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Sample records for helical peptides carrying

  1. Interaction of 18-residue peptides derived from amphipathic helical ...

    Madhsudhan

    interaction of proteins and peptides with membranes (Segrest ... favour surface activity have been described by Eisenberg et ... amphipathicity and propensity for α-helical conformation ..... Membrane destabilisation occurs due to electrostatic.

  2. Molecular dynamics simulations of the helical antimicrobial peptide ovispirin-1 in a zwitterionic dodecylphosphocholine micelle

    Khandelia, Himanshu; Kaznessis, Yiannis N

    2005-01-01

    We have carried out a 40-ns all-atom molecular dynamics simulation of the helical antimicrobial peptide ovispirin-1 (OVIS) in a zwitterionic diphosphocholine (DPC) micelle. The DPC micelle serves as an economical and effective model for a cellular membrane owing to the presence of a choline...... headgroup, which resembles those of membrane phospholipids. OVIS, which was initially placed along a micelle diameter, diffuses out to the water-DPC interface, and the simulation stabilizes to an interface-bound steady state in 40 ns. The helical content of the peptide marginally increases in the process...... in the micellar core and the polar side chains protruding into the aqueous phase. There is overwhelming evidence that points to the significant and indispensable participation of hydrophobic residues in binding to the zwitterionic interface. The simulation starts with a conformation that is unbiased toward...

  3. Structures and related properties of helical, disulfide-stabilized peptides

    Pagel, Mark D. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

    1993-11-01

    The three dimensional structure of several peptides were determined by NMR spectroscopy and distance geometry calculations. Each peptide formed a predictable, rigid structure, consisting of an α-helix, a "scaffold" region which packed along one face of the helix, and two disulfide bridges which covalently connect the helix and scaffold regions. The peptide Apa-M5 was designed to constrain the M5 peptide from MLCK in a helical geometry using the apamin disulfide scaffold. This scaffold constrains the N- terminal end of the helix with two disulfide bridges and a reverse turn. Like the M5 peptide, Apa-M5 was found to bind calmodulin in a Ca2+-dependent 1:1 stoichiometry. However, the dissociation constant of the (Apa-M5)-calmodulin complex, 107 nM, was 100-fold higher than the dissociation constant of the M5-calmodulin complex. This difference was due to a putative steric overlap between the Apa-M5 scaffold and calmodulin. The peptide Apa-Cro was designed to replace the large structural protein matrix of λ Cro with the apamin disulfide scaffold. However, Apa-Cro did not bind the consensus DNA operator half-site of λ Cro, probably due to a steric overlap between the Apa-Cro disulfide framework and the DNA. The amino acid sequence of the scaffold-disulfide bridge arrangement of the peptide Max was derived from the core sequence of scyllatoxin, which contains an α-helix constrained at the C-terminal end by two disulfide bridges and a two-stranded βsheet scaffold. Max was shown to fold with >84% yield to form a predictable, stable structure that is similar to scyllatoxin. The folding and stability properties of Max make this scaffold and disulfide bridge arrangement an ideal candidate for the development of hybrid sequence peptides. The dynamics of a fraying C-terminal end of the helix of the peptide Apa-AlaN was determined by analysis of 15N NMR relaxation properties.

  4. Improving cell penetration of helical peptides stabilized by N-terminal crosslinked aspartic acids.

    Zhao, Hui; Jiang, Yanhong; Tian, Yuan; Yang, Dan; Qin, Xuan; Li, Zigang

    2017-01-04

    Cell penetration and nucleus translocation efficiency are important for the cellular activities of peptide therapeutics. For helical peptides stabilized by N-terminal crosslinked aspartic acid, correlations between their penetration efficiency/nucleus translocation and physicochemical properties were studied. An increase in hydrophobicity and isoelectric point will promote cellular uptake and nucleus translocation of stabilized helices.

  5. Hexagonally Ordered Arrays of α-Helical Bundles Formed from Peptide-Dendron Hybrids

    Barkley, Deborah A. [Department; Rokhlenko, Yekaterina [Department; Marine, Jeannette E. [Department; David, Rachelle [Department; Sahoo, Dipankar [Department; Watson, Matthew D. [Department; Koga, Tadanori [Department; Department; Osuji, Chinedum O. [Department; Rudick, Jonathan G. [Department

    2017-10-24

    Combining monodisperse building blocks that have distinct folding properties serves as a modular strategy for controlling structural complexity in hierarchically organized materials. We combine an α-helical bundle-forming peptide with self-assembling dendrons to better control the arrangement of functional groups within cylindrical nanostructures. Site-specific grafting of dendrons to amino acid residues on the exterior of the α-helical bundle yields monodisperse macromolecules with programmable folding and self-assembly properties. The resulting hybrid biomaterials form thermotropic columnar hexagonal mesophases in which the peptides adopt an α-helical conformation. Bundling of the α-helical peptides accompanies self-assembly of the peptide-dendron hybrids into cylindrical nanostructures. The bundle stoichiometry in the mesophase agrees well with the size found in solution for α-helical bundles of peptides with a similar amino acid sequence.

  6. Antimicrobial peptides: the role of hydrophobicity in the alpha helical structure

    Pandurangan Perumal

    2013-12-01

    Full Text Available The antimicrobial peptides (AMPs are a class of molecule obtained from plants, insects, animals, and humans. These peptides have been classified into five categories: 1. Anionic peptide, 2. Linear alpha helical cationic peptide, 3. Cationic peptide, 4. Anionic and cationic peptides with disulphide bonds, and 5. Anionic and cationic peptide fragments of larger proteins. Factors affecting AMPs are sequence, size, charge, hydrophobicity, amphipathicity, structure and conformation. Synthesis of these peptides is convenient by using solid phase peptide synthesis by using FMOC chemistry protocol. The secondary structures of three synthetic peptides were determined by circular dichroism. Also, it was compared the stability of the α-helical structure and confirmed the percentage of helix of these peptides by using circular dichroism. Some of these AMPs show therapeutic properties like antimicrobial, antiviral, contraceptive, and anticancer. The formulations of some peptides have been entered into the phase I, II, or III of clinical trials. This article to review briefly the sources, classification, factors affecting AMPs activity, synthesis, characterization, mechanism of action and therapeutic concern of AMPs and mainly focussed on percentage of α-helical structure in various medium.

  7. Stabilized helical peptides: overview of the technologies and its impact on drug discovery.

    Klein, Mark

    2017-11-01

    Protein-protein interactions are predominant in the workings of all cells. Until now, there have been a few successes in targeting protein-protein interactions with small molecules. Peptides may overcome some of the challenges of small molecules in disrupting protein-protein interactions. However, peptides present a new set of challenges in drug discovery. Thus, the study of the stabilization of helical peptides has been extensive. Areas covered: Several technological approaches to helical peptide stabilization have been studied. In this review, stapled peptides, foldamers, and hydrogen bond surrogates are discussed. Issues regarding design principles are also discussed. Furthermore, this review introduces select computational techniques used to aid peptide design and discusses clinical trials of peptides in a more advanced stage of development. Expert opinion: Stabilized helical peptides hold great promise in a wide array of diseases. However, the field is still relatively new and new design principles are emerging. The possibilities of peptide modification are quite extensive and expanding, so the design of stabilized peptides requires great attention to detail in order to avoid a large number of failed lead peptides. The start of clinical trials with stapled peptides is a promising sign for the future.

  8. Buckwheat trypsin inhibitor with helical hairpin structure belongs to a new family of plant defence peptides.

    Oparin, Peter B; Mineev, Konstantin S; Dunaevsky, Yakov E; Arseniev, Alexander S; Belozersky, Mikhail A; Grishin, Eugene V; Egorov, Tsezi A; Vassilevski, Alexander A

    2012-08-15

    A new peptide trypsin inhibitor named BWI-2c was obtained from buckwheat (Fagopyrum esculentum) seeds by sequential affinity, ion exchange and reversed-phase chromatography. The peptide was sequenced and found to contain 41 amino acid residues, with four cysteine residues involved in two intramolecular disulfide bonds. Recombinant BWI-2c identical to the natural peptide was produced in Escherichia coli in a form of a cleavable fusion with thioredoxin. The 3D (three-dimensional) structure of the peptide in solution was determined by NMR spectroscopy, revealing two antiparallel α-helices stapled by disulfide bonds. Together with VhTI, a trypsin inhibitor from veronica (Veronica hederifolia), BWI-2c represents a new family of protease inhibitors with an unusual α-helical hairpin fold. The linker sequence between the helices represents the so-called trypsin inhibitory loop responsible for direct binding to the active site of the enzyme that cleaves BWI-2c at the functionally important residue Arg(19). The inhibition constant was determined for BWI-2c against trypsin (1.7×10(-1)0 M), and the peptide was tested on other enzymes, including those from various insect digestive systems, revealing high selectivity to trypsin-like proteases. Structural similarity shared by BWI-2c, VhTI and several other plant defence peptides leads to the acknowledgement of a new widespread family of plant peptides termed α-hairpinins.

  9. Molecular dynamics study of the solvation of an alpha-helical transmembrane peptide by DMSO

    Duarte, A.M.; Mierlo, van C.P.M.; Hemminga, M.A.

    2008-01-01

    10-ns molecular dynamics study of the solvation of a hydrophobic transmembrane helical peptide in dimethyl sulfoxide (DMSO) is presented. The objective is to analyze how this aprotic polar solvent is able to solvate three groups of amino acid residues (i.e., polar, apolar, and charged) that are

  10. Biodegradable copolymers carrying cell-adhesion peptide sequences.

    Proks, Vladimír; Machová, Lud'ka; Popelka, Stepán; Rypácek, Frantisek

    2003-01-01

    Amphiphilic block copolymers are used to create bioactive surfaces on biodegradable polymer scaffolds for tissue engineering. Cell-selective biomaterials can be prepared using copolymers containing peptide sequences derived from extracellular-matrix proteins (ECM). Here we discuss alternative ways for preparation of amphiphilic block copolymers composed of hydrophobic polylactide (PLA) and hydrophilic poly(ethylene oxide) (PEO) blocks with cell-adhesion peptide sequences. Copolymers PLA-b-PEO were prepared by a living polymerisation of lactide in dioxane with tin(II)2-ethylhexanoate as a catalyst. The following approaches for incorporation of peptides into copolymers were elaborated. (a) First, a side-chain protected Gly-Arg-Gly-Asp-Ser-Gly (GRGDSG) peptide was prepared by solid-phase peptide synthesis (SPPS) and then coupled with delta-hydroxy-Z-amino-PEO in solution. In the second step, the PLA block was grafted to it via a controlled polymerisation of lactide initiated by the hydroxy end-groups of PEO in the side-chain-protected GRGDSG-PEO. Deprotection of the peptide yielded a GRGDSG-b-PEO-b-PLA copolymer, with the peptide attached through its C-end. (b) A protected GRGDSG peptide was built up on a polymer resin and coupled with Z-carboxy-PEO using a solid-phase approach. After cleavage of the delta-hydroxy-PEO-GRGDSG copolymer from the resin, polymerisation of lactide followed by deprotection of the peptide yielded a PLA-b-PEO-b-GRGDSG block copolymer, in which the peptide is linked through its N-terminus.

  11. Antiviral activity of α-helical stapled peptides designed from the HIV-1 capsid dimerization domain

    Cowburn David

    2011-05-01

    Full Text Available Abstract Background The C-terminal domain (CTD of HIV-1 capsid (CA, like full-length CA, forms dimers in solution and CTD dimerization is a major driving force in Gag assembly and maturation. Mutations of the residues at the CTD dimer interface impair virus assembly and render the virus non-infectious. Therefore, the CTD represents a potential target for designing anti-HIV-1 drugs. Results Due to the pivotal role of the dimer interface, we reasoned that peptides from the α-helical region of the dimer interface might be effective as decoys to prevent CTD dimer formation. However, these small peptides do not have any structure in solution and they do not penetrate cells. Therefore, we used the hydrocarbon stapling technique to stabilize the α-helical structure and confirmed by confocal microscopy that this modification also made these peptides cell-penetrating. We also confirmed by using isothermal titration calorimetry (ITC, sedimentation equilibrium and NMR that these peptides indeed disrupt dimer formation. In in vitro assembly assays, the peptides inhibited mature-like virus particle formation and specifically inhibited HIV-1 production in cell-based assays. These peptides also showed potent antiviral activity against a large panel of laboratory-adapted and primary isolates, including viral strains resistant to inhibitors of reverse transcriptase and protease. Conclusions These preliminary data serve as the foundation for designing small, stable, α-helical peptides and small-molecule inhibitors targeted against the CTD dimer interface. The observation that relatively weak CA binders, such as NYAD-201 and NYAD-202, showed specificity and are able to disrupt the CTD dimer is encouraging for further exploration of a much broader class of antiviral compounds targeting CA. We cannot exclude the possibility that the CA-based peptides described here could elicit additional effects on virus replication not directly linked to their ability to bind

  12. Helical 1:1 α/Sulfono-γ-AA Heterogeneous Peptides with Antibacterial Activity

    She, Fengyu; Nimmagadda, Alekhya; Teng, Peng; Su, Ma; Zuo, Xiaobing; Cai, Jianfeng

    2016-05-09

    As one of the greatest threats facing in 21st century, antibiotic resistance is now a major public health concern. Host-defense peptides (HDPs) offer an alternative approach to combat emerging multidrug-resistant bacteria. It is known that helical HDPs such as magainin 2 and its analogs adopt cationic amphipathic conformations upon interaction with bacterial membranes, leading to membrane disruption and subsequent bacterial cell death. We have previously shown that amphipathic sulfono-γ-AApeptides could mimic magainin 2 and exhibit bactericidal activity. In this article, we demonstrate for the first time that amphipathic helical 1:1 α/sulfono-γ-AA heterogeneous peptides, in which regular amino acids and sulfono-γ-AApeptide building blocks are alternatively present in a 1:1 pattern, display potent antibacterial activity against both Gram-positive and Gram-negative bacterial pathogens. Small Angle X-ray Scattering (SAXS) suggests that the lead sequences adopt defined helical structures. The subsequent studies including 2 fluorescence microscopy and time-kill experiments indicate that these hybrid peptides exert antimicrobial activity by mimicking the mechanism of HDPs. Our findings may lead to the development of HDP-mimicking antimicrobial peptidomimetics that combat drug-resistant bacterial pathogens. In addition, our results also demonstrate the effective design of a new class of helical foldamer, which could be employed to interrogate other important biological targets such as protein-protein interactions in the future.

  13. Water-Floating Giant Nanosheets from Helical Peptide Pentamers

    Lee, Jaehun; Nam, Ki Tae

    One of the important challenges in the development of protein-mimetic materials is to understand the sequence specific assembly behavior and the dynamic folding change. Conventional strategies to construct two dimensional nanostructures from the peptides have been limited to beta-sheet forming sequences in use of basic building blocks because of their natural tendency to form sheet like aggregations. Here we identified a new peptide sequence, YFCFY that can form dimers by the disulfide bridge, fold into helix and assemble into macroscopic flat sheet at the air/water interface. Because of large driving force for two dimensional assembly and high elastic modulus of the resulting sheet, the peptide assembly induces the flattening of initially round water droplet. Additionally, we found that stabilization of helix by the dimerization is a key determinant for maintaining macroscopic flatness over a few tens centimeter even with a uniform thickness below 10 nm. Furthermore, the capability to transfer 2D film from water droplet to other substrates allows for the multiple stacking of 2D peptide nanostructure, suggesting possible applications in the biomimetic catalysts, biosensor and 2D related electronic devices. This work was supported by Samsung Research Funding Center of Samsung Electronics under Project Number SRFC-MA1401-01.

  14. Nonpolar interactions between trans-membrane helical EGF peptide and phosphatidylcholines, sphingomyelins and cholesterol. Molecular dynamics simulation studies

    Róg, T.; Murzyn, K.; Karttunen, M.E.J.; Pasenkiewicz-Gierula, M.

    2008-01-01

    A molecular dynamics simulation study of four lipid bilayers with inserted trans-membrane helical fragment of epithelial growth factor (EGF) receptor (EGF peptide) was performed. The lipid bilayers differ in their lipid composition and consist of (i) unsaturated phosphatidylcholine

  15. Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents.

    Hailey R Bureau

    Full Text Available Steered Molecular Dynamics (SMD has been seen to provide the potential of mean force (PMF along a peptide unfolding pathway effectively but at significant computational cost, particularly in all-atom solvents. Adaptive steered molecular dynamics (ASMD has been seen to provide a significant computational advantage by limiting the spread of the trajectories in a staged approach. The contraction of the trajectories at the end of each stage can be performed by taking a structure whose nonequilibrium work is closest to the Jarzynski average (in naive ASMD or by relaxing the trajectories under a no-work condition (in full-relaxation ASMD--namely, FR-ASMD. Both approaches have been used to determine the energetics and hydrogen-bonding structure along the pathway for unfolding of a benchmark peptide initially constrained as an α-helix in a water environment. The energetics are quite different to those in vacuum, but are found to be similar between implicit and explicit solvents. Surprisingly, the hydrogen-bonding pathways are also similar in the implicit and explicit solvents despite the fact that the solvent contact plays an important role in opening the helix.

  16. Molecular architecture with carbohydrate functionalized β-peptides adopting 314-helical conformation

    Nitin J. Pawar

    2014-04-01

    Full Text Available Carbohydrate recognition is essential in cellular interactions and biological processes. It is characterized by structural diversity, multivalency and cooperative effects. To evaluate carbohydrate interaction and recognition, the structurally defined attachment of sugar units to a rigid template is highly desired. β-Peptide helices offer conformationally stable templates for the linear presentation of sugar units in defined distances. The synthesis and β-peptide incorporation of sugar-β-amino acids are described providing the saccharide units as amino acid side chain. The respective sugar-β-amino acids are accessible by Michael addition of ammonia to sugar units derivatized as α,β-unsaturated esters. Three sugar units were incorporated in β-peptide oligomers varying the sugar (glucose, galactose, xylose and sugar protecting groups. The influence of sugar units and the configuration of sugar-β-amino acids on β-peptide secondary structure were investigated by CD spectroscopy.

  17. Antifungal Activity of 14-Helical β-Peptides against Planktonic Cells and Biofilms of Candida Species

    Namrata Raman

    2015-08-01

    Full Text Available Candida albicans is the most prevalent cause of fungal infections and treatment is further complicated by the formation of drug resistant biofilms, often on the surfaces of implanted medical devices. In recent years, the incidence of fungal infections by other pathogenic Candida species such as C. glabrata, C. parapsilosis and C. tropicalis has increased. Amphiphilic, helical β-peptide structural mimetics of natural antimicrobial α-peptides have been shown to exhibit specific planktonic antifungal and anti-biofilm formation activity against C. albicans in vitro. Here, we demonstrate that β-peptides are also active against clinically isolated and drug resistant strains of C. albicans and against other opportunistic Candida spp. Different Candida species were susceptible to β-peptides to varying degrees, with C. tropicalis being the most and C. glabrata being the least susceptible. β-peptide hydrophobicity directly correlated with antifungal activity against all the Candida clinical strains and species tested. While β-peptides were largely ineffective at disrupting existing Candida biofilms, hydrophobic β-peptides were able to prevent the formation of C. albicans, C. glabrata, C. parapsilosis and C. tropicalis biofilms. The broad-spectrum antifungal activity of β-peptides against planktonic cells and in preventing biofilm formation suggests the promise of this class of molecules as therapeutics.

  18. Rational design and application of responsive α-helical peptide hydrogels

    Banwell, Eleanor F.; Abelardo, Edgardo S.; Adams, Dave J.; Birchall, Martin A.; Corrigan, Adam; Donald, Athene M.; Kirkland, Mark; Serpell, Louise C.; Butler, Michael F.; Woolfson, Derek N.

    2009-01-01

    Biocompatible hydrogels have a wide variety of potential applications in biotechnology and medicine, such as the controlled delivery and release of cells, cosmetics and drugs; and as supports for cell growth and tissue engineering1. Rational peptide design and engineering are emerging as promising new routes to such functional biomaterials2-4. Here we present the first examples of rationally designed and fully characterized self-assembling hydrogels based on standard linear peptides with purely α-helical structures, which we call hydrogelating self-assembling fibres (hSAFs). These form spanning networks of α-helical fibrils that interact to give self-supporting physical hydrogels of >99% water content. The peptide sequences can be engineered to alter the underlying mechanism of gelation and, consequently, the hydrogel properties. Interestingly, for example, those with hydrogen-bonded networks melt upon heating, whereas those formed via hydrophobic interactions strengthen when warmed. The hSAFs are dual-peptide systems that only gel on mixing, which gives tight control over assembly5. These properties raise possibilities for using the hSAFs as substrates in cell culture. We have tested this in comparison with the widely used Matrigel substrate, and demonstrate that, like Matrigel, hSAFs support both growth and differentiation of rat adrenal pheochromocytoma cells for sustained periods in culture. PMID:19543314

  19. Molecular dynamics simulations of helical antimicrobial peptides in SDS micelles: what do point mutations achieve?

    Khandelia, Himanshu; Kaznessis, Yiannis N

    2005-01-01

    We report long time scale simulations of the 18-residue helical antimicrobial peptide ovispirin-1 and its analogs novispirin-G10 and novispirin-T7 in SDS micelles. The SDS micelle serves as an economical and effective model for a cellular membrane. Ovispirin, which is initially placed along...... a micelle diameter, diffuses out to the water-SDS interface and stabilizes to an interface-bound steady state in 16.35 ns of simulation. The final conformation, orientation, and the structure of ovispirin are in good agreement with the experimentally observed properties of the peptide in presence of lipid...... bilayers. The simulation succeeds in capturing subtle differences of the membrane-bound peptide structure as predicted by solid state NMR. The novispirins also undergo identical diffusion patterns and similar final conformations. Although the final interface-bound states are similar, the simulations...

  20. Cα chemical shift tensors in helical peptides by dipolar-modulated chemical shift recoupling NMR

    Yao Xiaolan; Yamaguchi, Satoru; Hong Mei

    2002-01-01

    The Cα chemical shift tensors of proteins contain information on the backbone conformation. We have determined the magnitude and orientation of the Cα chemical shift tensors of two peptides with α-helical torsion angles: the Ala residue in G*AL (φ=-65.7 deg., ψ=-40 deg.), and the Val residue in GG*V (φ=-81.5 deg., ψ=-50.7 deg.). The magnitude of the tensors was determined from quasi-static powder patterns recoupled under magic-angle spinning, while the orientation of the tensors was extracted from Cα-Hα and Cα-N dipolar modulated powder patterns. The helical Ala Cα chemical shift tensor has a span of 36 ppm and an asymmetry parameter of 0.89. Its σ 11 axis is 116 deg. ± 5 deg. from the Cα-Hα bond while the σ 22 axis is 40 deg. ± 5 deg. from the Cα-N bond. The Val tensor has an anisotropic span of 25 ppm and an asymmetry parameter of 0.33, both much smaller than the values for β-sheet Val found recently (Yao and Hong, 2002). The Val σ 33 axis is tilted by 115 deg. ± 5 deg. from the Cα-Hα bond and 98 deg. ± 5 deg. from the Cα-N bond. These represent the first completely experimentally determined Cα chemical shift tensors of helical peptides. Using an icosahedral representation, we compared the experimental chemical shift tensors with quantum chemical calculations and found overall good agreement. These solid-state chemical shift tensors confirm the observation from cross-correlated relaxation experiments that the projection of the Cα chemical shift tensor onto the Cα-Hα bond is much smaller in α-helices than in β-sheets

  1. Peptide design using alpha,beta-dehydro amino acids: from beta-turns to helical hairpins.

    Mathur, Puniti; Ramakumar, S; Chauhan, V S

    2004-01-01

    Incorporation of alpha,beta-dehydrophenylalanine (DeltaPhe) residue in peptides induces folded conformations: beta-turns in short peptides and 3(10)-helices in larger ones. A few exceptions-namely, alpha-helix or flat beta-bend ribbon structures-have also been reported in a few cases. The most favorable conformation of DeltaPhe residues are (phi,psi) approximately (-60 degrees, -30 degrees ), (-60 degrees, 150 degrees ), (80 degrees, 0 degrees ) or their enantiomers. DeltaPhe is an achiral and planar residue. These features have been exploited in designing DeltaPhe zippers and helix-turn-helix motifs. DeltaPhe can be incorporated in both right and left-handed helices. In fact, consecutive occurrence of three or more DeltaPhe amino acids induce left-handed screw sense in peptides containing L-amino acids. Weak interactions involving the DeltaPhe residue play an important role in molecular association. The C--H.O==C hydrogen bond between the DeltaPhe side-chain and backbone carboxyl moiety, pi-pi stacking interactions between DeltaPhe side chains belonging to enantiomeric helices have shown to stabilize folding. The unusual capability of a DeltaPhe ring to form the hub of multicentered interactions namely, a donor in aromatic C--H.pi and C--H.O==C and an acceptor in a CH(3).pi interaction suggests its exploitation in introducing long-range interactions in the folding of supersecondary structures. Copyright 2004 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2004

  2. Production of phytotoxic cationic α-helical antimicrobial peptides in plant cells using inducible promoters.

    Nuri Company

    Full Text Available Synthetic linear antimicrobial peptides with cationic α-helical structures, such as BP100, have potent and specific activities against economically important plant pathogenic bacteria. They are also recognized as valuable therapeutics and preservatives. However, highly active BP100 derivatives are often phytotoxic when expressed at high levels as recombinant peptides in plants. Here we demonstrate that production of recombinant phytotoxic peptides in transgenic plants is possible by strictly limiting transgene expression to certain tissues and conditions, and specifically that minimization of this expression during transformation and regeneration of transgenic plants is essential to obtain viable plant biofactories. On the basis of whole-genome transcriptomic data available online, we identified the Os.hsp82 promoter that fulfilled this requirement and was highly induced in response to heat shock. Using this strategy, we generated transgenic rice lines producing moderate yields of severely phytotoxic BP100 derivatives on exposure to high temperature. In addition, a threshold for gene expression in selected tissues and stages was experimentally established, below which the corresponding promoters should be suitable for driving the expression of recombinant phytotoxic proteins in genetically modified plants. In view of the growing transcriptomics data available, this approach is of interest to assist promoter selection for specific purposes.

  3. Modular design of synthetic protein mimics. Characterization of the helical conformation of a 13-residue peptide in crystals

    Karle, I.L.; Flippen-Anderson, J.L.; Uma, K.; Balaram, P.

    1989-01-01

    The incorporation of α-aminoisobutyryl (Aib) residues into peptide sequences facilitates helical folding. Aib-containing sequences have been chosen for the design of rigid helical segments in a modular approach to the construction of a synthetic protein mimic. The helical conformation of the synthetic peptide Boc-Aib-(Val-Ala-Leu-Aib) 3 -OMe in crystals is established by X-ray diffraction. The 13-residue apolar peptide adopts a helical form in the crystal with seven α-type hydrogen bonds in the middle and 3 10 -type hydrogen bonds at either end. The helices stack in columns, zigzag rather than linear, by means of direct NH hor-ellipsis OC head to tail hydrogen bonds. Leucyl side chains are extended on one side of the helix and valyl side chains on the other side. Water molecules form hydrogen bonds with several backbone carbonyl oxygens that also participate in α-helix hydrogen bonds. There is no apparent distortion of the helix caused by hydration

  4. Carry

    Koijen, Ralph S.J.; Moskowitz, Tobias J.; Heje Pedersen, Lasse

    that include global equities, global bonds, currencies, commodities, US Treasuries, credit, and equity index options. This predictability underlies the strong returns to "carry trades" that go long high-carry and short low-carry securities, applied almost exclusively to currencies, but shown here...

  5. Effect of the aminoacid composition of model α-helical peptides on the physical properties of lipid bilayers and peptide conformation: a molecular dynamics simulation

    Melicherčík, Milan; Holúbeková, A.; Hianik, T.; Urban, J.

    2013-01-01

    Roč. 19, č. 11 (2013), s. 4723-4730 ISSN 1610-2940 Institutional support: RVO:67179843 Keywords : Bilayer lipid membranes * Helical peptides * Molecular dynamics simulations * Phase transitions Subject RIV: BO - Biophysics Impact factor: 1.867, year: 2013

  6. Anti-plasmodial action of de novo-designed, cationic, lysine-branched, amphipathic, helical peptides

    Kaushik Naveen K

    2012-08-01

    Full Text Available Abstract Background A lack of vaccine and rampant drug resistance demands new anti-malarials. Methods In vitro blood stage anti-plasmodial properties of several de novo-designed, chemically synthesized, cationic, amphipathic, helical, antibiotic peptides were examined against Plasmodium falciparum using SYBR Green assay. Mechanistic details of anti-plasmodial action were examined by optical/fluorescence microscopy and FACS analysis. Results Unlike the monomeric decapeptides {(Ac-GXRKXHKXWA-NH2 (X = F,ΔF (Fm, ΔFm IC50 >100 μM}, the lysine-branched,dimeric versions showed far greater potency {IC50 (μM Fd 1.5 , ΔFd 1.39}. The more helical and proteolytically stable ΔFd was studied for mechanistic details. ΔFq, a K-K2 dendrimer of ΔFm and (ΔFm2 a linear dimer of ΔFm showed IC50 (μM of 0.25 and 2.4 respectively. The healthy/infected red cell selectivity indices were >35 (ΔFd, >20 (ΔFm2 and 10 (ΔFq. FITC-ΔFd showed rapid and selective accumulation in parasitized red cells. Overlaying DAPI and FITC florescence suggested that ΔFd binds DNA. Trophozoites and schizonts incubated with ΔFd (2.5 μM egressed anomalously and Band-3 immunostaining revealed them not to be associated with RBC membrane. Prematurely egressed merozoites from peptide-treated cultures were found to be invasion incompetent. Conclusion Good selectivity (>35, good resistance index (1.1 and low cytotoxicity indicate the promise of ΔFd against malaria.

  7. Solvent polarity controls the helical conformation of short peptides rich in Calpha-tetrasubstituted amino acids.

    Bellanda, Massimo; Mammi, Stefano; Geremia, Silvano; Demitri, Nicola; Randaccio, Lucio; Broxterman, Quirinus B; Kaptein, Bernard; Pengo, Paolo; Pasquato, Lucia; Scrimin, Paolo

    2007-01-01

    The two peptides, rich in C(alpha)-tetrasubstituted amino acids, Ac-[Aib-L-(alphaMe)Val-Aib](2)-L-His-NH(2) (1) and Ac-[Aib-L-(alphaMe)Val-Aib](2)-O-tBu (2 a) are prevalently helical. They present the unique property of changing their conformation from the alpha- to the 3(10)-helix as a function of the polarity of the solvent: alpha in more polar solvents, 3(10) in less polar ones. Conclusive evidence of this reversible change of conformation is reported on the basis of the circular dichroism (CD) spectra and a detailed two-dimensional NMR analysis in two solvents (trifluoroethanol and methanol) refined with molecular dynamics calculations. The X-ray diffractometric analysis of the crystals of both peptides reveals that they assume a prevalent 3(10)-helix conformation in the solid state. This conformation is practically superimposable on that obtained from the NMR analysis of 1 in methanol. The NMR results further validate the reported CD signature of the 3(10)-helix and the use of the CD technique for its assessment.

  8. Carry

    Koijen, Ralph S.J.; Moskowitz, Tobias; Pedersen, Lasse Heje

    2018-01-01

    -sectionally and in time series for a host of different asset classes, including global equities, global bonds, commodities, US Treasuries, credit, and options. Carry is not explained by known predictors of returns from these asset classes, and it captures many of these predictors, providing a unifying framework...... for return predictability. We reject a generalized version of Uncovered Interest Parity and the Expectations Hypothesis in favor of models with varying risk premia, in which carry strategies are commonly exposed to global recession, liquidity, and volatility risks, though none fully explains carry’s premium....

  9. Photoinduced electron transfer through peptide-based self-assembled monolayers chemisorbed on gold electrodes: directing the flow-in and flow-out of electrons through peptide helices.

    Venanzi, Mariano; Gatto, Emanuela; Caruso, Mario; Porchetta, Alessandro; Formaggio, Fernando; Toniolo, Claudio

    2014-08-21

    Photoinduced electron transfer (PET) experiments have been carried out on peptide self-assembled monolayers (SAM) chemisorbed on a gold substrate. The oligopeptide building block was exclusively formed by C(α)-tetrasubstituted α-aminoisobutyric residues to attain a helical conformation despite the shortness of the peptide chain. Furthermore, it was functionalized at the C-terminus by a pyrene choromophore to enhance the UV photon capture cross-section of the compound and by a lipoic group at the N-terminus for linking to gold substrates. Electron transfer across the peptide SAM has been studied by photocurrent generation experiments in an electrochemical cell employing a gold substrate modified by chemisorption of a peptide SAM as a working electrode and by steady-state and time-resolved fluorescence experiments in solution and on a gold-coated glass. The results show that the electronic flow through the peptide bridge is strongly asymmetric; i.e., PET from the C-terminus to gold is highly favored with respect to PET in the opposite direction. This effect arises from the polarity of the Au-S linkage (Au(δ+)-S(δ-), junction effect) and from the electrostatic field generated by the peptide helix.

  10. Probing alpha-helical and beta-sheet structures of peptides at solid/liquid interfaces with SFG.

    Chen, Xiaoyun; Wang, Jie; Sniadecki, Jason J; Even, Mark A; Chen, Zhan

    2005-03-29

    We demonstrated that sum frequency generation (SFG) vibrational spectroscopy can distinguish different secondary structures of proteins or peptides adsorbed at solid/liquid interfaces. The SFG spectrum for tachyplesin I at the polystyrene (PS)/solution interface has a fingerprint peak corresponding to the B1/B3 mode of the antiparallel beta-sheet. This peak disappeared upon the addition of dithiothreitol, which can disrupt the beta-sheet structure. The SFG spectrum indicative of the MSI594 alpha-helical structure was observed at the PS/MSI594 solution interface. This research validates SFG as a powerful technique for revealing detailed secondary structures of interfacial proteins and peptides.

  11. Ratio of ellipticities between 192 and 208 nm (R1 ): An effective electronic circular dichroism parameter for characterization of the helical components of proteins and peptides.

    Banerjee, Raja; Sheet, Tridip

    2017-11-01

    Circular dichroism (CD) spectroscopy represents an important tool for characterization of the peptide and protein secondary structures that mainly arise from the conformational disposition of the peptide backbone in solution. In 1991 Manning and Woody proposed that, in addition to the signal intensity, the ratio between [θ]nπ* and [θ]ππ*ǁ ((R 2 ) ≅ [θ] 222 /[θ] 208 ), along with [θ]ππ*⊥ and [θ]ππ*ǁ ((R 1 ) ≅ [θ] 192 /[θ] 208 ), may be utilized towards identifying the peptide/protein conformation (especially 3 10 - and α-helices). However, till date the use of the ratiometric ellipticity component for helical structure analysis of peptides and proteins has not been reported. We studied a series of temperature dependent CD spectra of a thermally stable, model helical peptide and its related analogs in water as a function of added 2,2,2-trifluoroethanol (TFE) in order to explore their landscape of helicity. For the first time, we have experimentally shown here that the R 1 parameter can characterize better the individual helices, while the other parameter R 2 and the signal intensity do not always converge. We emphasize the use of the R 1 ratio of ellipticities for helical characterization because of the common origin of these two bands (exciton splitting of the amide π→ π* transition in a helical polypeptide). This approach may become worthwhile and timely with the increasing accessibility of CD synchrotron sources. © 2017 Wiley Periodicals, Inc.

  12. Sequence-specific unusual (1-->2)-type helical turns in alpha/beta-hybrid peptides.

    Prabhakaran, Panchami; Kale, Sangram S; Puranik, Vedavati G; Rajamohanan, P R; Chetina, Olga; Howard, Judith A K; Hofmann, Hans-Jörg; Sanjayan, Gangadhar J

    2008-12-31

    This article describes novel conformationally ordered alpha/beta-hybrid peptides consisting of repeating l-proline-anthranilic acid building blocks. These oligomers adopt a compact, right-handed helical architecture determined by the intrinsic conformational preferences of the individual amino acid residues. The striking feature of these oligomers is their ability to display an unusual periodic pseudo beta-turn network of nine-membered hydrogen-bonded rings formed in the forward direction of the sequence by 1-->2 amino acid interactions both in solid-state and in solution. Conformational investigations of several of these oligomers by single-crystal X-ray diffraction, solution-state NMR, and ab initio MO theory suggest that the characteristic steric and dihedral angle restraints exerted by proline are essential for stabilizing the unusual pseudo beta-turn network found in these oligomers. Replacing proline by the conformationally flexible analogue alanine (Ala) or by the conformationally more constrained alpha-amino isobutyric acid (Aib) had an adverse effect on the stabilization of this structural architecture. These findings increase the potential to design novel secondary structure elements profiting from the steric and dihedral angle constraints of the amino acid constituents and help to augment the conformational space available for synthetic oligomer design with diverse backbone structures.

  13. Controlling noncovalent interactions between a lysine-rich α-helical peptide and self-assembled monolayers of alkanethiols on Au through functional group diversity

    Raigoza, Annette F.; Onyirioha, Kristeen; Webb, Lauren J., E-mail: lwebb@cm.utexas.edu

    2017-02-28

    Highlights: • Functional variety in SAMs control covalent binding of proteins to surfaces. • Peptide density on Au(111) surfaces controlled by SAM functional groups. • Affinity between biomolecule and SAM surface follows a Langmuir isotherm. • Surface chemistry can mimic functional group diversity in proteins and peptides. - Abstract: Reliably attaching a structured biomolecule to an inorganic substrate would enable the preparation of surfaces that incorporate both biological and inorganic functions and structures. To this end, we have previously developed a procedure using the copper(I)-catalyzed click reaction to tether synthetic α-helical peptides carrying two alkyne groups to well-ordered alkanethiol self-assembled monolayers (SAM) on a Au(111) surface, in which the SAM is composed of a mixture of methyl and azide termination. Proteins, however, are composed of many diverse functional groups, and this composition directly effects protein structure, interactions, and reactivity. Here, we explore the utility of mixed SAMs with alternative terminating functional groups to tune and direct the reactivity of the surface through noncovalent peptide-surface interactions. We study both polar surfaces (OH-terminated) and charged surfaces (COOH- and NH{sub 3}-terminated, which are negatively and positively charged, respectively, under our reaction conditions). Surfaces were functionalized with a bipolar peptide composed of Lys and Leu residues that could express different interactions through either hydrophilic and/or charge (Lys) or hydrophobic (Leu) influences. X-ray photoelectron spectroscopy (XPS) and surface infrared spectroscopy were used to characterize surfaces at all stages of the peptide functionalization procedure. This strategy resulted in a high density of surface-bound α-helices without aggregation. Mixed SAMs that included a positively charged alkanethiol along with the azide-terminated thiol resulted in a more efficient reaction and better

  14. Controlling noncovalent interactions between a lysine-rich α-helical peptide and self-assembled monolayers of alkanethiols on Au through functional group diversity

    Raigoza, Annette F.; Onyirioha, Kristeen; Webb, Lauren J.

    2017-01-01

    Highlights: • Functional variety in SAMs control covalent binding of proteins to surfaces. • Peptide density on Au(111) surfaces controlled by SAM functional groups. • Affinity between biomolecule and SAM surface follows a Langmuir isotherm. • Surface chemistry can mimic functional group diversity in proteins and peptides. - Abstract: Reliably attaching a structured biomolecule to an inorganic substrate would enable the preparation of surfaces that incorporate both biological and inorganic functions and structures. To this end, we have previously developed a procedure using the copper(I)-catalyzed click reaction to tether synthetic α-helical peptides carrying two alkyne groups to well-ordered alkanethiol self-assembled monolayers (SAM) on a Au(111) surface, in which the SAM is composed of a mixture of methyl and azide termination. Proteins, however, are composed of many diverse functional groups, and this composition directly effects protein structure, interactions, and reactivity. Here, we explore the utility of mixed SAMs with alternative terminating functional groups to tune and direct the reactivity of the surface through noncovalent peptide-surface interactions. We study both polar surfaces (OH-terminated) and charged surfaces (COOH- and NH_3-terminated, which are negatively and positively charged, respectively, under our reaction conditions). Surfaces were functionalized with a bipolar peptide composed of Lys and Leu residues that could express different interactions through either hydrophilic and/or charge (Lys) or hydrophobic (Leu) influences. X-ray photoelectron spectroscopy (XPS) and surface infrared spectroscopy were used to characterize surfaces at all stages of the peptide functionalization procedure. This strategy resulted in a high density of surface-bound α-helices without aggregation. Mixed SAMs that included a positively charged alkanethiol along with the azide-terminated thiol resulted in a more efficient reaction and better alignment

  15. Simultaneous inhibition of key growth pathways in melanoma cells and tumor regression by a designed bidentate constrained helical peptide.

    Dhar, Amlanjyoti; Mallick, Shampa; Ghosh, Piya; Maiti, Atanu; Ahmed, Israr; Bhattacharya, Seemana; Mandal, Tapashi; Manna, Asit; Roy, Koushik; Singh, Sandeep; Nayak, Dipak Kumar; Wilder, Paul T; Markowitz, Joseph; Weber, David; Ghosh, Mrinal K; Chattopadhyay, Samit; Guha, Rajdeep; Konar, Aditya; Bandyopadhyay, Santu; Roy, Siddhartha

    2014-07-01

    Protein-protein interactions are part of a large number of signaling networks and potential targets for drug development. However, discovering molecules that can specifically inhibit such interactions is a major challenge. S100B, a calcium-regulated protein, plays a crucial role in the proliferation of melanoma cells through protein-protein interactions. In this article, we report the design and development of a bidentate conformationally constrained peptide against dimeric S100B based on a natural tight-binding peptide, TRTK-12. The helical conformation of the peptide was constrained by the substitution of α-amino isobutyric acid--an amino acid having high helical propensity--in positions which do not interact with S100B. A branched bidentate version of the peptide was bound to S100B tightly with a dissociation constant of 8 nM. When conjugated to a cell-penetrating peptide, it caused growth inhibition and rapid apoptosis in melanoma cells. The molecule exerts antiproliferative action through simultaneous inhibition of key growth pathways, including reactivation of wild-type p53 and inhibition of Akt and STAT3 phosphorylation. The apoptosis induced by the bidentate constrained helix is caused by direct migration of p53 to mitochondria. At moderate intravenous dose, the peptide completely inhibits melanoma growth in a mouse model without any significant observable toxicity. The specificity was shown by lack of ability of a double mutant peptide to cause tumor regression at the same dose level. The methodology described here for direct protein-protein interaction inhibition may be effective for rapid development of inhibitors against relatively weak protein-protein interactions for de novo drug development. © 2014 Wiley Periodicals, Inc.

  16. Exploring biological effects of MoS{sub 2} nanosheets on native structures of α-helical peptides

    Gu, Zonglin; Li, Weifeng, E-mail: wfli@suda.edu.cn, E-mail: ruhong@us.ibm.com [School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123 (China); Hong, Linbi [Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598 (United States); Zhou, Ruhong, E-mail: wfli@suda.edu.cn, E-mail: ruhong@us.ibm.com [School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123 (China); Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598 (United States); Department of Chemistry, Columbia University, New York, New York 10027 (United States)

    2016-05-07

    Recent reports of mono- and few-layer molybdenum disulfide (MoS{sub 2}), a representative transition metal dichacogenide (TMD), as antibacterial and anticancer agents have shed light on their potential in biomedical applications. To better facilitate these promising applications, one needs to understand the biological effects of these TMDs as well, such as their potential adverse effects on protein structure and function. Here, we sought to understand the interaction of MoS{sub 2} nanosheets with peptides using molecular dynamics simulations and a simple model polyalanine with various lengths (PA{sub n}, n = 10, 20, 30, and 40; mainly α − helices). Our results demonstrated that MoS{sub 2} monolayer has an exceptional capability to bind all peptides in a fast and strong manner. The strong attraction from the MoS{sub 2} nanosheet is more than enough to compensate the energy needed to unfold the peptide, regardless of the length, which induces drastic disruptions to the intra-peptide hydrogen bonds and subsequent secondary structures of α − helices. This universal phenomenon may point to the potential nanotoxicity of MoS{sub 2} when used in biological systems. Moreover, these results aligned well with previous findings on the potential cytotoxicity of TMD nanomaterials.

  17. Blocking the RecA activity and SOS-response in bacteria with a short α-helical peptide.

    Yakimov, Alexander; Pobegalov, Georgii; Bakhlanova, Irina; Khodorkovskii, Mikhail; Petukhov, Michael; Baitin, Dmitry

    2017-09-19

    The RecX protein, a very active natural RecA protein inhibitor, can completely disassemble RecA filaments at nanomolar concentrations that are two to three orders of magnitude lower than that of RecA protein. Based on the structure of RecX protein complex with the presynaptic RecA filament, we designed a short first in class α-helical peptide that both inhibits RecA protein activities in vitro and blocks the bacterial SOS-response in vivo. The peptide was designed using SEQOPT, a novel method for global sequence optimization of protein α-helices. SEQOPT produces artificial peptide sequences containing only 20 natural amino acids with the maximum possible conformational stability at a given pH, ionic strength, temperature, peptide solubility. It also accounts for restrictions due to known amino acid residues involved in stabilization of protein complexes under consideration. The results indicate that a few key intermolecular interactions inside the RecA protein presynaptic complex are enough to reproduce the main features of the RecX protein mechanism of action. Since the SOS-response provides a major mechanism of bacterial adaptation to antibiotics, these results open new ways for the development of antibiotic co-therapy that would not cause bacterial resistance. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Exploring biological effects of MoS2 nanosheets on native structures of α-helical peptides

    Gu, Zonglin; Li, Weifeng; Hong, Linbi; Zhou, Ruhong

    2016-01-01

    Recent reports of mono- and few-layer molybdenum disulfide (MoS 2 ), a representative transition metal dichacogenide (TMD), as antibacterial and anticancer agents have shed light on their potential in biomedical applications. To better facilitate these promising applications, one needs to understand the biological effects of these TMDs as well, such as their potential adverse effects on protein structure and function. Here, we sought to understand the interaction of MoS 2 nanosheets with peptides using molecular dynamics simulations and a simple model polyalanine with various lengths (PA n , n = 10, 20, 30, and 40; mainly α − helices). Our results demonstrated that MoS 2 monolayer has an exceptional capability to bind all peptides in a fast and strong manner. The strong attraction from the MoS 2 nanosheet is more than enough to compensate the energy needed to unfold the peptide, regardless of the length, which induces drastic disruptions to the intra-peptide hydrogen bonds and subsequent secondary structures of α − helices. This universal phenomenon may point to the potential nanotoxicity of MoS 2 when used in biological systems. Moreover, these results aligned well with previous findings on the potential cytotoxicity of TMD nanomaterials.

  19. Structure-activity relationship study of Aib-containing amphipathic helical peptide-cyclic RGD conjugates as carriers for siRNA delivery.

    Wada, Shun-Ichi; Takesada, Anna; Nagamura, Yurie; Sogabe, Eri; Ohki, Rieko; Hayashi, Junsuke; Urata, Hidehito

    2017-12-15

    The conjugation of Aib-containing amphipathic helical peptide with cyclo(-Arg-Gly-Asp-d-Phe-Cys-) (cRGDfC) at the C-terminus of the helix peptide (PI) has been reported to be useful for constructing a carrier for targeted siRNA delivery into cells. In order to explore structure-activity relationships for the development of potential carriers for siRNA delivery, we synthesized conjugates of Aib-containing amphipathic helical peptide with cRGDfC at the N-terminus (PII) and both the N- and C-termini (PIII) of the helical peptide. Furthermore, to examine the influence of PI helical chain length on siRNA delivery, truncated peptides containing 16 (PIV), 12 (PV), and 8 (PVI) amino acid residues at the N-terminus of the helical chain were synthesized. PII and PIII, as well as PI, could deliver anti-luciferase siRNA into cells to induce the knockdown of luciferase stably expressed in cells. In contrast, all of the truncated peptides were unlikely to transport siRNA into cells. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Targeting EphA2-Sam and Its Interactome: Design and Evaluation of Helical Peptides Enriched in Charged Residues.

    Mercurio, Flavia A; Marasco, Daniela; Di Natale, Concetta; Pirone, Luciano; Costantini, Susan; Pedone, Emilia M; Leone, Marilisa

    2016-11-17

    The EphA2 receptor controls diverse physiological and pathological conditions and its levels are often upregulated in cancer. Targeting receptor overexpression, through modulation of endocytosis and consequent degradation, appears to be an appealing strategy for attacking tumor malignancy. In this scenario, the Sam domain of EphA2 plays a pivotal role because it is the site where protein regulators of endocytosis and stability are recruited by means of heterotypic Sam-Sam interactions. Because EphA2-Sam heterotypic complexes are largely based on electrostatic contacts, we have investigated the possibility of attacking these interactions with helical peptides enriched in charged residues. Several peptide sequences with high predicted helical propensities were designed, and detailed conformational analyses were conducted by diverse techniques including NMR, CD, and molecular dynamics (MD) simulations. Interaction studies were also performed by NMR, surface plasmon resonance (SPR), and microscale thermophoresis (MST) and led to the identification of two peptides capable of binding to the first Sam domain of Odin. These molecules represent early candidates for the generation of efficient Sam domain binders and antagonists of Sam-Sam interactions involving EphA2. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Self-Assembling Peptide Surfactants A6K and A6D Adopt a-Helical Structures Useful for Membrane Protein Stabilization

    Furen Zhuang

    2011-10-01

    Full Text Available Elucidation of membrane protein structures have been greatly hampered by difficulties in producing adequately large quantities of the functional protein and stabilizing them. A6D and A6K are promising solutions to the problem and have recently been used for the rapid production of membrane-bound G protein-coupled receptors (GPCRs. We propose that despite their short lengths, these peptides can adopt α-helical structures through interactions with micelles formed by the peptides themselves. These α-helices are then able to stabilize α-helical motifs which many membrane proteins contain. We also show that A6D and A6K can form β-sheets and appear as weak hydrogels at sufficiently high concentrations. Furthermore, A6D and A6K together in sodium dodecyl sulfate (SDS can form expected β-sheet structures via a surprising α-helical intermediate.

  2. Truncated Glucagon-like Peptide-1 and Exendin-4 α-Conotoxin pl14a Peptide Chimeras Maintain Potency and α-Helicity and Reveal Interactions Vital for cAMP Signaling in Vitro*

    Swedberg, Joakim E.; Schroeder, Christina I.; Mitchell, Justin M.; Fairlie, David P.; Edmonds, David J.; Griffith, David A.; Ruggeri, Roger B.; Derksen, David R.; Loria, Paula M.; Price, David A.; Liras, Spiros; Craik, David J.

    2016-01-01

    Glucagon-like peptide-1 (GLP-1) signaling through the glucagon-like peptide 1 receptor (GLP-1R) is a key regulator of normal glucose metabolism, and exogenous GLP-1R agonist therapy is a promising avenue for the treatment of type 2 diabetes mellitus. To date, the development of therapeutic GLP-1R agonists has focused on producing drugs with an extended serum half-life. This has been achieved by engineering synthetic analogs of GLP-1 or the more stable exogenous GLP-1R agonist exendin-4 (Ex-4). These synthetic peptide hormones share the overall structure of GLP-1 and Ex-4, with a C-terminal helical segment and a flexible N-terminal tail. Although numerous studies have investigated the molecular determinants underpinning GLP-1 and Ex-4 binding and signaling through the GLP-1R, these have primarily focused on the length and composition of the N-terminal tail or on how to modulate the helicity of the full-length peptides. Here, we investigate the effect of C-terminal truncation in GLP-1 and Ex-4 on the cAMP pathway. To ensure helical C-terminal regions in the truncated peptides, we produced a series of chimeric peptides combining the N-terminal portion of GLP-1 or Ex-4 and the C-terminal segment of the helix-promoting peptide α-conotoxin pl14a. The helicity and structures of the chimeric peptides were confirmed using circular dichroism and NMR, respectively. We found no direct correlation between the fractional helicity and potency in signaling via the cAMP pathway. Rather, the most important feature for efficient receptor binding and signaling was the C-terminal helical segment (residues 22–27) directing the binding of Phe22 into a hydrophobic pocket on the GLP-1R. PMID:27226591

  3. Synthesis and optical properties of pyrrolidinyl peptide nucleic acid carrying a clicked Nile red label

    Nattawut Yotapan

    2014-09-01

    Full Text Available DNA or its analogues with an environment-sensitive fluorescent label are potentially useful as a probe for studying the structure and dynamics of nucleic acids. In this work, pyrrolidinyl peptide nucleic acid (acpcPNA was labeled at its backbone with Nile red, a solvatochromic benzophenoxazine dye, by means of click chemistry. The optical properties of the Nile red-labeled acpcPNA were investigated by UV–vis and fluorescence spectroscopy in the absence and in the presence of DNA. In contrast to the usual quenching observed in Nile red-labeled DNA, the hybridization with DNA resulted in blue shifting and an enhanced fluorescence regardless of the neighboring bases. More pronounced blue shifts and fluorescence enhancements were observed when the DNA target carried a base insertion in close proximity to the Nile red label. The results indicate that the Nile red label is located in a more hydrophobic environment in acpcPNA–DNA duplexes than in the single-stranded acpcPNA. The different fluorescence properties of the acpcPNA hybrids of complementary DNA and DNA carrying a base insertion are suggestive of different interactions between the Nile red label and the duplexes.

  4. N-terminal diproline and charge group effects on the stabilization of helical conformation in alanine-based short peptides: CD studies with water and methanol as solvent.

    Goyal, Bhupesh; Srivastava, Kinshuk Raj; Durani, Susheel

    2017-06-01

    Protein folding problem remains a formidable challenge as main chain, side chain and solvent interactions remain entangled and have been difficult to resolve. Alanine-based short peptides are promising models to dissect protein folding initiation and propagation structurally as well as energetically. The effect of N-terminal diproline and charged side chains is assessed on the stabilization of helical conformation in alanine-based short peptides using circular dichroism (CD) with water and methanol as solvent. A1 (Ac-Pro-Pro-Ala-Lys-Ala-Lys-Ala-Lys-Ala-NH 2 ) is designed to assess the effect of N-terminal homochiral diproline and lysine side chains to induce helical conformation. A2 (Ac-Pro-Pro-Glu-Glu-Ala-Ala-Lys-Lys-Ala-NH 2 ) and A3 (Ac-dPro-Pro-Glu-Glu-Ala-Ala-Lys-Lys-Ala-NH 2 ) with N-terminal homochiral and heterochiral diproline, respectively, are designed to assess the effect of Glu...Lys (i, i + 4) salt bridge interactions on the stabilization of helical conformation. The CD spectra of A1, A2 and A3 in water manifest different amplitudes of the observed polyproline II (PPII) signals, which indicate different conformational distributions of the polypeptide structure. The strong effect of solvent substitution from water to methanol is observed for the peptides, and CD spectra in methanol evidence A2 and A3 as helical folds. Temperature-dependent CD spectra of A1 and A2 in water depict an isodichroic point reflecting coexistence of two conformations, PPII and β-strand conformation, which is consistent with the previous studies. The results illuminate the effect of N-terminal diproline and charged side chains in dictating the preferences for extended-β, semi-extended PPII and helical conformation in alanine-based short peptides. The results of the present study will enhance our understanding on stabilization of helical conformation in short peptides and hence aid in the design of novel peptides with helical structures. Copyright © 2017 European Peptide

  5. Consequences of non-uniformity in the stoichiometry of component fractions within one and two loops models of alpha-helical peptides

    Atoms in biomolecular structures like alpha helices contain an array of distances and angles which include abundant multiple patterns of redundancies. Thus all peptides backbones contain the three atom sequence N-C*C, whereas the repeating set of a four atom sequences (N-C*C-N, C*-C-N-C*, and C-N-C...

  6. Conformational Flexibility Determines Selectivity and Antibacterial, Antiplasmodial, and Anticancer Potency of Cationic α-Helical Peptides*

    Vermeer, Louic S.; Lan, Yun; Abbate, Vincenzo; Ruh, Emrah; Bui, Tam T.; Wilkinson, Louise J.; Kanno, Tokuwa; Jumagulova, Elmira; Kozlowska, Justyna; Patel, Jayneil; McIntyre, Caitlin A.; Yam, W. C.; Siu, Gilman; Atkinson, R. Andrew; Lam, Jenny K. W.; Bansal, Sukhvinder S.; Drake, Alex F.; Mitchell, Graham H.; Mason, A. James

    2012-01-01

    We used a combination of fluorescence, circular dichroism (CD), and NMR spectroscopies in conjunction with size exclusion chromatography to help rationalize the relative antibacterial, antiplasmodial, and cytotoxic activities of a series of proline-free and proline-containing model antimicrobial peptides (AMPs) in terms of their structural properties. When compared with proline-free analogs, proline-containing peptides had greater activity against Gram-negative bacteria, two mammalian cancer cell lines, and intraerythrocytic Plasmodium falciparum, which they were capable of killing without causing hemolysis. In contrast, incorporation of proline did not have a consistent effect on peptide activity against Mycobacterium tuberculosis. In membrane-mimicking environments, structures with high α-helix content were adopted by both proline-free and proline-containing peptides. In solution, AMPs generally adopted disordered structures unless their sequences comprised more hydrophobic amino acids or until coordinating phosphate ions were added. Proline-containing peptides resisted ordering induced by either method. The roles of the angle subtended by positively charged amino acids and the positioning of the proline residues were also investigated. Careful positioning of proline residues in AMP sequences is required to enable the peptide to resist ordering and maintain optimal antibacterial activity, whereas varying the angle subtended by positively charged amino acids can attenuate hemolytic potential albeit with a modest reduction in potency. Maintaining conformational flexibility improves AMP potency and selectivity toward bacterial, plasmodial, and cancerous cells while enabling the targeting of intracellular pathogens. PMID:22869378

  7. A Helix-Stabilizing Linker Improves Subcutaneous Bioavailability of a Helical Peptide Independent of Linker Lipophilicity

    Zhang, Liang; Navaratna, Tejas; Thurber, Greg M.

    2016-01-01

    Stabilized peptides address several limitations to peptide-based imaging agents and therapeutics such as poor stability and low affinity due to conformational flexibility. There is also active research in developing these compounds for intracellular drug targeting, and significant efforts have been invested to determine the effects of helix stabilization on intracellular delivery. However, much less is known about the impact on other pharmacokinetic parameters such as plasma clearance and bioavailability. We investigated the effect of different fluorescent helix-stabilizing linkers with varying lipophilicity on subcutaneous (SC) bioavailability using the glucagon-like peptide-1 (GLP-1) receptor ligand exendin as a model system. The stabilized peptides showed significantly higher protease resistance and increased bioavailability independent of linker hydrophilicity, and all subcutaneously delivered conjugates were able to successfully target the islets of Langerhans with high specificity. The lipophilic peptide variants had slower absorption and plasma clearance than their respective hydrophilic conjugates, and the absolute bioavailability was also lower likely due to the longer residence times in the skin. The ease and efficiency of double-click helix stabilization chemistries is a useful tool for increasing the bioavailability of peptide therapeutics, many of which suffer from rapid in vivo protease degradation. Helix stabilization using linkers of varying lipophilicity can further control SC absorption and clearance rates to customize plasma pharmacokinetics. PMID:27327034

  8. Paramagnetic particles carried by cell-penetrating peptide tracking of bone marrow mesenchymal stem cells, a research in vitro

    Liu Min; Guo Youmin; Wu Qifei; Yang Junle; Wang Peng; Wang Sicen; Guo Xiaojuan; Qiang Yongqian; Duan Xiaoyi

    2006-01-01

    The ability to track the distribution and differentiation of stem cells by high-resolution imaging techniques would have significant clinical and research implications. In this study, a model cell-penetrating peptide was used to carry gadolinium particles for magnetic resonance imaging of the mesenchymal stem cells. The mesenchymal stem cells were isolated from rat bone marrow by Percoll and identified by osteogenic differentiation in vitro. The cell-penetrating peptides labeled with fluorescein-5-isothiocyanate and gadolinium were synthesized by a solid-phase peptide synthesis method and the relaxivity of cell-penetrating peptide-gadolinium paramagnetic conjugate on 400 MHz nuclear magnetic resonance was 5.7311 ± 0.0122 mmol -1 s -1 , higher than that of diethylenetriamine pentaacetic acid gadolinium (p < 0.05). Fluorescein imaging confirmed that this new peptide could internalize into the cytoplasm and nucleus. Gadolinium was efficiently internalized into mesenchymal stem cells by the peptide in a time- or concentration-dependent fashion, resulting in intercellular T1 relaxation enhancement, which was obviously detected by 1.5 T magnetic resonance imaging. Cytotoxicity assay and flow cytometric analysis showed the intercellular contrast medium incorporation did not affect cell viability and membrane potential gradient. The research in vitro suggests that the newly constructed peptides could be a vector for tracking mesenchymal stem cells

  9. Conformational Flexibility Determines Selectivity and Antibacterial, Antiplasmodial, and Anticancer Potency of Cationic α-Helical Peptides*

    Vermeer, Louic S.; Lan, Yun; Abbate, Vincenzo; Ruh, Emrah; Bui, Tam T.; Wilkinson, Louise J.; Kanno, Tokuwa; Jumagulova, Elmira; Kozlowska, Justyna; Patel, Jayneil; McIntyre, Caitlin A.; Yam, W. C.; Siu, Gilman; Atkinson, R. Andrew; Lam, Jenny K. W.

    2012-01-01

    Background: Antimicrobial peptides (AMPs) have the potential to act against multiple pathogenic targets. Results: AMPs that maintain conformational flexibility are more potent against multiple pathogens and less hemolytic. Conclusion: Antimicrobial action and hemolysis proceed via differing mechanisms. Significance: The potency, selectivity, and ability of AMPs to reach intracellular pathogens can be modulated using general principles.

  10. How proteases from Enterococcus faecalis contribute to its resistance to short alpha-helical antimicrobial peptides

    Nešuta, Ondřej; Buděšínský, Miloš; Hadravová, Romana; Monincová, Lenka; Humpolíčková, Jana; Čeřovský, Václav

    2017-01-01

    Roč. 75, č. 7 (2017), č. článku ftx091. ISSN 2049-632X R&D Projects: GA TA ČR(CZ) TA04010638; GA MZd(CZ) NV16-27726A Institutional support: RVO:61388963 Keywords : antimicrobial peptides * biofilm * C-terminal deamidation * gelatinase * protease Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 2.335, year: 2016

  11. Lybatides from Lycium barbarum Contain An Unusual Cystine-stapled Helical Peptide Scaffold.

    Tan, Wei Liang; Wong, Ka H; Lei, Jian; Sakai, Naoki; Tan, Hong Wei; Hilgenfeld, Rolf; Tam, James P

    2017-07-12

    Cysteine-rich peptides (CRPs) of 2-6 kDa are generally thermally and proteolytically stable because of their multiple cross-bracing disulfide bonds. Here, we report the discovery and characterization of two novel cystine-stapled CRPs, designated lybatide 1 and 2 (lyba1 and lyba2), from the cortex of Lycium barbarum root. Lybatides, 32 to 33 amino acids in length, are hyperstable and display a novel disulfide connectivity with a cysteine motif of C-C-C-C-CC-CC which contains two pairs of adjacent cysteines (-CC-CC). X-ray structure analysis revealed the presence of a single cystine-stabilized (α + π)-helix in lyba2, a rare feature of CRPs. Together, our results suggest that lybatides, one of the smallest four-disulfide-constrained plant CRPs, is a new family of CRPs. Additionally, this study provides new insights into the molecular diversity of plant cysteine-rich peptides and the unusual lybatide scaffold could be developed as a useful template for peptide engineering and therapeutic development.

  12. Effect of TFE on the Helical Content of AK17 and HAL-1 Peptides: Theoretical Insights into the Mechanism of Helix Stabilization.

    Vymětal, Jiří; Bednárová, Lucie; Vondrášek, Jiří

    2016-02-18

    Fluorinated alcohols such as 2,2,2-trifluoroethanol (TFE) are among the most frequently used cosolvents in experiment studies of peptides. They have significant effects on secondary structure and a particularly strong promotion of α-helix is induced by TFE. In this study we validated recently proposed force field parameters for TFE in molecular dynamics simulations with two model peptides-alanine-rich AK-17 and antimicrobial peptide halictine-1 (HAL-1). In the case of HAL-1, we characterized the effect of TFE on this peptide experimentally by ECD spectroscopy. Our TFE model in question reproduced the helix-promoting effect of TFE and provided insight into the mechanisms of TFE action on peptides. Our simulations confirmed the preferential interaction of TFE molecules with α-helices, although the TFE molecules accumulate in the vicinity of the peptides in various conformations. Moreover, we observed a significant effect of TFE on the thermodynamics of the helix-coil transition and a change in local conformational preferences in the unfolded (coil) state induced by TFE. In addition, our simulation-based analysis suggests that different mechanisms participate in helix stabilization in both model peptides in water and TFE solution. Our results thus support the picture of complex TFE action on peptides that is further diversified by the identity and intrinsic properties of the peptide.

  13. Rational Design of Alpha-Helical Antimicrobial Peptides: Do's and Don'ts

    Uggerhøj, Lars Erik; Poulsen, Tanja Juul; Munk, Jens Kristian

    2015-01-01

    Antimicrobial peptides (AMPs) are promising candidates for battling multiresistant bacteria. Despite extensive research, structure–activity relationships of AMPs are not fully understood, and there is a lack of structural data relating to AMPs in lipids. Here we present the NMR structure of anoplin...... (GLLKRIKTLL-NH2) in a micellar environment. A vast library of substitutions was designed and tested for antimicrobial and hemolytic activity, as well as for changes in structure and lipid interactions. This showed that improvement of antimicrobial activity without concomitant introduction of strong hemolytic...

  14. Dodecylphosphocholine Micelles Induce Amyloid Formation of the PrP(110-136 Peptide via an α-Helical Metastable Conformation.

    Simon Sauvé

    Full Text Available A peptide encompassing the conserved hydrophobic region and the first β-strand of the prion protein (PrP(110-136 shown to interact with the surface of dodecylphosphocholine micelles adopts an α-helical conformation that is localized below the head-group layer. This surface-bound peptide has a half-life of one day, and readily initiates the formation of amyloid fibrils. The presence of the latter was confirmed using birefringence microscopy upon Congo red binding and thioflavin T-binding induced fluorescence. The observation of this metastable α-helical conformer provides a unique snapshot of the early steps of the inter-conversion pathway. These findings together with the body of evidence from the prion literature allowed us to propose a mechanism for the conversion of PrPC to amyloid material.

  15. Order through disorder: hyper-mobile C-terminal residues stabilize the folded state of a helical peptide. a molecular dynamics study.

    Kalliopi K Patapati

    Full Text Available Conventional wisdom has it that the presence of disordered regions in the three-dimensional structures of polypeptides not only does not contribute significantly to the thermodynamic stability of their folded state, but, on the contrary, that the presence of disorder leads to a decrease of the corresponding proteins' stability. We have performed extensive 3.4 µs long folding simulations (in explicit solvent and with full electrostatics of an undecamer peptide of experimentally known helical structure, both with and without its disordered (four residue long C-terminal tail. Our simulations clearly indicate that the presence of the apparently disordered (in structural terms C-terminal tail, increases the thermodynamic stability of the peptide's folded (helical state. These results show that at least for the case of relatively short peptides, the interplay between thermodynamic stability and the apparent structural stability can be rather subtle, with even disordered regions contributing significantly to the stability of the folded state. Our results have clear implications for the understanding of peptide energetics and the design of foldable peptides.

  16. Exploring the Changes in the Structure of α-Helical Peptides ...

    sathish

    Method: Molecular dynamics. Package: Gromacs 4.0.3 .... The abovementioned observation is verified by carrying out simulation in two different force fields. ... using their saturated RMSD values and also by using the cluster analysis. 25.

  17. Disulfide-stabilized Helical Hairpin Structure and Activity of a Novel Antifungal Peptide EcAMP1 from Seeds of Barnyard Grass (Echinochloa crus-galli)*

    Nolde, Svetlana B.; Vassilevski, Alexander A.; Rogozhin, Eugene A.; Barinov, Nikolay A.; Balashova, Tamara A.; Samsonova, Olga V.; Baranov, Yuri V.; Feofanov, Alexey V.; Egorov, Tsezi A.; Arseniev, Alexander S.; Grishin, Eugene V.

    2011-01-01

    This study presents purification, activity characterization, and 1H NMR study of the novel antifungal peptide EcAMP1 from kernels of barnyard grass Echinochloa crus-galli. The peptide adopts a disulfide-stabilized α-helical hairpin structure in aqueous solution and thus represents a novel fold among naturally occurring antimicrobial peptides. Micromolar concentrations of EcAMP1 were shown to inhibit growth of several fungal phytopathogens. Confocal microscopy revealed intensive EcAMP1 binding to the surface of fungal conidia followed by internalization and accumulation in the cytoplasm without disturbance of membrane integrity. Close spatial structure similarity between EcAMP1, the trypsin inhibitor VhTI from seeds of Veronica hederifolia, and some scorpion and cone snail toxins suggests natural elaboration of different functions on a common fold. PMID:21561864

  18. Disulfide-stabilized helical hairpin structure and activity of a novel antifungal peptide EcAMP1 from seeds of barnyard grass (Echinochloa crus-galli).

    Nolde, Svetlana B; Vassilevski, Alexander A; Rogozhin, Eugene A; Barinov, Nikolay A; Balashova, Tamara A; Samsonova, Olga V; Baranov, Yuri V; Feofanov, Alexey V; Egorov, Tsezi A; Arseniev, Alexander S; Grishin, Eugene V

    2011-07-15

    This study presents purification, activity characterization, and (1)H NMR study of the novel antifungal peptide EcAMP1 from kernels of barnyard grass Echinochloa crus-galli. The peptide adopts a disulfide-stabilized α-helical hairpin structure in aqueous solution and thus represents a novel fold among naturally occurring antimicrobial peptides. Micromolar concentrations of EcAMP1 were shown to inhibit growth of several fungal phytopathogens. Confocal microscopy revealed intensive EcAMP1 binding to the surface of fungal conidia followed by internalization and accumulation in the cytoplasm without disturbance of membrane integrity. Close spatial structure similarity between EcAMP1, the trypsin inhibitor VhTI from seeds of Veronica hederifolia, and some scorpion and cone snail toxins suggests natural elaboration of different functions on a common fold.

  19. Effects on in vitro and in vivo angiogenesis induced by small peptides carrying adhesion sequences.

    Conconi, Maria Teresa; Ghezzo, Francesca; Dettin, Monica; Urbani, Luca; Grandi, Claudio; Guidolin, Diego; Nico, Beatrice; Di Bello, Carlo; Ribatti, Domenico; Parnigotto, Pier Paolo

    2010-07-01

    It is well known that tumor growth is strictly dependent on neo-vessel formation inside the tumor mass and that cell adhesion is required to allow EC proliferation and migration inside the tumor. In this work, we have evaluated the in vitro and in vivo effects on angiogenesis of some peptides, originally designed to promote cell adhesion on biomaterials, containing RGD motif mediating cell adhesion via integrin receptors [RGD, GRGDSPK, and (GRGDSP)(4)K] or the heparin-binding sequence of human vitronectin that interacts with HSPGs [HVP(351-359)]. Cell adhesion, proliferation, migration, and capillary-like tube formation in Matrigel were determined on HUVECs, whereas the effects on in vivo angiogenesis were evaluated using the CAM assay. (GRGDSP)(4)K linear sequence inhibited cell adhesion, decreased cell proliferation, migration and morphogenesis in Matrigel, and induced anti-angiogenic responses on CAM at higher degree than that determined after incubation with RGD or GRGDSPK. Moreover, it counteracted both in vitro and in vivo the pro-angiogenic effects induced by the Fibroblast growth factor (FGF-2). On the other hand, HVP was not able to affect cell adhesion and appeared less effective than (GRGDSP)(4)K. Our data indicate that the activity of RGD-containing peptides is related to their adhesive properties, and their effects are modulated by the number of cell adhesion motifs and the aminoacidic residues next to these sequences. The anti-angiogenic properties of (GRGDSP)(4)K seem to depend on its interaction with integrins, whereas the effects of HVP may be partially due to an impairment of HSPGs/FGF-2.

  20. Investigating the role of GXXXG motifs in helical folding and self-association of plasticins, Gly/Leu-rich antimicrobial peptides.

    Carlier, Ludovic; Joanne, Pierre; Khemtémourian, Lucie; Lacombe, Claire; Nicolas, Pierre; El Amri, Chahrazade; Lequin, Olivier

    2015-01-01

    Plasticins (PTC) are dermaseptin-related antimicrobial peptides characterized by a large number of leucine and glycine residues arranged in GXXXG motifs that are often described to promote helix association within biological membranes. We report the structure and interaction properties of two plasticins, PTC-B1 from Phyllomedusa bicolor and a cationic analog of PTC-DA1 from Pachymedusa dacnicolor, which exhibit membrane-lytic activities on a broad range of microorganisms. Despite a high number of glycine, CD and NMR spectroscopy show that the two plasticins adopt mainly alpha-helical conformations in a wide variety of environments such as trifluoroethanol, detergent micelles and lipid vesicles. In DPC and SDS, plasticins adopt well-defined helices that lie parallel to the micelle surface, all glycine residues being located on the solvent-exposed face. Spectroscopic data and cross-linking experiments indicate that the GXXXG repeats in these amphipathic helices do not provide a strong oligomerization interface, suggesting a different role from GXXXG motifs found in transmembrane helices. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Alpha-helical destabilization of the Bcl-2-BH4-domain peptide abolishes its ability to inhibit the IP3 receptor.

    Giovanni Monaco

    Full Text Available The anti-apoptotic Bcl-2 protein is the founding member and namesake of the Bcl-2-protein family. It has recently been demonstrated that Bcl-2, apart from its anti-apoptotic role at mitochondrial membranes, can also directly interact with the inositol 1,4,5-trisphosphate receptor (IP3R, the primary Ca(2+-release channel in the endoplasmic reticulum (ER. Bcl-2 can thereby reduce pro-apoptotic IP3R-mediated Ca(2+ release from the ER. Moreover, the Bcl-2 homology domain 4 (Bcl-2-BH4 has been identified as essential and sufficient for this IP3R-mediated anti-apoptotic activity. In the present study, we investigated whether the reported inhibitory effect of a Bcl-2-BH4 peptide on the IP 3R1 was related to the distinctive α-helical conformation of the BH4 domain peptide. We therefore designed a peptide with two glycine "hinges" replacing residues I14 and V15, of the wild-type Bcl-2-BH4 domain (Bcl-2-BH4-IV/GG. By comparing the structural and functional properties of the Bcl-2-BH4-IV/GG peptide with its native counterpart, we found that the variant contained reduced α-helicity, neither bound nor inhibited the IP 3R1 channel, and in turn lost its anti-apoptotic effect. Similar results were obtained with other substitutions in Bcl-2-BH4 that destabilized the α-helix with concomitant loss of IP3R inhibition. These results provide new insights for the further development of Bcl-2-BH4-derived peptides as specific inhibitors of the IP3R with significant pharmacological implications.

  2. Molecular dynamics investigation of the influence of anionic and zwitterionic interfaces on antimicrobial peptides' structure: implications for peptide toxicity and activity

    Khandelia, Himanshu; Kaznessis, Yiannis N

    2006-01-01

    Molecular dynamics simulations of three related helical antimicrobial peptides have been carried out in zwitterionic diphosphocholine (DPC) micelles and anionic sodiumdodecylsulfate (SDS) micelles. These systems can be considered as model mammalian and bacterial membrane interfaces, respectively...

  3. Folding control in cyclic peptides through N-methylation pattern selection: formation of antiparallel beta-sheet dimers, double reverse turns and supramolecular helices by 3alpha,gamma cyclic peptides.

    Amorín, Manuel; Castedo, Luis; Granja, Juan R

    2008-01-01

    Peptide foldamers constitute a growing class of nanomaterials with potential applications in a wide variety of chemical, medical and technological fields. Here we describe the preparation and structural characteristics of a new class of cyclic peptide foldamers (3alpha,gamma-CPs) that, depending on their backbone N-methylation patterns and the medium, can either remain as flat rings that dimerize through arrays of hydrogen bonds of antiparallel beta-sheet type, or can fold into twisted double reverse turns that, in the case of double gamma-turns, associate in nonpolar solvents to form helical supramolecular structures. A 3alpha,gamma-CP consists of a number of multiples of a repeat unit made up of four amino acid residues of alternating chirality: three corresponding to alpha-amino acids and one to a gamma-amino acid (a cis-3-aminocycloalkanecarboxylic acid).

  4. Effect of hydrocarbon stapling on the properties of alpha-helical antimicrobial peptides isolated from the venom of hymenoptera

    Chapuis, Hubert Jean; Slaninová, Jiřina; Bednárová, Lucie; Monincová, Lenka; Buděšínský, Miloš; Čeřovský, Václav

    2012-01-01

    Roč. 43, č. 5 (2012), s. 2047-2058 ISSN 0939-4451 R&D Projects: GA ČR GA203/08/0536 Institutional research plan: CEZ:AV0Z40550506 Keywords : antimicrobial peptides * stapled peptides * amphipathic helix * CD spectroscopy Subject RIV: CC - Organic Chemistry Impact factor: 3.914, year: 2012

  5. The feasibility of a targeted ultrasound contrast agent carrying genes and cell-penetrating peptides to hypoxic HUVEC

    Tian Ju; Wang Zhigang; Ren Jianli; Zhang Qingfeng; Liu Li

    2012-01-01

    Objective: To prepare an anti-P-selectin targeted ultrasound contrast agent carrying genes and cell-penetrating peptides (CPP) and to investigate its feasibility of delivery to hypoxic human umbilical vein endothelial cells (HUVEC). Methods: Anti-P-selectin targeted ultrasound contrast agent carrying a green fluorescent protein gene (pEGFP-N1) and CPP was prepared by mechanical vibration and carbodiimide techniques. The appearance, distribution, concentration and diameter of the ultrasound contrast agent were measured. The gene and CPP distribution on the agent was investigated using confocal laser scanning microscopy (CLSM). The efficiency of the ultrasound contrast agent to carry the gene and CPP was investigated by fluorospectrophotometry. HUVEC were cultured in vitro and hypoxic HUVEC were prepared using hydrogen peroxide (H 2 O 2 ). Hypoxic HUVEC were randomly assigned targeted ultrasound contrast agents and non-targeted ultrasound contrast agents for transfection. The transfection effect of green fluorescent protein in the two groups was observed using fluorescence microscopy and flow cytometry. T-test and linear correlation analysis were used for statistical analysis. Results: The average diameter of anti-P-selectin targeted ultrasound contrast agents carrying gene and CPP was (2.15 ±0.36) μm and the concentration was (1.58 ± 0.23) × 10 7 /ml.The results of CLSM showed that gene and CPP were distributed on the shell of the agent. The gene encapsulation efficiency was 28% (y=0.932x-0.09, r=0.993, P<0.05), and the CPP encapsulation efficiency was 25% (y=5.875x-0.81, r=0.987, P<0.05). EGFP expression was observed using fluorescence microscopy in targeted ultrasound contrast agents and non-targeted ultrasound contrast agents. The average transfection efficiencies of targeted ultrasound contrast agents and non-targeted ultrasound contrast agents were (18.74 ± 0.47) % and (15.34 ± 0.22) % after 24 h (t=10.923, P<0.001). Conclusions: The in vitro studies

  6. Expanding the peptide beta-turn in alphagamma hybrid sequences: 12 atom hydrogen bonded helical and hairpin turns.

    Chatterjee, Sunanda; Vasudev, Prema G; Raghothama, Srinivasarao; Ramakrishnan, Chandrasekharan; Shamala, Narayanaswamy; Balaram, Padmanabhan

    2009-04-29

    Hybrid peptide segments containing contiguous alpha and gamma amino acid residues can form C(12) hydrogen bonded turns which may be considered as backbone expanded analogues of C(10) (beta-turns) found in alphaalpha segments. Exploration of the regular hydrogen bonded conformations accessible for hybrid alphagamma sequences is facilitated by the use of a stereochemically constrained gamma amino acid residue gabapentin (1-aminomethylcyclohexaneacetic acid, Gpn), in which the two torsion angles about C(gamma)-C(beta) (theta(1)) and C(beta)-C(alpha) (theta(2)) are predominantly restricted to gauche conformations. The crystal structures of the octapeptides Boc-Gpn-Aib-Gpn-Aib-Gpn-Aib-Gpn-Aib-OMe (1) and Boc-Leu-Phe-Val-Aib-Gpn-Leu-Phe-Val-OMe (2) reveal two distinct conformations for the Aib-Gpn segment. Peptide 1 forms a continuous helix over the Aib(2)-Aib(6) segment, while the peptide 2 forms a beta-hairpin structure stabilized by four cross-strand hydrogen bonds with the Aib-Gpn segment forming a nonhelical C(12) turn. The robustness of the helix in peptide 1 in solution is demonstrated by NMR methods. Peptide 2 is conformationally fragile in solution with evidence of beta-hairpin conformations being obtained in methanol. Theoretical calculations permit delineation of the various C(12) hydrogen bonded structures which are energetically feasible in alphagamma and gammaalpha sequences.

  7. The PDB database is a rich source of alpha-helical anti-microbial peptides to combat disease causing pathogens [version 2; referees: 2 approved, 1 approved with reservations

    Sandeep Chakraborty

    2015-06-01

    Full Text Available The therapeutic potential of α-helical anti-microbial peptides (AH-AMP to combat pathogens is fast gaining prominence. Based on recently published open access software for characterizing α-helical peptides (PAGAL, we elucidate a search methodology (SCALPEL that leverages the massive structural data pre-existing in the PDB database to obtain AH-AMPs belonging to the host proteome. We provide in vitro validation of SCALPEL on plant pathogens (Xylella fastidiosa, Xanthomonas arboricola and Liberibacter crescens by identifying AH-AMPs that mirror the function and properties of cecropin B, a well-studied AH-AMP. The identified peptides include a linear AH-AMP present within the existing structure of phosphoenolpyruvate carboxylase (PPC20, and an AH-AMP mimicing the properties of the two α-helices of cecropin B from chitinase (CHITI25. The minimum inhibitory concentration of these peptides are comparable to that of cecropin B, while anionic peptides used as control failed to show any inhibitory effect on these pathogens. Substitute therapies in place of conventional chemotherapies using membrane permeabilizing peptides like these might also prove effective to target cancer cells. The use of native structures from the same organism could possibly ensure that administration of such peptides will be better tolerated and not elicit an adverse immune response. We suggest a similar approach to target Ebola epitopes, enumerated using PAGAL recently, by selecting suitable peptides from the human proteome, especially in wake of recent reports of cationic amphiphiles inhibiting virus entry and infection.

  8. Phosphorylated peptides occur in a non-helical portion of the tail of a catch muscle myosin

    Castellani, L.; Elliott, B.W. Jr.; Cohen, C.

    1987-01-01

    Myosin from a molluscan catch muscle (the Anterior Byssus Retractor (ABRM) of Mytilus edulis) is unusual in being phosphorylated in the rod by an endogenous heavy-chain kinase. This phosphorylation enhances myosin solubility at low ionic strength and induces molecular folding of the myosin tail. Papain and chymotryptic cleavage of this myosin, phosphorylated with [γ- 32 P]ATP, indicates that the phosphorylated residues are associated with the carboxy-terminal end of the light meromyosin. Ion-exchange and reverse-phase HPLC of radiolabeled chymotryptic peptides allow the isolation of two different peptides with high specific activity. One of these peptides is rich in lysine and arginine residues, a finding consistent with the observation that basic residues often determine the substrate specificity of protein kinases. The second peptide contains proline residues. Taken together, these results suggest that, as in the case of Acanthamoeba myosin, phosphorylation occurs in a nonhelical portion of the rod that may also control solubility. Identification of the residues that are phosphorylated and their location in the rod may reveal how the phosphorylation-dependent changes observed in the myosin in vitro are related to changes in intermolecular interactions in the thick filaments in vivo

  9. Site-specific Orientation of an α-helical Peptide Ovispirin-1 from Isotope Labeled SFG Spectroscopy

    Ding, Bei; Laaser, Jennifer E.; Liu, Yuwei; Wang, Pengrui; Zanni, Martin T.; Chen, Zhan

    2013-01-01

    Sum-frequency generation (SFG) vibrational spectroscopy is often used to probe the backbone structures and orientations of polypeptides at surfaces. Using the ovispirin-1 polypeptide at the solid/liquid interface of polystyrene, we demonstrate for the first time that SFG can probe the polarization response of a single isotope labeled residue. To interpret the spectral intensities, we simulated the spectra using an excitonic Hamiltonian approach. We show that the polarization dependence of either the label or the unlabeled amide I band alone does not provide sufficient structural constraints to obtain both the tilt and the twist of the ovispirin helix at a solid/liquid interface, but that both can be determined from the polarization dependence of the complete spectrum. For ovispirin, the detailed analysis of the polarized SFG experimental data shows that the helix axis is tilted at roughly 138 degrees from the surface normal, and the transition dipole of the isotope labeled C=O group is tilted at 23 degrees from the surface normal, with the hydrophobic region facing the polystyrene surface. We further demonstrated that the Hamiltonian approach is able to address the coupling effect and the structural disorder. For comparison, we also collected the FTIR spectrum of ovispirin under similar conditions, which reveals the enhanced sensitivity of SFG for structural studies of single monolayer peptide surfaces. Our study provides insight into how structural and environmental effects appear in SFG spectra of the amide I band and establishes that SFG of isotope labeled peptides will be a powerful technique for elucidating secondary structures with residue-by-residue resolution. PMID:24228619

  10. Site-specific orientation of an α-helical peptide ovispirin-1 from isotope-labeled SFG spectroscopy.

    Ding, Bei; Laaser, Jennifer E; Liu, Yuwei; Wang, Pengrui; Zanni, Martin T; Chen, Zhan

    2013-11-27

    Sum-frequency generation (SFG) vibrational spectroscopy is often used to probe the backbone structures and orientations of polypeptides at surfaces. Using the ovispirin-1 polypeptide at the solid/liquid interface of polystyrene, we demonstrate for the first time that SFG can probe the polarization response of a single-isotope-labeled residue. To interpret the spectral intensities, we simulated the spectra using an excitonic Hamiltonian approach. We show that the polarization dependence of either the label or the unlabeled amide I band alone does not provide sufficient structural constraints to obtain both the tilt and the twist of the ovispirin helix at a solid/liquid interface, but that both can be determined from the polarization dependence of the complete spectrum. For ovispirin, the detailed analysis of the polarized SFG experimental data shows that the helix axis is tilted at roughly 138° from the surface normal, and the transition dipole of the isotope-labeled C═O group is tilted at 23° from the surface normal, with the hydrophobic region facing the polystyrene surface. We further demonstrate that the Hamiltonian approach is able to address the coupling effect and the structural disorder. For comparison, we also collected the FTIR spectrum of ovispirin under similar conditions, which reveals the enhanced sensitivity of SFG for structural studies of single monolayer peptide surfaces. Our study provides insight into how structural and environmental effects appear in SFG spectra of the amide I band and establishes that SFG of isotope-labeled peptides will be a powerful technique for elucidating secondary structures with residue-by-residue resolution.

  11. Solid-state nuclear magnetic resonance measurements of HIV fusion peptide 13CO to lipid 31P proximities support similar partially inserted membrane locations of the α helical and β sheet peptide structures.

    Gabrys, Charles M; Qiang, Wei; Sun, Yan; Xie, Li; Schmick, Scott D; Weliky, David P

    2013-10-03

    Fusion of the human immunodeficiency virus (HIV) membrane and the host cell membrane is an initial step of infection of the host cell. Fusion is catalyzed by gp41, which is an integral membrane protein of HIV. The fusion peptide (FP) is the ∼25 N-terminal residues of gp41 and is a domain of gp41 that plays a key role in fusion catalysis likely through interaction with the host cell membrane. Much of our understanding of the FP domain has been accomplished with studies of "HFP", i.e., a ∼25-residue peptide composed of the FP sequence but lacking the rest of gp41. HFP catalyzes fusion between membrane vesicles and serves as a model system to understand fusion catalysis. HFP binds to membranes and the membrane location of HFP is likely a significant determinant of fusion catalysis perhaps because the consequent membrane perturbation reduces the fusion activation energy. In the present study, many HFPs were synthesized and differed in the residue position that was (13)CO backbone labeled. Samples were then prepared that each contained a singly (13)CO labeled HFP incorporated into membranes that lacked cholesterol. HFP had distinct molecular populations with either α helical or oligomeric β sheet structure. Proximity between the HFP (13)CO nuclei and (31)P nuclei in the membrane headgroups was probed by solid-state NMR (SSNMR) rotational-echo double-resonance (REDOR) measurements. For many samples, there were distinct (13)CO shifts for the α helical and β sheet structures so that the proximities to (31)P nuclei could be determined for each structure. Data from several differently labeled HFPs were then incorporated into a membrane location model for the particular structure. In addition to the (13)CO labeled residue position, the HFPs also differed in sequence and/or chemical structure. "HFPmn" was a linear peptide that contained the 23 N-terminal residues of gp41. "HFPmn_V2E" contained the V2E mutation that for HIV leads to greatly reduced extent of fusion and

  12. Beta-helical polymers from isocyanopeptides

    Cornelissen, J.J.L.M.; Donners, J.J.J.M.; Gelder, de R.; Graswinckel, W.S.; Metselaar, G.A.; Rowan, A.E.; Sommerdijk, N.A.J.M.; Nolte, R.J.M.

    2001-01-01

    Polymerization of isocyanopeptides results in the formation of high molecular mass polymers that fold in a proteinlike fashion to give helical strands in which the peptide chains are arranged in ß-sheets. The ß-helical polymers retain their structure in water and unfold in a cooperative process at

  13. Molecular basis for endotoxin neutralization by amphipathic peptides derived from the alpha-helical cationic core-region of NK-lysin.

    Brandenburg, Klaus; Garidel, Patrick; Fukuoka, Satoshi; Howe, Jörg; Koch, Michel H J; Gutsmann, Thomas; Andrä, Jörg

    2010-08-01

    An analysis of the interaction of the NK-lysin derived peptide NK-2 and of analogs thereof with bacterial lipopolysaccharide (LPS, endotoxin) was performed to determine the most important biophysical parameters for an effective LPS neutralization. We used microcalorimetry, FTIR spectroscopy, Zeta potential measurements, and small-angle X-ray scattering to analyze the peptide:LPS binding enthalpy, the accessible LPS surface charge, the fluidity of the LPS hydrocarbon chains, their phase transition enthalpy change, the aggregate structure of LPS, and how these parameters are modulated by the peptides. We conclude that (i) a high peptide:LPS binding affinity, which is facilitated by electrostatic and hydrophobic interactions and which leads to a positive Zeta potential, (ii) the formation of peptide-enriched domains, which destabilize the lipid packing, demonstrated by a drastic decrease of phase transition enthalpy change of LPS, and (iii) the multilamellarization of the LPS aggregate structure are crucial for an effective endotoxin neutralization by cationic peptides.

  14. Helical filaments

    Barbieri, Nicholas; Lim, Khan; Durand, Magali; Baudelet, Matthieu; Richardson, Martin [Townes Laser Institute, CREOL—The College of Optics and Photonics, University of Central Florida, Orlando, Florida 32816 (United States); Hosseinimakarem, Zahra; Johnson, Eric [Micro-Photonics Laboratory – Center for Optical Material Science, Clemson, Anderson, South Carolina 29634 (United States)

    2014-06-30

    The shaping of laser-induced filamenting plasma channels into helical structures by guiding the process with a non-diffracting beam is demonstrated. This was achieved using a Bessel beam superposition to control the phase of an ultrafast laser beam possessing intensities sufficient to induce Kerr effect driven non-linear self-focusing. Several experimental methods were used to characterize the resulting beams and confirm the observed structures are laser air filaments.

  15. Pregnancy Vaccination with Gold Glyco-Nanoparticles Carrying Listeria monocytogenes Peptides Protects against Listeriosis and Brain- and Cutaneous-Associated Morbidities

    Ricardo Calderón-Gonzalez

    2016-08-01

    Full Text Available Listeriosis is a fatal infection for fetuses and newborns with two clinical main morbidities in the neonatal period, meningitis and diffused cutaneous lesions. In this study, we vaccinated pregnant females with two gold glyconanoparticles (GNP loaded with two peptides, listeriolysin peptide 91–99 (LLO91–99 or glyceraldehyde-3-phosphate dehydrogenase 1–22 peptide (GAPDH1–22. Neonates born to vaccinated mothers were free of bacteria and healthy, while non-vaccinated mice presented clear brain affections and cutaneous diminishment of melanocytes. Therefore, these nanoparticle vaccines are effective measures to offer pregnant mothers at high risk of listeriosis interesting therapies that cross the placenta.

  16. Pregnancy Vaccination with Gold Glyco-Nanoparticles Carrying Listeria monocytogenes Peptides Protects against Listeriosis and Brain- and Cutaneous-Associated Morbidities

    Calderón-Gonzalez, Ricardo; Terán-Navarro, Héctor; Frande-Cabanes, Elisabet; Ferrández-Fernández, Eva; Freire, Javier; Penadés, Soledad; Marradi, Marco; García, Isabel; Gomez-Román, Javier; Yañez-Díaz, Sonsoles; Álvarez-Domínguez, Carmen

    2016-01-01

    Listeriosis is a fatal infection for fetuses and newborns with two clinical main morbidities in the neonatal period, meningitis and diffused cutaneous lesions. In this study, we vaccinated pregnant females with two gold glyconanoparticles (GNP) loaded with two peptides, listeriolysin peptide 91–99 (LLO91–99) or glyceraldehyde-3-phosphate dehydrogenase 1–22 peptide (GAPDH1–22). Neonates born to vaccinated mothers were free of bacteria and healthy, while non-vaccinated mice presented clear brain affections and cutaneous diminishment of melanocytes. Therefore, these nanoparticle vaccines are effective measures to offer pregnant mothers at high risk of listeriosis interesting therapies that cross the placenta. PMID:28335280

  17. Structure determination of a peptide model of the repeated helical domain in Samia cynthia ricini silk fibroin before spinning by a combination of advanced solid-state NMR methods.

    Nakazawa, Yasumoto; Asakura, Tetsuo

    2003-06-18

    Fibrous proteins unlike globular proteins, contain repetitive amino acid sequences, giving rise to very regular secondary protein structures. Silk fibroin from a wild silkworm, Samia cynthia ricini, consists of about 100 repeats of alternating polyalanine (poly-Ala) regions of 12-13 residues in length and Gly-rich regions. In this paper, the precise structure of the model peptide, GGAGGGYGGDGG(A)(12)GGAGDGYGAG, which is a typical repeated sequence of the silk fibroin, was determined using a combination of three kinds of solid-state NMR studies; a quantitative use of (13)C CP/MAS NMR chemical shift with conformation-dependent (13)C chemical shift contour plots, 2D spin diffusion (13)C solid-state NMR under off magic angle spinning and rotational echo double resonance. The structure of the model peptide corresponding to the silk fibroin structure before spinning was determined. The torsion angles of the central Ala residue, Ala(19), in the poly-Ala region were determined to be (phi, psi) = (-59 degrees, -48 degrees ) which are values typically associated with alpha-helical structures. However, the torsion angles of the Gly(25) residue adjacent to the C-terminal side of the poly-Ala chain were determined to be (phi, psi) = (-66 degrees, -22 degrees ) and those of Gly(12) and Ala(13) residues at the N-terminal of the poly-Ala chain to be (phi, psi) = (-70 degrees, -30 degrees ). In addition, REDOR experiments indicate that the torsion angles of the two C-terminal Ala residues, Ala(23) and Ala(24), are (phi, psi) = (-66 degrees, -22 degrees ) and those of N-terminal two Ala residues, Ala(13) and Ala(14) are (phi, psi) = (-70 degrees, -30 degrees ). Thus, the local structure of N-terminal and C-terminal residues, and also the neighboring residues of alpha-helical poly-Ala chain in the model peptide is a more strongly wound structure than found in typical alpha-helix structures.

  18. Helicity content and tokamak applications of helicity

    Boozer, A.H.

    1986-05-01

    Magnetic helicity is approximately conserved by the turbulence associated with resistive instabilities of plasmas. To generalize the application of the concept of helicity, the helicity content of an arbitrary bounded region of space will be defined. The definition has the virtues that both the helicity content and its time derivative have simple expressions in terms of the poloidal and toroidal magnetic fluxes, the average toroidal loop voltage and the electric potential on the bounding surface, and the volume integral of E-B. The application of the helicity concept to tokamak plasmas is illustrated by a discussion of so-called MHD current drive, an example of a stable tokamak q profile with q less than one in the center, and a discussion of the possibility of a natural steady-state tokamak due to the bootstrap current coupling to tearing instabilities

  19. Key interactions by conserved polar amino acids located at the transmembrane helical boundaries in Class B GPCRs modulate activation, effector specificity and biased signalling in the glucagon-like peptide-1 receptor.

    Wootten, Denise; Reynolds, Christopher A; Smith, Kevin J; Mobarec, Juan C; Furness, Sebastian G B; Miller, Laurence J; Christopoulos, Arthur; Sexton, Patrick M

    2016-10-15

    Class B GPCRs can activate multiple signalling effectors with the potential to exhibit biased agonism in response to ligand stimulation. Previously, we highlighted key TM domain polar amino acids that were crucial for the function of the GLP-1 receptor, a key therapeutic target for diabetes and obesity. Using a combination of mutagenesis, pharmacological characterisation, mathematical and computational molecular modelling, this study identifies additional highly conserved polar residues located towards the TM helical boundaries of Class B GPCRs that are important for GLP-1 receptor stability and/or controlling signalling specificity and biased agonism. This includes (i) three positively charged residues (R3.30 227 , K4.64 288 , R5.40 310 ) located at the extracellular boundaries of TMs 3, 4 and 5 that are predicted in molecular models to stabilise extracellular loop 2, a crucial domain for ligand affinity and receptor activation; (ii) a predicted hydrogen bond network between residues located in TMs 2 (R2.46 176 ), 6 (R6.37 348 ) and 7 (N7.61 406 and E7.63 408 ) at the cytoplasmic face of the receptor that is important for stabilising the inactive receptor and directing signalling specificity, (iii) residues at the bottom of TM 5 (R5.56 326 ) and TM6 (K6.35 346 and K6.40 351 ) that are crucial for receptor activation and downstream signalling; (iv) residues predicted to be involved in stabilisation of TM4 (N2.52 182 and Y3.52 250 ) that also influence cell signalling. Collectively, this work expands our understanding of peptide-mediated signalling by the GLP-1 receptor. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  20. Helical Antimicrobial Sulfono- {gamma} -AApeptides

    Li, Yaqiong; Wu, Haifan; Teng, Peng; Bai, Ge; Lin, Xiaoyang; Zuo, Xiaobing; Cao, Chuanhai; Cai, Jianfeng

    2015-06-11

    Host-defense peptides (HDPs) such as magainin 2 have emerged as potential therapeutic agents combating antibiotic resistance. Inspired by their structures and mechanism of action, herein we report the fi rst example of antimicrobial helical sulfono- γ - AApeptide foldamers. The lead molecule displays broad-spectrum and potent antimicrobial activity against multi-drug-resistant Gram- positive and Gram-negative bacterial pathogens. Time-kill studies and fl uorescence microscopy suggest that sulfono- γ -AApeptides eradicate bacteria by taking a mode of action analogous to that of HDPs. Clear structure - function relationships exist in the studied sequences. Longer sequences, presumably adopting more-de fi ned helical structures, are more potent than shorter ones. Interestingly, the sequence with less helical propensity in solution could be more selective than the stronger helix-forming sequences. Moreover, this class of antimicrobial agents are resistant to proteolytic degradation. These results may lead to the development of a new class of antimicrobial foldamers combating emerging antibiotic-resistant pathogens.

  1. Flexible helical yarn swimmers.

    Zakharov, A P; Leshansky, A M; Pismen, L M

    2016-09-01

    We investigate the motion of a flexible Stokesian flagellar swimmer realised as a yarn made of two intertwined elastomer fibres, one active, that can reversibly change its length in response to a local excitation causing transition to the nematic state or swelling, and the other one, a passive isotropic elastomer with identical mechanical properties. A propagating chemical wave may provide an excitation mechanism ensuring a constant length of the excited region. Generally, the swimmer moves along a helical trajectory, and the propagation and rotation velocity are very sensitive to the ratio of the excited region to the pitch of the yarn, as well as to the size of a carried load. External excitation by a moving actuating beam is less effective, unless the direction of the beam is adjusted to rotation of the swimmer.

  2. Helical type vacuum container

    Owada, Kimio.

    1989-01-01

    Helical type vacuum containers in the prior art lack in considerations for thermal expansion stresses to helical coils, and there is a possibility of coil ruptures. The object of the present invention is to avoid the rupture of helical coils wound around the outer surface of a vacuum container against heat expansion if any. That is, bellows or heat expansion absorbing means are disposed to a cross section of a helical type vacuum container. With such a constitution, thermal expansion of helical coils per se due to temperature elevation of the coils during electric supply can be absorbed by expansion of the bellows or absorption of the heat expansion absorbing means. Further, this can be attained by arranging shear pins in the direction perpendicular to the bellows axis so that the bellows are not distorted when the helical coils are wound around the helical type vacuum container. (I.S.)

  3. Carrying Capacity

    Schroll, Henning; Andersen, Jan; Kjærgård, Bente

    2012-01-01

    A spatial planning act was introduced inIndonesia 1992 and renewed in 2008. It emphasised the planning role of decentralised authorities. The spatial planning act covers both spatial and environmental issues. It defines the concept of carrying capacity and includes definitions of supportive....../cities. Four different sectors (water, food production, waste, and forests) were selected as core areas for decentralised spatial planning. Indicators for SCC and ACC were identified and assessed with regard to relevance and quantifiability. For each of the indicators selected, a legal threshold or guiding...... was introduced inIndonesia 1992 and renewed in 2008. It emphasised the planning role of decentralised authorities. The spatial planning act covers both spatial and environmental issues. It defines the concept of carrying capacity and includes definitions of supportive carrying capacity (SCC) and assimilative...

  4. Pyrolysis of Helical Coordination Polymers for Metal-Sulfide-Based Helices with Broadband Chiroptical Activity.

    Hirai, Kenji; Yeom, Bongjun; Sada, Kazuki

    2017-06-27

    Fabrication of chiroptical materials with broadband response in the visible light region is vital to fully realize their potential applications. One way to achieve broadband chiroptical activity is to fabricate chiral nanostructures from materials that exhibit broadband absorption in the visible light region. However, the compounds used for chiroptical materials have predominantly been limited to materials with narrowband spectral response. Here, we synthesize Ag 2 S-based nanohelices derived from helical coordination polymers. The right- and left-handed coordination helices used as precursors are prepared from l- and d-glutathione with Ag + and a small amount of Cu 2+ . The pyrolysis of the coordination helices yields right- and left-handed helices of Cu 0.12 Ag 1.94 S/C, which exhibit chiroptical activity spanning the entire visible light region. Finite element method simulations substantiate that the broadband chiroptical activity is attributed to synergistic broadband light absorption and light scattering. Furthermore, another series of Cu 0.10 Ag 1.90 S/C nanohelices are synthesized by choosing the l- or d-Glu-Cys as starting materials. The pitch length of nanohelicies is controlled by changing the peptides, which alters their chiroptical properties. The pyrolysis of coordination helices enables one to fabricate helical Ag 2 S-based materials that enable broadband chiroptical activity but have not been explored owing to the lack of synthetic routes.

  5. A real-scale helical coil winding trial of the Large Helical Device

    Senba, T.; Yamamoto, T.; Tamaki, T.; Asano, K.; Suzuki, S.; Yamauchi, T.; Uchida, K.; Nakanishi, K.; Yamagiwa, T.; Suzuki, S.; Miyoshi, R.; Sasa, H.; Watanabe, S.; Tatemura, M.; Hatada, N.; Yamaguchi, S.; Imagawa, S.; Yanagi, N.; Satow, T.; Yamamoto, J.; Motojima, O.

    1995-01-01

    A real-scale helical coil winding trial of the Large Helical Device (LHD) has been conducted for a study of coil winding configuration and winding methods and for exhibiting the state of the art. It includes construction and test run of a specifically designed winding machine and development of various manufacturing methods for accurate coil winding. It has been carried out in Hitachi Works before in situ winding, and has provided much needed engineering data for construction of the LHD. (orig.)

  6. A note on helicity

    Bialynicki-Birula, I.; Newmann, E.T.; Porter, J.; Winicour, J.; Lukacs, B.; Perjes, Z.; Sebestyen, A.

    1981-03-01

    The authors give a formal definition of the helicity operator for integral spin fields, which does not involve their momentum-space decomposition. The discussion is based upon a representation of the Pauli-Lubanski operator in terms of the action on tensor fields by the Killing vectors associated with the generators of the Poincare group. This leads to an identification of the helicity operator with the duality operator defined by the space-time alternating tensor. Helicity eigenstates then correspond to self-dual or anti-self-dual fields, in agreement with usage implicit in the literature. In addiition, the relationship between helicity eigenstates which are intrinsically non-classical, and states of right or left circular polarization in classical electrodynamics are discussed. (author)

  7. Helical CT defecography

    Ferrando, R.; Fiorini, G.; Beghello, A.; Cicio, G.R.; Derchi, L.E.; Consigliere, M.; Resasco, M.; Tornago, S.

    1999-01-01

    The purpose of this work is to investigate the possible role of Helical CT defecography in pelvic floor disorders by comparing the results of the investigations with those of conventional defecography. The series analyzed consisted of 90 patients, namely 62 women and 28 men, ranging in age 24-82 years. They were all submitted to conventional defecography, and 18 questionable cases were also studied with Helical CT defecography. The conventional examination was performed during the 4 standard phases of resting, squeezing, Valsalva and straining; it is used a remote-control unit. The parameters for Helical CT defecography were: 5 mm beam collimation, pitch 2, 120 KV, 250 m As and 18-20 degrees gantry inclination to acquire coronal images of the pelvic floor. The rectal ampulla was distended with a bolus of 300 mL nonionic iodinated contrast agent (dilution: 3g/cc). The patient wore a napkin and was seated on the table, except for those who could not hold the position and were thus examined supine. Twenty-second helical scans were performed at rest and during evacuation; multiplanar reconstructions were obtained especially on the sagittal plane for comparison with conventional defecographic images. Coronal Helical CT defecography images permitted to map the perineal floor muscles, while sagittal reconstructions provided information on the ampulla and the levator ani. To conclude, Helical CT defecography performed well in study of pelvic floor disorders and can follow conventional defecography especially in questionable cases [it

  8. Helicity, Reconnection, and Dynamo Effects

    Ji, Hantao

    1998-01-01

    The inter-relationships between magnetic helicity, magnetic reconnection, and dynamo effects are discussed. In laboratory experiments, where two plasmas are driven to merge, the helicity content of each plasma strongly affects the reconnection rate, as well as the shape of the diffusion region. Conversely, magnetic reconnection events also strongly affect the global helicity, resulting in efficient helicity cancellation (but not dissipation) during counter-helicity reconnection and a finite helicity increase or decrease (but less efficiently than dissipation of magnetic energy) during co-helicity reconnection. Close relationships also exist between magnetic helicity and dynamo effects. The turbulent electromotive force along the mean magnetic field (alpha-effect), due to either electrostatic turbulence or the electron diamagnetic effect, transports mean-field helicity across space without dissipation. This has been supported by direct measurements of helicity flux in a laboratory plasma. When the dynamo effect is driven by electromagnetic turbulence, helicity in the turbulent field is converted to mean-field helicity. In all cases, however, dynamo processes conserve total helicity except for a small battery effect, consistent with the observation that the helicity is approximately conserved during magnetic relaxation

  9. Microwave-assisted synthesis of triple-helical, collagen-mimetic lipopeptides

    Banerjee, Jayati; Hanson, Andrea J; Muhonen, Wallace W; Shabb, John B; Mallik, Sanku

    2018-01-01

    Collagen-mimetic peptides and lipopeptides are widely used as substrates for matrix degrading enzymes, as new biomaterials for tissue engineering, as drug delivery systems and so on. However, the preparation and subsequent purification of these peptides and their fatty-acid conjugates are really challenging. Herein, we report a rapid microwave-assisted, solid-phase synthetic protocol to prepare the fatty-acid conjugated, triple-helical peptides containing the cleavage site for the enzyme matrix metalloproteinase-9 (MMP-9). We employed a PEG-based resin as the solid support and the amino acids were protected with Fmoc- and tert-butyl groups. The amino acids were coupled at 50 °C (25 W of microwave power) for 5 min. The deprotection reactions were carried out at 75 °C (35 W of microwave power) for 3 min. Using this protocol, a peptide containing 23 amino acids was synthesized and then conjugated to stearic acid in 14 h. PMID:20057380

  10. Helical-D pinch

    Schaffer, M.J.

    1997-08-01

    A stabilized pinch configuration is described, consisting of a D-shaped plasma cross section wrapped tightly around a guiding axis. The open-quotes helical-Dclose quotes geometry produces a very large axial (toroidal) transform of magnetic line direction that reverses the pitch of the magnetic lines without the need of azimuthal (poloidal) plasma current. Thus, there is no need of a open-quotes dynamoclose quotes process and its associated fluctuations. The resulting configuration has the high magnetic shear and pitch reversal of the reversed field pinch (RFP). (Pitch = P = qR, where R = major radius). A helical-D pinch might demonstrate good confinement at q << 1

  11. Review of the helicity formalism

    Barreiro, F.; Cerrada, M.; Fernandez, E.

    1972-01-01

    Our purpose in these notes has been to present a brief and general review of the helicity formalism. We begin by discussing Lorentz invariance, spin and helicity ideas, in section 1 . In section 2 we deal with the construction of relativistic states and scattering amplitudes in the helicity basis and we study their transformation properties under discrete symmetries. Finally we present some more sophisticated topics like kinematical singularities of helicity amplitudes, kinematical constraints and crossing relations 3, 4, 5 respectively. (Author) 8 refs

  12. Constraining cyclic peptides to mimic protein structure motifs

    Hill, Timothy A.; Shepherd, Nicholas E.; Diness, Frederik

    2014-01-01

    peptides can have protein-like biological activities and potencies, enabling their uses as biological probes and leads to therapeutics, diagnostics and vaccines. This Review highlights examples of cyclic peptides that mimic three-dimensional structures of strand, turn or helical segments of peptides...... and proteins, and identifies some additional restraints incorporated into natural product cyclic peptides and synthetic macrocyclic pepti-domimetics that refine peptide structure and confer biological properties....

  13. Helical Confinement Concepts

    Beidler, C; Brakel, R; Burhenn, R; Dinklage, A; Erckmann, V; Feng, Y; Geiger, J; Hartmann, D; Hirsch, M; Jaenicke, R; Koenig, R; Laqua, H P; Maassberg, H; Wagner, F; Weller, A; Wobig, H [Max-Planck Institut fuer Plasmaphysik, EURATOM Association, Greifswald (Germany)

    2012-09-15

    Stellarators, conceived 1951 by Lyman Spitzer in Princeton, are toroidal devices that confine a plasma in a magnetic field which originates from currents in coils outside the plasma. A plasma current driven by external means, for example by an ohmic transformer, is not required for confinement. Supplying the desired poloidal field component by external coils leads to a helically structured plasma topology. Thus stellarators - or helical confinement devices - are fully three-dimensional in contrast to the toroidal (rotational) symmetry of tokamaks. As stellarators can be free of an inductive current, whose radial distribution depends on the plasma parameters, their equilibrium must not be established via the evolving plasma itself, but to a first order already given by the vacuum magnetic field. They do not need an active control (like positional feedback) and therefore cannot suffer from its failure. The outstanding conceptual advantage of stellarators is the potential of steady state plasma operation without current drive. As there is no need for current drive, the recirculating power is expected to be smaller than in equivalent tokamaks. The lack of a net current avoids current driven instabilities; specifically, no disruptions, no resistive wall modes and no conventional or neoclassical tearing modes appear. Second order pressure-driven currents (Pfirsch-Schlueter, bootstrap) exist but they can be modified and even minimized by the magnetic design. The magnetic configuration of helical devices naturally possesses a separatrix, which allows the implementation of a helically structured divertor for exhaust and impurity control. (author)

  14. Acetone-Linked Peptides: A Convergent Approach for Peptide Macrocyclization and Labeling.

    Assem, Naila; Ferreira, David J; Wolan, Dennis W; Dawson, Philip E

    2015-07-20

    Macrocyclization is a broadly applied approach for overcoming the intrinsically disordered nature of linear peptides. Herein, it is shown that dichloroacetone (DCA) enhances helical secondary structures when introduced between peptide nucleophiles, such as thiols, to yield an acetone-linked bridge (ACE). Aside from stabilizing helical structures, the ketone moiety embedded in the linker can be modified with diverse molecular tags by oxime ligation. Insights into the structure of the tether were obtained through co-crystallization of a constrained S-peptide in complex with RNAse S. The scope of the acetone-linked peptides was further explored through the generation of N-terminus to side chain macrocycles and a new approach for generating fused macrocycles (bicycles). Together, these studies suggest that acetone linking is generally applicable to peptide macrocycles with a specific utility in the synthesis of stabilized helices that incorporate functional tags. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Helical modes generate antimagnetic rotational spectra in nuclei

    Malik, Sham S.

    2018-03-01

    A systematic analysis of the antimagnetic rotation band using r -helicity formalism is carried out for the first time. The observed octupole correlation in a nucleus is likely to play a role in establishing the antimagnetic spectrum. Such octupole correlations are explained within the helical orbits. In a rotating field, two identical fermions (generally protons) with paired spins generate these helical orbits in such a way that its positive (i.e., up) spin along the axis of quantization refers to one helicity (right-handedness) while negative (down) spin along the same quantization-axis decides another helicity (left-handedness). Since the helicity remains invariant under rotation, therefore, the quantum state of a fermion is represented by definite angular momentum and helicity. These helicity represented states support a pear-shaped structure of a rotating system having z axis as the symmetry axis. A combined operation of parity, time-reversal, and signature symmetries ensures an absence of one of the signature partner band from the observed antimagnetic spectrum. This formalism has also been tested for the recently observed negative parity Δ I =2 antimagnetic spectrum in odd-A 101Pd nucleus and explains nicely its energy spectrum as well as the B (E 2 ) values. Further, this formalism is found to be fully consistent with twin-shears mechanism popularly known for such type of rotational bands. It also provides significant clue for extending these experiments in various mass regions spread over the nuclear chart.

  16. Radiation Field of a Square, Helical Beam Antenna

    Knudsen, Hans Lottrup

    1952-01-01

    square helices are used. Further, in connection with corresponding rigorous formulas for the field from a circular, helical antenna with a uniformly progressing current wave of constant amplitude the present formulas may be used for an investigation of the magnitude of the error introduced in Kraus......' approximate calculation of the field from a circular, helical antenna by replacing this antenna with an ``equivalent'' square helix. This investigation is carried out by means of a numerical example. The investigation shows that Kraus' approximate method of calculation yields results in fair agreement...

  17. Coulomb double helical structure

    Kamimura, Tetsuo; Ishihara, Osamu

    2012-01-01

    Structures of Coulomb clusters formed by dust particles in a plasma are studied by numerical simulation. Our study reveals the presence of various types of self-organized structures of a cluster confined in a prolate spheroidal electrostatic potential. The stable configurations depend on a prolateness parameter for the confining potential as well as on the number of dust particles in a cluster. One-dimensional string, two-dimensional zigzag structure and three-dimensional double helical structure are found as a result of the transition controlled by the prolateness parameter. The formation of stable double helical structures resulted from the transition associated with the instability of angular perturbations on double strings. Analytical perturbation study supports the findings of numerical simulations.

  18. Helically linked mirror arrangement

    Ranjan, P.

    1986-08-01

    A scheme is described for helical linking of mirror sections, which endeavors to combine the better features of toroidal and mirror devices by eliminating the longitudinal loss of mirror machines, having moderately high average β and steady state operation. This scheme is aimed at a device, with closed magnetic surfaces having rotational transform for equilibrium, one or more axisymmetric straight sections for reduced radial loss, a simple geometrical axis for the links and an overall positive magnetic well depth for stability. We start by describing several other attempts at linking of mirror sections, made both in the past and the present. Then a description of our helically linked mirror scheme is given. This example has three identical straight sections connected by three sections having helical geometric axes. A theoretical analysis of the magnetic field and single-particle orbits in them leads to the conclusion that most of the passing particles would be confined in the device and they would have orbits independent of pitch angle under certain conditions. Numerical results are presented, which agree well with the theoretical results as far as passing particle orbits are concerned

  19. Primary structure and conformational analysis of peptide methionine-tyrosine, a peptide related to neuropeptide Y and peptide YY isolated from lamprey intestine

    Conlon, J M; Bjørnholm, B; Jørgensen, Flemming Steen

    1991-01-01

    A peptide belonging to the pancreatic-polypeptide-fold family of regulatory peptides has been isolated from the intestine of an Agnathan, the sea lamprey (Petromyzon marinus). The primary structure of the peptide (termed peptide methionine-tyrosine) was established as Met-Pro-Pro-Lys-Pro-Asp-Asn-...... in a preferred structure in which the conformation of the beta-turn between the two helical domains (residues 9-14) is appreciably different....

  20. Geometric analysis of alloreactive HLA α-helices.

    Ribarics, Reiner; Karch, Rudolf; Ilieva, Nevena; Schreiner, Wolfgang

    2014-01-01

    Molecular dynamics (MD) is a valuable tool for the investigation of functional elements in biomolecules, providing information on dynamic properties and processes. Previous work by our group has characterized static geometric properties of the two MHC α-helices comprising the peptide binding region recognized by T cells. We build upon this work and used several spline models to approximate the overall shape of MHC α-helices. We applied this technique to a series of MD simulations of alloreactive MHC molecules that allowed us to capture the dynamics of MHC α-helices' steric configurations. Here, we discuss the variability of spline models underlying the geometric analysis with varying polynomial degrees of the splines.

  1. Toxins and antimicrobial peptides: interactions with membranes

    Schlamadinger, Diana E.; Gable, Jonathan E.; Kim, Judy E.

    2009-08-01

    The innate immunity to pathogenic invasion of organisms in the plant and animal kingdoms relies upon cationic antimicrobial peptides (AMPs) as the first line of defense. In addition to these natural peptide antibiotics, similar cationic peptides, such as the bee venom toxin melittin, act as nonspecific toxins. Molecular details of AMP and peptide toxin action are not known, but the universal function of these peptides to disrupt cell membranes of pathogenic bacteria (AMPs) or a diverse set of eukaryotes and prokaryotes (melittin) is widely accepted. Here, we have utilized spectroscopic techniques to elucidate peptide-membrane interactions of alpha-helical human and mouse AMPs of the cathelicidin family as well as the peptide toxin melittin. The activity of these natural peptides and their engineered analogs was studied on eukaryotic and prokaryotic membrane mimics consisting of resistant pathogens.

  2. The dominant role of side chains in supramolecular double helical organisation in synthetic tripeptides

    Sharma, Ankita; Tiwari, Priyanka; Dutt Konar, Anita

    2018-06-01

    Peptide self-assembled nanostructures have attracted attention recently owing to their promising applications in diversified avenues. To validate the importance of sidechains in supramolecular architectural stabilization, herein this report describes the self-assembly propensities involving weak interactions in a series of model tripeptides Boc-Xaa-Aib-Yaa-OMe I-IV, (where Xaa = 4-F-Phe/NMeSer/Ile & Yaa = Tyr in peptide I-III respectively and Xaa = 4-F-Phe & Yaa = Ile in peptide IV) differing in terminal side chains. The solid state structural analysis reveals that tripeptide (I) displays supramolecular preference for double helical architecture. However, when slight modification has been introduced in the N-terminal side chains disfavour the double helical organisation (Peptide II and III). Indeed the peptides display sheet like ensemble within the framework. Besides replacement of C-terminal Tyr by Ile in peptide I even do not promote the architecture, emphasizing the dominant role of balance of side chains in stabilizing double helical organisation. The CD measurements, concentration dependant studies, NMR titrations and ROESY spectra are well in agreement with the solid state conformational investigation. Moreover the morphological experiments utilizing FE-SEM, support the heterogeneity present in the peptides. Thus this work may not only hold future promise in understanding the structure and function of neurodegenerative diseases but also assist in rational design of protein modification in biologically active peptides.

  3. Helical Tomotherapy Quality Assurance

    Balog, John; Soisson, Emilie

    2008-01-01

    Helical tomotherapy uses a dynamic delivery in which the gantry, treatment couch, and multileaf collimator leaves are all in motion during treatment. This results in highly conformal radiotherapy, but the complexity of the delivery is partially hidden from the end-user because of the extensive integration and automation of the tomotherapy control systems. This presents a challenge to the medical physicist who is expected to be both a system user and an expert, capable of verifying relevant aspects of treatment delivery. A related issue is that a clinical tomotherapy planning system arrives at a customer's site already commissioned by the manufacturer, not by the clinical physicist. The clinical physicist and the manufacturer's representative verify the commissioning at the customer site before acceptance. Theoretically, treatment could begin immediately after acceptance. However, the clinical physicist is responsible for the safe and proper use of the machine. In addition, the therapists and radiation oncologists need to understand the important machine characteristics before treatment can proceed. Typically, treatment begins about 2 weeks after acceptance. This report presents an overview of the tomotherapy system. Helical tomotherapy has unique dosimetry characteristics, and some of those features are emphasized. The integrated treatment planning, delivery, and patient-plan quality assurance process is described. A quality assurance protocol is proposed, with an emphasis on what a clinical medical physicist could and should check. Additionally, aspects of a tomotherapy quality assurance program that could be checked automatically and remotely because of its inherent imaging system and integrated database are discussed

  4. Driving engineering of novel antimicrobial peptides from simulations of peptide-micelle interactions

    Khandelia, Himanshu; Langham, Allison A; Kaznessis, Yiannis N

    2006-01-01

    Simulations of antimicrobial peptides in membrane mimics can provide the high resolution, atomistic picture that is necessary to decipher which sequence and structure components are responsible for activity and toxicity. With such detailed insight, engineering new sequences that are active but non...... peptides and their interaction with membrane mimics. In this article, we discuss the promise and the challenges of widely used models and detail our recent work on peptide-micelle simulations as an attractive alternative to peptide-bilayer simulations. We detail our results with two large structural...... classes of peptides, helical and beta-sheet and demonstrate how simulations can assist in engineering of novel antimicrobials with therapeutic potential....

  5. Ten tandem repeats of β-hCG 109-118 enhance immunogenicity and anti-tumor effects of β-hCG C-terminal peptide carried by mycobacterial heat-shock protein HSP65

    Zhang Yankai; Yan Rong; He Yi; Liu Wentao; Cao Rongyue; Yan Ming; Li Taiming; Liu Jingjing; Wu Jie

    2006-01-01

    The β-subunit of human chorionic gonadotropin (β-hCG) is secreted by many kinds of tumors and it has been used as an ideal target antigen to develop vaccines against tumors. In view of the low immunogenicity of this self-peptide,we designed a method based on isocaudamer technique to repeat tandemly the 10-residue sequence X of β-hCG (109-118), then 10 tandemly repeated copies of the 10-residue sequence combined with β-hCG C-terminal 37 peptides were fused to mycobacterial heat-shock protein 65 to construct a fusion protein HSP65-X10-βhCGCTP37 as an immunogen. In this study, we examined the effect of the tandem repeats of this 10-residue sequence in eliciting an immune by comparing the immunogenicity and anti-tumor effects of the two immunogens, HSP65-X10-βhCGCTP37 and HSP65-βhCGCTP37 (without the 10 tandem repeats). Immunization of mice with the fusion protein HSP65-X10-βhCGCTP37 elicited much higher levels of specific anti-β-hCG antibodies and more effectively inhibited the growth of Lewis lung carcinoma (LLC) in vivo than with HSP65-βhCGCTP37, which should suggest that HSP65-X10-βhCGCTP37 may be an effective protein vaccine for the treatment of β-hCG-dependent tumors and multiple tandem repeats of a certain epitope are an efficient method to overcome the low immunogenicity of self-peptide antigens

  6. Employing Helicity Amplitudes for Resummation

    Moult, I.; Stewart, I.W.; Tackmann, F.J.; Waalewijn, W.J.

    2015-01-01

    Many state-of-the-art QCD calculations for multileg processes use helicity amplitudes as their fundamental ingredients. We construct a simple and easy-to-use helicity operator basis in soft-collinear effective theory (SCET), for which the hard Wilson coefficients from matching QCD onto SCET are

  7. LHD helical divertor

    Ohyabu, N.; Watanabe, T.; Ji Hantao

    1993-07-01

    The Large Helical Device (LHD) now under construction is a heliotron/torsatron device with a closed divertor system. The edge LHD magnetic structure has been studied in detail. A peculiar feature of the configuration is existence of edge surface layers, a complicated three dimensional magnetic structure which does not, however, seem to hamper the expected divertor functions. Two divertor operational modes are being considered for the LHD experiment, high density, cold radiative divertor operation as a safe heat removal scheme and high temperature divertor plasma operation. In the latter operation, a divertor plasma with temperature of a few kev, generated by efficient pumping, expects to lead to significant improvement in core plasma confinement. Conceptual designs of the LHD divertor components are under way. (author)

  8. Structural and functional characterization of a multifunctional alanine-rich peptide analogue from Pleuronectes americanus.

    Ludovico Migliolo

    Full Text Available Recently, defense peptides that are able to act against several targets have been characterized. The present work focuses on structural and functional evaluation of the peptide analogue Pa-MAP, previously isolated as an antifreeze peptide from Pleuronectes americanus. Pa-MAP showed activities against different targets such as tumoral cells in culture (CACO-2, MCF-7 and HCT-116, bacteria (Escherichia coli ATCC 8739 and Staphylococcus aureus ATCC 25923, viruses (HSV-1 and HSV-2 and fungi (Candida parapsilosis ATCC 22019, Trichophyton mentagrophytes (28d&E and T. rubrum (327. This peptide did not show toxicity against mammalian cells such as erythrocytes, Vero and RAW 264.7 cells. Molecular mechanism of action was related to hydrophobic residues, since only the terminal amino group is charged at pH 7 as confirmed by potentiometric titration. In order to shed some light on its structure-function relations, in vitro and in silico assays were carried out using circular dichroism and molecular dynamics. Furthermore, Pa-MAP showed partial unfolding of the peptide changes in a wide pH (3 to 11 and temperature (25 to 95°C ranges, although it might not reach complete unfolding at 95°C, suggesting a high conformational stability. This peptide also showed a conformational transition with a partial α-helical fold in water and a full α-helical core in SDS and TFE environments. These results were corroborated by spectral data measured at 222 nm and by 50 ns dynamic simulation. In conclusion, data reported here show that Pa-MAP is a potential candidate for drug design against pathogenic microorganisms due to its structural stability and wide activity against a range of targets.

  9. Peptides Interfering 3A Protein Dimerization Decrease FMDV Multiplication.

    Mónica González-Magaldi

    Full Text Available Nonstructural protein 3A is involved in relevant functions in foot-and-mouth disease virus (FMDV replication. FMDV 3A can form homodimers and preservation of the two hydrophobic α-helices (α1 and α2 that stabilize the dimer interface is essential for virus replication. In this work, small peptides mimicking residues involved in the dimer interface were used to interfere with dimerization and thus gain insight on its biological function. The dimer interface peptides α1, α2 and that spanning the two hydrophobic α-helices, α12, impaired in vitro dimer formation of a peptide containing the two α-helices, this effect being higher with peptide α12. To assess the effect of dimer inhibition in cultured cells, the interfering peptides were N-terminally fused to a heptaarginine (R7 sequence to favor their intracellular translocation. Thus, when fused to R7, interference peptides (100 μM were able to inhibit dimerization of transiently expressed 3A, the higher inhibitions being found with peptides α1 and α12. The 3A dimerization impairment exerted by the peptides correlated with significant, specific reductions in the viral yield recovered from peptide-treated FMDV infected cells. In this case, α2 was the only peptide producing significant reductions at concentrations lower than 100 μM. Thus, dimer interface peptides constitute a tool to understand the structure-function relationship of this viral protein and point to 3A dimerization as a potential antiviral target.

  10. Theoretical aspects of magnetic helicity

    Hammer, J.H.

    1985-01-01

    The magnetic helicity, usually defined as K=integralA.Bdv, where A is the vector potential and B the magnetic field, measures the topological linkage of magnetic fluxes. Helicity manifests itself in the twistedness and knottedness of flux tubes. Its significance is that it is an ideal MHD invariant. While the helicity formalism has proven very useful in understanding reversed field pinch and spheromak behavior, some problems exist in applying the method consistently for complex (e.g., toroidal) conductor geometries or in situations where magnetic flux penetrates conducting walls. Recent work has attempted to generalize K to allow for all possible geometries

  11. Design windows and cost analysis on helical reactors

    Kozaki, Y.; Imagawa, S.; Sagara, A.

    2007-01-01

    The LHD type helical reactors are characterized by a large major radius but slender helical coil, which give us different approaches for power plants from tokamak reactors. For searching design windows of helical reactors and discussing their potential as power plants, we have developed a mass-cost estimating model linked with system design code (HeliCos), thorough studying the relationships between major plasma parameters and reactor parameters, and weight of major components. In regard to cost data we have much experience through preparing ITER construction. To compare the weight and cost of magnet systems between tokamak and helical reactors, we broke down magnet systems and cost factors, such as weights of super conducting strands, conduits, support structures, and winding unit costs, through estimating ITER cost data basis. Based on FFHR2m1 deign we considered a typical 3 GWth helical plant (LHD type) with the same magnet size, coil major radius Rc 14 m, magnetic energy 120 GJ, but increasing plasma densities. We evaluated the weight and cost of magnet systems of 3 GWth helical plant, the total magnet weights of 16,000ton and costs of 210 BYen, which are similar values of tokamak reactors (10,200 ton, 110 BYen in ITER 2002 report, and 21,900 ton, 275 BYen in ITER FDR1999). The costs of strands and winding occupy 70% of total magnet costs, and influence entire power plants economics. The design windows analysis and comparative economics studies to optimize the main reactor parameters have been carried out. Economics studies show that it is misunderstanding to consider helical coils are too large and too expensive to achieve power plants. But we should notice that the helical reactor design windows and economics are very sensitive to allowable blanket space (depend on ergodic layer conditions) and diverter configuration for decreasing heat loads. (orig.)

  12. Godbillon Vey Helicity and Magnetic Helicity in Magnetohydrodynamics

    Webb, G. M.; Hu, Q.; Anco, S.; Zank, G. P.

    2017-12-01

    The Godbillon-Vey invariant arises in homology theory, and algebraic topology, where conditions for a layered family of 2D surfaces forms a 3D manifold were elucidated. The magnetic Godbillon-Vey helicity invariant in magnetohydrodynamics (MHD) is a helicity invariant that occurs for flows, in which the magnetic helicity density hm= A\\cdotB=0 where A is the magnetic vector potential and B is the magnetic induction. Our purpose is to elucidate the evolution of the magnetic Godbillon-Vey field η =A×B/|A|2 and the Godbillon-Vey helicity hgv}= η \\cdot∇ × η in general MHD flows in which the magnetic helicity hm≠q 0. It is shown that hm acts as a source term in the Godbillon-Vey helicity transport equation, in which hm is coupled to hgv via the shear tensor of the background flow. The transport equation for hgv depends on the electric field potential ψ , which is related to the gauge for A, which takes its simplest form for the advected A gauge in which ψ =A\\cdot u where u is the fluid velocity.

  13. Bis-polymer lipid-peptide conjugates and nanoparticles thereof

    Xu, Ting; Dong, He; Shu, Jessica; Dube, Nikhil

    2018-04-24

    The present invention provides bis-polymer lipid-peptide conjugates containing a hydrophobic block and headgroup containing a helical peptide and two polymer blocks. The conjugates can self-assemble to form helix bundle subunits, which in turn assemble to provide micellar nanocarriers for drug cargos and other agents. Particles containing the conjugates and methods for forming the particles are also disclosed.

  14. Helicity multiplexed broadband metasurface holograms.

    Wen, Dandan; Yue, Fuyong; Li, Guixin; Zheng, Guoxing; Chan, Kinlong; Chen, Shumei; Chen, Ming; Li, King Fai; Wong, Polis Wing Han; Cheah, Kok Wai; Pun, Edwin Yue Bun; Zhang, Shuang; Chen, Xianzhong

    2015-09-10

    Metasurfaces are engineered interfaces that contain a thin layer of plasmonic or dielectric nanostructures capable of manipulating light in a desirable manner. Advances in metasurfaces have led to various practical applications ranging from lensing to holography. Metasurface holograms that can be switched by the polarization state of incident light have been demonstrated for achieving polarization multiplexed functionalities. However, practical application of these devices has been limited by their capability for achieving high efficiency and high image quality. Here we experimentally demonstrate a helicity multiplexed metasurface hologram with high efficiency and good image fidelity over a broad range of frequencies. The metasurface hologram features the combination of two sets of hologram patterns operating with opposite incident helicities. Two symmetrically distributed off-axis images are interchangeable by controlling the helicity of the input light. The demonstrated helicity multiplexed metasurface hologram with its high performance opens avenues for future applications with functionality switchable optical devices.

  15. Employing helicity amplitudes for resummation

    Moult, Ian; Stewart, Iain W.; Tackmann, Frank J.; Waalewijn, Wouter J.; Amsterdam Univ.

    2015-08-01

    Many state-of-the-art QCD calculations for multileg processes use helicity amplitudes as their fundamental ingredients. We construct a simple and easy-to-use helicity operator basis in soft-collinear effective theory (SCET), for which the hard Wilson coefficients from matching QCD onto SCET are directly given in terms of color-ordered helicity amplitudes. Using this basis allows one to seamlessly combine fixed-order helicity amplitudes at any order they are known with a resummation of higher-order logarithmic corrections. In particular, the virtual loop amplitudes can be employed in factorization theorems to make predictions for exclusive jet cross sections without the use of numerical subtraction schemes to handle real-virtual infrared cancellations. We also discuss matching onto SCET in renormalization schemes with helicities in 4- and d-dimensions. To demonstrate that our helicity operator basis is easy to use, we provide an explicit construction of the operator basis, as well as results for the hard matching coefficients, for pp → H+0,1,2 jets, pp → W/Z/γ+0,1,2 jets, and pp → 2,3 jets. These operator bases are completely crossing symmetric, so the results can easily be applied to processes with e + e - and e - p collisions.

  16. Amide I SFG Spectral Line Width Probes the Lipid-Peptide and Peptide-Peptide Interactions at Cell Membrane In Situ and in Real Time.

    Zhang, Baixiong; Tan, Junjun; Li, Chuanzhao; Zhang, Jiahui; Ye, Shuji

    2018-06-13

    The balance of lipid-peptide and peptide-peptide interactions at cell membrane is essential to a large variety of cellular processes. In this study, we have experimentally demonstrated for the first time that sum frequency generation vibrational spectroscopy can be used to probe the peptide-peptide and lipid-peptide interactions in cell membrane in situ and in real time by determination of the line width of amide I band of protein backbone. Using a "benchmark" model of α-helical WALP23, it is found that the dominated lipid-peptide interaction causes a narrow line width of the amide I band, whereas the peptide-peptide interaction can markedly broaden the line width. When WALP23 molecules insert into the lipid bilayer, a quite narrow line width of the amide I band is observed because of the lipid-peptide interaction. In contrast, when the peptide lies down on the bilayer surface, the line width of amide I band becomes very broad owing to the peptide-peptide interaction. In terms of the real-time change in the line width, the transition from peptide-peptide interaction to lipid-peptide interaction is monitored during the insertion of WALP23 into 1,2-dipalmitoyl- sn-glycero-3-phospho-(1'- rac-glycerol) (DPPG) lipid bilayer. The dephasing time of a pure α-helical WALP23 in 1-palmitoyl-2-oleoyl- sn-glycero-3-phospho-(1'- rac-glycerol) and DPPG bilayer is determined to be 2.2 and 0.64 ps, respectively. The peptide-peptide interaction can largely accelerate the dephasing time.

  17. Double quick, double click reversible peptide "stapling".

    Grison, Claire M; Burslem, George M; Miles, Jennifer A; Pilsl, Ludwig K A; Yeo, David J; Imani, Zeynab; Warriner, Stuart L; Webb, Michael E; Wilson, Andrew J

    2017-07-01

    The development of constrained peptides for inhibition of protein-protein interactions is an emerging strategy in chemical biology and drug discovery. This manuscript introduces a versatile, rapid and reversible approach to constrain peptides in a bioactive helical conformation using BID and RNase S peptides as models. Dibromomaleimide is used to constrain BID and RNase S peptide sequence variants bearing cysteine (Cys) or homocysteine ( h Cys) amino acids spaced at i and i + 4 positions by double substitution. The constraint can be readily removed by displacement of the maleimide using excess thiol. This new constraining methodology results in enhanced α-helical conformation (BID and RNase S peptide) as demonstrated by circular dichroism and molecular dynamics simulations, resistance to proteolysis (BID) as demonstrated by trypsin proteolysis experiments and retained or enhanced potency of inhibition for Bcl-2 family protein-protein interactions (BID), or greater capability to restore the hydrolytic activity of the RNAse S protein (RNase S peptide). Finally, use of a dibromomaleimide functionalized with an alkyne permits further divergent functionalization through alkyne-azide cycloaddition chemistry on the constrained peptide with fluorescein, oligoethylene glycol or biotin groups to facilitate biophysical and cellular analyses. Hence this methodology may extend the scope and accessibility of peptide stapling.

  18. Designing anticancer peptides by constructive machine learning.

    Grisoni, Francesca; Neuhaus, Claudia; Gabernet, Gisela; Müller, Alex; Hiss, Jan; Schneider, Gisbert

    2018-04-21

    Constructive machine learning enables the automated generation of novel chemical structures without the need for explicit molecular design rules. This study presents the experimental application of such a generative model to design membranolytic anticancer peptides (ACPs) de novo. A recurrent neural network with long short-term memory cells was trained on alpha-helical cationic amphipathic peptide sequences and then fine-tuned with 26 known ACPs. This optimized model was used to generate unique and novel amino acid sequences. Twelve of the peptides were synthesized and tested for their activity on MCF7 human breast adenocarcinoma cells and selectivity against human erythrocytes. Ten of these peptides were active against cancer cells. Six of the active peptides killed MCF7 cancer cells without affecting human erythrocytes with at least threefold selectivity. These results advocate constructive machine learning for the automated design of peptides with desired biological activities. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Study on reinforced concrete beams with helical transverse reinforcement

    Kaarthik Krishna, N.; Sandeep, S.; Mini, K. M.

    2018-02-01

    In a Reinforced Concrete (R.C) structure, major reinforcement is used for taking up tensile stresses acting on the structure due to applied loading. The present paper reports the behavior of reinforced concrete beams with helical reinforcement (transverse reinforcement) subjected to monotonous loading by 3-point flexure test. The results were compared with identically similar reinforced concrete beams with rectangular stirrups. During the test crack evolution, load carrying capacity and deflection of the beams were monitored, analyzed and compared. Test results indicate that the use of helical reinforcement provides enhanced load carrying capacity and a lower deflection proving to be more ductile, clearly indicating the advantage in carrying horizontal loads. An analysis was also carried out using ANSYS software in order to compare the test results of both the beams.

  20. Studi Eksperimental Perancangan Turbin Air Terapung Tipe Helical Blade

    Muhammad, Andi Haris; Had, Abdul Latief; Terti, Wayan

    2016-01-01

    This research describes the design of floating helical water turbine for electric power generation in free flow and low head water operation. The design involves the use of strips attached to the blades of turbine. The efficiency of turbine (??) investigation was carried out using empirical formulas. The rotation of turbine (n) of the calculation with variation strips angles (450, 900, and 1350) were obtained through captive model tests carried out in towing tank. The result indicated the eff...

  1. Pulling Helices inside Bacteria: Imperfect Helices and Rings

    Allard, Jun F.; Rutenberg, Andrew D.

    2009-04-01

    We study steady-state configurations of intrinsically-straight elastic filaments constrained within rod-shaped bacteria that have applied forces distributed along their length. Perfect steady-state helices result from axial or azimuthal forces applied at filament ends, however azimuthal forces are required for the small pitches observed for MreB filaments within bacteria. Helix-like configurations can result from distributed forces, including coexistence between rings and imperfect helices. Levels of expression and/or bundling of the polymeric protein could mediate this coexistence.

  2. Magnetic Helicity Estimations in Models and Observations of the Solar Magnetic Field. III. Twist Number Method

    Guo, Y. [School of Astronomy and Space Science and Key Laboratory of Modern Astronomy and Astrophysics in Ministry of Education, Nanjing University, Nanjing 210023 (China); Pariat, E.; Moraitis, K. [LESIA, Observatoire de Paris, PSL Research University, CNRS, Sorbonne Université, UPMC Univ. Paris 06, Univ. Paris Diderot, Sorbonne Paris Cité, F-92190 Meudon (France); Valori, G. [University College London, Mullard Space Science Laboratory, Holmbury St. Mary, Dorking, Surrey, RH5 6NT (United Kingdom); Anfinogentov, S. [Institute of Solar-Terrestrial Physics SB RAS 664033, Irkutsk, P.O. box 291, Lermontov Street, 126a (Russian Federation); Chen, F. [Max-Plank-Institut für Sonnensystemforschung, D-37077 Göttingen (Germany); Georgoulis, M. K. [Research Center for Astronomy and Applied Mathematics of the Academy of Athens, 4 Soranou Efesiou Street, 11527 Athens (Greece); Liu, Y. [W. W. Hansen Experimental Physics Laboratory, Stanford University, Stanford, CA 94305 (United States); Thalmann, J. K. [Institute of Physics, Univeristy of Graz, Universitätsplatz 5/II, A-8010 Graz (Austria); Yang, S., E-mail: guoyang@nju.edu.cn [Key Laboratory of Solar Activity, National Astronomical Observatories, Chinese Academy of Sciences, Beijing 100012 (China)

    2017-05-01

    We study the writhe, twist, and magnetic helicity of different magnetic flux ropes, based on models of the solar coronal magnetic field structure. These include an analytical force-free Titov–Démoulin equilibrium solution, non-force-free magnetohydrodynamic simulations, and nonlinear force-free magnetic field models. The geometrical boundary of the magnetic flux rope is determined by the quasi-separatrix layer and the bottom surface, and the axis curve of the flux rope is determined by its overall orientation. The twist is computed by the Berger–Prior formula, which is suitable for arbitrary geometry and both force-free and non-force-free models. The magnetic helicity is estimated by the twist multiplied by the square of the axial magnetic flux. We compare the obtained values with those derived by a finite volume helicity estimation method. We find that the magnetic helicity obtained with the twist method agrees with the helicity carried by the purely current-carrying part of the field within uncertainties for most test cases. It is also found that the current-carrying part of the model field is relatively significant at the very location of the magnetic flux rope. This qualitatively explains the agreement between the magnetic helicity computed by the twist method and the helicity contributed purely by the current-carrying magnetic field.

  3. Helicity and potential vorticity in the surface boundary layer turbulence

    Chkhetiani, Otto; Kurgansky, Michael; Koprov, Boris; Koprov, Victor

    2016-04-01

    An experimental measurement of all three components of the velocity and vorticity vectors, as well as the temperature and its gradient, and potential vorticity, has been developed using four acoustic anemometers. Anemometers were placed at vertices of a tetrahedron, the horizontal base of which was a rectangular triangle with equal legs, and the upper point was exactly above the top of the right angle. The distance from the surface to the tetrahedron its base was 5.5 m, and the lengths of legs and a vertical edge were 5 m. The measurements were carried out of total duration near 100 hours both in stable and unstable stratification conditions (at the Tsimlyansk Scientific Station in a uniform area of virgin steppe 700 x 650 m, August 2012). A covariance-correlation matrix for turbulent variations in all measured values has been calculated. In the daytime horizontal and vertical components of the helicity are of the order of -0.03 and +0.01 m s-2, respectively. The nighttime signs remain unchanged, but the absolute values are several times smaller. It is confirmed also by statistics of a relative helicity. The cospectra and spectral correlation coefficients have been calculated for all helicity components. The time variations in the components of "instantaneous" relative helicity and potential vorticity are considered. Connections of helicity with Monin-Obukhov length and the wind vertical profile structure are discussed. This work was supported by the Russian Science Foundation (Project No 14-27-00134).

  4. Molecular Origin of Gerstmann-Str ussler-Scheinker Syndrome: Insight from Computer Simulation of an Amyloidogenic Prion Peptide

    Diadone, Isabella [University of L' Aquila, L' Aquila, Italy; DiNola, Alfredo [University of Rome; Smith, Jeremy C [ORNL

    2011-01-01

    Prion proteins become pathogenic through misfolding. Here, we characterize the folding of a peptide consisting of residues 109 122 of the Syrian hamster prion protein (the H1 peptide) and of a more amyloidogenic A117V point mutant that leads in humans to an inheritable form of the Gerstmann-Straeussler-Scheinker syndrome. Atomistic molecular dynamics simulations are performed for 2.5 s. Both peptides lose their -helical starting conformations and assume a -hairpin that is structurally similar in both systems. In each simulation several unfolding/refolding events occur, leading to convergence of the thermodynamics of the conformational states to within 1 kJ/mol. The similar stability of the -hairpin relative to the unfolded state is observed in the two peptides. However, substantial differences are found between the two unfolded states. A local minimum is found within the free energy unfolded basin of the A117V mutant populated by misfolded collapsed conformations of comparable stability to the -hairpin state, consistent with increased amyloidogenicity. This population, in which V117 stabilizes a hydrophobic core, is absent in the wild-type peptide. These results are supported by simulations of oligomers showing a slightly higher stability of the associated structures and a lower barrier to association for the mutated peptide. Hence, a single point mutation carrying only two additional methyl groups is here shown to be responsible for rather dramatic differences of structuring within the unfolded (misfolded) state.

  5. Cysteine-containing peptides having antioxidant properties

    Bielicki, John K [Castro Valley, CA

    2008-10-21

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

  6. Transport barrier in Helical system

    Ida, Katsumi

    1998-01-01

    Experiments on the transport barrier in Helical plasmas are reviewed. There are two mechanisms of transport improvement, that results in the formation of the transport barrier. One is the improvement of neoclassical transport by reducing the ripple loss with radial electric field, which exist only in helical plasma. The other is the improvement of anomalous transport due to the suppression of fluctuations associated with a radial electric field shear both in tokamak and helical plasma. The formation of the transport barrier can be triggered by the radial electric field shear associated with the transition of the radial electric field (L/H transition or ion-electron root transition) or the peaked density or the optimization of magnetic field shear. The mechanisms of transport barrier formation are also discussed. (author). 60 refs

  7. Generalized helicity and Beltrami fields

    Buniy, Roman V., E-mail: roman.buniy@gmail.com [Schmid College of Science, Chapman University, Orange, CA 92866 (United States); Isaac Newton Institute, University of Cambridge, Cambridge, CB3 0EH (United Kingdom); Kephart, Thomas W., E-mail: tom.kephart@gmail.com [Department of Physics and Astronomy, Vanderbilt University, Nashville, TN 37235 (United States); Isaac Newton Institute, University of Cambridge, Cambridge, CB3 0EH (United Kingdom)

    2014-05-15

    We propose covariant and non-abelian generalizations of the magnetic helicity and Beltrami equation. The gauge invariance, variational principle, conserved current, energy–momentum tensor and choice of boundary conditions elucidate the subject. In particular, we prove that any extremal of the Yang–Mills action functional 1/4 ∫{sub Ω}trF{sub μν}F{sup μν}d{sup 4}x subject to the local constraint ε{sup μναβ}trF{sub μν}F{sub αβ}=0 satisfies the covariant non-abelian Beltrami equation. -- Highlights: •We introduce the covariant non-abelian helicity and Beltrami equation. •The Yang–Mills action and instanton term constraint lead to the Beltrami equation. •Solutions of the Beltrami equation conserve helicity.

  8. Generalized helicity and Beltrami fields

    Buniy, Roman V.; Kephart, Thomas W.

    2014-01-01

    We propose covariant and non-abelian generalizations of the magnetic helicity and Beltrami equation. The gauge invariance, variational principle, conserved current, energy–momentum tensor and choice of boundary conditions elucidate the subject. In particular, we prove that any extremal of the Yang–Mills action functional 1/4 ∫ Ω trF μν F μν d 4 x subject to the local constraint ε μναβ trF μν F αβ =0 satisfies the covariant non-abelian Beltrami equation. -- Highlights: •We introduce the covariant non-abelian helicity and Beltrami equation. •The Yang–Mills action and instanton term constraint lead to the Beltrami equation. •Solutions of the Beltrami equation conserve helicity

  9. Toroidal helical quartz forming machine

    Hanks, K.W.; Cole, T.R.

    1977-01-01

    The Scyllac fusion experimental machine used 10 cm diameter smooth bore discharge tubes formed into a simple toroidal shape prior to 1974. At about that time, it was discovered that a discharge tube was required to follow the convoluted shape of the load coil. A machine was designed and built to form a fused quartz tube with a toroidal shape. The machine will accommodate quartz tubes from 5 cm to 20 cm diameter forming it into a 4 m toroidal radius with a 1 to 5 cm helical displacement. The machine will also generate a helical shape on a linear tube. Two sets of tubes with different helical radii and wavelengths have been successfully fabricated. The problems encountered with the design and fabrication of this machine are discussed

  10. Collagenolytic Matrix Metalloproteinase Activities toward Peptomeric Triple-Helical Substrates.

    Stawikowski, Maciej J; Stawikowska, Roma; Fields, Gregg B

    2015-05-19

    Although collagenolytic matrix metalloproteinases (MMPs) possess common domain organizations, there are subtle differences in their processing of collagenous triple-helical substrates. In this study, we have incorporated peptoid residues into collagen model triple-helical peptides and examined MMP activities toward these peptomeric chimeras. Several different peptoid residues were incorporated into triple-helical substrates at subsites P3, P1, P1', and P10' individually or in combination, and the effects of the peptoid residues were evaluated on the activities of full-length MMP-1, MMP-8, MMP-13, and MMP-14/MT1-MMP. Most peptomers showed little discrimination between MMPs. However, a peptomer containing N-methyl Gly (sarcosine) in the P1' subsite and N-isobutyl Gly (NLeu) in the P10' subsite was hydrolyzed efficiently only by MMP-13 [nomenclature relative to the α1(I)772-786 sequence]. Cleavage site analysis showed hydrolysis at the Gly-Gln bond, indicating a shifted binding of the triple helix compared to the parent sequence. Favorable hydrolysis by MMP-13 was not due to sequence specificity or instability of the substrate triple helix but rather was based on the specific interactions of the P7' peptoid residue with the MMP-13 hemopexin-like domain. A fluorescence resonance energy transfer triple-helical peptomer was constructed and found to be readily processed by MMP-13, not cleaved by MMP-1 and MMP-8, and weakly hydrolyzed by MT1-MMP. The influence of the triple-helical structure containing peptoid residues on the interaction between MMP subsites and individual substrate residues may provide additional information about the mechanism of collagenolysis, the understanding of collagen specificity, and the design of selective MMP probes.

  11. Helical axis stellarator equilibrium model

    Koniges, A.E.; Johnson, J.L.

    1985-02-01

    An asymptotic model is developed to study MHD equilibria in toroidal systems with a helical magnetic axis. Using a characteristic coordinate system based on the vacuum field lines, the equilibrium problem is reduced to a two-dimensional generalized partial differential equation of the Grad-Shafranov type. A stellarator-expansion free-boundary equilibrium code is modified to solve the helical-axis equations. The expansion model is used to predict the equilibrium properties of Asperators NP-3 and NP-4. Numerically determined flux surfaces, magnetic well, transform, and shear are presented. The equilibria show a toroidal Shafranov shift

  12. Resonant helical fields in tokamaks

    Okano, V.

    1990-01-01

    Poincare maps of magnetic field lines of a toroidal helical system were made. The magnetic field is a linear superposition of the magnetic fields produced by a toroidal plasma in equilibrium and by external helical currents. Analytical expression for the Poincare maps was no obtained since the magnetic field do not have symmetry. In order to obtain the maps, the equation minus derivative of l vector times B vector = 0 was numerically integrated. In the Poincare maps, the principal and the secondary magnetic island were observed. (author)

  13. Helical system. History and current state of helical research

    Yokoyama, Masayuki

    2017-01-01

    This paper described the following: (1) history of nuclear fusion research of Japan's original heliotron method, (2) worldwide development of nuclear fusion research based on helical system such as stellarator, and (3) worldwide meaning of large helical device (LHD) aiming to demonstrate the steady-state performance of heliotron type in the parameter area extrapolable to the core plasma, and research results of LHD. LHD demonstrated that the helical system is excellent in steady operation performance at the world's most advanced level. In an experiment using deuterium gas in 2017, LHD achieved to reach 120 million degrees of ion temperature, which is one index of nuclear fusion condition, demonstrated the realization of high-performance plasma capable of extrapolating to future nuclear fusion reactors, and established the foundation for full-scale research toward the realization of nuclear fusion reactor. Besides experimental research, this paper also described the helical-type stationary nuclear fusion prototype reactor, FFHR-d1, which was based on progress of large-scale simulation at the world's most advanced level. A large-scale superconducting stellarator experimental device, W7-X, with the same scale as LHD, started experiment in December 2015, whose current state is also touched on here. (A.O.)

  14. Helicity and evanescent waves. [Energy transport velocity, helicity, Lorentz transformation

    Agudin, J L; Platzeck, A M [La Plata Univ. Nacional (Argentina); Albano, J R [Instituto de Astronomia y Fisica del Espacio, Buenos Aires, Argentina

    1978-02-20

    It is shown that the projection of the angular momentum of a circularly polarized electromagnetic evanescent wave along the mean velocity of energy transport (=helicity) can be reverted by a Lorentz transformation, in spite of the fact that this velocity is c.

  15. On the motion of multiple helical vortices

    Wood, D. H.; Boersma, J.

    2001-11-01

    The analysis of the self-induced velocity of a single helical vortex (Boersma & Wood 1999) is extended to include equally spaced multiple vortices. This arrangement approximates the tip vortices in the far wake of multi-bladed wind turbines, propellers, or rotors in ascending, descending, or hovering flight. The problem is reduced to finding, from the Biot Savart law, the additional velocity of a helix due to an identical helix displaced azimuthally. The resulting Biot Savart integral is further reduced to a Mellin Barnes integral representation which allows the asymptotic expansions to be determined for small and for large pitch. The Biot Savart integral is also evaluated numerically for a total of two, three and four vortices over a range of pitch values. The previous finding that the self-induced velocity at small pitch is dominated by a term inversely proportional to the pitch carries over to multiple vortices. It is shown that a far wake dominated by helical tip vortices is consistent with the one-dimensional representation that leads to the Betz limit on the power output of wind turbines. The small-pitch approximation then allows the determination of the blade&s bound vorticity for optimum power extraction. The present analysis is shown to give reasonable estimates for the vortex circulation in experiments using a single hovering rotor and a four-bladed propeller.

  16. Parameterization and measurements of helical magnetic fields

    Fischer, W.; Okamura, M.

    1997-01-01

    Magnetic fields with helical symmetry can be parameterized using multipole coefficients (a n , b n ). We present a parameterization that gives the familiar multipole coefficients (a n , b n ) for straight magnets when the helical wavelength tends to infinity. To measure helical fields all methods used for straight magnets can be employed. We show how to convert the results of those measurements to obtain the desired helical multipole coefficients (a n , b n )

  17. Applications of 2D helical vortex dynamics

    Okulov, Valery; Sørensen, Jens Nørkær

    2010-01-01

    In the paper, we show how the assumption of helical symmetry in the context of 2D helical vortices can be exploited to analyse and to model various cases of rotating flows. From theory, examples of three basic applications of 2D dynamics of helical vortices embedded in flows with helical symmetry...... of the vorticity field are addressed. These included some of the problems related to vortex breakdown, instability of far wakes behind rotors and vortex theory of ideal rotors....

  18. ICRF heating on helical devices

    Rasmussen, D.A.; Lyon, J.F.; Hoffman, D.J.; Murakami, M.; England, A.C.; Wilgen, J.B.; Jaeger, E.F.; Wang, C.; Batchelor, D.B.

    1995-01-01

    Ion cyclotron range of frequency (ICRF) heating is currently in use on CHS and W7-AS and is a major element of the heating planned for steady state helical devices. In helical devices, the lack of a toroidal current eliminates both disruptions and the need for ICRF current drive, simplifying the design of antenna structures as compared to tokamak applications. However the survivability of plasma facing components and steady state cooling issues are directly applicable to tokamak devices. Results from LHD steady state experiments should be available on a time scale to strongly influence the next generation of steady state tokamak experiments. The helical plasma geometry provides challenges not faced with tokamak ICRF heating, including the potential for enhanced fast ion losses, impurity accumulation, limited access for antenna structures, and open magnetic field lines in the plasma edge. The present results and near term plans provide the basis for steady state ICRF heating of larger helical devices. An approach which includes direct electron, mode conversion, ion minority and ion Bernstein wave heating addresses these issues

  19. ICRF heating on helical devices

    Rasmussen, D.A.; Lyon, J.F.; Hoffman, D.J.

    1995-01-01

    Ion cyclotron range of frequency (ICRF) heating is currently in use on CHS and W7AS and is a major element of the heating planned for steady state helical devices. In helical devices, the lack of a toroidal current eliminates both disruptions and the need for ICRF current drive, simplifying the design of antenna structures as compared to tokamak applications. However the survivability of plasma facing components and steady state cooling issues are directly applicable to tokamak devices. Results from LHD steady state experiments should be available on a time scale to strongly influence the next generation of steady state tokamak experiments. The helical plasma geometry provides challenges not faced with tokamak ICRF heating, including the potential for enhanced fast ion losses, impurity accumulation, limited access for antenna structures, and open magnetic field lines in the plasma edge. The present results and near term plans provide the basis for steady state ICRF heating of larger helical devices. An approach which includes direct electron, mode conversion, ion minority and ion Bernstein wave heating addresses these issues

  20. The helical tomotherapy thread effect

    Kissick, M.W.; Fenwick, J.; James, J.A.; Jeraj, R.; Kapatoes, J.M.; Keller, H.; Mackie, T.R.; Olivera, G.; Soisson, E.T.

    2005-01-01

    Inherent to helical tomotherapy is a dose variation pattern that manifests as a 'ripple' (peak-to-trough relative to the average). This ripple is the result of helical beam junctioning, completely unique to helical tomotherapy. Pitch is defined as in helical CT, the couch travel distance for a complete gantry rotation relative to the axial beam width at the axis of rotation. Without scattering or beam divergence, an analytical posing of the problem as a simple integral predicts minima near a pitch of 1/n where n is an integer. A convolution-superposition dose calculator (TomoTherapy, Inc.) included all the physics needed to explore the ripple magnitude versus pitch and beam width. The results of the dose calculator and some benchmark measurements demonstrate that the ripple has sharp minima near p=0.86(1/n). The 0.86 factor is empirical and caused by a beam junctioning of the off-axis dose profiles which differ from the axial profiles as well as a long scatter tail of the profiles at depth. For very strong intensity modulation, the 0.86 factor may vary. The authors propose choosing particular minima pitches or using a second delivery that starts 180 deg off-phase from the first to reduce these ripples: 'Double threading'. For current typical pitches and beam widths, however, this effect is small and not clinically important for most situations. Certain extremely large field or high pitch cases, however, may benefit from mitigation of this effect

  1. Peptide dendrimers

    Niederhafner, Petr; Šebestík, Jaroslav; Ježek, Jan

    2005-01-01

    Roč. 11, - (2005), 757-788 ISSN 1075-2617 R&D Projects: GA ČR(CZ) GA203/03/1362 Institutional research plan: CEZ:AV0Z40550506 Keywords : multiple antigen peptides * peptide dendrimers * synthetic vaccine * multipleantigenic peptides Subject RIV: CC - Organic Chemistry Impact factor: 1.803, year: 2005

  2. Intravenous digital subtraction angiography and helical computed tomography in evaluation of living renal donors

    Watarai, Yoshihiko; Usuki, Tomoaki; Takeuchi, Ichiro; Nonomura, Katsuya; Koyanagi, Tomohiko; Kubo, Kozo; Hirano, Tetsuo; Togashi, Masaki; Ohashi, Nobuo

    2001-01-01

    The present study was carried out to evaluate the accuracy of helical computed tomography (CT) and intravenous digital subtraction angiography (IV-DSA) on anatomical assessment of renal vasculature for living renal donors. Forty-two healthy potential renal donors were prospectively evaluated and 35 subsequently underwent donor nephrectomy after helical CT and IV-DSA evaluation. The vascular and non-vascular findings were compared between the findings on helical CT, IV-DSA and surgery. Ten prehilar branches and five accessory renal arteries were found at nephrectomy. Overall, operative findings agreed with the findings by IV-DSA in 89% and by helical CT in 83%. In delineating accessory arteries, IV-DSA had a sensitivity of 60% and specificity of 97%, whereas helical CT had a sensitivity of 40% and specificity of 100%. In delineating prehilar branches, IV-DSA had a sensitivity of 90% and specificity of 100%, whereas helical CT had a sensitivity of 70% and specificity of 100%. Accessory arteries and prehilar branches that were not detected by helical CT or IV-DSA, were less than 2 mm in diameter and did not require vascular reconstruction. Renal veins were delineated in 63% by IV-DSA, whereas they were clearly imaged by helical CT in all cases, including a case with a circumaortic renal vein. Non-vascular findings were obtained in 64% by helical CT, including two renal tumors. None of these findings were obtained by IV-DSA. Helical CT and IV-DSA provide comparably sufficient information on renal artery vasculature. However, helical CT provides significantly more information on venous and non-vascular findings as a single-imaging modality. (author)

  3. Salt-bridging effects on short amphiphilic helical structure and introducing sequence-based short beta-turn motifs.

    Guarracino, Danielle A; Gentile, Kayla; Grossman, Alec; Li, Evan; Refai, Nader; Mohnot, Joy; King, Daniel

    2018-02-01

    Determining the minimal sequence necessary to induce protein folding is beneficial in understanding the role of protein-protein interactions in biological systems, as their three-dimensional structures often dictate their activity. Proteins are generally comprised of discrete secondary structures, from α-helices to β-turns and larger β-sheets, each of which is influenced by its primary structure. Manipulating the sequence of short, moderately helical peptides can help elucidate the influences on folding. We created two new scaffolds based on a modestly helical eight-residue peptide, PT3, we previously published. Using circular dichroism (CD) spectroscopy and changing the possible salt-bridging residues to new combinations of Lys, Arg, Glu, and Asp, we found that our most helical improvements came from the Arg-Glu combination, whereas the Lys-Asp was not significantly different from the Lys-Glu of the parent scaffold, PT3. The marked 3 10 -helical contributions in PT3 were lessened in the Arg-Glu-containing peptide with the beginning of cooperative unfolding seen through a thermal denaturation. However, a unique and unexpected signature was seen for the denaturation of the Lys-Asp peptide which could help elucidate the stages of folding between the 3 10 and α-helix. In addition, we developed a short six-residue peptide with β-turn/sheet CD signature, again to help study minimal sequences needed for folding. Overall, the results indicate that improvements made to short peptide scaffolds by fine-tuning the salt-bridging residues can enhance scaffold structure. Likewise, with the results from the new, short β-turn motif, these can help impact future peptidomimetic designs in creating biologically useful, short, structured β-sheet-forming peptides.

  4. Ruby-Helix: an implementation of helical image processing based on object-oriented scripting language.

    Metlagel, Zoltan; Kikkawa, Yayoi S; Kikkawa, Masahide

    2007-01-01

    Helical image analysis in combination with electron microscopy has been used to study three-dimensional structures of various biological filaments or tubes, such as microtubules, actin filaments, and bacterial flagella. A number of packages have been developed to carry out helical image analysis. Some biological specimens, however, have a symmetry break (seam) in their three-dimensional structure, even though their subunits are mostly arranged in a helical manner. We refer to these objects as "asymmetric helices". All the existing packages are designed for helically symmetric specimens, and do not allow analysis of asymmetric helical objects, such as microtubules with seams. Here, we describe Ruby-Helix, a new set of programs for the analysis of "helical" objects with or without a seam. Ruby-Helix is built on top of the Ruby programming language and is the first implementation of asymmetric helical reconstruction for practical image analysis. It also allows easier and semi-automated analysis, performing iterative unbending and accurate determination of the repeat length. As a result, Ruby-Helix enables us to analyze motor-microtubule complexes with higher throughput to higher resolution.

  5. EVOLUTION OF SPINNING AND BRAIDING HELICITY FLUXES IN SOLAR ACTIVE REGION NOAA 10930

    Ravindra, B. [Indian Institute of Astrophysics, Koramangala, Bangalore 560 034 (India); Yoshimura, Keiji [Department of Physics, Montana State University Bozeman, MT 59717 (United States); Dasso, Sergio, E-mail: ravindra@iiap.res.in, E-mail: yosimura@solar.physics.montana.edu, E-mail: dasso@df.uba.ar [Instituto de Astronomia y Fisica del Espacio (CONICET-UBA), 1428 Buenos Aires (Argentina)

    2011-12-10

    Multiplication-Sign 10{sup 43} Mx{sup 2}. The observed reversal in the sign of spinning and braiding helicity fluxes could be the signature of the emergence of a twisted flux tube, which acquires the writhe of an opposite sign. The magnetic cloud associated with the ejected mass has carried about -7 Multiplication-Sign 10{sup 41} Mx{sup 2} of helicity. A time integration of helicity flux of about 1.2 hr integrated backward in time of the observation of the coronal mass ejection is sufficient for this event.

  6. Plasmodium vivax antigen discovery based on alpha-helical coiled coil protein motif.

    Nora Céspedes

    Full Text Available Protein α-helical coiled coil structures that elicit antibody responses, which block critical functions of medically important microorganisms, represent a means for vaccine development. By using bioinformatics algorithms, a total of 50 antigens with α-helical coiled coil motifs orthologous to Plasmodium falciparum were identified in the P. vivax genome. The peptides identified in silico were chemically synthesized; circular dichroism studies indicated partial or high α-helical content. Antigenicity was evaluated using human sera samples from malaria-endemic areas of Colombia and Papua New Guinea. Eight of these fragments were selected and used to assess immunogenicity in BALB/c mice. ELISA assays indicated strong reactivity of serum samples from individuals residing in malaria-endemic regions and sera of immunized mice, with the α-helical coiled coil structures. In addition, ex vivo production of IFN-γ by murine mononuclear cells confirmed the immunogenicity of these structures and the presence of T-cell epitopes in the peptide sequences. Moreover, sera of mice immunized with four of the eight antigens recognized native proteins on blood-stage P. vivax parasites, and antigenic cross-reactivity with three of the peptides was observed when reacted with both the P. falciparum orthologous fragments and whole parasites. Results here point to the α-helical coiled coil peptides as possible P. vivax malaria vaccine candidates as were observed for P. falciparum. Fragments selected here warrant further study in humans and non-human primate models to assess their protective efficacy as single components or assembled as hybrid linear epitopes.

  7. Optical Carry Adder.

    1987-03-01

    AOM’s) with the deflected beam as the modulator "on" state. These AOM’s ( TeO2 crystals, manufactured by Newport E.O. Systems) have high deflection...caused by the slow acoustic propagation (4.2 - 105 cm/s for TeO2 ), but this delay can be minimized by placing the laser beam close to the acoustic...dependent jitter in the optical carry to below 1 ns, the total carry path must be less than 30 cm long (or 20 cm in glass , 14 cm in LiNbO 3). Thus, a 32

  8. NMR studies of the fifth transmembrane segment of Na+,K+-ATPase reveals a non-helical ion-binding region

    Underhaug, Jarl; Jakobsen, Louise Odgaard; Esmann, Mikael

    2006-01-01

    The structure of a synthetic peptide corresponding to the fifth membrane-spanning segment (M5) in Na(+),K(+)-ATPase in sodium dodecyl sulfate (SDS) micelles was determined using liquid-state nuclear magnetic resonance (NMR) spectroscopy. The spectra reveal that this peptide is substantially less...... transmembrane element of the Ca(2+)-ATPase. Furthermore, this region spans the residues implicated in Na(+) and K(+) transport, where they are likely to offer the flexibility needed to coordinate Na(+) as well as K(+) during active transport....... alpha-helical than the corresponding M5 peptide of Ca(2+)-ATPase. A well-defined alpha-helix is shown in the C-terminal half of the peptide. Apart from a short helical stretch at the N-terminus, the N-terminal half contains a non-helical region with two proline residues and sequence similarity to a non-structured...

  9. Antimicrobial peptides design by evolutionary multiobjective optimization.

    Giuseppe Maccari

    Full Text Available Antimicrobial peptides (AMPs are an abundant and wide class of molecules produced by many tissues and cell types in a variety of mammals, plant and animal species. Linear alpha-helical antimicrobial peptides are among the most widespread membrane-disruptive AMPs in nature, representing a particularly successful structural arrangement in innate defense. Recently, AMPs have received increasing attention as potential therapeutic agents, owing to their broad activity spectrum and their reduced tendency to induce resistance. The introduction of non-natural amino acids will be a key requisite in order to contrast host resistance and increase compound's life. In this work, the possibility to design novel AMP sequences with non-natural amino acids was achieved through a flexible computational approach, based on chemophysical profiles of peptide sequences. Quantitative structure-activity relationship (QSAR descriptors were employed to code each peptide and train two statistical models in order to account for structural and functional properties of alpha-helical amphipathic AMPs. These models were then used as fitness functions for a multi-objective evolutional algorithm, together with a set of constraints for the design of a series of candidate AMPs. Two ab-initio natural peptides were synthesized and experimentally validated for antimicrobial activity, together with a series of control peptides. Furthermore, a well-known Cecropin-Mellitin alpha helical antimicrobial hybrid (CM18 was optimized by shortening its amino acid sequence while maintaining its activity and a peptide with non-natural amino acids was designed and tested, demonstrating the higher activity achievable with artificial residues.

  10. Generalized helicity and its time derivative

    Jarboe, T.R.; Marklin, G.J.

    1985-01-01

    Spheromaks can be sustained against resistive decay by helicity injection because they tend to obey the minimum energy principle. This principle states that a plasma-laden magnetic configuration will relax to a state of minimum energy subject to the constraint that the magnetic helicity is conserved. Use of helicity as a constraint on the minimization of energy was first proposed by Woltjer in connection with astrophysical phenomena. Helicity does decay on the resistive diffusion time. However, if helicity is created and made to flow continuoiusly into a confinement geometry, these additional linked fluxes can relax and sustain the configuration indefinitely against the resistive decay. In this paper we will present an extension of the definition of helicity to include systems where B vector can penetrate the boundary and the penetration can be varying in time. We then discuss the sustainment of RFPs and spheromaks in terms of helicity injection

  11. Influence of drill helical direction on exit damage development in drilling carbon fiber reinforced plastic

    Bai, Y.; Jia, Z. Y.; Wang, F. J.; Fu, R.; Guo, H. B.; Cheng, D.; Zhang, B. Y.

    2017-06-01

    Drilling is inevitable for CFRP components’ assembling process in the aviation industry. The exit damage frequently occurs and affects the load carrying capacity of components. Consequently, it is of great urgency to enhance drilling exit quality on CFRP components. The article aims to guide the reasonable choice of drill helical direction and effectively reduce exit damage. Exit observation experiments are carried out with left-hand helical, right-hand helical and straight one-shot drill drilling T800S CFRP laminates separately. The development rules of exit damage and delamination factor curves are obtained. Combined with loading conditions and fracture modes of push-out burrs, and thrust force curves, the influence of drill helical direction on exit damage development is derived. It is found that the main fracture modes for left-hand helical, right-hand helical, and straight one-shot drill are mode I, extrusive fracture, mode III respectively. Among them, mode III has the least effect on exit damage development. Meanwhile, the changing rate of thrust force is relative slow for right-hand helical and straight one-shot drill in the thrust force increasing phase of stage II, which is disadvantaged for exit damage development. Therefore, straight one-shot drill’s exit quality is the best.

  12. New mode of operating a magnetized coaxial plasma gun for injecting magnetic helicity into a spheromak

    Woodruff, S.; Hill, D.N.; Stallard, B.W.; Bulmer, R.; Cohen, B.; Holcomb, C.T.; Hooper, E.B.; McLean, H.S.; Moller, J.; Wood, R.D.

    2003-01-01

    By operating a magnetized coaxial plasma gun continuously with just sufficient current to enable plasma ejection, large gun-voltage spikes (∼1 kV) are produced, giving the highest sustained voltage ∼500 V and highest sustained helicity injection rate observed in the Sustained Spheromak Physics Experiment. The spheromak magnetic field increases monotonically with time, exhibiting the lowest fluctuation levels observed during formation of any spheromak (B-tilde)/B≥2%). The results suggest an important mechanism for field generation by helicity injection, namely, the merging of helicity-carrying filaments

  13. New mode of operating a magnetized coaxial plasma gun for injecting magnetic helicity into a spheromak.

    Woodruff, S; Hill, D N; Stallard, B W; Bulmer, R; Cohen, B; Holcomb, C T; Hooper, E B; McLean, H S; Moller, J; Wood, R D

    2003-03-07

    By operating a magnetized coaxial plasma gun continuously with just sufficient current to enable plasma ejection, large gun-voltage spikes (approximately 1 kV) are produced, giving the highest sustained voltage approximately 500 V and highest sustained helicity injection rate observed in the Sustained Spheromak Physics Experiment. The spheromak magnetic field increases monotonically with time, exhibiting the lowest fluctuation levels observed during formation of any spheromak (B/B>/=2%). The results suggest an important mechanism for field generation by helicity injection, namely, the merging of helicity-carrying filaments.

  14. A helical scintillating fiber hodoscope

    Altmeier, M; Bisplinghoff, J; Bissel, T; Bollmann, R; Busch, M; Büsser, K; Colberg, T; Demiroers, L; Diehl, O; Dohrmann, F; Engelhardt, H P; Eversheim, P D; Felden, O; Gebel, R; Glende, M; Greiff, J; Gross, A; Gross-Hardt, R; Hinterberger, F; Jahn, R; Jeske, M; Jonas, E; Krause, H; Lahr, U; Langkau, R; Lindemann, T; Lindlein, J; Maier, R; Maschuw, R; Mayer-Kuckuck, T; Meinerzhagen, A; Naehle, O; Pfuff, M; Prasuhn, D; Rohdjess, H; Rosendaal, D; Von Rossen, P; Sanz, B; Schirm, N; Schulz-Rojahn, M; Schwarz, V; Scobel, W; Thomas, S; Trelle, H J; Weise, E; Wellinghausen, A; Wiedmann, W; Woller, K; Ziegler, R

    1999-01-01

    A novel scintillating fiber hodoscope in helically cylindric geometry has been developed for detection of low multiplicity events of fast protons and other light charged particles in the internal target experiment EDDA at the Cooler Synchrotron COSY. The hodoscope consists of 640 scintillating fibers (2.5 mm diameter), arranged in four layers surrounding the COSY beam pipe. The fibers are helically wound in opposing directions and read out individually using 16-channel photomultipliers connected to a modified commercial encoding system. The detector covers an angular range of 9 deg. <= THETA<=72 deg. and 0 deg. <=phi (cursive,open) Greek<=360 deg. in the lab frame. The detector length is 590 mm, the inner diameter 161 mm. Geometry and granularity of the hodoscope afford a position resolution of about 1.3 mm. The detector design took into consideration a maximum of reliability and a minimum of maintenance. An LED array may be used for monitoring purposes. (author)

  15. Helical CT of ureteral disease

    Cikman, Pablo; Bengio, Ruben; Bulacio, Javier; Zirulnik, Esteban; Garimaldi, Jorge

    2000-01-01

    Among the new applications of helical CT is the study of the ureteral pathology. The objective of this paper was to evaluate patients with suspected pathology of this organ and the repercussion in the therapeutic plans. We studied 23 patients with a helical CT protocol, without IV contrast injection and performed multiplanar reconstruction (MPR). We called this procedure Pielo CT. Thirteen ureteral stones were detected, 6 calculi, 2 urinary tract tumors, dilatation of the system in a patient with neo-bladder. In 2 patients, in whom ureteral pathology was ruled out, we found other alterations that explained the symptoms, (gallbladder stones, disk protrusion). The Pielo CT let decide a therapeutical approach in 20 or 21 patients with ureteral pathology. (author)

  16. Self-assembling monolayers of helical oligopeptides with applications in molecular electronics

    Strong, A.E.

    1997-01-01

    The aim of this project was to develop a generic method of preparing a 'molecular architecture' containing functional groups on a surface at predetermined relative positions several nm apart. This would be of great utility in molecular electronics, chemical sensors and other fields. It was proposed that such an architecture could be prepared on gold using linked, helical oligopeptides that contained the components of interest and sulphur functions able to form monolayers on gold by the self-assembly technique. Towards this ultimate aim Self-Assembled Monolayers (SAMs) of monomeric oligopeptides (13-17 residues) were prepared and characterised. Peptides containing three Met residues spaced in the sequence so that their side-chains lay on the same side of the helix were shown by circular dichroism (CD) to be strongly helical in organic solvents. Their self-assembled films on gold were characterised by Reflection-Absorption Infrared Spectroscopy (RAIRS) which showed the peptides adsorbed with the helix axes parallel to the surface, the orientation expected for self-assembly. However the surface coverage measured by cyclic voltammetry (CV) of the peptides' ferrocenyl derivatives on gold electrodes were less than expected for monolayers. Comparison of the films of ferrocenyl derivatives of Met and Cys showed that the thiolate bound more strongly than the thioether. Accordingly an oligopeptide containing two Cys residues at i, i+3, designed to be 3 10 -helical, was prepared. Transformation of the two (Trt)Cys residues of the resin-bound peptide to the intramolecular disulphide by iodine was achieved in acetonitrile but not in DMF. CD suggested that the conformation of this peptide was a mixture of helix and random coil. Films of the peptide-disulphide and the peptide-dithiol adsorbed from protic solvents were characterised as multilayers by ellipsometry. However CV and ellipsometry showed that a monolayer was successfully prepared from acetonitrile. Future targets for

  17. Helicity formalism and spin effects

    Anselmino, M.; Caruso, F.; Piovano, U.

    1990-01-01

    The helicity formalism and the technique to compute amplitudes for interaction processes involving leptons, quarks, photons and gluons are reviewed. Explicit calculations and examples of exploitation of symmetry properties are shown. The formalism is then applied to the discussion of several hadronic processes and spin effects: the experimental data, when related to the properties of the elementary constituent interactions, show many not understood features. Also the nucleon spin problem is briefly reviewed. (author)

  18. Radiation characteristics of helical tomotherapy

    Jeraj, Robert; Mackie, Thomas R.; Balog, John; Olivera, Gustavo; Pearson, Dave; Kapatoes, Jeff; Ruchala, Ken; Reckwerdt, Paul

    2004-01-01

    Helical tomotherapy is a dedicated intensity modulated radiation therapy (IMRT) system with on-board imaging capability (MVCT) and therefore differs from conventional treatment units. Different design goals resulted in some distinctive radiation field characteristics. The most significant differences in the design are the lack of flattening filter, increased shielding of the collimators, treatment and imaging operation modes and narrow fan beam delivery. Radiation characteristics of the helical tomotherapy system, sensitivity studies of various incident electron beam parameters and radiation safety analyses are presented here. It was determined that the photon beam energy spectrum of helical tomotherapy is similar to that of more conventional radiation treatment units. The two operational modes of the system result in different nominal energies of the incident electron beam with approximately 6 MeV and 3.5 MeV in the treatment and imaging modes, respectively. The off-axis mean energy dependence is much lower than in conventional radiotherapy units with less than 5% variation across the field, which is the consequence of the absent flattening filter. For the same reason the transverse profile exhibits the characteristic conical shape resulting in a 2-fold increase of the beam intensity in the center. The radiation leakage outside the field was found to be negligible at less than 0.05% because of the increased shielding of the collimators. At this level the in-field scattering is a dominant source of the radiation outside the field and thus a narrow field treatment does not result in the increased leakage. The sensitivity studies showed increased sensitivity on the incident electron position because of the narrow fan beam delivery and high sensitivity on the incident electron energy, as common to other treatment systems. All in all, it was determined that helical tomotherapy is a system with some unique radiation characteristics, which have been to a large extent

  19. Lipid-peptide-polymer conjugates and nanoparticles thereof

    Xu, Ting; Dong, He; Shu, Jessica

    2015-06-02

    The present invention provides a conjugate having a peptide with from about 10 to about 100 amino acids, wherein the peptide adopts a helical structure. The conjugate also includes a first polymer covalently linked to the peptide, and a hydrophobic moiety covalently linked to the N-terminus of the peptide, wherein the hydrophobic moiety comprises a second polymer or a lipid moiety. The present invention also provides helix bundles form by self-assembling the conjugates, and particles formed by self-assembling the helix bundles. Methods of preparing the helix bundles and particles are also provided.

  20. Hamiltonian theory of vacuum helical torus lines of magnetic force

    Gnudi, Giovanni; Hatori, Tadatsugu

    1994-01-01

    For making plasma into equilibrium state, the lines of magnetic force must have magnetic surfaces. However in a helical system, space is divided into the region having magnetic surface structure and the region that does not have it. Accordingly, it is an important basic research for the plasma confinement in a helical system to examine where is the boundary of both regions and how is the large area structure of the lines of magnetic force in the boundary region. The lines of magnetic force can be treated as a Hamilton mechanics system, and it has been proved that the Hamiltonian for the lines of magnetic force can be expressed by a set of canonical variables and the function of time. In this research, the Hamiltonian that describes the lines of magnetic force of helical system torus coordination in vacuum was successfully determined concretely. Next, the development of new linear symplectic integration method was carried out. The important supports for the theory of determining Hamiltonian are Lie transformation and paraxial expansion. The procedure is explained. In Appendix, Lie transformation, Hamiltonian for the lines of magnetic force, magnetic potential, Taylor expansion of the potential, cylindrical limit approximation, helical toroidal potential and integrable model are described. (K.I.)

  1. Institute for Fusion Research and Large Helical Device program

    Iiyoshi, Atsuo

    1989-01-01

    In the research on nuclear fusion, the final objective is to materialize nuclear fusion reactors, and for the purpose, it is necessary to cause nuclear combustion by making the plasma of higher than 100 million deg and confine it for a certain time. So far in various universities, the researches on diversified fusion processes have been advanced, but in February, 1986, the Science Council issued the report 'Nuclear fusion research in universities hereafter'. As the next large scale device, an external conductor system helical device was decided, and it is desirable to found the organization for joint utilization by national universities to promote the project. The researches on the other processes are continued by utilizing the existing facilitie. The reason of selecting a helical device is the data base of the researches carried out so far can be utilized sufficiently, it is sufficiently novel even after 10 years from now, and many researchers can be collected. The place of the research is Toki City, Gifu Prefecture, where the Institute of Plasma Physics, Nagoya University, is to be moved. The basic concept of the superconducting helical device project, the trend of nuclear fusion development in the world, the physical research using a helical system and so on are reported. (Kako, I.)

  2. Metamorphosis of helical magnetorotational instability in the presence axial electric current

    Priede, Jānis

    2014-01-01

    This paper presents numerical linear stability analysis of a cylindrical Taylor-Couette flow of liquid metal carrying axial electric current in a generally helical external magnetic field. Axially symmetric disturbances are considered in the inductionless approximation corresponding to zero magnetic Prandtl number. Axial symmetry allows us to reveal an entirely new electromagnetic instability. First, we show that the electric current passing through the liquid can extend the range of helical ...

  3. Magnetic helicity and active filament configuration

    Romano, P.; Zuccarello, F.; Poedts, S.; Soenen, A.; Zuccarello, F. P.

    2009-11-01

    Context: The role of magnetic helicity in active filament formation and destabilization is still under debate. Aims: Although active filaments usually show a sigmoid shape and a twisted configuration before and during their eruption, it is unclear which mechanism leads to these topologies. In order to provide an observational contribution to clarify these issues, we describe a filament evolution whose characteristics seem to be directly linked to the magnetic helicity transport in corona. Methods: We applied different methods to determine the helicity sign and the chirality of the filament magnetic field. We also computed the magnetic helicity transport rate at the filament footpoints. Results: All the observational signatures provided information on the positive helicity and sinistral chirality of the flux rope containing the filament material: its forward S shape, the orientation of its barbs, the bright and dark threads at 195 Å. Moreover, the magnetic helicity transport rate at the filament footpoints showed a clear accumulation of positive helicity. Conclusions: The study of this event showed a correspondence between several signatures of the sinistral chirality of the filament and several evidences of the positive magnetic helicity of the filament magnetic field. We also found that the magnetic helicity transported along the filament footpoints showed an increase just before the change of the filament shape observed in Hα images. We argued that the photospheric regions where the filament was rooted might be the preferential ways where the magnetic helicity was injected along the filament itself and where the conditions to trigger the eruption were yielded.

  4. Representing environment-induced helix-coil transitions in a coarse grained peptide model

    Dalgicdir, Cahit; Globisch, Christoph; Sayar, Mehmet; Peter, Christine

    2016-10-01

    Coarse grained (CG) models are widely used in studying peptide self-assembly and nanostructure formation. One of the recurrent challenges in CG modeling is the problem of limited transferability, for example to different thermodynamic state points and system compositions. Understanding transferability is generally a prerequisite to knowing for which problems a model can be reliably used and predictive. For peptides, one crucial transferability question is whether a model reproduces the molecule's conformational response to a change in its molecular environment. This is of particular importance since CG peptide models often have to resort to auxiliary interactions that aid secondary structure formation. Such interactions take care of properties of the real system that are per se lost in the coarse graining process such as dihedral-angle correlations along the backbone or backbone hydrogen bonding. These auxiliary interactions may then easily overstabilize certain conformational propensities and therefore destroy the ability of the model to respond to stimuli and environment changes, i.e. they impede transferability. In the present paper we have investigated a short peptide with amphiphilic EALA repeats which undergoes conformational transitions between a disordered and a helical state upon a change in pH value or due to the presence of a soft apolar/polar interface. We designed a base CG peptide model that does not carry a specific (backbone) bias towards a secondary structure. This base model was combined with two typical approaches of ensuring secondary structure formation, namely a C α -C α -C α -C α pseudodihedral angle potential or a virtual site interaction that mimics hydrogen bonding. We have investigated the ability of the two resulting CG models to represent the environment-induced conformational changes in the helix-coil equilibrium of EALA. We show that with both approaches a CG peptide model can be obtained that is environment-transferable and that

  5. New formulae for magnetic relative helicity and field line helicity

    Aly, Jean-Jacques

    2018-01-01

    We consider a magnetic field {B} occupying the simply connected domain D and having all its field lines tied to the boundary S of D. We assume here that {B} has a simple topology, i.e., the mapping {M} from positive to negative polarity areas of S associating to each other the two footpoints of any magnetic line, is continuous. We first present new formulae for the helicity H of {B} relative to a reference field {{B}}r having the same normal component {B}n on S, and for its field line helicity h relative to a reference vector potential {{C}}r of {{B}}r. These formulae make immediately apparent the well known invariance of these quantities under all the ideal MHD deformations that preserve the positions of the footpoints on S. They express indeed h and H either in terms of {M} and {B}n, or in terms of the values on S of a pair of Euler potentials of {B}. We next show that, for a specific choice of {{C}}r, the field line helicity h of {B} fully characterizes the magnetic mapping {M} and then the topology of the lines. Finally, we give a formula that describes the rate of change of h in a situation where the plasma moves on the perfectly conducting boundary S without changing {B}n and/or non-ideal processes, described by an unspecified term {N} in Ohm’s law, are at work in some parts of D.

  6. Plasma transport simulation modeling for helical confinement systems

    Yamazaki, K.; Amano, T.

    1991-08-01

    New empirical and theoretical transport models for helical confinement systems are developed based on the neoclassical transport theory including the effect of radial electric field and multi-helicity magnetic components, and the drift wave turbulence transport for electrostatic and electromagnetic modes, or the anomalous semi-empirical transport. These electron thermal diffusivities are compared with CHS (Compact Helical System) experimental data, which indicates that the central transport coefficient of the ECH plasma agrees with the neoclassical axi-symmetric value and the transport outside the half radius is anomalous. On the other hand, the transport of NBI-heated plasmas is anomalous in the whole plasma region. This anomaly is not explained by the electrostatic drift wave turbulence models in these flat-density-profile discharges. For the detailed prediction of plasma parameters in LHD (Large Helical Device), 3-D(dimensional) equilibrium/1-D transport simulations including empirical or drift wave turbulence models are carried out, which suggests that the global confinement time of LHD is determined mainly by the electron anomalous transport near the plasma edge region rather than the helical ripple transport in the core region. Even if the ripple loss can be eliminated, the increase of the global confinement is 10%. However, the rise in the central ion temperature is more than 20%. If the anomalous loss can be reduced to the half level of the present scaling, like so-called 'H-mode' of the tokamak discharge, the neoclassical ripple loss through the ion channel becomes important even in the plasma core. The 5% radial inward shift of the plasma column with respect to the major radius is effective for improving plasma confinement and raising more than 50% of the fusion product by reducing this neoclassical asymmetric ion transport loss and increasing 10% in the plasma radius. (author)

  7. Examining the Conservation of Kinks in Alpha Helices.

    Eleanor C Law

    Full Text Available Kinks are a structural feature of alpha-helices and many are known to have functional roles. Kinks have previously tended to be defined in a binary fashion. In this paper we have deliberately moved towards defining them on a continuum, which given the unimodal distribution of kink angles is a better description. From this perspective, we examine the conservation of kinks in proteins. We find that kink angles are not generally a conserved property of homologs, pointing either to their not being functionally critical or to their function being related to conformational flexibility. In the latter case, the different structures of homologs are providing snapshots of different conformations. Sequence identity between homologous helices is informative in terms of kink conservation, but almost equally so is the sequence identity of residues in spatial proximity to the kink. In the specific case of proline, which is known to be prevalent in kinked helices, loss of a proline from a kinked helix often also results in the loss of a kink or reduction in its kink angle. We carried out a study of the seven transmembrane helices in the GPCR family and found that changes in kinks could be related both to subfamilies of GPCRs and also, in a particular subfamily, to the binding of agonists or antagonists. These results suggest conformational change upon receptor activation within the GPCR family. We also found correlation between kink angles in different helices, and the possibility of concerted motion could be investigated further by applying our method to molecular dynamics simulations. These observations reinforce the belief that helix kinks are key, functional, flexible points in structures.

  8. MHD stability analysis of helical system plasmas

    Nakamura, Yuji

    2000-01-01

    Several topics of the MHD stability studies in helical system plasmas are reviewed with respect to the linear and ideal modes mainly. Difference of the method of the MHD stability analysis in helical system plasmas from that in tokamak plasmas is emphasized. Lack of the cyclic (symmetric) coordinate makes an analysis more difficult. Recent topic about TAE modes in a helical system is also described briefly. (author)

  9. Employing helicity amplitudes for resummation in SCET

    Moult, Ian; Stewart, Iain W.; Tackmann, Frank J.; Waalewijn, Wouter J.; Nikhef, Amsterdam

    2016-05-01

    Helicity amplitudes are the fundamental ingredients of many QCD calculations for multi-leg processes. We describe how these can seamlessly be combined with resummation in Soft-Collinear Effective Theory (SCET), by constructing a helicity operator basis for which the Wilson coefficients are directly given in terms of color-ordered helicity amplitudes. This basis is crossing symmetric and has simple transformation properties under discrete symmetries.

  10. EVOLUTION OF MAGNETIC HELICITY AND ENERGY SPECTRA OF SOLAR ACTIVE REGIONS

    Zhang, Hongqi; Brandenburg, Axel; Sokoloff, D. D.

    2016-01-01

    We adopt an isotropic representation of the Fourier-transformed two-point correlation tensor of the magnetic field to estimate the magnetic energy and helicity spectra as well as current helicity spectra of two individual active regions (NOAA 11158 and NOAA 11515) and the change of the spectral indices during their development as well as during the solar cycle. The departure of the spectral indices of magnetic energy and current helicity from 5/3 are analyzed, and it is found that it is lower than the spectral index of the magnetic energy spectrum. Furthermore, the fractional magnetic helicity tends to increase when the scale of the energy-carrying magnetic structures increases. The magnetic helicity of NOAA 11515 violates the expected hemispheric sign rule, which is interpreted as an effect of enhanced field strengths at scales larger than 30–60 Mm with opposite signs of helicity. This is consistent with the general cycle dependence, which shows that around the solar maximum the magnetic energy and helicity spectra are steeper, emphasizing the large-scale field

  11. EVOLUTION OF MAGNETIC HELICITY AND ENERGY SPECTRA OF SOLAR ACTIVE REGIONS

    Zhang, Hongqi [Key Laboratory of Solar Activity, National Astronomical Observatories, Chinese Academy of Sciences, Beijing 100012 (China); Brandenburg, Axel [Nordita, KTH Royal Institute of Technology and Stockholm University, Roslagstullsbacken 23, SE-10691 Stockholm (Sweden); Sokoloff, D. D., E-mail: hzhang@bao.ac.cn [Department of Physics, Moscow University, 119992 Moscow (Russian Federation)

    2016-03-10

    We adopt an isotropic representation of the Fourier-transformed two-point correlation tensor of the magnetic field to estimate the magnetic energy and helicity spectra as well as current helicity spectra of two individual active regions (NOAA 11158 and NOAA 11515) and the change of the spectral indices during their development as well as during the solar cycle. The departure of the spectral indices of magnetic energy and current helicity from 5/3 are analyzed, and it is found that it is lower than the spectral index of the magnetic energy spectrum. Furthermore, the fractional magnetic helicity tends to increase when the scale of the energy-carrying magnetic structures increases. The magnetic helicity of NOAA 11515 violates the expected hemispheric sign rule, which is interpreted as an effect of enhanced field strengths at scales larger than 30–60 Mm with opposite signs of helicity. This is consistent with the general cycle dependence, which shows that around the solar maximum the magnetic energy and helicity spectra are steeper, emphasizing the large-scale field.

  12. New Modular Heliotron system compatible with closed helical divertor and good plasma confinement

    Yamazaki, K.; Watanabe, K.Y.

    1994-04-01

    A new helical system ('Modular Heliotron') with improved modular coils compatible with efficient closed helical divertor and good plasma confinement property is proposed based on a Heliotron system with continuous helical coils and one pair of poloidal coils. The physics optimization of this system as a function of the gap angle between adjacent modular coils has been carried out by means of vacuum magnetic surface calculations and finite-beta plasma analyses, and a new improved coil system is invented by combining sectored helical field coils with sectored returning poloidal field coils. The Modular Heliotron with standard coil winding law (reference Modular Heliotron) was previously proposed, but it is found that this is not appropriate to keep clean helical divertor and high beta configuration when the coil gap becomes large. By modulating the modular coil winding with outside-plus and inside-minus pitch modulation, almost the same good magnetic configuration as that of a conventional Heliotron can be produced. The optimal gap angle is determined as a function of the modulation parameter. This improved Modular Heliotron permits larger gap angle between adjacent modules and produces more clean helical divertor configuration than the reference Modular Heliotron. All these helical system are created by only modular coils without poloidal coils. (author)

  13. New modular heliotron system compatible with closed helical divertor and good plasma confinement

    Yamazaki, K.; Watanabe, K.Y.

    1995-01-01

    A new helical system ('modular heliotron') with improved modular coils compatible with an efficient closed helical divertor and a good plasma confinement property is proposed, based on a heliotron system with continuous helical coils and one pair of poloidal coils. The physics optimization of this system as a function of the gap angle between adjacent modular coils has been carried out by means of vacuum magnetic surface calculations and finite-beta plasma analyses, and a new improved coil system is invented by combining sectored helical field coils with sectored returning poloidal field coils. A modular heliotron with standard coil winding law (the reference modular heliotron) was previously proposed, but it is found that this was not appropriate to keep a clean helical divertor and high beta configuration when the coil gap becomes large. By modulating the modular coil winding with outside-plus and inside-minus pitch modulation, almost the same good magnetic configuration as that of a conventional heliotron can be produced. The optimal gap angle is determined as a function of the modulation parameter. This improved modular heliotron permits a larger gap angle between adjacent modules and produces a cleaner helical divertor configuration than the reference modular heliotron. All these helical systems are created by only modular coils without poloidal coils. (author). Letter-to-the-editor. 11 refs, 7 figs

  14. Novel antimicrobial peptides from the venom of eusocial bee Halictus sexcinctus (Hymenoptera: Halictidae)

    Monincová, Lenka; Hovorka, Oldřich; Cvačka, Josef; Voburka, Zdeněk; Fučík, Vladimír; Borovičková, Lenka; Bednárová, Lucie; Buděšínský, Miloš; Slaninová, Jiřina; Straka, J.; Čeřovský, Václav

    2009-01-01

    Roč. 92, č. 4 (2009), s. 364-364 ISSN 0006-3525. [American Peptide Symposium /21./. 07.06.2009-12.06.2009, Bloomington] Institutional research plan: CEZ:AV0Z40550506 Keywords : antimicrobial peptide * bee venom * alpha-helical structure Subject RIV: CC - Organic Chemistry

  15. On the diffusion of alpha-helical proteins in solvents

    Barredo, Wilson I.; Bornales, Jinky B.; Bernido, Christopher C.; Aringa, Henry P.

    2015-01-01

    The winding probability function for a biopolymer diffusing in a crowded cell is obtained with the drift coefficient f(s) involving Bessel functions of general form f(s) = kJ2p+1 (νs). The variable s is the length along the chain and ν is a constant which can be used to simulate the frequency of appearance of a certain type of amino acid. Application of a particular case p = 3 to protein chains is carried out for different alpha helical proteins found in the Protein Data Bank (PDB). Analysis of our results leads us to an empirical formula that can be used to conveniently predict k/D and ν, where D is the diffusion coefficient of various α-helical proteins in solvents.

  16. Small-x Asymptotics of the Quark Helicity Distribution.

    Kovchegov, Yuri V; Pitonyak, Daniel; Sievert, Matthew D

    2017-02-03

    We construct a numerical solution of the small-x evolution equations derived in our recent work [J. High Energy Phys. 01 (2016) 072.JHEPFG1029-847910.1007/JHEP01(2016)072] for the (anti)quark transverse momentum dependent helicity TMDs and parton distribution functions (PDFs) as well as the g_{1} structure function. We focus on the case of large N_{c}, where one finds a closed set of equations. Employing the extracted intercept, we are able to predict directly from theory the behavior of the quark helicity PDFs at small x, which should have important phenomenological consequences. We also give an estimate of how much of the proton's spin carried by the quarks may be at small x and what impact this has on the spin puzzle.

  17. THE EFFECT OF ELECTRON THERMAL PRESSURE ON THE OBSERVED MAGNETIC HELICITY IN THE SOLAR WIND

    Markovskii, S. A.; Vasquez, Bernard J.; Smith, Charles W., E-mail: sergei.markovskii@unh.edu, E-mail: bernie.vasquez@unh.edu, E-mail: charles.smith@unh.edu [Space Science Center, University of New Hampshire, Durham, NH 03824 (United States)

    2016-12-20

    Statistical analysis of magnetic helicity spectra in the solar wind at 1 au is carried out. A large database of the solar wind intervals assembled from Wind spacecraft magnetic and plasma data is used. The effect of the electron thermal pressure on the wavenumber position of the helicity signature, i.e., the peak of the spectrum, is studied. The position shows a statistically significant dependence on both the electron and proton pressures. However, the strongest dependence is seen when the two pressures are summed. These findings confirm that the generation of the magnetic helicity is associated with an increasing compressibility of the turbulent fluctuations at smaller kinetic scales. It is argued that instrumental artifacts do not contribute to the helicity signature.

  18. Evidence for α-helices in the gas phase: a case study using Melittin from honey bee venom.

    Florance, Hannah V; Stopford, Andrew P; Kalapothakis, Jason M; McCullough, Bryan J; Bretherick, Andrew; Barran, Perdita E

    2011-09-07

    Gas phase methodologies are increasingly used to study the structure of proteins and peptides. A challenge to the mass spectrometrist is to preserve the structure of the system of interest intact and unaltered from solution into the gas phase. Small peptides are very flexible and can present a number of conformations in solution. In this work we examine Melittin a 26 amino acid peptide that forms the active component of honey bee venom. Melittin is haemolytic and has been shown to form an α-helical tetrameric structure by X-ray crystallography [M. Gribskov et al., The RCSB Protein Data Bank, 1990] and to be helical in high concentrations of methanol. Here we use ion mobility mass spectrometry, molecular dynamics and gas-phase HDX to probe its structure in the gas phase and specifically interrogate whether the helical form can be preserved. All low energy calculated structures possess some helicity. In our experiments we examine the peptide following nano-ESI from solutions with varying methanol content. Ion mobility gives collision cross sections (CCS) that compare well with values found from molecular modelling and from other reported structures, but with inconclusive results regarding the effect of solvent. There is only a slight increase in CCS with charge, showing minimal coloumbically driven unfolding. HDX supports preservation of some helical content into the gas phase and again shows little difference in the exchange rates of species sprayed from different solvents. The [M + 3H](3+) species has two exchanging populations both of which exhibit faster exchange rates than observed for the [M + 2H](2+) species. One interpretation for these results is that the time spent being analysed is sufficient for this peptide to form a helix in the 'ultimate' hydrophobic environment of a vacuum.

  19. DNA-like double helix formed by peptide nucleic acid

    Wittung, P; Nielsen, Peter E.; Buchardt, O

    1994-01-01

    Although the importance of the nucleobases in the DNA double helix is well understood, the evolutionary significance of the deoxyribose phosphate backbone and the contribution of this chemical entity to the overall helical structure and stability of the double helix is not so clear. Peptide nucleic...

  20. Folding and insertion thermodynamics of the transmembrane WALP peptide

    Bereau, T.; Bennett, W.F.D.; Pfaendtner, J.; Deserno, M.; Karttunen, M.E.J.

    2015-01-01

    The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA)$_n$(L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural

  1. Folding and insertion thermodynamics of the transmembrane WALP peptide

    Bereau, T.; Bennett, W.F.D. Drew; Pfaendtner, J.; Deserno, M.; Karttunen, M.

    2015-01-01

    The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA)n (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural

  2. Novel antimicrobial peptides isolated from the venom of wild bees

    Čeřovský, Václav; Monincová, Lenka; Slaninová, Jiřina; Fučík, Vladimír; Borovičková, Lenka; Hovorka, Oldřich; Voburka, Zdeněk; Cvačka, Josef; Bednárová, Lucie; Buděšínský, Miloš; Straka, J.

    2009-01-01

    Roč. 276, Suppl. 1 (2009), s. 106-106 ISSN 1742-464X. [FEBS Congress /34/. 04.07.2009-09.07.2009, Praha] Institutional research plan: CEZ:AV0Z40550506 Keywords : linear cationic alpha-helical antimicrobial peptides * Edman degradation * mass spectrometry Subject RIV: CC - Organic Chemistry

  3. Magnetic islands created by resonant helical windings

    Fernandes, A.S.; Heller, M.V.; Caldas, I.L.

    1986-01-01

    The triggering of disruptive instabilities by resonant helical windings in large aspect-ratio tokamaks is associated to destruction of magnetic surfaces. The Chirikov condition is applied to estimate analytically the helical winding current thresholds for ergodization of the magnetic field lines. (Autor) [pt

  4. Helicity amplitudes for matter-coupled gravity

    Aldrovandi, R.; Novaes, S.F.; Spehler, D.

    1992-07-01

    The Weyl-van der Waerden spinor formalism is applied to the evaluation of helicity invariant amplitudes in the framework of linearized gravitation. The graviton couplings to spin-0, 1 - 2 , 1, and 3 - 2 particles are given, and, to exhibit the reach of this method, the helicity amplitudes for the process electron + positron → photon + graviton are obtained. (author)

  5. Stiffness versus architecture of single helical polyisocyanopeptides

    Buul, van A.M.; Schwartz, E.; Brocorens, P.; Koepf, M.; Beljonne, D.; Maan, J.C.; Christianen, P.C.M.; Kouwer, P.H.J.; Nolte, R.J.M.; Engelkamp, H.; Blank, K.; Rowan, A.E.

    2013-01-01

    Helical structures play a vital role in nature, offering mechanical rigidity, chirality and structural definition to biological systems. Little is known about the influence of the helical architecture on the intrinsic properties of polymers. Here, we offer an insight into the nano architecture of

  6. Dynamics of zonal flows in helical systems.

    Sugama, H; Watanabe, T-H

    2005-03-25

    A theory for describing collisionless long-time behavior of zonal flows in helical systems is presented and its validity is verified by gyrokinetic-Vlasov simulation. It is shown that, under the influence of particles trapped in helical ripples, the response of zonal flows to a given source becomes weaker for lower radial wave numbers and deeper helical ripples while a high-level zonal-flow response, which is not affected by helical-ripple-trapped particles, can be maintained for a longer time by reducing their bounce-averaged radial drift velocity. This implies a possibility that helical configurations optimized for reducing neoclassical ripple transport can simultaneously enhance zonal flows which lower anomalous transport.

  7. Three-residue turns in alpha/beta-peptides and their application in the design of tertiary structures.

    Sharma, Gangavaram V M; Nagendar, Pendem; Ramakrishna, Kallaganti V S; Chandramouli, Nagula; Choudhary, Madavi; Kunwar, Ajit C

    2008-06-02

    A new three-residue turn was serendipitously discovered in alpha/beta hybrid peptides derived from alternating C-linked carbo-beta-amino acids (beta-Caa) and L-Ala residues. The three-residue beta-alpha-beta turn at the C termini, nucleated by a helix at the N termini, resulted in helix-turn (HT) supersecondary structures in these peptides. The turn in the HT motif is stabilized by two H bonds-CO(i-2)-NH(i), with a seven-membered pseudoring (gamma turn) in the backward direction, and NH(i-2)-CO(i), with a 13-membered pseudoring in the forward direction (i being the last residue)--at the C termini. The study was extended to generalize the new three-residue turn (beta-alpha-beta) by using different alpha- and beta-amino acids. Furthermore, the HT motifs were efficiently converted, by an extension with helical oligomers at the C termini, into peptides with novel helix-turn-helix (HTH) tertiary structures. However, this resulted in the destabilization of the beta-alpha-beta turn with the concomitant nucleation of another three-residue turn, alpha-beta-beta, which is stabilized by 11- and 15-membered bifurcated H bonds. Extensive NMR spectroscopic studies were carried out to delineate the secondary and tertiary structures in these peptides, which are further supported by molecular dynamics (MD) investigations.

  8. Topology of helical fluid flow

    Andersen, Morten; Brøns, Morten

    2014-01-01

    function for the topology of the streamline pattern in incompressible flows. On this basis, we perform a comprehensive study of the topology of the flow field generated by a helical vortex filament in an ideal fluid. The classical expression for the stream function obtained by Hardin (Hardin, J. C. 1982...... the zeroes of a single real function of one variable, and we show that three different flow topologies can occur, depending on a single dimensionless parameter. By including the self-induced velocity on the vortex filament by a localised induction approximation, the stream function is slightly modified...... and an extra parameter is introduced. In this setting two new flow topologies arise, but not more than two critical points occur for any combination of parameters....

  9. Helically coiled tube heat exchanger

    Harris, A.M.

    1981-01-01

    In a heat exchanger such as a steam generator for a nuclear reactor, two or more bundles of helically coiled tubes are arranged in series with the tubes in each bundle integrally continuing through the tube bundles arranged in series therewith. Pitch values for the tubing in any pair of tube bundles, taken transverse to the path of the reactor coolant flow about the tubes, are selected as a ratio of two unequal integers to permit efficient operation of each tube bundle while maintaining the various tube bundles of the heat exchanger within a compact envelope. Preferably, the helix angle and tube pitch parallel to the path of coolant flow are constant for all tubes in a single bundle so that the tubes are of approximately the same length within each bundle

  10. The quantum Hall effect helicity

    Shrivastava, Keshav N., E-mail: keshav1001@yahoo.com [Department of Physics, University of Malaya, Kuala Lumpur 50603 (Malaysia); School of Physics, University of Hyderabad, Hyderabad 500046 (India)

    2015-04-16

    The quantum Hall effect in semiconductor heterostructures is explained by two signs in the angular momentum j=l±s and g=(2j+1)/(2l+1) along with the Landau factor (n+1/2). These modifications in the existing theories explain all of the fractional charges. The helicity which is the sign of the product of the linear momentum with the spin p.s plays an important role for the understanding of the data at high magnetic fields. In particular it is found that particles with positive sign in the spin move in one direction and those with negative sign move in another direction which explains the up and down stream motion of the particles.

  11. Influence of 63Ser phosphorylation and dephosphorylation on the structure of the stathmin helical nucleation sequence: a molecular dynamics study.

    Missimer, John H; Steinmetz, Michel O; van Gunsteren, Wilfred F; Dolenc, Jožica

    2012-10-23

    Phosphorylation is an important mechanism regulating protein-protein interactions involving intrinsically disordered protein regions. Stathmin, an archetypical example of an intrinsically disordered protein, is a key regulator of microtubule dynamics in which phosphorylation of 63Ser within the helical nucleation sequence strongly down-regulates the tubulin binding and microtubule destabilizing activities of the protein. Experimental studies on a peptide encompassing the 19-residue helical nucleation sequence of stathmin (residues 55-73) indicate that phosphorylation of 63Ser destabilizes the peptide's secondary structure by disrupting the salt bridges supporting its helical conformation. In order to investigate this hypothesis at atomic resolution, we performed molecular dynamics simulations of nonphosphorylated and phosphorylated stathmin-[55-73] at room temperature and pressure, neutral pH, and explicit solvation using the recently released GROMOS force field 54A7. In the simulations of nonphosphorylated stathmin-[55-73] emerged salt bridges associated with helical configurations. In the simulations of 63Ser phosphorylated stathmin-[55-73] these configurations dispersed and were replaced by a proliferation of salt bridges yielding disordered configurations. The transformation of the salt bridges was accompanied by emergence of numerous interactions between main and side chains, involving notably the oxygen atoms of the phosphorylated 63Ser. The loss of helical structure induced by phosphorylation is reversible, however, as a final simulation showed. The results extend the hypothesis of salt bridge derangement suggested by experimental observations of the stathmin nucleation sequence, providing new insights into regulation of intrinsically disordered protein systems mediated by phosphorylation.

  12. Heat transfer analysis of short helical borehole heat exchangers

    Zarrella, Angelo; De Carli, Michele

    2013-01-01

    Highlights: ► Vertical ground heat exchanger with a helical shaped pipe is analyzed. ► The model considers the interaction between the ground and the environment. ► The results of the model are in good agreement with the experimental values. ► The weather conditions considerably affect the fluid heat carrier temperature. ► The pitch between the turns does not affect the behaviour of the heat exchanger. -- Abstract: In this paper a numerical model to analyze the thermal behaviour of vertical ground heat exchangers with a helical shaped pipe is presented. This type of configuration can be a suitable alternative to conventional ground heat exchangers, especially when the heating and cooling loads of the building are very low. The model describes the heat transfer problem by means of a network of interconnected thermal resistances and capacitances. Moreover, as the investigated ground heat exchanger is usually installed in shallow depth, the model takes into account the interaction between the ground and the ambient environment which affects the fluid heat carrier temperature into the heat exchanger and, as a consequence, the energy efficiency of the heat pump. After a sensitivity analysis on the mesh parameters, the presented model is compared with experimental data and the simulation results show good agreement with the measurements. Finally, analyses to investigate the influence of the weather conditions, of the axial heat transfer and of the pitch between the turns of the helical pipe for two types of ground are carried out.

  13. Helical CT scan for emergent patients with cerebrovascular diseases

    Matsumoto, Masato; Sato, Naoki; Nakano, Masayuki; Watanabe, Youichi; Kodama, Namio

    1995-01-01

    We studied 44 emergent patients with cerebrovascular diseases (18 cases of subarachnoid hemorrhage, 15 of occlusive lesions, 7 of intracerebral hematoma and 4 of suspected subarachnoid hemorrhage) using helical CT scan. The helical CT scan was performed with contrast medium at a rate of 3 ml/sec with a delay of 20 sec, and was carried out before conventional angiography. The reconstruction time of 3D-CTA was within 10 min. We were able to obtain findings for the lesion on 3D-CTA before those on conventional angiography. The 3D-CTA yielded excellent images of the vascular structures and anatomical relationships of the aneurysm, its neck and parent artery, and surrounding arteries. However, it proved difficult to visualize vessels of less than 1 mm in diameter, especially the perforating arteries. In occlusive diseases, the degree of stenosis depended on the changes in CT number threshold: at present, evaluations of the lesions should be made by conventional angiography. 3D-CTA using helical CT scan can thus be applied for emergent patients with cerebrovascular diseases. Surgical simulation images of 3D-CTA were especially useful at the time of operation. (author)

  14. Helical CT scan for emergent patients with cerebrovascular diseases

    Matsumoto, Masato; Sato, Naoki; Nakano, Masayuki; Watanabe, Youichi; Kodama, Namio [Fukushima Medical Coll. (Japan)

    1995-08-01

    We studied 44 emergent patients with cerebrovascular diseases (18 cases of subarachnoid hemorrhage, 15 of occlusive lesions, 7 of intracerebral hematoma and 4 of suspected subarachnoid hemorrhage) using helical CT scan. The helical CT scan was performed with contrast medium at a rate of 3 ml/sec with a delay of 20 sec, and was carried out before conventional angiography. The reconstruction time of 3D-CTA was within 10 min. We were able to obtain findings for the lesion on 3D-CTA before those on conventional angiography. The 3D-CTA yielded excellent images of the vascular structures and anatomical relationships of the aneurysm, its neck and parent artery, and surrounding arteries. However, it proved difficult to visualize vessels of less than 1 mm in diameter, especially the perforating arteries. In occlusive diseases, the degree of stenosis depended on the changes in CT number threshold: at present, evaluations of the lesions should be made by conventional angiography. 3D-CTA using helical CT scan can thus be applied for emergent patients with cerebrovascular diseases. Surgical simulation images of 3D-CTA were especially useful at the time of operation. (author).

  15. Secondary structure of cell-penetrating peptides during interaction with fungal cells.

    Gong, Zifan; Ikonomova, Svetlana P; Karlsson, Amy J

    2018-03-01

    Cell-penetrating peptides (CPPs) are peptides that cross cell membranes, either alone or while carrying molecular cargo. Although their interactions with mammalian cells have been widely studied, much less is known about their interactions with fungal cells, particularly at the biophysical level. We analyzed the interactions of seven CPPs (penetratin, Pep-1, MPG, pVEC, TP-10, MAP, and cecropin B) with the fungal pathogen Candida albicans using experiments and molecular simulations. Circular dichroism (CD) of the peptides revealed a structural transition from a random coil or weak helix to an α-helix occurs for all peptides when the solvent is changed from aqueous to hydrophobic. However, CD performed in the presence of C. albicans cells showed that proximity to the cell membrane is not necessarily sufficient to induce this structural transition, as penetratin, Pep-1, and MPG did not display a structural shift in the presence of cells. Monte Carlo simulations were performed to further probe the molecular-level interaction with the cell membrane, and these simulations suggested that pVEC, TP-10, MAP, and cecropin B strongly penetrate into the hydrophobic domain of the membrane lipid bilayer, inducing a transition to an α-helical conformation. In contrast, penetratin, Pep-1 and MPG remained in the hydrophilic region without a shift in conformation. The experimental data and MC simulations combine to explain how peptide structure affects their interaction with cells and their mechanism of translocation into cells (direct translocation vs. endocytosis). Our work also highlights the utility of combining biophysical experiments, biological experiments, and molecular modeling to understand biological phenomena. © 2017 The Protein Society.

  16. Evidence for Mixed Helicity in Erupting Filaments

    Muglach, K.; Wang, Y.-M.; Kliem, B.

    2009-09-01

    Erupting filaments are sometimes observed to undergo a rotation about the vertical direction as they rise. This rotation of the filament axis is generally interpreted as a conversion of twist into writhe in a kink-unstable magnetic flux rope. Consistent with this interpretation, the rotation is usually found to be clockwise (as viewed from above) if the post-eruption arcade has right-handed helicity, but counterclockwise if it has left-handed helicity. Here, we describe two non-active-region filament events recorded with the Extreme-Ultraviolet Imaging Telescope on the Solar and Heliospheric Observatory in which the sense of rotation appears to be opposite to that expected from the helicity of the post-event arcade. Based on these observations, we suggest that the rotation of the filament axis is, in general, determined by the net helicity of the erupting system, and that the axially aligned core of the filament can have the opposite helicity sign to the surrounding field. In most cases, the surrounding field provides the main contribution to the net helicity. In the events reported here, however, the helicity associated with the filament "barbs" is opposite in sign to and dominates that of the overlying arcade.

  17. HEMISPHERIC HELICITY TREND FOR SOLAR CYCLE 24

    Hao Juan; Zhang Mei

    2011-01-01

    Using vector magnetograms obtained with the Spectro-polarimeter (SP) on board Hinode satellite, we studied two helicity parameters (local twist and current helicity) of 64 active regions that occurred in the descending phase of solar cycle 23 and the ascending phase of solar cycle 24. Our analysis gives the following results. (1) The 34 active regions of the solar cycle 24 follow the so-called hemispheric helicity rule, whereas the 30 active regions of the solar cycle 23 do not. (2) When combining all 64 active regions as one sample, they follow the hemispheric helicity sign rule as in most other observations. (3) Despite the so-far most accurate measurement of vector magnetic field given by SP/Hinode, the rule is still weak with large scatters. (4) The data show evidence of different helicity signs between strong and weak fields, confirming previous result from a large sample of ground-based observations. (5) With two example sunspots we show that the helicity parameters change sign from the inner umbra to the outer penumbra, where the sign of penumbra agrees with the sign of the active region as a whole. From these results, we speculate that both the Σ-effect (turbulent convection) and the dynamo have contributed in the generation of helicity, whereas in both cases turbulence in the convection zone has played a significant role.

  18. Influence of helical external driven current on nonlinear resistive tearing mode evolution and saturation in tokamaks

    Zhang, W.; Wang, S.; Ma, Z. W.

    2017-06-01

    The influences of helical driven currents on nonlinear resistive tearing mode evolution and saturation are studied by using a three-dimensional toroidal resistive magnetohydrodynamic code (CLT). We carried out three types of helical driven currents: stationary, time-dependent amplitude, and thickness. It is found that the helical driven current is much more efficient than the Gaussian driven current used in our previous study [S. Wang et al., Phys. Plasmas 23(5), 052503 (2016)]. The stationary helical driven current cannot persistently control tearing mode instabilities. For the time-dependent helical driven current with f c d = 0.01 and δ c d < 0.04 , the island size can be reduced to its saturated level that is about one third of the initial island size. However, if the total driven current increases to about 7% of the total plasma current, tearing mode instabilities will rebound again due to the excitation of the triple tearing mode. For the helical driven current with time dependent strength and thickness, the reduction speed of the radial perturbation component of the magnetic field increases with an increase in the driven current and then saturates at a quite low level. The tearing mode is always controlled even for a large driven current.

  19. Chiral charge erasure via thermal fluctuations of magnetic helicity

    Long, Andrew J.; Sabancilar, Eray

    2016-01-01

    We consider a relativistic plasma of fermions coupled to an Abelian gauge field and carrying a chiral charge asymmetry, which might arise in the early Universe through baryogenesis. It is known that on large length scales, λ≳1/(αμ_5), the chiral anomaly opens an instability toward the erasure of chiral charge and growth of magnetic helicity. Here the chemical potential μ_5 parametrizes the chiral asymmetry and α is the fine-structure constant. We study the process of chiral charge erasure through the thermal fluctuations of magnetic helicity and contrast with the well-studied phenomenon of Chern-Simons number diffusion. Through the fluctuation-dissipation theorem we estimate the amplitude and time scale of helicity fluctuations on the length scale λ, finding δ H∼λT and τ∼αλ"3T"2 for a relativistic plasma at temperature T. We argue that the presence of a chiral asymmetry allows the helicity to grow diffusively for a time t∼T"3/(α"5μ_5"4) until it reaches an equilibrium value H∼μ_5T"2/α, and the chiral asymmetry is partially erased. If the chiral asymmetry is small, μ_5< T/α, this avenue for chiral charge erasure is found to be slower than the chiral magnetic effect for which t∼T/(α"3μ_5"2). This mechanism for chiral charge erasure can be important for the hypercharge sector of the Standard Model as well as extensions including U(1) gauge interactions, such as asymmetric dark matter models.

  20. Cylindrical Taylor states conserving total absolute magnetic helicity

    Low, B. C.; Fang, F.

    2014-09-01

    The Taylor state of a three-dimensional (3D) magnetic field in an upright cylindrical domain V is derived from first principles as an extremum of the total magnetic energy subject to a conserved, total absolute helicity Habs. This new helicity [Low, Phys. Plasmas 18, 052901 (2011)] is distinct from the well known classical total helicity and relative total helicity in common use to describe wholly-contained and anchored fields, respectively. A given field B, tangential along the cylindrical side of V, may be represented as a unique linear superposition of two flux systems, an axially extended system along V and a strictly transverse system carrying information on field-circulation. This specialized Chandrasekhar-Kendall representation defines Habs and permits a neat formulation of the boundary-value problem (BVP) for the Taylor state as a constant-α force-free field, treating 3D wholly-contained and anchored fields on the same conceptual basis. In this formulation, the governing equation is a scalar integro-partial differential equation (PDE). A family of series solutions for an anchored field is presented as an illustration of this class of BVPs. Past treatments of the constant-α field in 3D cylindrical geometry are based on a scalar Helmholtz PDE as the governing equation, with issues of inconsistency in the published field solutions discussed over time in the journal literature. The constant-α force-free equation reduces to a scalar Helmholtz PDE only as special cases of the 3D integro-PDE derived here. In contrast, the constant-α force-free equation and the scalar Helmholtz PDE are absolutely equivalent in the spherical domain as discussed in Appendix. This theoretical study is motivated by the investigation of the Sun's corona but the results are also relevant to laboratory plasmas.

  1. Polymorphic transformation of helical flagella of bacteria

    Lim, Sookkyung; Howard Berg Collaboration; William Ko Collaboration; Yongsam Kim Collaboration; Wanho Lee Collaboration; Charles Peskin Collaboration

    2016-11-01

    Bacteria such as E. coli swim in an aqueous environment by utilizing the rotation of flagellar motors and alternate two modes of motility, runs and tumbles. Runs are steady forward swimming driven by bundles of flagellar filaments whose motors are turning CCW; tumbles involve a reorientation of the direction of swimming triggered by motor reversals. During tumbling, the helical flagellum undergoes polymorphic transformations, which is a local change in helical pitch, helical radius, and handedness. In this work, we investigate the underlying mechanism of structural conformation and how this polymorphic transition plays a role in bacterial swimming. National Science Foundation.

  2. Modelling simple helically delivered dose distributions

    Fenwick, John D; Tome, Wolfgang A; Kissick, Michael W; Mackie, T Rock

    2005-01-01

    In a previous paper, we described quality assurance procedures for Hi-Art helical tomotherapy machines. Here, we develop further some ideas discussed briefly in that paper. Simple helically generated dose distributions are modelled, and relationships between these dose distributions and underlying characteristics of Hi-Art treatment systems are elucidated. In particular, we describe the dependence of dose levels along the central axis of a cylinder aligned coaxially with a Hi-Art machine on fan beam width, couch velocity and helical delivery lengths. The impact on these dose levels of angular variations in gantry speed or output per linear accelerator pulse is also explored

  3. Plasmoid behavior in helical plasmas

    Ishizaki, R.; Nakajima, N.

    2009-01-01

    Full text: It is well known that an ablation cloud; a high density and low temperature plasmoid, drifts to the lower field side in tokamak plasmas, which leads to a good performance on fueling in tokamak. Such a good performance, however, has not been obtained yet in the planar axis heliotron; Large Helical Device (LHD) experiments, even if a pellet has been injected from the high field side. The purpose of the study is to clarify the difference on the plasmoid motion between tokamak and LHD plasmas by using the MHD simulation including ablation processes. It is found in tokamaks that the drift motion is induced by a tire tube force and 1/R force in the major radius direction, and that the pressure and density of the plasmoid have oscillation due to fast compressional Alfven wave. On the other hand, the upper and lower portions surrounding the plasmoid center drift to the higher field side, because 1/R force by magnetic field becomes negative in the major radius direction since the magnetic field surrounding the plasmoid is accumulated by the extremely large ablation pressure and the magnetic pressure perturbation becomes positive. It is also found that the plasmoid does not drift when the perturbation of the plasmoid is small. In addition, the motion of the plasmoid is investigated in LHD plasmas in four cases that the plasmoids are initially located at the inner and outer sides of the torus on the vertically and horizontally elongated poloidal cross sections. The plasmoids drift to the lower field sides in all cases. However, in the case that it is located at the inner side of the torus on the horizontally elongated poloidal cross section, it is found that the plasmoid drifts in the negative direction of the major radius and subsequently drifts in the positive direction of it. In other words, the plasmoid finally drifts in the positive direction of the major radius the same as the plasmoid located at the outer side of the torus. This fact might be one of the

  4. Sticky water surfaces: Helix-​coil transitions suppressed in a cell-​penetrating peptide at the air-​water interface

    Schach, D.; Globisch, C.; Roeters, S.J.; Woutersen, S.; Fuchs, A.; Weiss, C.K.; Backus, E.H.G.; Landfester, K.; Bonn, M.; Peter, C.; Weidner, T.

    2014-01-01

    GALA is a 30 amino acid synthetic peptide consisting of a Glu-​Ala-​Leu-​Ala repeat and is known to undergo a reversible structural transition from a disordered to an α-​helical structure when changing the pH from basic to acidic values. In its helical state GALA can insert into and disintegrate

  5. Helicity and Filament Channels? The Straight Twist!

    Antiochos, Spiro K.

    2010-01-01

    One of the most important and most puzzling features of the coronal magnetic field is that it appears to have smooth magnetic structure with little evidence for non-potentiality except at special locations, photospheric polarity inversions lines where the non-potentiality is observed as a filament channel. This characteristic feature of the closed-field corona is highly unexpected given that photospheric motions continuously tangle its magnetic field. Although reconnection can eliminate some of the injected structure, it cannot destroy the helicity, which should build up to produce observable complexity. We propose that an inverse cascade process transports the injected helicity from the interior of closed flux regions to their boundaries, polarity inversion lines, creating filament channels. We describe how the helicity is injected and transported and calculate the relevant rates. We argue that one process, helicity transport, can explain both the observed lack and presence of structure in the coronal magnetic field.

  6. Spin versus helicity in processes involving transversity

    Mekhfi, Mustapha

    2011-01-01

    We construct the spin formalism in order to deal in a direct and natural way with processes involving transversity which are now of increasing popularity. The helicity formalism which is more appropriate for collision processes of definite helicity has been so far used also to manage processes with transversity, but at the price of computing numerous helicity amplitudes generally involving unnecessary kinematical variables.In a second step we work out the correspondence between both formalisms and retrieve in another way all results of the helicity formalism but in simpler forms.We then compute certain processes for comparison.A special process:the quark dipole magnetic moment is shown to be exclusively treated within the spin formalism as it is directly related to the transverse spin of the quark inside the baryon.

  7. Helical magnetized wiggler for synchrotron radiation laser

    Wang Mei; Park, S.Y.; Hirshfield, J.L.

    1999-01-01

    A helical magnetized iron wiggler has been built for a novel infrared synchrotron radiation laser (SRL) experiment. The wiggler consists of four periods of helical iron structure immersed in a solenoid field. This wiggler is to impart transverse velocity to a prebunched 6 MeV electron beam, and thus to obtain a desired high orbit pitch ratio for the SRL. Field tapering at beam entrance is considered and tested on a similar wiggler. Analytic and simulated characteristics of wigglers of this type are discussed and the performance of the fabricated wigglers is demonstrated experimentally. A 4.7 kG peak field was measured for a 6.4 mm air gap and a 5.4 cm wiggler period at a 20 kG solenoid field. The measured helical fields compare favorably with the analytical solution. This type of helical iron wigglers has the potential to be scaled to small periods with strong field amplitude

  8. Helical magnetized wiggler for synchrotron radiation laser

    Wang Mei; Hirshfield, J L

    1999-01-01

    A helical magnetized iron wiggler has been built for a novel infrared synchrotron radiation laser (SRL) experiment. The wiggler consists of four periods of helical iron structure immersed in a solenoid field. This wiggler is to impart transverse velocity to a prebunched 6 MeV electron beam, and thus to obtain a desired high orbit pitch ratio for the SRL. Field tapering at beam entrance is considered and tested on a similar wiggler. Analytic and simulated characteristics of wigglers of this type are discussed and the performance of the fabricated wigglers is demonstrated experimentally. A 4.7 kG peak field was measured for a 6.4 mm air gap and a 5.4 cm wiggler period at a 20 kG solenoid field. The measured helical fields compare favorably with the analytical solution. This type of helical iron wigglers has the potential to be scaled to small periods with strong field amplitude.

  9. Using helical compressors for coke gas condensation

    Privalov, V E; Rezunenko, Yu I; Lelyanov, N V; Zarnitzkii, G Eh; Gordienko, A A; Derebenko, I F; Venzhega, A G; Leonov, N P; Gorokhov, N N

    1982-08-01

    Coke oven gas compression is discussed. Presently used multilevel piston compressors are criticized. The paper recommends using helical machines which combine advantages of using volume condensing compressors and compact high-efficiency centrifugal machines. Two kinds of helical compressors are evaluated: dry and oil-filled; their productivities and coke oven gas chemical composition are analyzed. Experiments using helical compressors were undertaken at the Yasinovskii plant. Flowsheet of the installation is shown. Performance results are given in a table. For all operating conditions content of insolubles in oil compounds is found to be lower than the acceptable value (0.08%). Compressor productivity measurements with variable manifold pressure are evaluated. Figures obtained show that efficient condensation of raw coke oven gas is possible. Increasing oil-filled compressor productivity is recommended by decreasing amount of oil injected and simultaneously increasing rotation speed. The dry helical compressor with water seal is found to be most promising for raw coke oven gas condensation. (10 refs.)

  10. Applications of Circular Dichroism for Structural Analysis of Gelatin and Antimicrobial Peptides

    Yoonkyung Park

    2012-03-01

    Full Text Available Circular dichroism (CD is a useful technique for monitoring changes in the conformation of antimicrobial peptides or gelatin. In this study, interactions between cationic peptides and gelatin were observed without affecting the triple helical content of the gelatin, which was more strongly affected by anionic surfactant. The peptides did not adopt a secondary structure in the presence of aqueous solution or Tween 80, but a peptide secondary structure formed upon the addition of sodium dodecyl sulfate (SDS. The peptides bound to the phosphate group of lipopolysaccharide (LPS and displayed an alpha-helical conformation while (KW4 adopted a folded conformation. Further, the peptides did not specifically interact with the fungal cell wall components of mannan or laminarin. Tryptophan blue shift assay indicated that these peptides interacted with SDS, LPS, and gelatin but not with Tween 80, mannan, or laminarin. The peptides also displayed antibacterial activity against P. aeruginosa without cytotoxicity against HaCaT cells at MIC, except for HPA3NT3-analog peptide. In this study, we used a CD spectroscopic method to demonstrate the feasibility of peptide characterization in numerous environments. The CD method can thus be used as a screening method of gelatin-peptide interactions for use in wound healing applications.

  11. Helicity evolution at small x

    Kovchegov, Yuri V.; Pitonyak, Daniel; Sievert, Matthew D.

    2016-01-01

    We construct small-x evolution equations which can be used to calculate quark and anti-quark helicity TMDs and PDFs, along with the g 1 structure function. These evolution equations resum powers of α s ln 2  (1/x) in the polarization-dependent evolution along with the powers of α s ln (1/x) in the unpolarized evolution which includes saturation effects. The equations are written in an operator form in terms of polarization-dependent Wilson line-like operators. While the equations do not close in general, they become closed and self-contained systems of non-linear equations in the large-N c and large-N c   N f limits. As a cross-check, in the ladder approximation, our equations map onto the same ladder limit of the infrared evolution equations for the g 1 structure function derived previously by Bartels, Ermolaev and Ryskin http://dx.doi.org/10.1007/s002880050285.

  12. Early clinical phase of patient's management after polytrauma using 1- and 4-slice helical CT

    Kloeppel, R.; Kahn, T.; Schreiter, D.; Dietrich, J.; Josten, C.

    2002-01-01

    In the early clinical phase the comprehensive imaging of patients with multiple trauma using helical CT is already established. Aim of this study was to assess whether MSCT may improve the patient management and the diagnostic results.The procedure is designed as follows: after life-thretening treatment x-ray of chest and ultrasound are carried out in the emergency room. Then the patient is moved to CT. From 1998 to december 2000 241 patients were examined using a single slice helical CT (Somatom plus 4), in 2001 79 patients using a 4-slice helical CT (Somatom VZ, Siemens Med.Sol.). After CT selected radiograms of the extremities were taken.359 of 360 procedures were carried out successfully. Excluding 1 case (death during 1-sl. h CT) all relevant lesions of head, neck, and body were diagnosed. Although the patients had an injury severity score of ∼30. The change from 1slice-helical CT to 4 slice-helical CT allowed us to reduce the stay in the CT room from 28 to 16 min. The total lethality decreased by ∼4%.Advantages for the patient arose from the standardized examination protocol using multislice CT. If integrated in an interdisciplinary management concept, it is a good compromise between examination time, comprehensive diagnostic imaging, life-saving therapeutic procedures, and therapy planning. (orig.) [de

  13. Dynamics of helicity transport and Taylor relaxation

    Diamond, P.H.; Malkov, M.

    2003-01-01

    A simple model of the dynamics of Taylor relaxation is derived using symmetry principles alone. No statistical closure approximations are invoked or detailed plasma model properties assumed. Notably, the model predicts several classes of nondiffusive helicity transport phenomena, including traveling nonlinear waves and superdiffusive turbulent pulses. A universal expression for the scaling of the effective magnetic Reynolds number of a system undergoing Taylor relaxation is derived. Some basic properties of intermittency in helicity transport are examined

  14. Multiple helical modes of vortex breakdown

    Sørensen, Jens Nørkær; Naumov, I. V.; Okulov, Valery

    2011-01-01

    Experimental observations of vortex breakdown in a rotating lid-driven cavity are presented. The results show that vortex breakdown for cavities with high aspect ratios is associated with the appearance of stable helical vortex multiplets. By using results from stability theory generalizing Kelvi......’s problem on vortex polygon stability, and systematically exploring the cavity flow, we succeeded in identifying two new stable vortex breakdown states consisting of triple and quadruple helical multiplets....

  15. Tuning peptide self-assembly by an in-tether chiral center

    Hu, Kuan; Xiong, Wei; Li, Hu; Zhang, Pei-Yu; Yin, Feng; Zhang, Qianling; Jiang, Fan; Li, Zigang

    2018-01-01

    The self-assembly of peptides into ordered nanostructures is important for understanding both peptide molecular interactions and nanotechnological applications. However, because of the complexity and various self-assembling pathways of peptide molecules, design of self-assembling helical peptides with high controllability and tunability is challenging. We report a new self-assembling mode that uses in-tether chiral center-induced helical peptides as a platform for tunable peptide self-assembly with good controllability. It was found that self-assembling behavior was governed by in-tether substitutional groups, where chirality determined the formation of helical structures and aromaticity provided the driving force for self-assembly. Both factors were essential for peptide self-assembly to occur. Experiments and theoretical calculations indicate long-range crystal-like packing in the self-assembly, which was stabilized by a synergy of interpeptide π-π and π-sulfur interactions and hydrogen bond networks. In addition, the self-assembled peptide nanomaterials were demonstrated to be promising candidate materials for applications in biocompatible electrochemical supercapacitors.

  16. On the helicity of open magnetic fields

    Prior, C.; Yeates, A. R.

    2014-01-01

    We reconsider the topological interpretation of magnetic helicity for magnetic fields in open domains, and relate this to the relative helicity. Specifically, our domains stretch between two parallel planes, and each of these ends may be magnetically open. It is demonstrated that, while the magnetic helicity is gauge-dependent, its value in any gauge may be physically interpreted as the average winding number among all pairs of field lines with respect to some orthonormal frame field. In fact, the choice of gauge is equivalent to the choice of reference field in the relative helicity, meaning that the magnetic helicity is no less physically meaningful. We prove that a particular gauge always measures the winding with respect to a fixed frame, and propose that this is normally the best choice. For periodic fields, this choice is equivalent to measuring relative helicity with respect to a potential reference field. However, for aperiodic fields, we show that the potential field can be twisted. We prove by construction that there always exists a possible untwisted reference field.

  17. Peptide folding in the presence of interacting protein crowders

    Bille, Anna, E-mail: anna.bille@thep.lu.se; Irbäck, Anders, E-mail: anders@thep.lu.se [Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund (Sweden); Mohanty, Sandipan, E-mail: s.mohanty@fz-juelich.de [Jülich Supercomputing Centre, Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich (Germany)

    2016-05-07

    Using Monte Carlo methods, we explore and compare the effects of two protein crowders, BPTI and GB1, on the folding thermodynamics of two peptides, the compact helical trp-cage and the β-hairpin-forming GB1m3. The thermally highly stable crowder proteins are modeled using a fixed backbone and rotatable side-chains, whereas the peptides are free to fold and unfold. In the simulations, the crowder proteins tend to distort the trp-cage fold, while having a stabilizing effect on GB1m3. The extent of the effects on a given peptide depends on the crowder type. Due to a sticky patch on its surface, BPTI causes larger changes than GB1 in the melting properties of the peptides. The observed effects on the peptides stem largely from attractive and specific interactions with the crowder surfaces, and differ from those seen in reference simulations with purely steric crowder particles.

  18. Diffusion in a tokamak with helical magnetic cells

    Wakatani, Masahiro

    1975-05-01

    In a tokamak with helical magnetic cells produced by a resonant helical magnetic field, diffusion in the collisional regime is studied. The diffusion coefficient is greatly enhanced near the resonant surface even for a weak helical magnetic field. A theoretical model for disruptive instabilities based on the enhanced transport due to helical magnetic cells is discussed. This may explain experiments of the tokamak with resonant helical fields qualitatively. (author)

  19. Right-Handed Helical Foldamers Consisting of De Novo d -AApeptides

    Teng, Peng; Ma, Ning; Cerrato, Darrell Cole; She, Fengyu; Odom, Timothy; Wang, Xiang; Ming, Li-June; van der Vaart, Arjan; Wojtas, Lukasz; Xu, Hai; Cai, Jianfeng

    2017-05-16

    New types of foldamer scaffolds are formidably challenging to design and synthesize, yet highly desirable as structural mimics of peptides/proteins with a wide repertoire of functions. In particular, the development of peptidomimetic helical foldamers holds promise for new biomaterials, catalysts, and drug molecules. Unnatural l-sulfono-γ-AApeptides were recently developed and shown to have potential applications in both biomedical and material sciences. However, d-sulfono-γ-AApeptides, the enantiomers of l-sulfono-γ-AApeptides, have never been studied due to the lack of high-resolution three-dimensional structures to guide structure-based design. Herein, we report the first synthesis and X-ray crystal structures of a series of 2:1 l-amino acid/d-sulfono-γ-AApeptide hybrid foldamers, and elucidate their folded conformation at the atomic level. Single-crystal X-ray crystallography indicates that this class of oligomers folds into well-defined right-handed helices with unique helical parameters. The helical structures were consistent with data obtained from solution 2D NMR, CD studies, and molecular dynamics simulations. Our findings are expected to inspire the structure-based design of this type of unique folding biopolymers for biomaterials and biomedical applications.

  20. Prediction of twin-arginine signal peptides

    Bendtsen, Jannick Dyrløv; Nielsen, Henrik; Widdick, D.

    2005-01-01

    expressions, whereas hydrophobicity discrimination of Tat- and Sec- signal peptides is carried out by an artificial neural network. A potential cleavage site of the predicted Tat signal peptide is also reported. The TatP prediction server is available as a public web server at http://www.cbs.dtu.dk/services/TatP/....

  1. Peptide chemistry toolbox - Transforming natural peptides into peptide therapeutics.

    Erak, Miloš; Bellmann-Sickert, Kathrin; Els-Heindl, Sylvia; Beck-Sickinger, Annette G

    2018-06-01

    The development of solid phase peptide synthesis has released tremendous opportunities for using synthetic peptides in medicinal applications. In the last decades, peptide therapeutics became an emerging market in pharmaceutical industry. The need for synthetic strategies in order to improve peptidic properties, such as longer half-life, higher bioavailability, increased potency and efficiency is accordingly rising. In this mini-review, we present a toolbox of modifications in peptide chemistry for overcoming the main drawbacks during the transition from natural peptides to peptide therapeutics. Modifications at the level of the peptide backbone, amino acid side chains and higher orders of structures are described. Furthermore, we are discussing the future of peptide therapeutics development and their impact on the pharmaceutical market. Copyright © 2018 Elsevier Ltd. All rights reserved.

  2. Study of Pelvicaliceal Anatomy by Helical Computerized Tomography

    Al-Qahtani, Fahd N.; Ali, Gaber A.; Kamal, Baher A.; Taha, Saud A.

    2003-01-01

    To evaluate the role of 3-dimensional images produced by computerized tomography (CT), using intravenous contrast, to study pelvicaliceal anatomy.This might be of help in endourological procedure. The study was conducted in the King Fahd Hospital of the University, King Faisal University. Dammam,Kingdom of Saudi Arabia. The study took place from July 2002 through to October 2002 .Helical CT was carried for patients who were investigated using excretory urography for any reason. A CT was carried out to the kidneys only within 10 minutes ( between 5 and 15 minute films of excretory urography).Images were reprocessed by 3-dimension construction after subtracting all structures except for the palvicaliceal system. Thity-six normal kidneys were studied. The upper pole was drained by a single caliceal infundibulum in all 36(100%) kidneys.the middle segement of the kidney was drained by 2 infundibula in 32 (89%) kidneys. Four (11%) kidneys have no middle caliceal infudibula. The lower pole was drained by 2 caliceal infundibula in 23 (64%) and a single infundibulum in 13 (36%) kidneys. The minor calices draining each renal segment were seen clearly. Three-dimensional images derived by helical CT are feasible for evaluating the anatomy of palvicaliceal system,and, can be of help in endourological procedures. (author)/

  3. Neoclassical transport in a multiple-helicity torsatron in the low-collisionality (1/#betta#) regime

    Shaing, K.C.; Hokin, S.A.

    1983-02-01

    For a sufficiently high number of field periods (m/iota > l), the magnetic field of a multiple helicity torsatron can be reduced to a simple form such that the second adiabatic invariant J can be calculated. It is found that the particle and the heat fluxes for a multiple helicity torsatron in the low collisionality (1/#betta#) regime have the same geometric dependences. An optimization of both quantities is carried out for a given equilibrium constraint. It is shown that the transport fluxes can be smaller than those of the conventional stellarator by an order of magnitude. The effect of finite plasma beta on the neoclassical fluxes is also studied

  4. Pulsed currents carried by whistlers. IV. Electric fields and radiation excited by an electrode

    Stenzel, R.L.; Urrutia, J.M.; Rousculp, C.L.

    1995-01-01

    Electromagnetic properties of current pulses carried by whistler wave packets are obtained from a basic laboratory experiment. While the magnetic field and current density are described in the preceding companion paper (Part III), the present analysis starts with the electric field. The inductive and space charge electric field contributions are separately calculated in Fourier space from the measured magnetic field and Ohm's law along B 0 . Inverse Fourier transformation yields the total electric field in space and time, separated into rotational and divergent contributions. The space-charge density in whistler wave packets is obtained. The cross-field tensor conductivity is determined. The frozen-in condition is nearly satisfied, E+v e xB congruent 0. The dissipation is obtained from Poynting's theorem. The waves are collisionally damped; Landau damping is negligible. A radiation resistance for the electrode is determined. Analogous to Poynting's theorem, the transport of helicity is analyzed. Current helicity is generated by a flow of helicity between pulses traveling in opposite directions which carry opposite signs of helicity. Helicity is dissipated by collisions. These observations complete a detailed description of whistler/current pulses which can occur in various laboratory and space plasmas. copyright 1995 American Institute of Physics

  5. Recurrent Neural Network Model for Constructive Peptide Design.

    Müller, Alex T; Hiss, Jan A; Schneider, Gisbert

    2018-02-26

    We present a generative long short-term memory (LSTM) recurrent neural network (RNN) for combinatorial de novo peptide design. RNN models capture patterns in sequential data and generate new data instances from the learned context. Amino acid sequences represent a suitable input for these machine-learning models. Generative models trained on peptide sequences could therefore facilitate the design of bespoke peptide libraries. We trained RNNs with LSTM units on pattern recognition of helical antimicrobial peptides and used the resulting model for de novo sequence generation. Of these sequences, 82% were predicted to be active antimicrobial peptides compared to 65% of randomly sampled sequences with the same amino acid distribution as the training set. The generated sequences also lie closer to the training data than manually designed amphipathic helices. The results of this study showcase the ability of LSTM RNNs to construct new amino acid sequences within the applicability domain of the model and motivate their prospective application to peptide and protein design without the need for the exhaustive enumeration of sequence libraries.

  6. MH2c: Characterization of major histocompatibility α-helices - an information criterion approach.

    Hischenhuber, B; Frommlet, F; Schreiner, W; Knapp, B

    2012-07-01

    Major histocompatibility proteins share a common overall structure or peptide binding groove. Two binding groove domains, on the same chain for major histocompatibility class I or on two different chains for major histocompatibility class II, contribute to that structure that consists of two α -helices ("wall") and a sheet of eight anti-parallel beta strands ("floor"). Apart from the peptide presented in the groove, the major histocompatibility α -helices play a central role for the interaction with the T cell receptor. This study presents a generalized mathematical approach for the characterization of these helices. We employed polynomials of degree 1 to 7 and splines with 1 to 2 nodes based on polynomials of degree 1 to 7 on the α -helices projected on their principal components. We evaluated all models with a corrected Akaike Information Criterion to determine which model represents the α -helices in the best way without overfitting the data. This method is applicable for both the stationary and the dynamic characterization of α -helices. By deriving differential geometric parameters from these models one obtains a reliable method to characterize and compare α -helices for a broad range of applications. Program title: MH 2 c (MH helix curves) Catalogue identifier: AELX_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AELX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 327 565 No. of bytes in distributed program, including test data, etc.: 17 433 656 Distribution format: tar.gz Programming language: Matlab Computer: Personal computer architectures Operating system: Windows, Linux, Mac (all systems on which Matlab can be installed) RAM: Depends on the trajectory size, min. 1 GB (Matlab) Classification: 2.1, 4.9, 4.14 External routines: Curve

  7. Peptide stabilized amphotericin B nanodisks

    Tufteland, Megan; Pesavento, Joseph B.; Bermingham, Rachelle L.; Hoeprich, Paul D.; Ryan, Robert O.

    2007-01-01

    Nanometer scale apolipoprotein A-I stabilized phospholipid disk complexes (nanodisks; ND) have been formulated with the polyene antibiotic amphotericin B (AMB). The present studies were designed to evaluate if a peptide can substitute for the function of the apolipoprotein component of ND with respect to particle formation and stability. An 18-residue synthetic amphipathic α-helical peptide, termed 4F (Ac-D-W-F-K-A-F-Y-D-K-V-A-E-K-F-K-E-A-F-NH2), solubilized vesicles comprised of egg phosphatidylcholine (egg PC), dipentadecanoyl PC or dimyristoylphosphatidylcholine (DMPC) at rates greater than or equal to solubilization rates observed with human apolipoprotein A-I (apoA-I; 243 amino acids). Characterization studies revealed that interaction with DMPC induced a near doubling of 4F tryptophan fluorescence emission quantum yield (excitation 280 nm) and a ~7 nm blue shift in emission wavelength maximum. Inclusion of AMB in the vesicle substrate resulted in formation of 4F AMB-ND. Spectra of AMB containing particles revealed the antibiotic is a highly effective quencher of 4F tryptophan fluorescence emission, giving rise to a Ksv = 7.7 × 104. Negative stain electron microscopy revealed that AMB-ND prepared with 4F possessed a disk shaped morphology similar to ND prepared without AMB or prepared with apoA-I. In yeast and pathogenic fungi growth inhibition assays, 4F AMB-ND was as effective as apoA-I AMB-ND. The data indicate that AMB-ND generated using an amphipathic peptide in lieu of apoA-I form a discrete population of particles that possess potent biological activity. Given their intrinsic versatility, peptides may be preferred for scale up and clinical application of AMB-ND. PMID:17293004

  8. Hydrogen recycling and transport in the helical divertor of TEXTOR

    Clever, Meike

    2010-07-01

    The aim of this thesis was to investigate the hydrogen recycling at the target plates of the helical divertor in TEXTOR and by this the capability of this divertor configuration to access such favourable operational regimes. In order to study the different divertor density regimes in TEXTOR, discharges were performed in which the total plasma density was increased continuously up to the density limit. The recycling was investigated in a fixed helical divertor structure where four helical strike points with a poloidal width of about 8-10 cm are created at the divertor target plates. The experimental investigation of the hydrogen recycling was carried out using mainly spectroscopic methods supplemented by Langmuir probe, interferometric and atomic beam measurements. In the framework of this thesis a spectroscopic multi camera system has been built that facilitates the simultaneous observation of four different spectral lines, recording images of the divertor target plates and the plasma volume close to the target. The system facilitates the simultaneous measurement of the poloidal and toroidal pattern of the recycling flux at the divertor target without the need for sweeping the plasma structure. The simultaneous observation of different spectral lines reduces the uncertainty in the analysis based on several lines, as the contribution from uncertainties in the reproducibility of plasma parameters in different discharges are eliminated and only the uncertainty of the measurement method limits the accuracy. The spatial resolution of the system in poloidal and toroidal direction (0.8 mm{+-}0.01 mm) is small compared to the separation of the helical strike points, the capability of the measurement method to resolve these structures is therefore limited by the line-of-sight integration and the penetration depth of the light emitting species. The measurements showed that the recycling flux increases linearly with increasing plasma density, a high recycling regime is not

  9. Hydrogen recycling and transport in the helical divertor of TEXTOR

    Clever, Meike

    2010-01-01

    The aim of this thesis was to investigate the hydrogen recycling at the target plates of the helical divertor in TEXTOR and by this the capability of this divertor configuration to access such favourable operational regimes. In order to study the different divertor density regimes in TEXTOR, discharges were performed in which the total plasma density was increased continuously up to the density limit. The recycling was investigated in a fixed helical divertor structure where four helical strike points with a poloidal width of about 8-10 cm are created at the divertor target plates. The experimental investigation of the hydrogen recycling was carried out using mainly spectroscopic methods supplemented by Langmuir probe, interferometric and atomic beam measurements. In the framework of this thesis a spectroscopic multi camera system has been built that facilitates the simultaneous observation of four different spectral lines, recording images of the divertor target plates and the plasma volume close to the target. The system facilitates the simultaneous measurement of the poloidal and toroidal pattern of the recycling flux at the divertor target without the need for sweeping the plasma structure. The simultaneous observation of different spectral lines reduces the uncertainty in the analysis based on several lines, as the contribution from uncertainties in the reproducibility of plasma parameters in different discharges are eliminated and only the uncertainty of the measurement method limits the accuracy. The spatial resolution of the system in poloidal and toroidal direction (0.8 mm±0.01 mm) is small compared to the separation of the helical strike points, the capability of the measurement method to resolve these structures is therefore limited by the line-of-sight integration and the penetration depth of the light emitting species. The measurements showed that the recycling flux increases linearly with increasing plasma density, a high recycling regime is not

  10. Dynamic helical CT mammography of breast cancer

    Yamamoto, Akira; Fukushima, Hitoshi; Okamura, Ryuji; Nakamura, Yoshiaki; Morimoto, Taisuke; Urata, Yoji; Mukaihara, Sumio; Hayakawa, Katsumi

    2006-01-01

    The purpose of this study was to determine whether dynamic helical computed tomography (CT)-mammography could assist in selecting the most appropriate surgical method in women with breast cancer. Preoperative contrast-enhanced helical CT scanning of the breast was performed on 133 female patients with suspicion of breast cancer at the same time as clinical, mammographic, and/or ultrasonographic examinations. The patients were scanned in the prone position with a specially designed CT-compatible device. A helical scan was made with rapid intravenous bolus injection (3 ml/s) of 100 ml of iodine contrast material. Three-dimensional maximum intensity projection (MIP) images were reconstructed, and CT findings were correlated with surgical and histopathological findings. Histopathological analysis revealed 84 malignant lesions and seven benign lesions. The sensitivity, specificity, and accuracy levels of the CT scanning were 94.6%, 58.6%, and 78.9%. Helical scanning alone revealed additional contralateral carcinomas in three of four patients and additional ipsilateral carcinomas in three of five patients. However, the technique gave false-positive readings in 24 patients. The preoperative CT-mammogram altered the surgical method in six patients. Dynamic helical CT-mammography in the prone position may be one of the choices of adjunct imaging in patients with suspected breast cancer scheduled for surgery. (author)

  11. Introduction to the m = 1 helicity source

    Platts, D.A.; Jarboe, T.R.; Wright, B.L.

    1985-01-01

    The m = 1 Helicity Source, formerly called the Kinked Z-pinch, was developed as part of the Electrode Studies program at Los Alamos. The Electrode Studies program was initiated to study the control of electrode erosion in long discharge duration spheromak sources. Erosion control is necessary to reduce plasma impurities and to obtain adequate electrode lifetimes. The first task of the Electrode Studies program is to determine, from among a variety of configurations including the coaxial one, a helicity source geometry with good prospects for erosion control. The more efficient the helicity source the easier it will be to control erosion, but the source most also be easy to diagnose and modify if it is to be a useful test bed. The various erosion control techniques which have been proposed will require extensive experimentation to evaluate and optimize. Proposed techniques include, using refractory metals, profiling of the electrodes and magnetic fields, and various gas injection schemes including porous electrodes. It is considered necessary to do these experiments on an optimized helicity source so that the electrode geometries and plasma properties will be relevant. Therefore the present Electrode Studies program is aimed at developing an improved helicity source design

  12. On the validity of the use of a localized approximation for helical beams. I. Formal aspects

    Gouesbet, Gérard; André Ambrosio, Leonardo

    2018-03-01

    The description of an electromagnetic beam for use in light scattering theories may be carried out by using an expansion over vector spherical wave functions with expansion coefficients expressed in terms of Beam Shape Coefficients (BSCs). A celebrated method to evaluate these BSCs has been the use of localized approximations (with several existing variants). We recently established that the use of any existing localized approximation is of limited validity in the case of Bessel and Mathieu beams. In the present paper, we address a warning against the use of any existing localized approximation in the case of helical beams. More specifically, we demonstrate that a procedure used to validate any existing localized approximation fails in the case of helical beams. Numerical computations in a companion paper will confirm that existing localized approximations are of limited validity in the case of helical beams.

  13. Cationic antimicrobial peptides inactivate Shiga toxin-encoding bacteriophages

    Del Cogliano, Manuel E.; Hollmann, Axel; Martinez, Melina; Semorile, Liliana; Ghiringhelli, Pablo D.; Maffía, Paulo C.; Bentancor, Leticia V.

    2017-12-01

    Shiga toxin (Stx) is the principal virulence factor during Shiga toxin-producing Escherichia coli (STEC) infections. We have previously reported the inactivation of bacteriophage encoding Stx after treatment with chitosan, a linear polysaccharide polymer with cationic properties. Cationic antimicrobial peptides (cAMPs) are short linear aminoacidic sequences, with a positive net charge, which display bactericidal or bacteriostatic activity against a wide range of bacterial species. They are promising novel antibiotics since they have shown bactericidal effects against multiresistant bacteria. To evaluate whether cationic properties are responsible for bacteriophage inactivation, we tested seven cationic peptides with proven antimicrobial activity as anti-bacteriophage agents, and one random sequence cationic peptide with no antimicrobial activity as a control. We observed bacteriophage inactivation after incubation with five cAMPs, but no inactivating activity was observed with the random sequence cationic peptide or with the non alpha helical cAMP Omiganan. Finally, to confirm peptide-bacteriophage interaction, zeta potential was analyzed by following changes on bacteriophage surface charges after peptide incubation. According to our results we could propose that: 1) direct interaction of peptides with phage is a necessary step for bacteriophage inactivation, 2) cationic properties are necessary but not sufficient for bacteriophage inactivation, and 3) inactivation by cationic peptides could be sequence (or structure) specific. Overall our data suggest that these peptides could be considered a new family of molecules potentially useful to decrease bacteriophage replication and Stx expression.

  14. Cationic Antimicrobial Peptides Inactivate Shiga Toxin-Encoding Bacteriophages

    Manuel E. Del Cogliano

    2017-12-01

    Full Text Available Shiga toxin (Stx is the principal virulence factor during Shiga toxin-producing Escherichia coli (STEC infections. We have previously reported the inactivation of bacteriophage encoding Stx after treatment with chitosan, a linear polysaccharide polymer with cationic properties. Cationic antimicrobial peptides (cAMPs are short linear aminoacidic sequences, with a positive net charge, which display bactericidal or bacteriostatic activity against a wide range of bacterial species. They are promising novel antibiotics since they have shown bactericidal effects against multiresistant bacteria. To evaluate whether cationic properties are responsible for bacteriophage inactivation, we tested seven cationic peptides with proven antimicrobial activity as anti-bacteriophage agents, and one random sequence cationic peptide with no antimicrobial activity as a control. We observed bacteriophage inactivation after incubation with five cAMPs, but no inactivating activity was observed with the random sequence cationic peptide or with the non-alpha helical cAMP Omiganan. Finally, to confirm peptide-bacteriophage interaction, zeta potential was analyzed by following changes on bacteriophage surface charges after peptide incubation. According to our results we could propose that: (1 direct interaction of peptides with phage is a necessary step for bacteriophage inactivation, (2 cationic properties are necessary but not sufficient for bacteriophage inactivation, and (3 inactivation by cationic peptides could be sequence (or structure specific. Overall our data suggest that these peptides could be considered a new family of molecules potentially useful to decrease bacteriophage replication and Stx expression.

  15. Clinical application of helical CT colonography

    Zeng Huiliang; Zhu Xinjin; Liang Rujian; Liang Jianhao; Ou Weiqian; Wen Haomao

    2009-01-01

    Objective: To investigate the clinical value of 16-slice helical CT colonography in the diagnosis of colon tumor and polypus. Methods: 16-slice helical CT volumetric scanning was performed in 18 patients with colonic disease, including colonic tumor (n=16) and colonic polypus (n=2). 3D images, virtual endoscopy and multiplanar reformation were obtained in the AW4.1 workstation. CT appearances were compared with operation and fiberoptic colonoscopy. Results: Satisfied results were achieved from 18 patients, no difference found in results between CT colonography and operation in 16 patients with colonic tumor. Conclusion: 16-slice helical CT colonography is of great value in preoperative staging of colonic tumor and have a high value in clinical application. (authors)

  16. Helicity antenna showers for hadron colliders

    Fischer, Nadine; Skands, Peter [Monash University, School of Physics and Astronomy, Clayton, VIC (Australia); Lifson, Andrew [Monash University, School of Physics and Astronomy, Clayton, VIC (Australia); ETH Zuerich, Zurich (Switzerland)

    2017-10-15

    We present a complete set of helicity-dependent 2 → 3 antenna functions for QCD initial- and final-state radiation. The functions are implemented in the Vincia shower Monte Carlo framework and are used to generate showers for hadron-collider processes in which helicities are explicitly sampled (and conserved) at each step of the evolution. Although not capturing the full effects of spin correlations, the explicit helicity sampling does permit a significantly faster evaluation of fixed-order matrix-element corrections. A further speed increase is achieved via the implementation of a new fast library of analytical MHV amplitudes, while matrix elements from Madgraph are used for non-MHV configurations. A few examples of applications to QCD 2 → 2 processes are given, comparing the newly released Vincia 2.200 to Pythia 8.226. (orig.)

  17. Manipulation of wavefront using helical metamaterials.

    Yang, Zhenyu; Wang, Zhaokun; Tao, Huan; Zhao, Ming

    2016-08-08

    Helical metamaterials, a kind of 3-dimensional structure, has relatively strong coupling effect among the helical nano-wires. Therefore, it is expected to be a good candidate for generating phase shift and controlling wavefront with high efficiency. In this paper, using the finite-difference time-domain (FDTD) method, we studied the phase shift properties in the helical metamaterials. It is found that the phase shift occurs for both transmitted and reflected light waves. And the maximum of reflection coefficients can reach over 60%. In addition, the phase shift (φ) is dispersionless in the range of 600 nm to 860 nm, that is, it is only dominated by the initial angle (θ) of the helix. The relationship between them is φ = ± 2θ. Using Jones calculus we give a further explanation for these properties. Finally, by arranging the helixes in an array with a constant phase gradient, the phenomenon of anomalous refraction was also observed in a broad wavelength range.

  18. Helicity antenna showers for hadron colliders

    Fischer, Nadine; Lifson, Andrew; Skands, Peter

    2017-10-01

    We present a complete set of helicity-dependent 2→ 3 antenna functions for QCD initial- and final-state radiation. The functions are implemented in the Vincia shower Monte Carlo framework and are used to generate showers for hadron-collider processes in which helicities are explicitly sampled (and conserved) at each step of the evolution. Although not capturing the full effects of spin correlations, the explicit helicity sampling does permit a significantly faster evaluation of fixed-order matrix-element corrections. A further speed increase is achieved via the implementation of a new fast library of analytical MHV amplitudes, while matrix elements from Madgraph are used for non-MHV configurations. A few examples of applications to QCD 2→ 2 processes are given, comparing the newly released Vincia 2.200 to Pythia 8.226.

  19. Neutrino's helicity in a gravitational field

    Pansart, J.P.

    1996-01-01

    By using approximated solutions of Dirac's equation, we show that there is no helicity reversal for light neutrinos in the Schwarzschild metric nor in an expanding universe. The actual coupling between a particle spin and the angular momentum of a heavy rotating body induces a possible helicity reversal but with an unobservable probability proportional to m 2 p / E 2 , where m p is the particle mass and E its energy. In these calculations, the helicity is defined through the spin orientation with respect to the current and not with respect to the linear momentum. This definition gives simple expressions and is equal to the usual definition in the case of a flat space. (N.T.)

  20. Single-superfield helical-phase inflation

    Ketov, Sergei V., E-mail: ketov@tmu.ac.jp [Department of Physics, Tokyo Metropolitan University, Minami-ohsawa 1-1, Hachioji-shi, Tokyo 192-0397 (Japan); Kavli Institute for the Physics and Mathematics of the Universe (IPMU), The University of Tokyo, Chiba 277-8568 (Japan); Institute of Physics and Technology, Tomsk Polytechnic University, 30 Lenin Ave., Tomsk 634050 (Russian Federation); Terada, Takahiro, E-mail: takahiro@hep-th.phys.s.u-tokyo.ac.jp [Department of Physics, The University of Tokyo, Tokyo 113-0033 (Japan); Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg (Germany)

    2016-01-10

    Large-field inflation in supergravity requires the approximate global symmetry needed to protect flatness of the scalar potential. In helical-phase inflation, the U(1) symmetry of the Kähler potential is assumed, the phase part of the complex scalar of a chiral superfield plays the role of inflaton, and the radial part is strongly stabilized. The original model of helical phase inflation, proposed by Li, Li and Nanopoulos (LLN), employs an extra (stabilizer) superfield. We propose a more economical new class of the helical phase inflationary models without a stabilizer superfield. As the specific examples, the quadratic, the natural, and the Starobinsky-type inflationary models are studied in our approach.

  1. Resonant helical fields in the TBR tokamak

    Bender, O.W.

    1986-01-01

    The influence of external resonant helical fields (RHF) in the tokamak TBR plasma discharges was investigated. These fields were created by helical windings wounded on the TBR vessel with the same helicity of rational magnetic surfaces, producing resonant efects on these surfaces. The characteristics of the MHZ activity (amplitude, frequency and poloidal and toroidal wave numbers, m=2,3,4 and n=1, respectively) during the plasma discharges were modified by eletrical winding currents of the order of 2% of the plasma current. These characterisitics were measured for diferent discharges safety factors at the limiter (q) between 3 and 4, with and without the RHF, with the atenuation of the oscillation amplitudes and the increasing of their frequencies. The existente of expontaneous and induced magnetic islands were investigated. The data were compared with results obtained in other tokamaks. (author) [pt

  2. The helical structure of DNA facilitates binding

    Berg, Otto G; Mahmutovic, Anel; Marklund, Emil; Elf, Johan

    2016-01-01

    The helical structure of DNA imposes constraints on the rate of diffusion-limited protein binding. Here we solve the reaction–diffusion equations for DNA-like geometries and extend with simulations when necessary. We find that the helical structure can make binding to the DNA more than twice as fast compared to a case where DNA would be reactive only along one side. We also find that this rate advantage remains when the contributions from steric constraints and rotational diffusion of the DNA-binding protein are included. Furthermore, we find that the association rate is insensitive to changes in the steric constraints on the DNA in the helix geometry, while it is much more dependent on the steric constraints on the DNA-binding protein. We conclude that the helical structure of DNA facilitates the nonspecific binding of transcription factors and structural DNA-binding proteins in general. (paper)

  3. Turbulent Helicity in the Atmospheric Boundary Layer

    Chkhetiani, Otto G.; Kurgansky, Michael V.; Vazaeva, Natalia V.

    2018-05-01

    We consider the assumption postulated by Deusebio and Lindborg (J Fluid Mech 755:654-671, 2014) that the helicity injected into the Ekman boundary layer undergoes a cascade, with preservation of its sign (right- or alternatively left-handedness), which is a signature of the system rotation, from large to small scales, down to the Kolmogorov microscale of turbulence. At the same time, recent direct field measurements of turbulent helicity in the steppe region of southern Russia near Tsimlyansk Reservoir show the opposite sign of helicity from that expected. A possible explanation for this phenomenon may be the joint action of different scales of atmospheric flows within the boundary layer, including the sea-breeze circulation over the test site. In this regard, we consider a superposition of the classic Ekman spiral solution and Prandtl's jet-like slope-wind profile to describe the planetary boundary-layer wind structure. The latter solution mimics a hydrostatic shallow breeze circulation over a non-uniformly heated surface. A 180°-wide sector on the hodograph plane exists, within which the relative orientation of the Ekman and Prandtl velocity profiles favours the left rotation with height of the resulting wind velocity vector in the lowermost part of the boundary layer. This explains the negative (left-handed) helicity cascade toward small-scale turbulent motions, which agrees with the direct field measurements of turbulent helicity in Tsimlyansk. A simple turbulent relaxation model is proposed that explains the measured positive values of the relatively minor contribution to turbulent helicity from the vertical components of velocity and vorticity.

  4. Nonideal, helical, vortical magnetohydrodynamic steady states

    Agim, Y.Z.; Montgomery, D.

    1991-01-01

    The helically-deformed profiles of driven, dissipative magnetohydrodynamic equilibria are constructed through second order in helical amplitude. The resultant plasma configurations are presented in terms of contour plots of magnetic flux function, pressure, current flux function and the mass flux function, along with the stability boundary at which they are expected to appear. For the Wisconsin Phaedrus-T Tokamak, plasma profiles with significant m = 3, n = 1 perturbation seem feasible; for these, the plasma pressure peaks off-axis. For the smaller aspect ratio case, the configuration with m 1,n =1 is thought to be relevant to the density perturbation observed in JET after a pellet injection. (author)

  5. Equilibrium calculations for helical axis stellarators

    Hender, T.C.; Carreras, B.A.

    1984-04-01

    An average method based on a vacuum flux coordinate system is presented. This average method permits the study of helical axis stellarators with toroidally dominated shifts. An ordering is introduced, and to lowest order the toroidally averaged equilibrium equations are reduced to a Grad-Shafranov equation. Also, to lowest order, a Poisson-type equation is obtained for the toroidally varying corrections to the equilibium. By including these corrections, systems that are toroidally dominated, but with significant helical distortion to the equilibrium, may be studied. Numerical solutions of the average method equations are shown to agree well with three-dimensional calculations

  6. Helical post stellarator. Part 1: Vacuum configuration

    Moroz, P.E.

    1997-08-01

    Results on a novel type of stellarator configuration, the Helical Post Stellarator (HPS), are presented. This configuration is different significantly from all previously known stellarators due to its unique geometrical characteristics and unique physical properties. Among those are: the magnetic field has only one toroidal period (M = 1), the plasma has an extremely low aspect ratio, A ∼ 1, and the variation of the magnetic field, B, along field lines features a helical ripple on the inside of the torus. Among the main advantages of a HPS for a fusion program are extremely compact, modular, and simple design compatible with significant rotational transform, large plasma volume, and improved particle transport characteristics

  7. Equilibrium studies of helical axis stellarators

    Hender, T.C.; Carreras, B.A.; Garcia, L.; Harris, J.H.; Rome, J.A.; Cantrell, J.L.; Lynch, V.E.

    1984-01-01

    The equilibrium properties of helical axis stellarators are studied with a 3-D equilibrium code and with an average method (2-D). The helical axis ATF is shown to have a toroidally dominated equilibrium shift and good equilibria up to at least 10% peak beta. Low aspect ratio heliacs, with relatively large toroidal shifts, are shown to have low equilibrium beta limits (approx. 5%). Increasing the aspect ratio and number of field periods proportionally is found to improve the equilibrium beta limit. Alternatively, increasing the number of field periods at fixed aspect ratio which raises and lowers the toroidal shift improves the equilibrium beta limit

  8. Conversion from mutual helicity to self-helicity observed with IRIS

    Li, L. P.; Peter, H.; Chen, F.; Zhang, J.

    2014-10-01

    Context. In the upper atmosphere of the Sun observations show convincing evidence for crossing and twisted structures, which are interpreted as mutual helicity and self-helicity. Aims: We use observations with the new Interface Region Imaging Spectrograph (IRIS) to show the conversion of mutual helicity into self-helicity in coronal structures on the Sun. Methods: Using far UV spectra and slit-jaw images from IRIS and coronal images and magnetograms from SDO, we investigated the evolution of two crossing loops in an active region, in particular, the properties of the Si IV line profile in cool loops. Results: In the early stage two cool loops cross each other and accordingly have mutual helicity. The Doppler shifts in the loops indicate that they wind around each other. As a consequence, near the crossing point of the loops (interchange) reconnection sets in, which heats the plasma. This is consistent with the observed increase of the line width and of the appearance of the loops at higher temperatures. After this interaction, the two new loops run in parallel, and in one of them shows a clear spectral tilt of the Si IV line profile. This is indicative of a helical (twisting) motion, which is the same as to say that the loop has self-helicity. Conclusions: The high spatial and spectral resolution of IRIS allowed us to see the conversion of mutual helicity to self-helicity in the (interchange) reconnection of two loops. This is observational evidence for earlier theoretical speculations. Movie associated with Fig. 1 and Appendix A are available in electronic form at http://www.aanda.org

  9. Conformational analysis by theoretical calculations of distinctin, an antimicrobial peptide isolated from Phyllomedusa distincta

    Munhoz, Victor H. de Oliveira; Alcantara, Antonio F. de Carvalho; Pilo-Veloso, Dorila

    2008-01-01

    Various studies demonstrate that different frog species produce distinct classes of biologically active peptides. These peptides can act as alternative agents against pathogenic bacteria and fungi by membrane permeability. Although studies have recently demonstrated that this process is utterly related to the secondary structure adopted by the peptide (in this case, the α-helical structure) when in contact with the bacterial membrane, the detailed mechanism is still unknown. In this work we describe a conformational analysis of distinctin, a heterodimeric peptide isolated from the skin of Phyllomedusa distincta, an anuran found in the Brazilian Atlantic Forest. The study yielded a stable geometry with a high content of the α-helical structure both in chains 1 and 2 of distinctin, showing strong interaction between them. (author)

  10. Aortic non communicating dissections. A study with helical CT

    Midiri, M.; Strada, A.; Stabile Ianora, A.A.; Rotondo, A.; Angelelli, G.; D'Agostino, D.; De Luca Tupputi Schinosa, L.

    2000-01-01

    The evaluate the signs of aortic intramural hematoma with helical CT and the diagnostic role of this technique in patients with this condition. It was reviewed the CT findings of 396 patients submitted to emergency examinations for suspected aortic dissection from 1995 to 1999. Only 18 patients (6 women and 12 men) had CT signs of aortic intramural hematoma. Helical CT studies were carried out with the following parameters: slice thickness 10 mm, reconstruction index 10, feed 1.5 mm, conventional algorithm with minimum values of 130 kV and 125mA. All patients were examined with dynamic contrast-enhanced CT, before and after a power injection of 130 mL ionic contrast material. It was studied: hematoma localization and longitudinal extension; thickness and density of aortic wall; presence and location of intimal calcifications; integrity of intimal wall; hemo mediastinum and/or hemo thorax. Aortic wall thickening appeared as a high density crescent-shaped area at baseline CT and had low density on enhanced images in all patients. Thickening was eccentric in 14/18 patients and concentric in 4/18 only; it always exceeded 4 mm. It was found some intimal calcifications in 8 patients and hemo thorax and/or hemo mediastinum in 9 patients. A patient with type A hematoma died of cardiac tamponade a few hours after CT diagnosis. Six patients (5 type B and 1 type A) underwent anti-hypertensive treatment and radiological follow-up. Eleven patients (6 type A and 5 type B) underwent prosthesis replacement and 5 of them (3 type A and 2 type B) died of postoperative complications. In the 5 type B patients surgery was performed because of treatment-resistant pain and of the onset of ischemic complications to abdominal organs caused by involvement of the main collateral branches of the aorta. One patient with type A hematoma was submitted to drug treatment because it was judged unresectable. Intramural hematoma of the aorta is a distinct pathological entity, which should not be

  11. Dynamics and deformability of α-, 310- and π-helices

    Narwani Tarun Jairaj

    2018-01-01

    Full Text Available Protein structures are often represented as seen in crystals as (i rigid macromolecules (ii with helices, sheets and coils. However, both definitions are partial because (i proteins are highly dynamic macromolecules and (ii the description of protein structures could be more precise. With regard to these two points, we analyzed and quantified the stability of helices by considering α-helices as well as 310- and π-helices. Molecular dynamic (MD simulations were performed on a large set of 169 representative protein domains. The local protein conformations were followed during each simulation and analyzed. The classical flexibility index (B-factor was confronted with the MD root mean square flexibility (RMSF index. Helical regions were classified according to their level of helicity from high to none. For the first time, a precise quantification showed the percentage of rigid and flexible helices that underlie unexpected behaviors. Only 76.4% of the residues associated with α-helices retain the conformation, while this tendency drops to 40.5% for 310-helices and is never observed for π-helices. α-helix residues that do not remain as an α-helix have a higher tendency to assume β-turn conformations than 310- or π-helices. The 310-helices that switch to the α-helix conformation have a higher B-factor and RMSF values than the average 310-helix but are associated with a lower accessibility. Rare π-helices assume a β-turn, bend and coil conformations, but not α- or 310-helices. The view on π-helices drastically changes with the new DSSP (Dictionary of Secondary Structure of Proteins assignment approach, leading to behavior similar to 310-helices, thus underlining the importance of secondary structure assignment methods.

  12. Review of the helicity formalism; Revision del formalismo de helicidad

    Barreiro, F; Cerrada, M; Fernandez, E

    1972-07-01

    Our purpose in these notes has been to present a brief and general review of the helicity formalism. We begin by discussing Lorentz invariance, spin and helicity ideas, in section 1 . In section 2 we deal with the construction of relativistic states and scattering amplitudes in the helicity basis and we study their transformation properties under discrete symmetries. Finally we present some more sophisticated topics like kinematical singularities of helicity amplitudes, kinematical constraints and crossing relations 3, 4, 5 respectively. (Author) 8 refs.

  13. Paramagnetic relaxation enhancements in NMR peptide-membrane interaction studies

    Kosol, S.

    2011-01-01

    Small membrane-bound proteins or peptides are involved in numerous essential biological processes, like cellular recognition, signaling, channel formation, and cytolysis. The secondary structure, orientation, mode of interaction and dynamics of these peptides can be as varied as their functions. Their localization in the membrane, the immersion depth, and their binding mode are factors critical to the function of these peptides. The atomic 3D solution structure of peptides bound to micelles can be determined by NMR spectroscopy. However, by employing paramagnetic relaxation enhancements (PREs) information on the complete topology of peptide bound to a micelle can be obtained. The antimicrobial peptide maximin H6, fst, a bacterial toxin, and the human peptide hormone ghrelin served as membrane-bound model peptides of similar sizes but strongly differing amino acid sequences. Their structures and binding behavior were determined and compared.The measured PREs provided suitable data for determining and distinguishing the different topologies of the investigated peptides bound to micelles. Maximin H6 and fst fold into α-helices upon insertion into a membrane, whereas the unstructured ghrelin is freely mobile in solution and interacts only via a covalently bound octanoyl group with the lipids. Maximin H6 is oriented parallel to the membrane surface, enabling the peptide to aggregate at the membrane water interface. Fst binds in transmembrane orientation with a protruding intrinsically disordered region near the C-terminus. Aside from determining the orientation of the bound peptides from the PREs, the moieties critical for membrane binding could be mapped in ghrelin. If suitable relaxation-edited spectra are acquired, the complete orientation and immersion depth of a peptide bound to a micelle can readily be obtained. (author) [de

  14. Synergistic Efficacy of Aedes aegypti Antimicrobial Peptide Cecropin A2 and Tetracycline against Pseudomonas aeruginosa

    Zheng, Zhaojun; Tharmalingam, Nagendran; Liu, Qingzhong; Jayamani, Elamparithi; Kim, Wooseong; Fuchs, Beth Burgwyn; Zhang, Rijun; Vilcinskas, Andreas; Mylonakis, Eleftherios

    2017-01-01

    The increasing prevalence of antibiotic resistance has created an urgent need for alternative drugs with new mechanisms of action. Antimicrobial peptides (AMPs) are promising candidates that could address the spread of multidrug-resistant bacteria, either alone or in combination with conventional antibiotics. We studied the antimicrobial efficacy and bactericidal mechanism of cecropin A2, a 36-residue α-helical cationic peptide derived from Aedes aegypti cecropin A, focusing on the common pat...

  15. Exabyte helical scan devices at Fermilab

    Constanta-Fanourakis, P.; Kaczar, K.; Oleynik, G.; Petravick, D.; Votava, M.; White, V.; Hockney, G.; Bracker, S.; de Miranda, J.M.

    1989-05-01

    Exabyte 8mm helical scan storage devices are in use at Fermilab in a number of applications. These devices have the functionality of magnetic tape, but use media which is much more economical and much more dense than conventional 9 track tape. 6 refs., 3 figs

  16. Helical axial injection concept for cyclotrons

    Hudson, E.D.

    1981-01-01

    A concept for an external beam injection system using a helical beam path centered on the cyclotron axis is described. This system could be used to couple two accelerator stages, with or without intermediate stripping, in cases where conventional axial injection or radial injection are not practical.

  17. Helical axial injection concept for cyclotrons

    Hudson, E.D.

    1981-01-01

    A concept for an external beam injection system using a helical beam path centered on the cyclotron axis is described. This system could be used to couple two accelerator stages, with or without intermediate stripping, in cases where conventional axial injection or radial injection are not practical

  18. Electron image reconstruction of helical protein assemblies

    Cremers, A.F.M.

    1980-01-01

    The analysis of projections of large ordered biological systems obtained by electron microscopy of negatively stained specimens is described. The biological structures amenable to this approach are constructed from a large number of identical protein molecules, which are arranged according to helical symmetry. Electron images of these structures generally contain sufficient information in order to calculate a three-dimensional density map. (Auth.)

  19. Adaptive radiotherapy using helical tomotherapy system

    Jeswani, Sam; Ruchala, Kenneth; Olivera, Gustavo; Mackie, T.R.

    2008-01-01

    As commonly known in the field, adaptive radiation therapy (ART) is the use of feedback to modify a radiotherapy treatment. There are numerous ways in which this feedback can be received and used, and this presentation will discuss some of the implementations of ART being investigated with a helical TomoTherapy system

  20. Topological characteristics of helical repeat proteins

    Groves, M R; Barford, D

    The recent elucidation of protein structures based upon repeating amino acid motifs, including the armadillo motif, the HEAT motif and tetratricopeptide repeats, reveals that they belong to the class of helical repeat proteins. These proteins share the common property of being assembled from tandem

  1. A Prospective Evaluation of Helical Tomotherapy

    Bauman, Glenn; Yartsev, Slav; Rodrigues, George; Lewis, Craig; Venkatesan, Varagur M.; Yu, Edward; Hammond, Alex; Perera, Francisco; Ash, Robert; Dar, A. Rashid; Lock, Michael; Baily, Laura; Coad, Terry C; Trenka, Kris C.; Warr, Barbara; Kron, Tomas; Battista, Jerry; Van Dyk, Jake

    2007-01-01

    Purpose: To report results from two clinical trials evaluating helical tomotherapy (HT). Methods and Materials: Patients were enrolled in one of two prospective trials of HT (one for palliative and one for radical treatment). Both an HT plan and a companion three-dimensional conformal radiotherapy (3D-CRT) plan were generated. Pretreatment megavoltage computed tomography was used for daily image guidance. Results: From September 2004 to January 2006, a total of 61 sites in 60 patients were treated. In all but one case, a clinically acceptable tomotherapy plan for treatment was generated. Helical tomotherapy plans were subjectively equivalent or superior to 3D-CRT in 95% of plans. Helical tomotherapy was deemed equivalent or superior in two thirds of dose-volume point comparisons. In cases of inferiority, differences were either clinically insignificant and/or reflected deliberate tradeoffs to optimize the HT plan. Overall imaging and treatment time (median) was 27 min (range, 16-91 min). According to a patient questionnaire, 78% of patients were satisfied to very satisfied with the treatment process. Conclusions: Helical tomotherapy demonstrated clear advantages over conventional 3D-CRT in this diverse patient group. The prospective trials were helpful in deploying this technology in a busy clinical setting

  2. Helicity-flip in particle production on nuclei

    Faeldt, G.

    1977-01-01

    Coherent nuclear production processes are generally analyzed assuming helicity conserving production amplitudes. In view of the uncertainties of the actual helicity structure this could be a dangerous assumption. It is shown that helicity-flip contributions might be part of the explanation of the small effective (pππ)-nucleon cross sections observed in coherent production. (Auth.)

  3. Dual-purpose linker for alpha helix stabilization and imaging agent conjugation to glucagon-like peptide-1 receptor ligands.

    Zhang, Liang; Navaratna, Tejas; Liao, Jianshan; Thurber, Greg M

    2015-02-18

    Peptides display many characteristics of efficient imaging agents such as rapid targeting, fast background clearance, and low non-specific cellular uptake. However, poor stability, low affinity, and loss of binding after labeling often preclude their use in vivo. Using glucagon-like peptide-1 receptor (GLP-1R) ligands exendin and GLP-1 as a model system, we designed a novel α-helix-stabilizing linker to simultaneously address these limitations. The stabilized and labeled peptides showed an increase in helicity, improved protease resistance, negligible loss or an improvement in binding affinity, and excellent in vivo targeting. The ease of incorporating azidohomoalanine in peptides and efficient reaction with the dialkyne linker enable this technique to potentially be used as a general method for labeling α helices. This strategy should be useful for imaging beta cells in diabetes research and in developing and testing other peptide targeting agents.

  4. Structure-activity relationships of an antimicrobial peptide plantaricin s from two-peptide class IIb bacteriocins.

    Soliman, Wael; Wang, Liru; Bhattacharjee, Subir; Kaur, Kamaljit

    2011-04-14

    Class IIb bacteriocins are ribosomally synthesized antimicrobial peptides comprising two different peptides synergistically acting in equal amounts for optimal potency. In this study, we demonstrate for the first time potent (nanomolar) antimicrobial activity of a representative class IIb bacteriocin, plantaricin S (Pls), against four pathogenic gram-positive bacteria, including Listeria monocytogenes. The structure-activity relationships for Pls were studied using activity assays, circular dichroism (CD), and molecular dynamics (MD) simulations. The two Pls peptides and five Pls derived fragments were synthesized. The CD spectra of the Pls and selected fragments revealed helical conformations in aqueous 2,2,2-trifluoroethanol. The MD simulations showed that when the two Pls peptides are in antiparallel orientation, the helical regions interact and align, mediated by strong attraction between conserved GxxxG/AxxxA motifs. The results strongly correlate with the antimicrobial activity suggesting that helix-helix alignment of the two Pls peptides and interaction between the conserved motifs are crucial for interaction with the target cell membrane.

  5. Bearing capacity of helical pile foundation in peat soil from different, diameter and spacing of helical plates

    Fatnanta, F.; Satibi, S.; Muhardi

    2018-03-01

    In an area dominated by thick peat soil layers, driven piles foundation is often used. These piles are generally skin friction piles where the pile tips do not reach hard stratum. Since the bearing capacity of the piles rely on the resistance of their smooth skin, the bearing capacity of the piles are generally low. One way to increase the bearing capacity of the piles is by installing helical plates around the pile tips. Many research has been performed on helical pile foundation. However, literature on the use of helical pile foundation on peat soil is still hardly found. This research focus on the study of axial bearing capacity of helical pile foundation in peat soil, especially in Riau Province. These full-scale tests on helical pile foundation were performed in a rectangular box partially embedded into the ground. The box is filled with peat soil, which was taken from Rimbo Panjang area in the district of Kampar, Riau Province. Several helical piles with different number, diameter and spacing of the helical plates have been tested and analysed. The tests result show that helical pile with three helical plates of uniform diameter has better bearing capacity compared to other helical piles with varying diameter and different number of helical plates. The bearing capacity of helical pile foundation is affected by the spacing between helical plates. It is found that the effective helical plates spacing for helical pile foundation with diameter of 15cm to 35cm is between 20cm to 30cm. This behaviour may be considered to apply to other type of helical pile foundations in peat soil.

  6. Ion temperature gradient modes in toroidal helical systems

    Kuroda, T. [Graduate University for Advanced Studies, Toki, Gifu (Japan); Sugama, H.; Kanno, R.; Okamoto, M.

    2000-04-01

    Linear properties of ion temperature gradient (ITG) modes in helical systems are studied. The real frequency, growth rate, and eigenfunction are obtained for both stable and unstable cases by solving a kinetic integral equation with proper analytic continuation performed in the complex frequency plane. Based on the model magnetic configuration for toroidal helical systems like the Large Helical Device (LHD), dependences of the ITG mode properties on various plasma equilibrium parameters are investigated. Particularly, relative effects of {nabla}B-curvature drifts driven by the toroidicity and by the helical ripples are examined in order to compare the ITG modes in helical systems with those in tokamaks. (author)

  7. Ion temperature gradient modes in toroidal helical systems

    Kuroda, T.; Sugama, H.; Kanno, R.; Okamoto, M.

    2000-04-01

    Linear properties of ion temperature gradient (ITG) modes in helical systems are studied. The real frequency, growth rate, and eigenfunction are obtained for both stable and unstable cases by solving a kinetic integral equation with proper analytic continuation performed in the complex frequency plane. Based on the model magnetic configuration for toroidal helical systems like the Large Helical Device (LHD), dependences of the ITG mode properties on various plasma equilibrium parameters are investigated. Particularly, relative effects of ∇B-curvature drifts driven by the toroidicity and by the helical ripples are examined in order to compare the ITG modes in helical systems with those in tokamaks. (author)

  8. Solution Structure of LXXLL-related Cofactor Peptide of Orphan Nuclear Receptor FTZ-F1

    Yun, Ji Hye; Lee, Chul Jin; Jung, Jin Won; Lee, Weon Tae [Yonsei University, Seoul (Korea, Republic of)

    2012-02-15

    Functional interaction between Drosophila orphan receptor FTZ-F1 (NR5A3) and a segmentation gene product fushi tarazu (FTZ) is crucial for regulating genes related to define the identities of alternate segmental regions in the Drosophila embryo. FTZ binding to the ligand-binding domain (LBD) of FTZ-F1 is of essence in activating its transcription process. We determined solution structures of the cofactor peptide (FTZ{sup PEP}) derived from FTZ by NMR spectroscopy. The cofactor peptide showed a nascent helical conformation in aqueous solution, however, the helicity was increased in the presence of TFE. Furthermore, FTZ{sup PEP} formed α- helical conformation upon FTZ-F1 binding, which provides a receptor bound structure of FTZ{sup PEP}. The solution structure of FTZ{sup PEP} in the presence of FTZ-F1 displays a long stretch of the α-helix with a bend in the middle of helix.

  9. Solution Structure of LXXLL-related Cofactor Peptide of Orphan Nuclear Receptor FTZ-F1

    Yun, Ji Hye; Lee, Chul Jin; Jung, Jin Won; Lee, Weon Tae

    2012-01-01

    Functional interaction between Drosophila orphan receptor FTZ-F1 (NR5A3) and a segmentation gene product fushi tarazu (FTZ) is crucial for regulating genes related to define the identities of alternate segmental regions in the Drosophila embryo. FTZ binding to the ligand-binding domain (LBD) of FTZ-F1 is of essence in activating its transcription process. We determined solution structures of the cofactor peptide (FTZ PEP ) derived from FTZ by NMR spectroscopy. The cofactor peptide showed a nascent helical conformation in aqueous solution, however, the helicity was increased in the presence of TFE. Furthermore, FTZ PEP formed α- helical conformation upon FTZ-F1 binding, which provides a receptor bound structure of FTZ PEP . The solution structure of FTZ PEP in the presence of FTZ-F1 displays a long stretch of the α-helix with a bend in the middle of helix

  10. Biot-Savart helicity versus physical helicity: A topological description of ideal flows

    Sahihi, Taliya; Eshraghi, Homayoon

    2014-08-01

    For an isentropic (thus compressible) flow, fluid trajectories are considered as orbits of a family of one parameter, smooth, orientation-preserving, and nonsingular diffeomorphisms on a compact and smooth-boundary domain in the Euclidian 3-space which necessarily preserve a finite measure, later interpreted as the fluid mass. Under such diffeomorphisms the Biot-Savart helicity of the pushforward of a divergence-free and tangent to the boundary vector field is proved to be conserved and since these circumstances present an isentropic flow, the conservation of the "Biot-Savart helicity" is established for such flows. On the other hand, the well known helicity conservation in ideal flows which here we call it "physical helicity" is found to be an independent constant with respect to the Biot-Savart helicity. The difference between these two helicities reflects some topological features of the domain as well as the velocity and vorticity fields which is discussed and is shown for simply connected domains the two helicities coincide. The energy variation of the vorticity field is shown to be formally the same as for the incompressible flow obtained before. For fluid domains consisting of several disjoint solid tori, at each time, the harmonic knot subspace of smooth vector fields on the fluid domain is found to have two independent base sets with a special type of orthogonality between these two bases by which a topological description of the vortex and velocity fields depending on the helicity difference is achieved since this difference is shown to depend only on the harmonic knot parts of velocity, vorticity, and its Biot-Savart vector field. For an ideal magnetohydrodynamics (MHD) flow three independent constant helicities are reviewed while the helicity of magnetic potential is generalized for non-simply connected domains by inserting a special harmonic knot field in the dynamics of the magnetic potential. It is proved that the harmonic knot part of the vorticity

  11. A novel chimeric peptide with antimicrobial activity.

    Alaybeyoglu, Begum; Akbulut, Berna Sariyar; Ozkirimli, Elif

    2015-04-01

    Beta-lactamase-mediated bacterial drug resistance exacerbates the prognosis of infectious diseases, which are sometimes treated with co-administration of beta-lactam type antibiotics and beta-lactamase inhibitors. Antimicrobial peptides are promising broad-spectrum alternatives to conventional antibiotics in this era of evolving bacterial resistance. Peptides based on the Ala46-Tyr51 beta-hairpin loop of beta-lactamase inhibitory protein (BLIP) have been previously shown to inhibit beta-lactamase. Here, our goal was to modify this peptide for improved beta-lactamase inhibition and cellular uptake. Motivated by the cell-penetrating pVEC sequence, which includes a hydrophobic stretch at its N-terminus, our approach involved the addition of LLIIL residues to the inhibitory peptide N-terminus to facilitate uptake. Activity measurements of the peptide based on the 45-53 loop of BLIP for enhanced inhibition verified that the peptide was a competitive beta-lactamase inhibitor with a K(i) value of 58 μM. Incubation of beta-lactam-resistant cells with peptide decreased the number of viable cells, while it had no effect on beta-lactamase-free cells, indicating that this peptide had antimicrobial activity via beta-lactamase inhibition. To elucidate the molecular mechanism by which this peptide moves across the membrane, steered molecular dynamics simulations were carried out. We propose that addition of hydrophobic residues to the N-terminus of the peptide affords a promising strategy in the design of novel antimicrobial peptides not only against beta-lactamase but also for other intracellular targets. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.

  12. Melectin: A novel antimicrobial peptide from the venom of the cleptoparasitic bee Melecta albifrons

    Čeřovský, Václav; Hovorka, Oldřich; Cvačka, Josef; Voburka, Zdeněk; Bednárová, Lucie; Borovičková, Lenka; Slaninová, Jiřina; Fučík, Vladimír

    2008-01-01

    Roč. 9, č. 17 (2008), s. 2815-2821 ISSN 1439-4227 R&D Projects: GA ČR(CZ) GA203/08/0536 Institutional research plan: CEZ:AV0Z40550506 Keywords : amphipathicity * antimicrobial activity * helical structures * peptides * solitary bee venom Subject RIV: CC - Organic Chemistry Impact factor: 3.322, year: 2008

  13. Divorcing folding from function: how acylation affects the membrane-perturbing properties of an antimicrobial peptide

    Vad, Brian Stougaard; Thomsen, Line Aagot Hede; Bertelsen, Kresten

    2010-01-01

    Many small cationic peptides, which are unstructured in aqueous solution, have antimicrobial properties. These properties are assumed to be linked to their ability to permeabilize bacterial membranes, accompanied by the transition to an alpha-helical folding state. Here we show that there is no d......Many small cationic peptides, which are unstructured in aqueous solution, have antimicrobial properties. These properties are assumed to be linked to their ability to permeabilize bacterial membranes, accompanied by the transition to an alpha-helical folding state. Here we show...... that there is no direct link between folding of the antimicrobial peptide Novicidin (Nc) and its membrane permeabilization. N-terminal acylation with C8-C16 alkyl chains and the inclusion of anionic lipids both increase Nc's ability to form alpha-helical structure in the presence of vesicles. Nevertheless, both acylation......, this cannot rationalize our results since permeabilization and antimicrobial activities are observed well below concentrations where aggregation occurs. This suggests that significant induction of alpha-helical structure is not a prerequisite for membrane perturbation in this class of antimicrobial peptides...

  14. Human peptide transporters

    Nielsen, Carsten Uhd; Brodin, Birger; Jørgensen, Flemming Steen

    2002-01-01

    Peptide transporters are epithelial solute carriers. Their functional role has been characterised in the small intestine and proximal tubules, where they are involved in absorption of dietary peptides and peptide reabsorption, respectively. Currently, two peptide transporters, PepT1 and PepT2, wh...

  15. Multiphasic helical CT of hepatocellular carcinoma. Evaluation after chemo embolization

    Catalano, O.; Esposito, M.; Sandomenico, F.; Siani, A.; Nunziata, A.

    2000-01-01

    The main purpose of this work is to report the personal experience with addition of contrast-enhanced multiphase helical CT to unenhanced CT (Lipiodol CT) in the evaluation of patients with hepatocellular carcinoma treated with chemoembolization and to analyze the present role of oily agent CT. It has been retrospectively reviewed the examinations of 42 consecutive patients submitted to globla chemoembolization over a 2-year period. CT was performed 18-30 days after the treatment. The Lipiodol CT study was carried out with volume acquisitions. It has been considered as nodules all well-defined areas with dense oily agent uptake; uptake itself was classified as: 0=absent, I=lower tha 10% of the tumor volume; II=lower than 50%, III=50%, IV=homogeneous. Contrast-enhanced helical CT was performed with the 2-phase technique in 28 patients and with the 3-phase technique in 14; it has been considered as nodules all well-defined and relatively homogeneous areas with hyperattenuation in the arterial phase and hypo-isoattenuation in the portal and/or delayed phase, or with hypo-isoattenuation in the arterial phase and in the portal and/or delayed phase. Lipiodol CT permitted to recognize 65 nodules (1-5/patient, mean 1.5), namely 15 grade I, 21 grade II, 20 grade III and 9 grade IV. Multiphase CT identified 6 additional nodules in 5 patients, 5 hypervascular and 1 hypovascular, and better assessed the correct morphology and volume of grade I nodules. Only 4 of 6 nodules missed on Lipiodol CT showed oily agent uptake after a new chemoembolization session. Moreover after retreatment, carried out in 6 of 9 patients with grade I uptake (11 nodules in all), it has been found persistence of the grade I pattern in 5 nodules, grade II in 5, and grade III in 1. Lipiodol CT may miss liver nodules and underestimate the volume of nodules with poor uptake. Though Lipiodol CT should still be considered slightly more sensitive than multiphase CT, in the general opinion this technique has

  16. Magnetic helicity balance in the Sustained Spheromak Plasma Experiment

    Stallard, B.W.; Hooper, E.B.; Woodruff, S.; Bulmer, R.H.; Hill, D.N.; McLean, H.S.; Wood, R.D.

    2003-01-01

    The magnetic helicity balance between the helicity input injected by a magnetized coaxial gun, the rate-of-change in plasma helicity content, and helicity dissipation in electrode sheaths and Ohmic losses have been examined in the Sustained Spheromak Plasma Experiment (SSPX) [E. B. Hooper, L. D. Pearlstein, and R. H. Bulmer, Nucl. Fusion 39, 863 (1999)]. Helicity is treated as a flux function in the mean-field approximation, allowing separation of helicity drive and losses between closed and open field volumes. For nearly sustained spheromak plasmas with low fluctuations, helicity balance analysis implies a decreasing transport of helicity from the gun input into the spheromak core at higher spheromak electron temperature. Long pulse discharges with continuously increasing helicity and larger fluctuations show higher helicity coupling from the edge to the spheromak core. The magnitude of the sheath voltage drop, inferred from cathode heating and a current threshold dependence of the gun voltage, shows that sheath losses are important and reduce the helicity injection efficiency in SSPX

  17. Amphiphilic cationic peptides mediate cell adhesion to plastic surfaces.

    Rideout, D C; Lambert, M; Kendall, D A; Moe, G R; Osterman, D G; Tao, H P; Weinstein, I B; Kaiser, E T

    1985-09-01

    Four amphiphilic peptides, each with net charges of +2 or more at neutrality and molecular weights under 4 kilodaltons, were found to mediate the adhesion of normal rat kidney fibroblasts to polystyrene surfaces. Two of these peptides, a model for calcitonin (peptide 1, MCT) and melittin (peptide 2, MEL), form amphiphilic alpha-helical structures at aqueous/nonpolar interfaces. The other two, a luteinizing hormone-releasing hormone model (peptide 3, LHM) and a platelet factor model (peptide 4, MPF) form beta-strand structures in amphiphilic environments. Although it contains only 10 residues, LHM mediated adhesion to surfaces coated with solutions containing as little as 10 pmoles/ml of peptide. All four of these peptides were capable of forming monolayers at air-buffer interfaces with collapse pressures greater than 20 dynes/cm. None of these four peptides contains the tetrapeptide sequence Arg-Gly-Asp-Ser, which has been associated with fibronectin-mediated cell adhesion. Ten polypeptides that also lacked the sequence Arg-Gly-Asp-Ser but were nonamphiphilic and/or had net charges less than +2 at neutrality were all incapable of mediating cell adhesion (Pierschbacher and Ruoslahti, 1984). The morphologies of NRK cells spread on polystyrene coated with peptide LHM resemble the morphologies on fibronectin-coated surfaces, whereas cells spread on surfaces coated with MCT or MEL exhibit strikingly different morphologies. The adhesiveness of MCT, MEL, LHM, and MPF implies that many amphiphilic cationic peptides could prove useful as well defined adhesive substrata for cell culture and for studies of the mechanism of cell adhesion.

  18. Nonlinear calculation of the M=1 internal kink instability in current carrying stellarators

    Wakatani, M.

    1978-02-01

    Nonlinear properties of the m = 1 internal kink mode are shown in a low β current carrying stellarator. The effects of the external helical magnetic fields are considered through a rotational transform and the magnetic surface is assumed to be circular. Magnetic surfaces inside the iota sub(h) + iota sub(σ) = 1 surface shift and deform non-circularly, while magnetic surfaces outside the iota sub(h) + iota sub(σ) = 1 are not disturbed, where iota sub(h) is a rotational transform due to helical magnetic fields and iota sub(σ) is due to a plasma current. Many higher harmonics are excited after the fundamental mode saturates. When the external helical magnetic fields are lowered, the m = 1 tearing mode similar to that in a low β tokamak grows and magnetic islands appear near the iota sub(h) + iota sub(σ) = 1 surface. For adequate helical magnetic fields, the current carrying stellarator becomes stable against both the m = 1 internal kink mode and the m = 1 tearing mode, without lowering the rotational transform. (auth.)

  19. Circulating elastin peptides, role in vascular pathology.

    Robert, L; Labat-Robert, J

    2014-12-01

    The atherosclerotic process starts with the degradation of elastic fibers. Their presence was demonstrated in the circulation as well as several of their biological properties elucidated. We described years ago a procedure to obtain large elastin peptides by organo-alkaline hydrolysis, κ-elastin. This method enabled also the preparation of specific antibodies used to determine elastin peptides, as well as anti-elastin antibodies in body fluids and tissue extracts. Elastin peptides were determined in a large number of human blood samples. Studies were carried out to explore their pharmacological properties. Similar recent studies by other laboratories confirmed our findings and arose new interest in circulating elastin peptides for their biological activities. This recent trend justified the publication of a review of the biological and pathological activities of elastin peptides demonstrated during our previous studies, subject of this article. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  20. Internal transport barrier formation and pellet injection simulation in helical and tokamak reactors

    Higashiyama, You; Yamazaki, Kozo; Arimoto, Hideki; Garcia, Jeronimo

    2008-01-01

    In the future fusion reactor, plasma density peaking is important for increase in the fusion power gain and for achievement of confinement improvement mode. Density control and internal transport barrier (ITB) formation due to pellet injection have been simulated in tokamak and helical reactors using the toroidal transport linkage code TOTAL. First, pellet injection simulation is carried out, including the neutral gas shielding model and the mass relocation model in the TOTAL code, and the effectiveness of high-field side (HFS) pellet injection is clarified. Second, ITB simulation with pellet injection is carried out with the confinement improvement model based on the E x B shear effects, and it is found that deep pellet penetration is helpful for ITB formation as well as plasma core fuelling in the reversed-shear tokamak and helical reactors. (author)

  1. Helical CT of congenital ossicular anomalies

    Osada, Hisato; Machida, Kikuo; Honda, Norinari

    2001-01-01

    Since January 1996 to December 2000, 26 cases of congenital ossicular anomaly could be diagnosed with helical CT. All cases were unilateral. In 8 patients with malformation of the external ear, CT showed malleoincudal fixation (n=5), malleoincudal fixation and deformed incuts long process (n=1), deformed incus long process (n=1), and partial fusion of malleus neck and incus long process (n=1). In 18 patients with normal external ear, CT showed defect of the incus long process (n=5), defect of both the incus long process and stapes superstructure (n=8, 2 patients with congenital cholesteatoma, 1 with hypoplastic oval window), defect of the stapes superstructure (n=2, 1 patient with oval window absence), defect of the malleus manubrium (n=1), ossification of the stampede's tendon (n=1), and monopod stapes (n=1). Helical CT can evaluate the auditory ossicular chain in detail and is useful for diagnosing congenital ossicular anomaly. (author)

  2. Weaving Knotted Vector Fields with Tunable Helicity.

    Kedia, Hridesh; Foster, David; Dennis, Mark R; Irvine, William T M

    2016-12-30

    We present a general construction of divergence-free knotted vector fields from complex scalar fields, whose closed field lines encode many kinds of knots and links, including torus knots, their cables, the figure-8 knot, and its generalizations. As finite-energy physical fields, they represent initial states for fields such as the magnetic field in a plasma, or the vorticity field in a fluid. We give a systematic procedure for calculating the vector potential, starting from complex scalar functions with knotted zero filaments, thus enabling an explicit computation of the helicity of these knotted fields. The construction can be used to generate isolated knotted flux tubes, filled by knots encoded in the lines of the vector field. Lastly, we give examples of manifestly knotted vector fields with vanishing helicity. Our results provide building blocks for analytical models and simulations alike.

  3. Vacuum systems for the ILC helical undulator

    Malyshev, O B; Clarke, J A; Bailey, I R; Dainton, J B; Malysheva, L I; Barber, D P; Cooke, P; Baynham, E; Bradshaw, T; Brummitt, A; Carr, S; Ivanyushenkov, Y; Rochford, J; Moortgat-Pick, G A

    2007-01-01

    The International Linear Collider (ILC) positron source uses a helical undulator to generate polarized photons of ∼10MeV∼10MeV at the first harmonic. Unlike many undulators used in synchrotron radiation sources, the ILC helical undulator vacuum chamber will be bombarded by photons, generated by the undulator, with energies mostly below that of the first harmonic. Achieving the vacuum specification of ∼100nTorr∼100nTorr in a narrow chamber of 4–6mm4–6mm inner diameter, with a long length of 100–200m100–200m, makes the design of the vacuum system challenging. This article describes the vacuum specifications and calculations of the flux and energy of photons irradiating the undulator vacuum chamber and considers possible vacuum system design solutions for two cases: cryogenic and room temperature.

  4. SUPERCONDUCTING HELICAL SNAKE MAGNETS: CONSTRUCTION AND MEASUREMENTS

    Mackay, W.W.; Anerella, M.; Courant, E.

    1999-01-01

    In order to collide polarized protons, the RHIC project will have two snakes in each ring and four rotators around each of two interaction regions. Two snakes on opposite sides of each ring can minimize depolarization during acceleration by keeping the spin tune at a half. Since the spin direction is normally along the vertical direction in a flat ring, spin rotators must be used around an interaction point to have longitudinal polarization in a collider experiment. Each snake or rotator will be composed of four helical dipoles to provide the required rotation of spin with minimal transverse orbit excursions in a compact length of 10m. The basic helical dipole is a superconducting magnet producing a transverse dipole field which is twisted about the magnet axis through 360 o in a length of 2.4 m. The design and construction of the magnets is described in this paper

  5. Buoyant Helical Twin-Axial Wire Antenna

    2016-11-15

    February 2017 The below identified patent application is available for licensing. Requests for information should be addressed to...300169 1 of 9 BUOYANT HELICAL TWIN-AXIAL WIRE ANTENNA CROSS REFERENCE TO OTHER PATENT APPLICATIONS [0001] This application is a divisional...application and claims the benefit of the filing date of United States Patent Application No. 14/280,889; filed on May 19, 2014; and entitled “Twin-Axial

  6. Molecular Dynamics with Helical Periodic Boundary Conditions

    Kessler, Jiří; Bouř, Petr

    2014-01-01

    Roč. 35, č. 21 (2014), s. 1552-1559 ISSN 0192-8651 R&D Projects: GA ČR GAP208/11/0105; GA MŠk(CZ) LH11033 Grant - others:GA AV ČR(CZ) M200551205; GA MŠk(CZ) LM2010005 Institutional support: RVO:61388963 Keywords : periodic boundary conditions * helical symmetry * molecular dynamics * protein structure * amyloid fibrils Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.589, year: 2014

  7. Simplification of the helical TEN2 laser

    Krahn, K.-H.

    1980-04-01

    The observation that the helical TEN2 laser can effectively be simplified by giving up the use of decoupling elements as well as by abolishing the segmentation of the electrode structure is examined. Although, as a consequence of this simplification, the operating pressure range was slightly decreased, the output power could be improved by roughly 30%, a result which is attributed to the new electrode geometry exhibiting lower inductance and lower damping losses.

  8. Field of a helical Siberian Snake

    Luccio, A. [Brookhaven National Lab., Upton, NY (United States)

    1995-02-01

    To preserve the spin polarization of a beam of high energy protons in a circular accelerator, magnets with periodic magnetic field, called Siberian Snakes are being used. Recently, it was proposed to build Siberian Snakes with superconducting helical dipoles. In a helical, or twisted dipole, the magnetic field is perpendicular to the axis of the helix and rotates around it as one proceeds along the magnet. In an engineering study of a 4 Tesla helical snake, the coil geometry is derived, by twisting, from the geometry of a cosine superconducting dipole. While waiting for magnetic measurement data on such a prototype, an analytical expression for the field of the helice is important, to calculate the particle trajectories and the spin precession in the helix. This model will also allow to determine the optical characteristics of the snake, as an insertion in the lattice of the accelerator. In particular, one can calculate the integrated multipoles through the magnet and the equivalent transfer matrix. An expression for the field in the helix body, i.e., excluding the fringe field was given in a classical paper. An alternate expression can be found by elaborating on the treatment of the field of a transverse wiggler obtained under the rather general conditions that the variables are separable. This expression exactly satisfies Maxwell`s div and curl equations for a stationary field, {del} {center_dot} B = 0, {del} x B = 0. This approach is useful in that it will allow one to use much of the work already done on the problem of inserting wigglers and undulators in the lattice of a circular accelerator.

  9. Effect of sequence and stereochemistry reversal on p53 peptide mimicry.

    Alessio Atzori

    Full Text Available Peptidomimetics effective in modulating protein-protein interactions and resistant to proteolysis have potential in therapeutic applications. An appealing yet underperforming peptidomimetic strategy is to employ D-amino acids and reversed sequences to mimic a lead peptide conformation, either separately or as the combined retro-inverso peptide. In this work, we examine the conformations of inverse, reverse and retro-inverso peptides of p53(15-29 using implicit solvent molecular dynamics simulation and circular dichroism spectroscopy. In order to obtain converged ensembles for the peptides, we find enhanced sampling is required via the replica exchange molecular dynamics method. From these replica exchange simulations, the D-peptide analogues of p53(15-29 result in a predominantly left-handed helical conformation. When the parent sequence is reversed sequence as either the L-peptide and D-peptide, these peptides display a greater helical propensity, feature reflected by NMR and CD studies in TFE/water solvent. The simulations also indicate that, while approximately similar orientations of the side-chains are possible by the peptide analogues, their ability to mimic the parent peptide is severely compromised by backbone orientation (for D-amino acids and side-chain orientation (for reversed sequences. A retro-inverso peptide is disadvantaged as a mimic in both aspects, and further chemical modification is required to enable this concept to be used fruitfully in peptidomimetic design. The replica exchange molecular simulation approach adopted here, with its ability to provide detailed conformational insights into modified peptides, has potential as a tool to guide structure-based design of new improved peptidomimetics.

  10. Dryout in sodium-heated helically-coiled steam generator tubes

    Tomita, Y.; Kosugi, T.; Kubota, J.; Nakajima, K.; Tsuchiya, T.

    1984-01-01

    Experimental research on the dryout phenomenon in sodium heated, helically coiled steam generator tubes was carried out. The fluctuation of the tube wall temperature caused by dryout was measured with thermocouples installed in the center of the tube wall. Empirical correlations of dryout quality were developed as functions of critical heat flux, water mass velocity and saturation pressure. These correlations confirmed that the design criterion of the MONJU steam generator was reasonable. (author)

  11. Helicity dependence of the total inclusive cross section on the deuteron

    Ahrens, J. [Institut fuer Kernphysik, Universitaet Mainz, D-55099 Mainz (Germany); Altieri, S. [INFN, Sezione di Pavia, I-27100 Pavia (Italy); Dipartimento di Fisica Nucleare e Teorica, Universita di Pavia, I-27100 Pavia (Italy); Annand, J.R.M. [Department of Physics and Astronomy, University of Glasgow (United Kingdom); Arends, H.-J.; Beck, R. [Institut fuer Kernphysik, Universitaet Mainz, D-55099 Mainz (Germany); Blackston, M.A. [Department of Physics, Duke University, Durham, NC 27708 (United States); Braghieri, A. [INFN, Sezione di Pavia, I-27100 Pavia (Italy); D' Hose, N. [CEA Saclay, DSM/DAPNIA/SPhN, F-91191 Gif-sur-Yvette Cedex (France); Dutz, H. [Physikalisches Institut, Universitaet Bonn, D-53115 Bonn (Germany); Heid, E.; Jahn, O. [Institut fuer Kernphysik, Universitaet Mainz, D-55099 Mainz (Germany); Klein, F. [Physikalisches Institut, Universitaet Bonn, D-53115 Bonn (Germany); Kondratiev, R. [INR, Academy of Science, Moscow (Russian Federation); Lang, M. [Institut fuer Kernphysik, Universitaet Mainz, D-55099 Mainz (Germany); Lisin, V. [INR, Academy of Science, Moscow (Russian Federation); Martinez Fabregate, M. [Institut fuer Kernphysik, Universitaet Mainz, D-55099 Mainz (Germany); McGeorge, J.C. [Department of Physics and Astronomy, University of Glasgow (United Kingdom); Meyer, W. [Inst. fuer Experimentalphysik, Ruhr-Universitaet Bochum, D-44801 Bochum (Germany); Panzeri, A. [INFN, Sezione di Pavia, I-27100 Pavia (Italy); Dipartimento di Fisica Nucleare e Teorica, Universita di Pavia, I-27100 Pavia (Italy); Pedroni, P. [INFN, Sezione di Pavia, I-27100 Pavia (Italy)], E-mail: pedroni@pv.infn.it (and others)

    2009-03-02

    A measurement of the helicity dependence of the total inclusive photoabsorption cross section on the deuteron was carried out at MAMI (Mainz) in the energy range 200

  12. Helicity dependence of the total inclusive cross section on the deuteron

    Ahrens, J.; Altieri, S.; Annand, J.R.M.; Arends, H.-J.; Beck, R.; Blackston, M.A.; Braghieri, A.; D'Hose, N.; Dutz, H.; Heid, E.; Jahn, O.; Klein, F.; Kondratiev, R.; Lang, M.; Lisin, V.; Martinez Fabregate, M.; McGeorge, J.C.; Meyer, W.; Panzeri, A.; Pedroni, P.

    2009-01-01

    A measurement of the helicity dependence of the total inclusive photoabsorption cross section on the deuteron was carried out at MAMI (Mainz) in the energy range 200 γ <800 MeV. The experiment used a 4π detection system, a circularly polarized tagged photon beam and a frozen spin target which provided longitudinally polarized deuterons. These new results are a significant improvement on the existing data and allow a detailed comparison with state-of-the-art calculations

  13. Helical waves in easy-plane antiferromagnets

    Semenov, Yuriy G.; Li, Xi-Lai; Xu, Xinyi; Kim, Ki Wook

    2017-12-01

    Effective spin torques can generate the Néel vector oscillations in antiferromagnets (AFMs). Here, it is theoretically shown that these torques applied at one end of a normal AFM strip can excite a helical type of spin wave in the strip whose properties are drastically different from characteristic spin waves. An analysis based on both a Néel vector dynamical equation and the micromagnetic simulation identifies the direction of magnetic anisotropy and the damping factor as the two key parameters determining the dynamics. Helical wave propagation requires the hard axis of the easy-plane AFM to be aligned with the traveling direction, while the damping limits its spatial extent. If the damping is neglected, the calculation leads to a uniform periodic domain wall structure. On the other hand, finite damping decelerates the helical wave rotation around the hard axis, ultimately causing stoppage of its propagation along the strip. With the group velocity staying close to spin-wave velocity at the wave front, the wavelength becomes correspondingly longer away from the excitation point. In a sufficiently short strip, a steady-state oscillation can be established whose frequency is controlled by the waveguide length as well as the excitation energy or torque.

  14. Helical CT in acute lower gastrointestinal bleeding

    Ernst, Olivier; Leroy, Christophe; Sergent, Geraldine; Bulois, Philippe; Saint-Drenant, Sophie; Paris, Jean-Claude

    2003-01-01

    The purpose of this study was to assess the usefulness of helical CT in depicting the location of acute lower gastrointestinal bleeding. A three-phase helical CT of the abdomen was performed in 24 patients referred for acute lower gastrointestinal bleeding. The diagnosis of the bleeding site was established by CT when there was at least one of the following criteria: spontaneous hyperdensity of the peribowel fat; contrast enhancement of the bowel wall; vascular extravasation of the contrast medium; thickening of the bowel wall; polyp or tumor; or vascular dilation. Diverticula alone were not enough to locate the bleeding site. The results of CT were compared with the diagnosis obtained by colonoscopy, enteroscopy, or surgery. A definite diagnosis was made in 19 patients. The bleeding site was located in the small bowel in 5 patients and the colon in 14 patients. The CT correctly located 4 small bowel hemorrhages and 11 colonic hemorrhages. Diagnosis of the primary lesion responsible for the bleeding was made in 10 patients. Our results suggest that helical CT could be a good diagnostic tool in acute lower gastrointestinal bleeding to help the physician to diagnose the bleeding site. (orig.)

  15. Superconducting Helical Snake Magnet for the AGS

    Willen, Erich; Escallier, John; Ganetis, George; Ghosh, Arup; Gupta, Ramesh C; Harrison, Michael; Jain, Animesh K; Luccio, Alfredo U; MacKay, William W; Marone, Andrew; Muratore, Joseph F; Okamura, Masahiro; Plate, Stephen R; Roser, Thomas; Tsoupas, Nicholaos; Wanderer, Peter

    2005-01-01

    A superconducting helical magnet has been built for polarized proton acceleration in the Brookhaven AGS. This "partial Snake" magnet will help to reduce the loss of polarization of the beam due to machine resonances. It is a 3 T magnet some 1940 mm in magnetic length in which the dipole field rotates with a pitch of 0.2053 degrees/mm for 1154 mm in the center and a pitch of 0.3920 degrees/mm for 393 mm in each end. The coil cross-section is made of two slotted cylinders containing superconductor. In order to minimize residual offsets and deflections of the beam on its orbit through the Snake, a careful balancing of the coil parameters was necessary. In addition to the main helical coils, a solenoid winding was built on the cold bore tube inside the main coils to compensate for the axial component of the field that is experienced by the beam when it is off-axis in this helical magnet. Also, two dipole corrector magnets were placed on the same tube with the solenoid. A low heat leak cryostat was built so that t...

  16. Total scalp irradiation using helical tomotherapy

    Orton, Nigel; Jaradat, Hazim; Welsh, James; Tome, Wolfgang

    2005-01-01

    Homogeneous irradiation of the scalp poses technical and dosimetric challenges due to the extensive, superficial, curved treatment volume. Conventional treatments on a linear accelerator use multiple matched electron fields or a combination of electron and photon fields. Problems with these techniques include dose heterogeneity in the target due to varying source-to-skin distance (SSD) and angle of beam incidence, significant dose to the brain, and the potential for overdose or underdose at match lines between the fields. Linac-based intensity-modulated radiation therapy (IMRT) plans have similar problems. This work presents treatment plans for total scalp irradiation on a helical tomotherapy machine. Helical tomotherapy is well-suited for scalp irradiation because it has the ability to deliver beamlets that are tangential to the scalp at all points. Helical tomotherapy also avoids problems associated with field matching and use of more than one modality. Tomotherapy treatment plans were generated and are compared to plans for treatment of the same patient on a linac. The resulting tomotherapy plans show more homogeneous target dose and improved critical structure dose when compared to state-of-the-art linac techniques. Target equivalent uniform dose (EUD) for the best tomotherapy plan was slightly higher than for the linac plan, while the volume of brain tissue receiving over 30 Gy was reduced by two thirds. Furthermore, the tomotherapy plan can be more reliably delivered than linac treatments, because the patient is aligned prior to each treatment based on megavoltage computed tomography (MVCT)

  17. THE EFFECTS OF SPATIAL SMOOTHING ON SOLAR MAGNETIC HELICITY PARAMETERS AND THE HEMISPHERIC HELICITY SIGN RULE

    Ocker, Stella Koch [Department of Physics, Oberlin College, Oberlin, OH 44074 (United States); Petrie, Gordon, E-mail: socker@oberlin.edu, E-mail: gpetrie@nso.edu [National Solar Observatory, Boulder, CO 80303 (United States)

    2016-12-01

    The hemispheric preference for negative/positive helicity to occur in the northern/southern solar hemisphere provides clues to the causes of twisted, flaring magnetic fields. Previous studies on the hemisphere rule may have been affected by seeing from atmospheric turbulence. Using Hinode /SOT-SP data spanning 2006–2013, we studied the effects of two spatial smoothing tests that imitate atmospheric seeing: noise reduction by ignoring pixel values weaker than the estimated noise threshold, and Gaussian spatial smoothing. We studied in detail the effects of atmospheric seeing on the helicity distributions across various field strengths for active regions (ARs) NOAA 11158 and NOAA 11243, in addition to studying the average helicities of 179 ARs with and without smoothing. We found that, rather than changing trends in the helicity distributions, spatial smoothing modified existing trends by reducing random noise and by regressing outliers toward the mean, or removing them altogether. Furthermore, the average helicity parameter values of the 179 ARs did not conform to the hemisphere rule: independent of smoothing, the weak-vertical-field values tended to be negative in both hemispheres, and the strong-vertical-field values tended to be positive, especially in the south. We conclude that spatial smoothing does not significantly affect the overall statistics for space-based data, and thus seeing from atmospheric turbulence seems not to have significantly affected previous studies’ ground-based results on the hemisphere rule.

  18. [Technique of complex mammary irradiation: Mono-isocentric 3D conformational radiotherapy and helical tomotherapy].

    Vandendorpe, B; Guilbert, P; Champagne, C; Antoni, T; Nguyen, T D; Gaillot-Petit, N; Servagi Vernat, S

    2017-12-01

    To evaluate the dosimetric contribution of helical tomotherapy for breast cancers compared with conformal radiotherapy in mono-isocentric technique. For 23 patients, the dosimetric results in mono-isocentric 3D conformational radiotherapy did not satisfy the constraints either of target volumes nor organs at risk. A prospective dosimetric comparison between mono-isocentric 3D conformational radiotherapy and helical tomotherapy was therefore carried out. The use of helical tomotherapy showed a benefit in these 23 patients, with either an improvement in the conformity index or homogeneity, but with an increase in low doses. Of the 23 patients, two had pectus excavatum, five had past thoracic irradiation and two required bilateral irradiation. The other 14 patients had a combination of morphology and/or indication of lymph node irradiation. For these patients, helical tomotherapy was therefore preferred to mono-isocentric 3D conformational radiotherapy. Tomotherapy appears to provide better homogeneity and tumour coverage. This technique of irradiation may be justified in the case of morphological situations such as pectus exavatum and in complex clinical situations. In other cases, conformal radiotherapy in mono-isocentric technique remains to be favoured. Copyright © 2017 Société française de radiothérapie oncologique (SFRO). Published by Elsevier SAS. All rights reserved.

  19. The use of helical heat exchanger for heat recovery domestic water-cooled air-conditioners

    Yi Xiaowen; Lee, W.L.

    2009-01-01

    An experimental study on the performance of a domestic water-cooled air-conditioner (WAC) using tube-in-tube helical heat exchanger for preheating of domestic hot water was carried out. The main aims are to identify the comprehensive energy performance (space cooling and hot water preheating) of the WAC and the optimum design of the helical heat exchanger taking into account the variation in tap water flow rate. A split-type WAC was set up for experimental study at different indoor and outdoor conditions. The cooling output, the amount of recovered heat, and the power consumption for different hot water flow rates were measured. The experimental results showed that the cooling coefficient of performance (COP) of the WAC improves with the inclusion of the heat recovery option by a minimum of 12.3%. This can be further improved to 20.6% by an increase in tap water flow rate. Same result was observed for the comprehensive COP of the WAC. The maximum achievable comprehensive COP was 4.92 when the tap water flow rate was set at 7.7 L/min. The overall heat transfer coefficient of the helical heat exchanger under various operating conditions were determined by Wilson plot. A mathematical model relating the over all heat transfer coefficient to the outer pipe diameter was established which provides a convenient way of optimising the design of the helical heat exchanger

  20. A proline-hinge alters the characteristics of the amphipathic α-helical AMPs.

    Lee, Jong Kook; Gopal, Ramamourthy; Park, Seong-Cheol; Ko, Hyun Sook; Kim, Yangmee; Hahm, Kyung-Soo; Park, Yoonkyung

    2013-01-01

    HP (2-20) is a 19-aa, amphipathic, α-helical peptide with antimicrobial properties that was derived from the N-terminus of Helicobacter pylori ribosomal protein L1. We previously showed that increasing the net hydrophobicity of HP (2-20) by substituting Trp for Gln(17) and Asp(19) (Anal 3) increased the peptide's antimicrobial activity. In hydrophobic medium, Anal 3 forms an amphipathic structure consisting of an N-terminal random coil region (residues 2-5) and an extended helical region (residues 6-20). To investigate the structure-activity relationship of Anal 3, we substituted Pro for Glu(9) (Anal 3-Pro) and then examined the new peptide's three-dimensional structure, antimicrobial activity and mechanism of action. Anal 3-Pro had an α-helical structure in the presence of trifluoroethanol (TFE) and sodium dodecyl sulfate (SDS). NMR spectroscopic analysis of Anal 3-Pro's tertiary structure in SDS micelles confirmed that the kink potential introduced by Pro(10) was responsible for the helix distortion. We also found that Anal 3-Pro exhibited about 4 times greater antimicrobial activity than Anal 3. Fluorescence activated flow cytometry and confocal fluorescence microscopy showed that incorporating a Pro-hinge into Anal 3 markedly reduced its membrane permeability so that it accumulated in the cytoplasm without remaining in the cell membrane. To investigate the translocation mechanism, we assessed its ability to release of FITC-dextran. The result showed Anal 3-Pro created a pore Candida albicans revealed that Anal 3-Pro and buforin II exert similar effects on cell membranes, whereas magainin 2 exerts a different, more damaging, effect. In addition, Anal 3-Pro assumed a helix-hinge-helix structure in the presence of biological membranes and formed micropores in both bacterial and fungal membranes, through which it entered the cytoplasm and tightly bound to DNA. These results indicate that the bending region of Anal 3- Pro peptide is prerequisite for effective

  1. A proline-hinge alters the characteristics of the amphipathic α-helical AMPs.

    Jong Kook Lee

    Full Text Available HP (2-20 is a 19-aa, amphipathic, α-helical peptide with antimicrobial properties that was derived from the N-terminus of Helicobacter pylori ribosomal protein L1. We previously showed that increasing the net hydrophobicity of HP (2-20 by substituting Trp for Gln(17 and Asp(19 (Anal 3 increased the peptide's antimicrobial activity. In hydrophobic medium, Anal 3 forms an amphipathic structure consisting of an N-terminal random coil region (residues 2-5 and an extended helical region (residues 6-20. To investigate the structure-activity relationship of Anal 3, we substituted Pro for Glu(9 (Anal 3-Pro and then examined the new peptide's three-dimensional structure, antimicrobial activity and mechanism of action. Anal 3-Pro had an α-helical structure in the presence of trifluoroethanol (TFE and sodium dodecyl sulfate (SDS. NMR spectroscopic analysis of Anal 3-Pro's tertiary structure in SDS micelles confirmed that the kink potential introduced by Pro(10 was responsible for the helix distortion. We also found that Anal 3-Pro exhibited about 4 times greater antimicrobial activity than Anal 3. Fluorescence activated flow cytometry and confocal fluorescence microscopy showed that incorporating a Pro-hinge into Anal 3 markedly reduced its membrane permeability so that it accumulated in the cytoplasm without remaining in the cell membrane. To investigate the translocation mechanism, we assessed its ability to release of FITC-dextran. The result showed Anal 3-Pro created a pore <1.8 nm in diameter, which is similar to buforin II. Notably, scanning electron microscopic observation of Candida albicans revealed that Anal 3-Pro and buforin II exert similar effects on cell membranes, whereas magainin 2 exerts a different, more damaging, effect. In addition, Anal 3-Pro assumed a helix-hinge-helix structure in the presence of biological membranes and formed micropores in both bacterial and fungal membranes, through which it entered the cytoplasm and tightly

  2. How honey bees carry pollen

    Matherne, Marguerite E.; Anyanwu, Gabriel; Leavey, Jennifer K.; Hu, David L.

    2017-11-01

    Honey bees are the tanker of the skies, carrying thirty percent of their weight in pollen per foraging trip using specialized orifices on their body. How do they manage to hang onto those pesky pollen grains? In this experimental study, we investigate the adhesion force of pollen to the honeybee. To affix pollen to themselves, honey bees form a suspension of pollen in nectar, creating a putty-like pollen basket that is skewered by leg hairs. We use tensile tests to show that the viscous force of the pollen basket is more than ten times the honeybee's flight force. This work may provide inspiration for the design of robotic flying pollinators.

  3. Cryo-EM Structure Determination Using Segmented Helical Image Reconstruction.

    Fromm, S A; Sachse, C

    2016-01-01

    Treating helices as single-particle-like segments followed by helical image reconstruction has become the method of choice for high-resolution structure determination of well-ordered helical viruses as well as flexible filaments. In this review, we will illustrate how the combination of latest hardware developments with optimized image processing routines have led to a series of near-atomic resolution structures of helical assemblies. Originally, the treatment of helices as a sequence of segments followed by Fourier-Bessel reconstruction revealed the potential to determine near-atomic resolution structures from helical specimens. In the meantime, real-space image processing of helices in a stack of single particles was developed and enabled the structure determination of specimens that resisted classical Fourier helical reconstruction and also facilitated high-resolution structure determination. Despite the progress in real-space analysis, the combination of Fourier and real-space processing is still commonly used to better estimate the symmetry parameters as the imposition of the correct helical symmetry is essential for high-resolution structure determination. Recent hardware advancement by the introduction of direct electron detectors has significantly enhanced the image quality and together with improved image processing procedures has made segmented helical reconstruction a very productive cryo-EM structure determination method. © 2016 Elsevier Inc. All rights reserved.

  4. Hydrodynamic studies of CNT nanofluids in helical coil heat exchanger

    Babita; Sharma, S. K.; Mital Gupta, Shipra; Kumar, Arinjay

    2017-12-01

    Helical coils are extensively used in several industrial processes such as refrigeration systems, chemical reactors, recovery processes etc to accommodate a large heat transfer area within a smaller space. Nanofluids are getting great attention due to their enhanced heat transfer capability. In heat transfer equipments, pressure drop is one of the major factors of consideration for pumping power calculations. So, the present work is aimed to study hydrodynamics of CNT nanofluids in helical coils. In this study, pressure drop characteristics of CNT nanofluid flowing inside horizontal helical coils are investigated experimentally. The helical coil to tube diameter was varied from 11.71 to 27.34 keeping pitch of the helical coil constant. Double distilled water was used as basefluid. SDBS and GA surfactants were added to stablilize CNT nanofluids. The volumetric fraction of CNT nanofluid was varied from 0.003 vol% to 0.051 vol%. From the experimental data, it was analyzed that the friction factor in helical coils is greater than that of straight tubes. Concentration of CNT in nanofluids also has a significant influence on the pressure drop/friction factor of helical coils. At a constant concentration of CNT, decreasing helical coil to tube diameter from 27.24 to 11.71, fanning friction factor of helical coil; f c increases for a constant value of p/d t. This increase in the value of fanning friction factor can be attributed to the secondary flow of CNT nanofluid in helical coils.

  5. Reverse engineering truncations of an antimicrobial peptide dimer to identify the origins of potency and broad spectrum of action.

    Anantharaman, Aparna; Sahal, Dinkar

    2010-08-26

    Antimicrobial peptides hold promise against antibiotic resistant pathogens. Here, to find the physicochemical origins of potency and broad spectrum antimicrobial action, we report the structure-activity relationships of synthetic intermediates (peptides A-D) of a potent lysine branched dimeric antibacterial peptide DeltaFd. Our studies show that a tetracationic character in a weak helical fold (peptide C) elicits potent but narrow spectrum antimicrobial activity [Minimum inhibitory concentrations (MICs) E. coli 10 microM, S. aureus>100 microM]. In contrast, a hexacationic character in a strong, amphipathic helix (DeltaFd) confers potent and broad spectrum action [MICs E. coli 2.5 microM, S. aureus 5 microM]. While DeltaFd caused rapid and potent permeabilization of the E. coli membranes, the less helical intermediates (peptides A-D) showed slow and weak to no responses. Two seminal findings that may aid future drug design are (a) at identical helicity, increasing charge enhanced outer membrane permeabilization, and (b) at identical charge, increasing helicity stimulated rate of outer membrane permeabilization and kill kinetics besides enhancing potency leading to broad spectrum action.

  6. Stabilization of magnetohydrodynamic instabilities in a current-carrying stellarator

    Matsuoka, K.; Miyamoto, K.

    1979-02-01

    Stable profiles against MHD instabilities are given in a cylindrical current-carrying stellarator. The comparison theorem, i.e., guiding principle for stabilization, is obtained in the same way as in a tokamak. As the external rotational transform due to an l = 2 helical field increases, MHD properties in a stellarator are improved than in a tokamak and the minimum value of q(a) which provides simultaneous stabilization of MHD modes can be lowered less than 2 even without a conducting shell. In an l = 3 stellarator, however, as shown from the Euler equation, the configuration becomes more unstable than in a tokamak and strong tailoring of the current profile is necessary in order to stabilize MHD modes. (author)

  7. Induction of a peptide with activity against a broad spectrum of pathogens in the Aedes aegypti salivary gland, following Infection with Dengue Virus.

    Natthanej Luplertlop

    2011-01-01

    Full Text Available The ultimate stage of the transmission of Dengue Virus (DENV to man is strongly dependent on crosstalk between the virus and the immune system of its vector Aedes aegypti (Ae. aegypti. Infection of the mosquito's salivary glands by DENV is the final step prior to viral transmission. Therefore, in the present study, we have determined the modulatory effects of DENV infection on the immune response in this organ by carrying out a functional genomic analysis of uninfected salivary glands and salivary glands of female Ae. aegypti mosquitoes infected with DENV. We have shown that DENV infection of salivary glands strongly up-regulates the expression of genes that encode proteins involved in the vector's innate immune response, including the immune deficiency (IMD and Toll signalling pathways, and that it induces the expression of the gene encoding a putative anti-bacterial, cecropin-like, peptide (AAEL000598. Both the chemically synthesized non-cleaved, signal peptide-containing gene product of AAEL000598, and the cleaved, mature form, were found to exert, in addition to antibacterial activity, anti-DENV and anti-Chikungunya viral activity. However, in contrast to the mature form, the immature cecropin peptide was far more effective against Chikungunya virus (CHIKV and, furthermore, had strong anti-parasite activity as shown by its ability to kill Leishmania spp. Results from circular dichroism analysis showed that the immature form more readily adopts a helical conformation which would help it to cause membrane permeabilization, thus permitting its transfer across hydrophobic cell surfaces, which may explain the difference in the anti-pathogenic activity between the two forms. The present study underscores not only the importance of DENV-induced cecropin in the innate immune response of Ae. aegypti, but also emphasizes the broad-spectrum anti-pathogenic activity of the immature, signal peptide-containing form of this peptide.

  8. Helical muon beam cooling channel engineering design

    Johnson, Rolland

    2015-01-01

    The Helical Cooling Channel (HCC) achieves effective ionization cooling of the six-dimensional (6d) phase space of a muon beam by means of a series of 21st century inventions. In the HCC, hydrogen-pressurized RF cavities enable high RF gradients in strong external magnetic fields. The theory of the HCC, which requires a magnetic field with solenoid, helical dipole, and helical quadrupole components, demonstrates that dispersion in the gaseous hydrogen energy absorber provides effective emittance exchange to enable longitudinal ionization cooling. The 10-year development of a practical implementation of a muon-beam cooling device has involved a series of technical innovations and experiments that imply that an HCC of less than 300 m length can cool the 6d emittance of a muon beam by six orders of magnitude. We describe the design and construction plans for a prototype HCC module based on oxygen-doped hydrogen-pressurized RF cavities that are loaded with dielectric, fed by magnetrons, and operate in a superconducting helical solenoid magnet. The first phase of this project saw the development of a conceptual design for the integration of 805 MHz RF cavities into a 10 T Nb 3 Sn-based HS test section. Two very novel ideas are required to realize the design. The first idea is the use of dielectric inserts in the RF cavities to make them smaller for a given frequency so that the cavities and associated plumbing easily fit inside the magnet cryostat. Calculations indicate that heat loads will be tolerable, while RF breakdown of the dielectric inserts will be suppressed by the pressurized hydrogen gas. The second new idea is the use of a multi-layer Nb 3 Sn helical solenoid. The technology demonstrations for the two aforementioned key components of a 10T, 805 MHz HCC were begun in this project. The work load in the Fermilab Technical Division made it difficult to test a multi-layer Nb 3 Sn solenoid as originally planned. Instead, a complementary project was approved by the

  9. Helical muon beam cooling channel engineering design

    Johnson, Rolland [Muons, Inc., Batavia, IL (United States)

    2015-08-07

    The Helical Cooling Channel (HCC) achieves effective ionization cooling of the six-dimensional (6d) phase space of a muon beam by means of a series of 21st century inventions. In the HCC, hydrogen-pressurized RF cavities enable high RF gradients in strong external magnetic fields. The theory of the HCC, which requires a magnetic field with solenoid, helical dipole, and helical quadrupole components, demonstrates that dispersion in the gaseous hydrogen energy absorber provides effective emittance exchange to enable longitudinal ionization cooling. The 10-year development of a practical implementation of a muon-beam cooling device has involved a series of technical innovations and experiments that imply that an HCC of less than 300 m length can cool the 6d emittance of a muon beam by six orders of magnitude. We describe the design and construction plans for a prototype HCC module based on oxygen-doped hydrogen-pressurized RF cavities that are loaded with dielectric, fed by magnetrons, and operate in a superconducting helical solenoid magnet. The first phase of this project saw the development of a conceptual design for the integration of 805 MHz RF cavities into a 10 T Nb3Sn-based HS test section. Two very novel ideas are required to realize the design. The first idea is the use of dielectric inserts in the RF cavities to make them smaller for a given frequency so that the cavities and associated plumbing easily fit inside the magnet cryostat. Calculations indicate that heat loads will be tolerable, while RF breakdown of the dielectric inserts will be suppressed by the pressurized hydrogen gas. The second new idea is the use of a multi-layer Nb3Sn helical solenoid. The technology demonstrations for the two aforementioned key components of a 10T, 805 MHz HCC were begun in this project. The work load in the Fermilab Technical Division made it difficult to test a multi-layer Nb3Sn solenoid as originally planned. Instead, a complementary

  10. Conformational study of melectin and antapin antimicrobial peptides in model membrane environments

    Kocourková, Lucie; Novotná, Pavlína; Čujová, Sabína; Čeřovský, Václav; Urbanová, Marie; Setnička, Vladimír

    2017-01-01

    Antimicrobial peptides have long been considered as promising compounds against drug-resistant pathogens. In this work, we studied the secondary structure of antimicrobial peptides melectin and antapin using electronic (ECD) and vibrational circular dichroism (VCD) spectroscopies that are sensitive to peptide secondary structures. The results from quantitative ECD spectral evaluation by Dichroweb and CDNN program and from the qualitative evaluation of the VCD spectra were compared. The antimicrobial activity of the selected peptides depends on their ability to adopt an amphipathic α-helical conformation on the surface of the bacterial membrane. Hence, solutions of different zwitterionic and negatively charged liposomes and micelles were used to mimic the eukaryotic and bacterial biological membranes. The results show a significant content of α-helical conformation in the solutions of negatively charged liposomes mimicking the bacterial membrane, thus correlating with the antimicrobial activity of the studied peptides. On the other hand in the solutions of zwitterionic liposomes used as models of the eukaryotic membranes, the fraction of α-helical conformation was lower, which corresponds with their moderate hemolytic activity.

  11. System assessment of helical reactors in comparison with tokamaks

    Yamazaki, K.; Imagawa, S.; Muroga, T.; Sagara, A.; Okamura, S.

    2002-10-01

    A comparative assessment of tokamak and helical reactors has been performed using equivalent physics/engineering model and common costing model. Higher-temperature plasma operation is required in tokamak reactors to increase bootstrap current fraction and to reduce current-drive (CD) power. In helical systems, lower-temperature operation is feasible and desirable to reduce helical ripple transport. The capital cost of helical reactor is rather high, however, the cost of electricity (COE) is almost same as that of tokamak reactor because of smaller re-circulation power (no CD power) and less-frequent blanket replacement (lower neutron wall loading). The standard LHD-type helical reactor with 5% beta value is economically equivalent to the standard tokamak with 3% beta. The COE of lower-aspect ratio helical reactor is on the same level of high-β N tokamak reactors. (author)

  12. Ultrasmall Peptides Self-Assemble into Diverse Nanostructures: Morphological Evaluation and Potential Implications

    Charlotte A.E. Hauser

    2011-09-01

    Full Text Available In this study, we perform a morphological evaluation of the diverse nanostructures formed by varying concentration and amino acid sequence of a unique class of ultrasmall self-assembling peptides. We modified these peptides by replacing the aliphatic amino acid at the C-aliphatic terminus with different aromatic amino acids. We tracked the effect of introducing aromatic residues on self-assembly and morphology of resulting nanostructures. Whereas aliphatic peptides formed long, helical fibers that entangle into meshes and entrap >99.9% water, the modified peptides contrastingly formed short, straight fibers with a flat morphology. No helical fibers were observed for the modified peptides. For the aliphatic peptides at low concentrations, different supramolecular assemblies such as hollow nanospheres and membrane blebs were found. Since the ultrasmall peptides are made of simple, aliphatic amino acids, considered to have existed in the primordial soup, study of these supramolecular assemblies could be relevant to understanding chemical evolution leading to the origin of life on Earth. In particular, we propose a variety of potential applications in bioengineering and nanotechnology for the diverse self-assembled nanostructures.

  13. A distributive peptide cyclase processes multiple microviridin core peptides within a single polypeptide substrate.

    Zhang, Yi; Li, Kunhua; Yang, Guang; McBride, Joshua L; Bruner, Steven D; Ding, Yousong

    2018-05-03

    Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important family of natural products. Their biosynthesis follows a common scheme in which the leader peptide of a precursor peptide guides the modifications of a single core peptide. Here we describe biochemical studies of the processing of multiple core peptides within a precursor peptide, rare in RiPP biosynthesis. In a cyanobacterial microviridin pathway, an ATP-grasp ligase, AMdnC, installs up to two macrolactones on each of the three core peptides within AMdnA. The enzyme catalysis occurs in a distributive fashion and follows an unstrict N-to-C overall directionality, but a strict order in macrolactonizing each core peptide. Furthermore, AMdnC is catalytically versatile to process unnatural substrates carrying one to four core peptides, and kinetic studies provide insights into its catalytic properties. Collectively, our results reveal a distinct biosynthetic logic of RiPPs, opening up the possibility of modular production via synthetic biology approaches.

  14. Structural similarity between β(3)-peptides synthesized from β(3)-homo-amino acids and aspartic acid monomers.

    Ahmed, Sahar; Sprules, Tara; Kaur, Kamaljit

    2014-07-01

    Formation of stable secondary structures by oligomers that mimic natural peptides is a key asset for enhanced biological response. Here we show that oligomeric β(3)-hexapeptides synthesized from L-aspartic acid monomers (β(3)-peptides 1, 5a, and 6) or homologated β(3)-amino acids (β(3)-peptide 2), fold into similar stable 14-helical secondary structures in solution, except that the former form right-handed 14-helix and the later form left-handed 14-helix. β(3)-Peptides from L-Asp monomers contain an additional amide bond in the side chains that provides opportunities for more hydrogen bonding. However, based on the NMR solution structures, we found that β(3)-peptide from L-Asp monomers (1) and from homologated amino acids (2) form similar structures with no additional side-chain interactions. These results suggest that the β(3)-peptides derived from L-Asp are promising peptide-mimetics that can be readily synthesized using L-Asp monomers as well as the right-handed 14-helical conformation of these β(3)-peptides (such as 1 and 6) may prove beneficial in the design of mimics for right-handed α-helix of α-peptides. © 2014 Wiley Periodicals, Inc.

  15. PeptideAtlas

    U.S. Department of Health & Human Services — PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass...

  16. Gating-by-rotation: a solution to the problem of intratreatment motion in helical tomotherapy

    Kapatoes, J.M.; Olivera, G.H.; Schloesser, E.A.; Pearson, D.W.; Balog, J.P.; Ruchala, K.J.; Schmidt, R.; Reckwerdt, P.J.; Mehta, M.P.; Mackie, T.R.

    2001-01-01

    Purpose: To assess the feasibility of addressing intratreatment motion issues in helical tomotherapy by gating the treatments by rotation. Intratreatment motion is a problem common to all IMRT techniques. Traditional methods of gating in conformal radiotherapy and some forms of IMRT are not applicable to helical tomotherapy due to the continuous rotation of the gantry. An alternative method is presented. Materials and Methods: Rotation-gating in helical tomotherapy is the process in which one rotation of treatment is immediately followed by a rotation of non-treatment. This on-off strategy is repeated for the full treatment volume. During the treatment rotations, the patient is required to hold their breath while the intensity-modulated fan beam deposits dose. For the non-treatment rotations, the patient is allowed to breathe freely as all leaves of the MLC will be closed, the accelerator disabled, or both. The couch indexes normally for treatment rotations and holds the patient stationary during non-treatment rotations. An investigation was conducted to assess the feasibility of rotation-gating. Film was placed between two hemispheres of a water phantom and a continuous helical delivery was carried out with all leaves opened. The film was replaced and another treatment was performed employing rotation-gating. The two films were compared to assess the process. The films were irradiated to dose levels within the linear region of the film response curve (maximum film dose ∼35 cGy). Films were also acquired with all leaves closed to quantify leakage dose through the collimation systems. Results: Central profiles for the inferior-superior direction (parallel to the direction of translation) for both films are displayed in Figure 1. The profiles agree very well, illustrating that a rotation-gated treatment closely mimics a continuous helical delivery. The only significant discrepancy lay in the tails of the profiles: a higher film dose is seen for the rotation

  17. Alteration of helical vortex core without change in flow topology

    Velte, Clara Marika; Okulov, Valery; Hansen, Martin Otto Laver

    2011-01-01

    topology. The helical symmetry as such is preserved, although the characteristic parameters of helical symmetry of the vortex core transfer from a smooth linear variation to a different trend under the influence of a non-uniform pressure gradient, causing an increase in helical pitch without changing its......The abrupt expansion of the slender vortex core with changes in flow topology is commonly known as vortex breakdown. We present new experimental observations of an alteration of the helical vortex core in wall bounded turbulent flow with abrupt growth in core size, but without change in flow...

  18. Helicity conservation under quantum reconnection of vortex rings.

    Zuccher, Simone; Ricca, Renzo L

    2015-12-01

    Here we show that under quantum reconnection, simulated by using the three-dimensional Gross-Pitaevskii equation, self-helicity of a system of two interacting vortex rings remains conserved. By resolving the fine structure of the vortex cores, we demonstrate that the total length of the vortex system reaches a maximum at the reconnection time, while both writhe helicity and twist helicity remain separately unchanged throughout the process. Self-helicity is computed by two independent methods, and topological information is based on the extraction and analysis of geometric quantities such as writhe, total torsion, and intrinsic twist of the reconnecting vortex rings.

  19. Superposition of helical beams by using a Michelson interferometer.

    Gao, Chunqing; Qi, Xiaoqing; Liu, Yidong; Weber, Horst

    2010-01-04

    Orbital angular momentum (OAM) of a helical beam is of great interests in the high density optical communication due to its infinite number of eigen-states. In this paper, an experimental setup is realized to the information encoding and decoding on the OAM eigen-states. A hologram designed by the iterative method is used to generate the helical beams, and a Michelson interferometer with two Porro prisms is used for the superposition of two helical beams. The experimental results of the collinear superposition of helical beams and their OAM eigen-states detection are presented.

  20. Progress with helicity injection current drive

    Jarboe, T.R.; Raman, R.; Nelson, B.A.

    2003-01-01

    Coaxial Helicity Injection (CHI) experiments in the NSTX and HIT-II devices are reported. NSTX has produced toroidal currents of 0.4 MA and pulse lengths of up to 0.33 s. These discharges nearly fill the NSTX main chamber, and show the n=1 rotating distortion characteristic of high-performance CHI plasmas. CHI has been used in HIT-II to provide a closed flux startup plasma for inductive drive. The CHI startup method saves transformer volt-seconds and greatly improves reproducibility and reliability of inductively driven discharges, even in the presence of diminishing wall conditions. (author)

  1. Heat loss by helicity injection in spheromaks

    Fowler, T.K.

    1994-01-01

    A model is presented for spheromak buildup and decay including thermal diffusivity associated with magnetic turbulence during helicity injection. It is shown that heat loss by magnetic turbulence scales more favorably than gyroBohm transport. Thus gyroBohm scaling for the proposed ignition experiment would be the conservative choice, though present experiments may be dominated by magnetic turbulence. Because of a change in boundary conditions when the gun is turned off, the model may account for the observed increase in electron temperature in CTX after turnoff

  2. Rotation influence on the plasma helical instability

    Gutkin, T.I.; Tsypin, V.S.; Boleslavskaya, G.I.

    1980-01-01

    The influence of the rotation on helical instability of a plasma with the fixed boundaries (HIFB) is investigated taking into account the compressibility. A case of infinitely long cylinder with distributed current is considered. Cases when a rotating plasma is confined by current magnetic field are analytically considered. It is shown that in the case of the fixed boundary taking into account the compressibility in the HIFB increment increases and the picture of the rotation influence on HIFB considerably changes. Besides, it is shown that in the case of high plasma pressures HIFB can stabilize as a result of the rotation

  3. A Dual-Purpose Linker for Alpha Helix Stabilization and Imaging Agent Conjugation to Glucagon-Like Peptide-1 Receptor Ligands

    Zhang, Liang; Navaratna, Tejas; Liao, Jianshan; Thurber, Greg M.

    2016-01-01

    Peptides display many characteristics of efficient imaging agents such as rapid targeting, fast background clearance, and low non-specific cellular uptake. However, poor stability, low affinity, and loss of binding after labeling often preclude their use in vivo. Using the glucagon-like peptide-1 receptor (GLP-1R) ligands exendin and GLP-1 as a model system, we designed a novel alpha helix stabilizing linker to simultaneously address these limitations. The stabilized and labeled peptides showed an increase in helicity, improved protease resistance, negligible loss or an improvement in binding affinity, and excellent in vivo targeting. The ease of incorporating azidohomoalanine in peptides and efficient reaction with the dialkyne linker enables this technique to potentially be used as a general method for labeling alpha helices. This strategy should be useful for imaging beta cells in diabetes research and in developing and testing other peptide targeting agents. PMID:25594741

  4. Peptide-Carrier Conjugation

    Hansen, Paul Robert

    2015-01-01

    To produce antibodies against synthetic peptides it is necessary to couple them to a protein carrier. This chapter provides a nonspecialist overview of peptide-carrier conjugation. Furthermore, a protocol for coupling cysteine-containing peptides to bovine serum albumin is outlined....

  5. PH dependent adhesive peptides

    Tomich, John; Iwamoto, Takeo; Shen, Xinchun; Sun, Xiuzhi Susan

    2010-06-29

    A novel peptide adhesive motif is described that requires no receptor or cross-links to achieve maximal adhesive strength. Several peptides with different degrees of adhesive strength have been designed and synthesized using solid phase chemistries. All peptides contain a common hydrophobic core sequence flanked by positively or negatively charged amino acids sequences.

  6. Peptide Nucleic Acids

    2003-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary ssDNA and RNA strands more strongly than a corresponding DNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker....

  7. Peptide Nucleic Acids

    1998-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary ssDNA and RNA strands more strongly than a corresponding DNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker....

  8. Peptide Nucleic Acids (PNA)

    2002-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary ssDNA and RNA strands more strongly than a corresponding DNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker....

  9. Peptide Nucleic Acid Synthons

    2004-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary ssDNA and RNA strands more strongly than a corresponding DNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker....

  10. Antimicrobial Peptides in 2014

    Guangshun Wang

    2015-03-01

    Full Text Available This article highlights new members, novel mechanisms of action, new functions, and interesting applications of antimicrobial peptides reported in 2014. As of December 2014, over 100 new peptides were registered into the Antimicrobial Peptide Database, increasing the total number of entries to 2493. Unique antimicrobial peptides have been identified from marine bacteria, fungi, and plants. Environmental conditions clearly influence peptide activity or function. Human α-defensin HD-6 is only antimicrobial under reduced conditions. The pH-dependent oligomerization of human cathelicidin LL-37 is linked to double-stranded RNA delivery to endosomes, where the acidic pH triggers the dissociation of the peptide aggregate to release its cargo. Proline-rich peptides, previously known to bind to heat shock proteins, are shown to inhibit protein synthesis. A model antimicrobial peptide is demonstrated to have multiple hits on bacteria, including surface protein delocalization. While cell surface modification to decrease cationic peptide binding is a recognized resistance mechanism for pathogenic bacteria, it is also used as a survival strategy for commensal bacteria. The year 2014 also witnessed continued efforts in exploiting potential applications of antimicrobial peptides. We highlight 3D structure-based design of peptide antimicrobials and vaccines, surface coating, delivery systems, and microbial detection devices involving antimicrobial peptides. The 2014 results also support that combination therapy is preferred over monotherapy in treating biofilms.

  11. Electronic transport in single-helical protein molecules: Effects of multiple charge conduction pathways and helical symmetry

    Kundu, Sourav, E-mail: sourav.kunduphy@gmail.com; Karmakar, S.N.

    2016-07-15

    We propose a tight-binding model to investigate electronic transport properties of single helical protein molecules incorporating both the helical symmetry and the possibility of multiple charge transfer pathways. Our study reveals that due to existence of both the multiple charge transfer pathways and helical symmetry, the transport properties are quite rigid under influence of environmental fluctuations which indicates that these biomolecules can serve as better alternatives in nanoelectronic devices than its other biological counterparts e.g., single-stranded DNA.

  12. Non-inductive current drive via helicity injection by Alfven waves in low aspects ratio Tokamak

    Cuperman, S.; Bruma, C.; Komoshvili, K.

    1996-01-01

    A theoretical investigation of radio frequency (RF) current drive via helicity injection in low aspect ratio tokamaks was carried out. A current-carrying cylindrical plasma surrounded by a helical sheet-current antenna and situated inside a perfectly conducting shell was considered. Toroidal features of low aspect ratio tokamaks were simulated by incorporation of the following effects: (i) arbitrarily small aspect ratio, R o /a ≡ 1/ε (ii) strongly sheared equilibrium magnetic field; and (iii) relatively large poloidal component of the equilibrium magnetic field. The study concentrates on the Alfven continuum, i.e. the case in which the wave frequency satisfies the condition {ω Alf (r)} min ≤ω≥{ω Alf (r)} max , where ω Alf (r)≡ω[n(r),B o (o)] is an eigenfrequency of the shear Alfven wave (SAW). Thus, using low-p, ideal magneto-hydrodynamics, the wave equation with correct boundary (matching) conditions was solved, the RF field components were found and subsequently, current drive , power deposition and efficiency were computed. The results of our investigation clearly demonstrate the possibility of generation of RF-driven currents via helicity injection by Alfven waves in low aspect ratio tokamaks, in the SAW mode. A special algorithm was developed which enables the selection of the antenna parameters providing optimal current drive efficiency. (authors)

  13. Antimicrobial peptides from the skins of North American frogs.

    Conlon, J Michael; Kolodziejek, Jolanta; Nowotny, Norbert

    2009-08-01

    North America is home to anuran species belonging to the families Bufonidae, Eleutherodactylidae, Hylidae, Leiopelmatidae, Ranidae, and Scaphiopodidae but antimicrobial peptides have been identified only in skin secretions and/or skin extracts of frogs belonging to the Leiopelmatidae ("tailed frogs") and Ranidae ("true frogs"). Eight structurally-related cationic alpha-helical peptides with broad-spectrum antibacterial activity, termed ascaphins, have been isolated from specimens of Ascaphus truei (Leiopelmatidae) occupying a coastal range. Characterization of orthologous antimicrobial peptides from Ascaphus specimens occupying an inland range supports the proposal that this population should be regarded as a separate species A. montanus. Ascaphin-8 shows potential for development into a therapeutically valuable anti-infective agent. Peptides belonging to the brevinin-1, esculentin-1, esculentin-2, palustrin-1, palustrin-2, ranacyclin, ranatuerin-1, ranatuerin-2, and temporin families have been isolated from North American ranids. It is proposed that "ranalexins" represent brevinin-1 peptides that have undergone a four amino acid residue internal deletion. Current taxonomic recommendations divide North American frogs from the family Ranidae into two genera: Lithobates and Rana. Cladistic analysis based upon the amino acid sequences of the brevinin-1 peptides provides strong support for this assignment.

  14. Splitting of α-Helical Structure as Molecular Basis for Abolishing an Amyloid Formation by Multiple Glycosylation: A Molecular Dynamics Simulation Study

    Choi, Youngjin [Hoseo University, Asan (Korea, Republic of); Cho, Eunae; Jung, Seunho [Konkuk University, Seoul (Korea, Republic of)

    2016-07-15

    Molecular details played by glycosylation are complicated by the subtle nature of variations in the glycan structure, and this complexity is one of the research barriers to establish structure-function relationship on the protein modification. This is particularly true for understanding the exact structural consequence of the glycosylation of the biological proteins. The present MD simulation revealed molecular-level mechanism of the glycosylation effect on the peptide to understand the experimentally observed phenomenon for inhibiting amyloid formation in the model peptide. The galactose residue on the Ser17 undermined the helical integrity of main protein region by enhancing sugar–amino acid interaction and perturbing natural interactions between amino acid residues.

  15. Membrane interactions and biological activity of antimicrobial peptides from Australian scorpion.

    Luna-Ramírez, Karen; Sani, Marc-Antoine; Silva-Sanchez, Jesus; Jiménez-Vargas, Juana María; Reyna-Flores, Fernando; Winkel, Kenneth D; Wright, Christine E; Possani, Lourival D; Separovic, Frances

    2014-09-01

    UyCT peptides are antimicrobial peptides isolated from the venom of the Australian scorpion. The activity of the UyCT peptides against Gram positive and Gram negative bacteria and red blood cells was determined. The membrane interactions of these peptides were evaluated by dye release (DR) of the fluorophore calcein from liposomes and isothermal titration calorimetry (ITC); and their secondary structure was determined by circular dichroism (CD). Three different lipid systems were used to mimic red blood cells, Escherichia coli and Staphylococcus aureus membranes. UyCT peptides exhibited broad spectrum antimicrobial activity with low MIC for S. aureus and multi-drug resistant Gram negative strains. Peptide combinations showed some synergy enhancing their potency but not hemolytic activity. The UyCT peptides adopted a helical structure in lipid environments and DR results confirmed that the mechanism of action is by disrupting the membrane. ITC data indicated that UyCT peptides preferred prokaryotic rather than eukaryotic membranes. The overall results suggest that UyCT peptides could be pharmaceutical leads for the treatment of Gram negative multiresistant bacterial infections, especially against Acinetobacter baumanni, and candidates for peptidomimetics to enhance their potency and minimize hemolysis. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova. © 2013.

  16. The design construction and installation of the helical winding for the CLEO stellarator

    Hunt, R.R.; Bayes, D.V.

    1979-03-01

    The CLEO stellarator has a torus 900mm major radius and 166mm minor radius, fitted externally with a 7 field period, l = 3, 120kAT helical winding of 179mm mean radius. The winding and torus have to withstand the large forces produced by the interaction of the current flowing in the winding with the toroidal magnetic field of 2 tesla produced by 24 coils spaced around the torus. To allow the torus to be divided the winding has to be split requiring a total of 240 demountable current-carrying joints at the torus vacuum joint positions. The design, development, manufacture, installation and operation of the helical winding is discussed. From the early development stages to installation took four years. When completed this was the largest installation of its type in Europe. (author)

  17. Investigation of Horizontal Velocity Fields in Stirred Vessels with Helical Coils by PIV

    Volker Bliem

    2014-01-01

    Full Text Available Horizontal velocity flow fields were measured by particle image velocimetry for a stirred vessel with baffles and two helical coils for enlargement of heat transfer area. The investigation was carried out in a cylindrical vessel with flat base and two different stirrers (radial-flow Rushton turbine and axial-flow propeller stirrer. Combined velocity plots for flow fields at different locations are presented. It was found that helical coils change the flow pattern significantly. Measurements for the axial-flow Rushton turbine showed a strong deflection by the coils, leading to a mainly tangential flow pattern. Behind baffles large areas of unused heat transfer area were found. First results for the axial-flow propeller reveal an extensive absence of fluid movement in the horizontal plane. Improved design considerations for enhanced heat transfer by more compatible equipment compilation are proposed.

  18. Observation of helical structure in a low energy plasma focus pinch

    Rout, R.K.; Shyam, A.

    1989-01-01

    Helical structure and hot spots were observed in a Mather-type plasma focus operated at 3 KJ of bank energy. The experiments were carried out with the help of a fast optical framing camera and two X-ray pin-hole cameras with different filters. It was observed that initially a conical pinch (with base diameter of 6 mm and length of 14 mm) with temperature of ≅ 10 2 eV was formed. This pinch disintegrated after ≅ 50 ns by a single lobe sausage instability into a central high temperature (≅ 10 3 eV) filament of 1 mm diameter and 8 mm length containing a high emissivity helical structure. This helix is probably responsible for generation of axial magnetic field and relaxation of the focus pinch. Hot spots of high X-ray intensity and temperature (≅ 10 3 eV) were also observed much beyond the filament region. (author)

  19. A self-biased 3D tunable helical antenna in ferrite LTCC substrate

    Ghaffar, Farhan A.; Shamim, Atif

    2015-01-01

    A ferrite LTCC based helical antenna which also provides magneto-static bias for its frequency tuning is presented in this work. The 3D helical-cum-bias winding design avoids the use of large external electromagnets which are traditionally used with ferrite based tunable antennas. This reduces the overall size of the design while making it efficient by getting rid of demagnetization effect experienced at the air-to-ferrite interface. RF choke and DC blocking capacitor, required to isolate the RF and DC passing through a single structure, are integrated within the multi-layer Ferrite LTCC substrate. Magnetostatic and microwave simulations have been carried out for the design optimization. The prototype antenna demonstrates a tuning range of 10 % around 13 GHz. An optimized design with an air cavity is also presented which reduces the biasing power requirement by 40 %.

  20. A self-biased 3D tunable helical antenna in ferrite LTCC substrate

    Ghaffar, Farhan A.

    2015-07-19

    A ferrite LTCC based helical antenna which also provides magneto-static bias for its frequency tuning is presented in this work. The 3D helical-cum-bias winding design avoids the use of large external electromagnets which are traditionally used with ferrite based tunable antennas. This reduces the overall size of the design while making it efficient by getting rid of demagnetization effect experienced at the air-to-ferrite interface. RF choke and DC blocking capacitor, required to isolate the RF and DC passing through a single structure, are integrated within the multi-layer Ferrite LTCC substrate. Magnetostatic and microwave simulations have been carried out for the design optimization. The prototype antenna demonstrates a tuning range of 10 % around 13 GHz. An optimized design with an air cavity is also presented which reduces the biasing power requirement by 40 %.

  1. CURRENT AND KINETIC HELICITY OF LONG-LIVED ACTIVITY COMPLEXES

    Komm, Rudolf; Gosain, Sanjay

    2015-01-01

    We study long-lived activity complexes and their current helicity at the solar surface and their kinetic helicity below the surface. The current helicity has been determined from synoptic vector magnetograms from the NSO/SOLIS facility, and the kinetic helicity of subsurface flows has been determined with ring-diagram analysis applied to full-disk Dopplergrams from NSO/GONG and SDO/HMI. Current and kinetic helicity of activity complexes follow the hemispheric helicity rule with mainly positive values (78%; 78%, respectively, with a 95% confidence level of 31%) in the southern hemisphere and negative ones (80%; 93%, respectively, with a 95% confidence level of 22% and 14%, respectively) in the northern hemisphere. The locations with the dominant sign of kinetic helicity derived from Global Oscillation Network Group (GONG) and SDO/HMI data are more organized than those of the secondary sign even if they are not part of an activity complex, while locations with the secondary sign are more fragmented. This is the case for both hemispheres even for the northern one where it is not as obvious visually due to the large amount of magnetic activity present as compared to the southern hemisphere. The current helicity shows a similar behavior. The dominant sign of current helicity is the same as that of kinetic helicity for the majority of the activity complexes (83% with a 95% confidence level of 15%). During the 24 Carrington rotations analyzed here, there is at least one longitude in each hemisphere where activity complexes occur repeatedly throughout the epoch. These ''active'' longitudes are identifiable as locations of strong current and kinetic helicity of the same sign

  2. Neutrino helicity flips via electroweak interactions

    Gaemers, K.J.F.; Gandhi, R.; Lattimer, J.M.; Department of Earth and Space Sciences, State University of New York, Stony Brook, New York 11794)

    1989-01-01

    Electroweak mechanisms via which neutrinos may flip helicity are examined in detail. Exact and approximate expressions for a variety of flip processes relevant in astrophysics and cosmology, mediated by W, Z, and γ exchange, including their interference, are derived for both Dirac and Majorana neutrinos (with emphasis on the former). It is shown that in general flip and nonflip cross sections differ by more than just a multiplicative factor of m/sub ν/ 2 /4E/sub ν/ 2 contrary to what might be expected and that this additional dependence on helicities can be significant. It is also shown that within the context of the standard model with massive neutrinos, for νe yields νe scattering, σ/sub Z//sup flip//σ/sub γ//sup flip/ ∼ 10 4 , independent of particle masses and energies to a good approximation. As an application, using some general considerations and the fact that the observed bar nu/sub e/ burst from SN 1987A lasted several seconds, these weak-interaction flip cross sections are used to rule out μ and tau neutrino masses above 30 keV. Finally, some other consequences for astrophysics in general and supernovae in particular are briefly discussed

  3. Helical type thermonuclear device and control method

    Ishigaki, Yukio.

    1990-01-01

    In a conventional helical type thermonuclear device, electric current flows in the toroidal direction under magnetic fields of helical coils and vertical magnetic coils, by which a circulating electric field is caused. Therefore, there is a problem that electrons as a seed are generated by cosmic rays, etc., the electrons are confined in a magnetic field boundary, are accelerated by the circulating electric field, to reach a high energy level, collide against structures in a vacuum vessel and emit a great amount of X-rays. Then, compensation coils for offsetting the magnetic fields generated upon energization and deenergization of the vertical magnetic coils and the power source therefor are disposed at the positions opposing to each other on both sides of the vertical magnetic coils for controlling the variation coefficient rate of electric current upon energization and deenergization of the vertical magnetic coils. Since the compensation coils also offset the magnetic field generated upon energization and deenergization of the vertical magnetic field coils by this control, the circulating magnetic field is not caused in the vacuum vessel to reduce the X-ray radiation by electrons at high energy level. (N.H.)

  4. Determining How Magnetic Helicity Injection Really Works

    Paul M Bellan

    2001-01-01

    OAK-B135 The goal of the Caltech program is to determine how helicity injection works by investigating the actual dynamics and topological evolution associated with magnetic relaxation. A new coaxial helicity injection source has been constructed and brought into operation. The key feature of this source is that it has maximum geometric simplicity. Besides being important for fusion research, this work also has astrophysical implications. Photos obtained using high-speed cameras show a clear sequence of events in the formation process. In particular, they show initial merging/reconnection processes, jet-like expansion, kinking, and separation of the plasma from the source. Various diagnostics have been developed, including laser induced fluorescence and soft x-ray detection using high speed diodes. Gas valves have been improved and a patent disclosure relating to puffed gas valves has been filed. Presentations on this work have been given in the form of invited talks at several university physics departments that were previously unfamiliar with laboratory plasma experiments

  5. Perspectives on confinement in helical systems

    Itoh, Kimitaka; Itoh, Sanae

    1989-01-01

    A review on recent experimental results and theoretical models on anomalous transport and density limit in toroidal helical devices is presented. Importance of transport problems is discussed. Experiments on Heliotron-E, Wendelstein-VIIA and new devices, i.e., ATF, Wendelstein-VIIAS and CHS, are reviewed and an overview on confinement property is given. From recent experimental results one sees that there are anomalous transport, which increases with temperature, and density limit, and that they limit the energy confinement time as well as the attainable beta value. The confinement characteristics of the scrape off layer plasma and loss cone loss are discussed, and perspectives on the high temperature plasma are given. These anomalous transport and density limit will be difficult obstacles in realizing a reactor grade plasma in helical systems. It is an urgent task to draw a realistic picture of the confinement based on the present data base. The relevant knowledge now would be critically essential for the successful development of the research in 1990's. (author) 102 refs

  6. Neutrino helicity reversal and fundamental symmetries

    Jentschura, U D; Wundt, B J

    2014-01-01

    A rather elusive helicity reversal occurs in a gedanken experiment in which a massive left-handed Dirac neutrino, traveling at a velocity u < c, is overtaken on a highway by a speeding vehicle (traveling at velocity v with u < v < c). Namely, after passing the neutrino, looking back, one would see a right-handed neutrino (which has never been observed in nature). The Lorentz-invariant mass of the right-handed neutrino is still the same as before the passing. The gedanken experiment thus implies the existence of right-handed, light neutrinos, which are not completely sterile. Furthermore, overtaking a bunch of massive right-handed Dirac neutrinos leads to gradual de-sterilization. We discuss the helicity reversal and the concomitant sterilization and de-sterilization mechanisms by way of an illustrative example calculation, with a special emphasis on massive Dirac and Majorana neutrinos. We contrast the formalism with a modified Dirac neutrino described by a Dirac equation with a pseudoscalar mass term proportional to the fifth current. (paper)

  7. Quality assurance of a helical tomotherapy machine

    Fenwick, J D; Tome, W A; Jaradat, H A; Hui, S K; James, J A; Balog, J P; DeSouza, C N; Lucas, D B; Olivera, G H; Mackie, T R; Paliwal, B R

    2004-01-01

    Helical tomotherapy has been developed at the University of Wisconsin, and 'Hi-Art II' clinical machines are now commercially manufactured. At the core of each machine lies a ring-gantry-mounted short linear accelerator which generates x-rays that are collimated into a fan beam of intensity-modulated radiation by a binary multileaf, the modulation being variable with gantry angle. Patients are treated lying on a couch which is translated continuously through the bore of the machine as the gantry rotates. Highly conformal dose-distributions can be delivered using this technique, which is the therapy equivalent of spiral computed tomography. The approach requires synchrony of gantry rotation, couch translation, accelerator pulsing and the opening and closing of the leaves of the binary multileaf collimator used to modulate the radiation beam. In the course of clinically implementing helical tomotherapy, we have developed a quality assurance (QA) system for our machine. The system is analogous to that recommended for conventional clinical linear accelerator QA by AAPM Task Group 40 but contains some novel components, reflecting differences between the Hi-Art devices and conventional clinical accelerators. Here the design and dosimetric characteristics of Hi-Art machines are summarized and the QA system is set out along with experimental details of its implementation. Connections between this machine-based QA work, pre-treatment patient-specific delivery QA and fraction-by-fraction dose verification are discussed

  8. Computational study of the fibril organization of polyglutamine repeats reveals a common motif identified in beta-helices.

    Zanuy, David; Gunasekaran, Kannan; Lesk, Arthur M; Nussinov, Ruth

    2006-04-21

    The formation of fibril aggregates by long polyglutamine sequences is assumed to play a major role in neurodegenerative diseases such as Huntington. Here, we model peptides rich in glutamine, through a series of molecular dynamics simulations. Starting from a rigid nanotube-like conformation, we have obtained a new conformational template that shares structural features of a tubular helix and of a beta-helix conformational organization. Our new model can be described as a super-helical arrangement of flat beta-sheet segments linked by planar turns or bends. Interestingly, our comprehensive analysis of the Protein Data Bank reveals that this is a common motif in beta-helices (termed beta-bend), although it has not been identified so far. The motif is based on the alternation of beta-sheet and helical conformation as the protein sequence is followed from the N to the C termini (beta-alpha(R)-beta-polyPro-beta). We further identify this motif in the ssNMR structure of the protofibril of the amyloidogenic peptide Abeta(1-40). The recurrence of the beta-bend suggests a general mode of connecting long parallel beta-sheet segments that would allow the growth of partially ordered fibril structures. The design allows the peptide backbone to change direction with a minimal loss of main chain hydrogen bonds. The identification of a coherent organization beyond that of the beta-sheet segments in different folds rich in parallel beta-sheets suggests a higher degree of ordered structure in protein fibrils, in agreement with their low solubility and dense molecular packing.

  9. Antimicrobial Peptides for Therapeutic Applications: A Review

    Tsogbadrakh Mishig-Ochir

    2012-10-01

    Full Text Available Antimicrobial peptides (AMPs have been considered as potential therapeutic sources of future antibiotics because of their broad-spectrum activities and different mechanisms of action compared to conventional antibiotics. Although AMPs possess considerable benefits as new generation antibiotics, their clinical and commercial development still have some limitations, such as potential toxicity, susceptibility to proteases, and high cost of peptide production. In order to overcome those obstacles, extensive efforts have been carried out. For instance, unusual amino acids or peptido-mimetics are introduced to avoid the proteolytic degradation and the design of short peptides retaining antimicrobial activities is proposed as a solution for the cost issue. In this review, we focus on small peptides, especially those with less than twelve amino acids, and provide an overview of the relationships between their three-dimensional structures and antimicrobial activities. The efforts to develop highly active AMPs with shorter sequences are also described.

  10. Possibility of simulation experiments for fast particle physics in the large helical device (LHD)

    Sato, K.N.; Murakami, S.; Nakajima, N.; Itoh, K.

    1995-01-01

    The confinement of fusion produced or high energy particles is one of the most important issues to be studied in the helical confinement system. A preliminary study has been carried out on the possibility of developing techniques for simulation experiments for the study of high energy particle physics in the Large Helical Device (LHD) project. Candidate methods have been considered as follows: (a) a high energy (∼ 3.5 MeV) He 0 beam injection method; (b) a medium energy (∼ 200 keV) H 0 beam injection method; (c) a method involving high energy tail production by an ICRF wave and/or a method of reaction rate enhancement by an ICRF wave; and (d) a method involving the combination of neutral beam injection and ICRF wave. Various features of each method have been considered. Although the high energy He 0 beam injection method has some advantages, the technique for production of this beam is extremely difficult because of the difficulties of the production of both negative helium and ground state neutral helium by neutralization. It is pointed out, on the other hand, that a wide range of simulation experiments for fast particle physics may be carried out even by the medium energy beam method, because the typical orbit deviation (e.g. equivalent super-banana size in a classical sense) can be largely controlled by controlling the magnetic field configuration in the case of a helical system, for example by shifting the magnetic axis. This is one of the unique features of a helical system in contrast to an axisymmetric system. (author). 12 refs, 6 figs, 2 tabs

  11. Membrane interaction and secondary structure of de novo designed arginine-and tryptophan peptides with dual function

    Rydberg, Hanna A.

    2012-10-01

    Cell-penetrating peptides and antimicrobial peptides are two classes of positively charged membrane active peptides with several properties in common. The challenge is to combine knowledge about the membrane interaction mechanisms and structural properties of the two classes to design peptides with membrane-specific actions, useful either as transporters of cargo or as antibacterial substances. Membrane active peptides are commonly rich in arginine and tryptophan. We have previously designed a series of arg/trp peptides and investigated how the position and number of tryptophans affect cellular uptake. Here we explore the antimicrobial properties and the interaction with lipid model membranes of these peptides, using minimal inhibitory concentrations assay (MIC), circular dichroism (CD) and linear dichroism (LD). The results show that the arg/trp peptides inhibit the growth of the two gram positive strains Staphylococcus aureus and Staphylococcus pyogenes, with some individual variations depending on the position of the tryptophans. No inhibition of the gram negative strains Proteus mirabilis or Pseudomonas aeruginosa was noticed. CD indicated that when bound to lipid vesicles one of the peptides forms an α-helical like structure, whereas the other five exhibited rather random coiled structures. LD indicated that all six peptides were somehow aligned parallel with the membrane surface. Our results do not reveal any obvious connection between membrane interaction and antimicrobial effect for the studied peptides. By contrast cell-penetrating properties can be coupled to both the secondary structure and the degree of order of the peptides. © 2012 Elsevier Inc.

  12. Targeted correction of a thalassemia-associated beta-globin mutation induced by pseudo-complementary peptide nucleic acids

    Lonkar, Pallavi; Kim, Ki-Hyun; Kuan, Jean Y

    2009-01-01

    Beta-thalassemia is a genetic disorder caused by mutations in the beta-globin gene. Triplex-forming oligonucleotides and triplex-forming peptide nucleic acids (PNAs) have been shown to stimulate recombination in mammalian cells via site-specific binding and creation of altered helical structures...

  13. Energy fluxes in helical magnetohydrodynamics and dynamo action

    ... large-scale magnetic field arising due to non-helical interactions and (2) inverse energy flux of magnetic energy caused by helical interactions. Based on our flux results, a primitive model for galactic dynamo has been constructed. Our calculations yield dynamo time-scale for a typical galaxy to be of the order of 108 years.

  14. Alpha-Effect, Current and Kinetic Helicities for Magnetically Driven ...

    tribpo

    Key words. Sun—dynamo, helicity, turbulent convection. Extended abstract. Recent numerical simulations lead to the result that turbulence is much more mag- netically driven than believed. ... positive (and negative in the northern hemisphere), this being just opposite to what occurs for the current helicity which is negative ...

  15. Space vehicle electromechanical system and helical antenna winding fixture

    Judd, Stephen; Dallmann, Nicholas; Guenther, David; Enemark, Donald; Seitz, Daniel; Martinez, John; Storms, Steven

    2017-12-26

    A space vehicle electromechanical system may employ an architecture that enables convenient and practical testing, reset, and retesting of solar panel and antenna deployment on the ground. A helical antenna winding fixture may facilitate winding and binding of the helical antenna.

  16. Low-energy properties of fractional helical Luttinger liquids

    Meng, T.; Fritz, L.|info:eu-repo/dai/nl/371569559; Schuricht, D.|info:eu-repo/dai/nl/369284690; Loss, D.

    2014-01-01

    We investigate the low-energy properties of (quasi) helical and fractional helical Luttinger liquids. In particular, we calculate the Drude peak of the optical conductivity, the density of states, as well as charge transport properties of the interacting system with and without attached Fermi liquid

  17. A helical naphthopyran dopant for photoresponsive cholesteric liquid crystals

    Kim, Yuna; Frigoli, Michel; Vanthuyne, Nicolas; Tamaoki, Nobuyuki

    2017-01-01

    The first photoresponsive cholesteric liquid crystal comprising a photoisomerizable helical naphthopyran derivative dopant and a nematic liquid crystal is reported. An unprecedented helical twisting power switching ratio of over 90% allowed us to demonstrate multi-cycle rotational motion of micro-objects by UV light irradiation.

  18. Experimental investigation of solar powered diaphragm and helical pumps

    For several years, many types of solar powered water pumping systems were evaluated, and in this paper, diaphragm and helical solar photovoltaic (PV) powered water pumping systems are discussed. Data were collected on diaphragm and helical pumps which were powered by different solar PV arrays at mul...

  19. Clicked bis-PEG-peptide conjugates for studying calmodulin-Kv7.2 channel binding.

    Bonache, M Angeles; Alaimo, Alessandro; Malo, Covadonga; Millet, Oscar; Villarroel, Alvaro; González-Muñiz, Rosario

    2014-11-28

    The recombinant Kv7.2 calmodulin (CaM) binding site (Q2AB CaMBD) shows a high tendency to aggregate, thus complicating biochemical and structural studies. To facilitate these studies we have conceived bis-PEG-peptide CaMBD-mimetics linking helices A and B in single, easy to handle molecules. Short PEG chains were selected as spacers between the two peptide molecules, and a Cu(i)-catalyzed cycloaddition (CuAAC) protocol was used to assemble the final bis-PEG-peptide conjugate, by the convenient functionalization of PEG arms with azide and alkyne groups. The resulting conjugates, with a certain helical character in TFE solutions (CD), showed nanomolar affinity in a fluorescence CaM binding in vitro assay, higher than just the sum of the precursor PEG-peptide affinities, thus validating our design. The approach to these first described examples of Kv7.2 CaMBD-mimetics could pave the way to chimeric conjugates merging helices A and B from different Kv7 subunits.

  20. Equilibrium and non-equilibrium conformations of peptides in lipid bilayers.

    Boden, N; Cheng, Y; Knowles, P F

    1997-04-22

    A synthetic, hydrophobic, 27-amino-acid-residue peptide 'K27', modelled on the trans-membrane domain of the slow voltage-gated potassium channel, IsK, has been incorporated into a lipid bilayer and its conformational properties studied using FT-IR spectroscopy. The conformation following reconstitution is found to be dependent on the nature of the solvent employed. When the reconstitution is conducted by solvent evaporation from a methanol solution, aggregates comprised of beta-strands are stabilised and their concentration is essentially invariant with time. By contrast, when trifluoroethanol is used, the initial conformation of the peptide is alpha-helical. This then relaxes to an equilibrium state between alpha-helices and beta-strands. The alpha-helix-to beta-strand conversion rate is relatively slow, and this allows the kinetics to be studied by FT-IR spectroscopy. The reverse process is much slower but again can be demonstrated by FT-IR. Thus, it appears that a true equilibrium structure can only be achieved by starting with peptide in the alpha-helical conformation. We believe this result should be of general validity for hydrophobic peptide reconstitution. The implications for conformational changes in membrane proteins are discussed.

  1. Stimuli-Directed Helical Chirality Inversion and Bio-Applications

    Ziyu Lv

    2016-08-01

    Full Text Available Helical structure is a sophisticated ubiquitous motif found in nature, in artificial polymers, and in supramolecular assemblies from microscopic to macroscopic points of view. Significant progress has been made in the synthesis and structural elucidation of helical polymers, nevertheless, a new direction for helical polymeric materials, is how to design smart systems with controllable helical chirality, and further use them to develop chiral functional materials and promote their applications in biology, biochemistry, medicine, and nanotechnology fields. This review summarizes the recent progress in the development of high-performance systems with tunable helical chirality on receiving external stimuli and discusses advances in their applications as drug delivery vesicles, sensors, molecular switches, and liquid crystals. Challenges and opportunities in this emerging area are also presented in the conclusion.

  2. Helicity conservation and twisted Seifert surfaces for superfluid vortices.

    Salman, Hayder

    2017-04-01

    Starting from the continuum definition of helicity, we derive from first principles its different contributions for superfluid vortices. Our analysis shows that an internal twist contribution emerges naturally from the mathematical derivation. This reveals that the spanwise vector that is used to characterize the twist contribution must point in the direction of a surface of constant velocity potential. An immediate consequence of the Seifert framing is that the continuum definition of helicity for a superfluid is trivially zero at all times. It follows that the Gauss-linking number is a more appropriate definition of helicity for superfluids. Despite this, we explain how a quasi-classical limit can arise in a superfluid in which the continuum definition for helicity can be used. This provides a clear connection between a microscopic and a macroscopic description of a superfluid as provided by the Hall-Vinen-Bekarevich-Khalatnikov equations. This leads to consistency with the definition of helicity used for classical vortices.

  3. High performance operational limits of tokamak and helical systems

    Yamazaki, Kozo; Kikuchi, Mitsuru

    2003-01-01

    The plasma operational boundaries of tokamak and helical systems are surveyed and compared with each other. Global confinement scaling laws are similar and gyro-Bohm like, however, local transport process is different due to sawtooth oscillations in tokamaks and ripple transport loss in helical systems. As for stability limits, achievable tokamak beta is explained by ideal or resistive MHD theories. On the other hand, beta values obtained so far in helical system are beyond ideal Mercier mode limits. Density limits in tokamak are often related to the coupling between radiation collapse and disruptive MHD instabilities, but the slow radiation collapse is dominant in the helical system. The pulse length of both tokamak and helical systems is on the order of hours in small machines, and the longer-pulsed good-confinement plasma operations compatible with radiative divertors are anticipated in both systems in the future. (author)

  4. On Helical Projection and Its Application in Screw Modeling

    Riliang Liu

    2014-04-01

    Full Text Available As helical surfaces, in their many and varied forms, are finding more and more applications in engineering, new approaches to their efficient design and manufacture are desired. To that end, the helical projection method that uses curvilinear projection lines to map a space object to a plane is examined in this paper, focusing on its mathematical model and characteristics in terms of graphical representation of helical objects. A number of interesting projective properties are identified in regard to straight lines, curves, and planes, and then the method is further investigated with respect to screws. The result shows that the helical projection of a cylindrical screw turns out to be a Jordan curve, which is determined by the screw's axial profile and number of flights. Based on the projection theory, a practical approach to the modeling of screws and helical surfaces is proposed and illustrated with examples, and its possible application in screw manufacturing is discussed.

  5. Competitor analogs for defined T cell antigens: peptides incorporating a putative binding motif and polyproline or polyglycine spacers.

    Maryanski, J L; Verdini, A S; Weber, P C; Salemme, F R; Corradin, G

    1990-01-12

    We describe a new approach for modeling antigenic peptides recognized by T cells. Peptide A24 170-182 can compete with other antigenic peptides that are recognized by H-2kd-restricted cytolytic T cells, presumably by binding to the Kd molecule. By comparing substituted A24 peptides as competitors in a functional competition assay, the A24 residues Tyr-171, Thr-178, and Leu-179 were identified as possible contact residues for Kd. A highly active competitor peptide analog was synthesized in which Tyr was separated from the Thr-Leu pair by a pentaproline spacer. The choice of proline allowed the prediction of a probable conformation for the analog when bound to the Kd molecule. The simplest conformation of the A24 peptide that allows the same spacing and orientation of the motif as in the analog would be a nearly extended polypeptide chain incorporating a single 3(10) helical turn or similar structural kink.

  6. [Plant signaling peptides. Cysteine-rich peptides].

    Ostrowski, Maciej; Kowalczyk, Stanisław

    2015-01-01

    Recent bioinformatic and genetic analyses of several model plant genomes have revealed the existence of a highly abundant group of signaling peptides that are defined as cysteine-rich peptides (CRPs). CRPs are usually in size between 50 and 90 amino acid residues, they are positively charged, and they contain 4-16 cysteine residues that are important for the correct conformational folding. Despite the structural differences among CRP classes, members from each class have striking similarities in their molecular properties and function. The present review presents the recent progress in research on signaling peptides from several families including: EPF/EPFL, SP11/SCR, PrsS, RALF, LURE, and some other peptides belonging to CRP group. There is convincing evidence indicating multiple roles for these CRPs as signaling molecules during the plant life cycle, ranging from stomata development and patterning, self-incompatibility, pollen tube growth and guidance, reproductive processes, and nodule formation.

  7. Internal transport barrier physics in helical systems

    Yokoyama, M.; Minami, T.; Fujisawa, A.; Herranz, J.; Ida, K.; Yamagishi, O.; Yamada, H.; Maaberg, H.; Beidler, C.D.; Dinklage, A.; Estrada, T.; Castejon, F.; Murakami, S.

    2005-01-01

    The electron internal transport barrier (eITB) has been observed in wide range of helical systems, such as CHS [eg.,1], LHD [eg., 2], TJ-II [eg., 3] and W7-AS [eg., 4]. The eITB isA defined as highly peaked electron temperature (Te) profile with strongly positive radial electric field (Er) in the central region. These observations are reviewed in this paper to understand the device-independent common findings and also to draw the main differences. This is the first report from the International Stellarator Profile Database Activity. The formation of the strong central positive Er has been understood mainly as a result of the ambipolarity of neoclassical electron and ion fluxes, although some additional convective electron flux such as driven by ECRH is required in some situations. This 'neoclassical' physics peculiar to low collisional regime of helical plasmas provides the commonly observed existence of the ECRH power threshold (which is also depending on the density). This is contrastive characteristics to the ITB observed in tokamaks. The dependence of the ECRH power threshold on the magnetic configuration and on the heating scenario among these devices are currently being examined by taking the effective ripple and the trapped particle fraction as parameters to achieve the comprehensive understanding. The roles of low order rational surfaces on the onset of eITB formation and also on its radial size (location of the footpoint of the eITB) have been indicated in inward shifted configurations in LHD (depending on the relative locations of heating position and 2/1 island) and TJ-II (eITB becomes possible at higher density when 3/2 rational is introduced in the plasma core region). It is speculated that, for the latter case, the resonance causes an extra electron flux to trigger the positive Er. The interplay between low order rational surfaces and the formation of eITB still waits for the systematic experiment and theoretical analysis. The external controllability

  8. Patterns of uterine enhancement with helical CT

    Kaur, H.; Loyer, E.M.; Charnsangavej, C. [Department of Diagnostic Radiology, Box 57, The University of Texas, M.D. Anderson Cancer Center, 1515 Holcombe Blvd. Houston, TX 77030 (United States); Minami, M. [Department of Radiology, Faculty of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113 (Japan)

    1998-10-01

    Objective: The purpose of this study was to evaluate the enhancement characteristics of the normal uterine body and cervix using dynamic contrast-enhanced helical CT. Methods: Thirty-eight women scheduled for pelvic CT for non-gynecologic malignancies underwent dynamic contrast-enhanced helical CT of the pelvis. Data acquisition was during the arterial phase (30-45 s after the start of injection), the parenchymal phase (90-120 s after the start of injection), and delayed phase (3-9 min after the start of injection). The images were evaluated by four radiologists for the pattern of myometrial and cervical enhancement. Correlation was made with the age and menstrual status of the patients. Results: In the uterine body, three types of enhancement were observed. Type 1 enhancement, seen in 16 patients (42%), was characterized by the visualization of a subendometrial zone of enhancement, 30-120 s after the start of injection. Eight of these patients also showed an enhancing zone in the outer myometrium. Both zones were transitory, and in all cases, the uterus became homogeneous in the delayed phase. This pattern was seen predominantly in premenopausal women with a mean age of 34 years. Type 2 enhancement, seen in 17 cases (45%), was defined by the absence of subendometrial enhancement in the early phase. Enhancement was either diffuse from the outset or originated in the outer myometrium. This pattern was seen nearly equally in premenopausal and postmenopausal women with a mean age of 40 years. Type 3 enhancement was seen in five postmenopausal patients (13%) with a mean age of 53 years and was characterized by faint diffuse enhancement. In the cervix, a zonal pattern of enhancement defining inner and outer stroma was seen in 23 patients (61%). Fifteen patients were premenopausal and eight were postmenopausal. Conclusion: In this study, we have shown a transitory zonal distribution of the contrast in the myometrium and cervix using dynamic contrast-enhanced helical CT

  9. Patterns of uterine enhancement with helical CT

    Kaur, H.; Loyer, E.M.; Charnsangavej, C.; Minami, M.

    1998-01-01

    Objective: The purpose of this study was to evaluate the enhancement characteristics of the normal uterine body and cervix using dynamic contrast-enhanced helical CT. Methods: Thirty-eight women scheduled for pelvic CT for non-gynecologic malignancies underwent dynamic contrast-enhanced helical CT of the pelvis. Data acquisition was during the arterial phase (30-45 s after the start of injection), the parenchymal phase (90-120 s after the start of injection), and delayed phase (3-9 min after the start of injection). The images were evaluated by four radiologists for the pattern of myometrial and cervical enhancement. Correlation was made with the age and menstrual status of the patients. Results: In the uterine body, three types of enhancement were observed. Type 1 enhancement, seen in 16 patients (42%), was characterized by the visualization of a subendometrial zone of enhancement, 30-120 s after the start of injection. Eight of these patients also showed an enhancing zone in the outer myometrium. Both zones were transitory, and in all cases, the uterus became homogeneous in the delayed phase. This pattern was seen predominantly in premenopausal women with a mean age of 34 years. Type 2 enhancement, seen in 17 cases (45%), was defined by the absence of subendometrial enhancement in the early phase. Enhancement was either diffuse from the outset or originated in the outer myometrium. This pattern was seen nearly equally in premenopausal and postmenopausal women with a mean age of 40 years. Type 3 enhancement was seen in five postmenopausal patients (13%) with a mean age of 53 years and was characterized by faint diffuse enhancement. In the cervix, a zonal pattern of enhancement defining inner and outer stroma was seen in 23 patients (61%). Fifteen patients were premenopausal and eight were postmenopausal. Conclusion: In this study, we have shown a transitory zonal distribution of the contrast in the myometrium and cervix using dynamic contrast-enhanced helical CT

  10. Pressure effect on the amide I frequency of the solvated α-helical structure in water

    Takekiyo, T; Yoshimura, Y; Shimizu, A; Koizumi, T; Kato, M; Taniguchi, Y

    2007-01-01

    As a model system of the pressure dependence of the amide I mode of the solvated α-helical structure in a helical peptide, we have calculated the frequency shifts of the amide I modes as a function of the distance between trans-N-methylacetamide (t-NMA) dimer and a water molecule (d C=O···H-O ) by the density-functional theory (DFT) method at the B3LYP/6-31G++(d,p) level. Two amide I frequencies at 1652 and 1700 cm -1 were observed under this calculation. The former is ascribed to the amide I mode forming the intermolecular hydrogen bond (H-bond) between t-NMA and H 2 O in addition to the intermolecular H-bond in the t-NMA dimer. The latter is due to the amide I mode forming only the intermolecular H-bond in the t-NMA dimer. We have found that the amide I frequency at 1652 cm -1 shifts to a lower frequency with decreasing d C=O···H-O ) (i.e., increasing pressure), whereas that at 1700 cm -1 shifts to a higher frequency. The amide I frequency shift of 1652 cm -1 is larger than that of 1700 cm -1 by the intermolecular H-bond. Thus, our results clearly indicate that the pressure-induced amide I frequency shift of the solvated α-helical structure correlates with the change in d C=O···H-O )

  11. Chaotic coordinates for the Large Helical Device

    Hudson, S. R., E-mail: shudson@pppl.gov [Princeton Plasma Physics Laboratory, P.O. Box 451, Princeton, New Jersey 08543 (United States); Suzuki, Y. [National Institute for Natural Sciences, National Institute for Fusion Sciences, 322-6 Oroshi, Toki, 509-5292 (Japan)

    2014-10-15

    The theory of quadratic-flux-minimizing (QFM) surfaces is reviewed, and numerical techniques that allow high-order QFM surfaces to be efficiently constructed for experimentally relevant, non-integrable magnetic fields are described. As a practical example, the chaotic edge of the magnetic field in the Large Helical Device (LHD) is examined. A precise technique for finding the boundary surface is implemented, the hierarchy of partial barriers associated with the near-critical cantori is constructed, and a coordinate system, which we call chaotic coordinates, that is based on a selection of QFM surfaces is constructed that simplifies the description of the magnetic field, so that flux surfaces become “straight” and islands become “square.”.

  12. Helical spin rotators and snakes for RHIC

    Ptitsin, V.I.; Shatunov, Yu.M.; Peggs, S.

    1995-01-01

    The RHIC collider, now under construction at BNL, will have the possibility of polarized proton-proton collisions up to a beam energy of 250 Gev. Polarized proton beams of such high energy can be only obtained with the use of siberian snakes, a special kind of spin rotator that rotates the particle spin by 180 degree around an axis lying in the horizontal plane. Siberian snakes help to preserve the beam polarization while numerous spin depolarizing resonances are crossed, during acceleration. In order to collide longitudinally polarized beams, it is also planned to install spin rotators around two interaction regions. This paper discusses snake and spin rotator designs based on sequences of four helical magnets. The schemes that were chosen to be applied at RHIC are presented

  13. ATLAS helicity analyses in beauty hadron decays

    Smizanska, M

    2000-01-01

    The ATLAS detector will allow a precise spatial reconstruction of the kinematics of B hadron decays. In combination with the efficient lepton identification applied already at trigger level, ATLAS is expected to provide large samples of exclusive decay channels cleanly separable from background. These data sets will allow spin-dependent analyses leading to the determination of production and decay parameters, which are not accessible if the helicity amplitudes are not separated. Measurement feasibility studies for decays B/sub s //sup 0/ to J/ psi phi and Lambda /sub b//sup 0/ to Lambda J/ psi , presented in this document, show the experimental precisions that can be achieved in determination of B/sub s//sup 0/ and Lambda /sub b //sup 0/ characteristics. (19 refs).

  14. Conditioner for a helically transported electron beam

    Wang, Changbiao.

    1992-05-01

    The kinetic theory is developed to investigate a conditioner for a helically transported electron beam. Linear expressions for axial velocity spread are derived. Numerical simulation is used to check the theoretical results and examine nonlinear aspects of the conditioning process. The results show that in the linear regime the action of the beam conditioner on a pulsed beam mainly depends on the phase at which the beam enters the conditioner and depends only slightly on the operating wavelength. In the nonlinear regime, however, the action of the conditioner strongly depends on the operating wavelength and only slightly upon the entrance phase. For a properly chosen operating wavelength, a little less than the electron's relativistic cyclotron wavelength, the conditioner can decrease the axial velocity spread of a pulsed beam down to less than one-third of its initial value

  15. Conditioner for a helically transported electron beam

    Wang, C.

    1992-05-01

    The kinetic theory is developed to investigate a conditioner for a helically imported electron beam. Linear expressions for axial velocity spread are derived. Numerical simulation is used to check the theoretical results and examine nonlinear aspects of the conditioning process. The results show that in the linear regime the action of the beam conditioner on a pulsed beam mainly depends on the phase at which the beam enters the conditioner and depends only slightly on the operating wavelength. In the nonlinear regime, however, the action of the conditioner strongly depends on the operating wavelength and only slightly upon the entrance phase. For a properly chosen operating wavelength, a little less than the electron's relativistic cyclotron wavelength, the conditioner can decrease the axial velocity spread of a pulsed beam down to less than one-third of its initial value

  16. Microinstability Studies for the Large Helical Device

    Rewoldt, G.; Ku, L.-P.; Tang, W.M.; Sugama, H.; Nakajima, N.; Watanabe, K.Y.; Murakami, S.; Yamada, H.; Cooper, W.A.

    2002-01-01

    Fully kinetic assessments of the stability properties of toroidal drift modes have been obtained for cases for the Large Helical Device (LHD). This calculation employs the comprehensive linear microinstability code FULL, as recently extended for nonaxisymmetric systems. The code retains the important effects in the linearized gyrokinetic equation, using the lowest-order ''ballooning representation'' for high toroidal mode number instabilities in the electrostatic limit. These effects include trapped particles, FLR, transit and bounce and magnetic drift frequency resonances, etc., for any number of plasma species. Results for toroidal drift waves destabilized by trapped electrons and ion temperature gradients are presented, using numerically-calculated three-dimensional MHD equilibria. These are reconstructed from experimental measurements. Quasilinear fluxes of particles and energy for each species are also calculated. Pairs of LHD discharges with different magnetic axis positions and with and without pellet injection are compared

  17. Characteristic features of edge transport barrier formed in helical divertor configuration of the Large Helical Device

    Toi, K.; Ohdachi, S.; Watanabe, F.

    2006-10-01

    In a helical divertor configuration of the Large Helical Device (LHD), transport barrier was formed through low to high confinement (L-H) transition in the plasma edge region including ergodic field layer of which region is in the magnetic hill. The plasma stored energy or the averaged bulk plasma beta dia > (derived from diamagnetic measurement) starts to increase just after the transition. In the case that both dia > and line-averaged electron density e > at the transition are relatively high as dia >≥1.5% and e >≥2x10 19 m -3 , the increase is hampered by rapid growth of edge MHD modes and/or small ELM like activities just after the transition. On the other hand, the transition at lower e > (≤1.5x10 19 m -3 ) and dia > (<2%) leads to a continuous increase in the stored energy with a time scale longer than the global energy confinement time, without suffering from these MHD activities near the edge. The ETB typically formed in electron density profile extends into ergodic field layer defined in the vacuum field. The width of ETB is almost independent of the toroidal field strength from 0.5T to 1.5T and is much larger than the poloidal ion gyro-radius. When resonant helical field perturbations are applied to expand a magnetic island size at the rational surface of the rotational transform ι/2π=1 near the edge, the L-H transition is triggered at lower electron density compared with the case without the field perturbations. The application of large helical field perturbations also suppresses edge MHD modes and ELM like activities. (author)

  18. NMR structure of the Arctic mutation of the Alzheimer's Aβ(1-40) peptide docked to SDS micelles

    Usachev, K. S.; Filippov, A. V.; Khairutdinov, B. I.; Antzutkin, O. N.; Klochkov, V. V.

    2014-11-01

    The “Arctic” point mutation of the Alzheimer's amyloid β-peptide is a rare mutation leading to an early onset of Alzheimer's disease. The peptide may interact with neuronal membranes, where it can provide its toxic effects. We used 2D NMR spectroscopy to investigate the conformation of the “Arctic” mutant of Aβ1-40 Alzheimer's amyloid peptide in sodium dodecyl sulfate micelle solutions, which are the type of amphiphilic structures mimicking some properties of biomembranes. The study showed that the Arctic mutant of Aβ1-40 interacts with the surface of SDS micelles mainly through the Leu17-Asn27 310-helical region, while the Ile31-Val40 region is buried in the hydrophobic interior of the micelle. In contrast, wild-type Aβ1-40 interacts with SDS micelles through the Lys16-Asp23 α-helical region and Gly29-Met35. Both the Arctic mutant and the wild-type Aβ1-40 peptides interactions with SDS micelles are hydrophobic in nature. Aβ peptides are thought to be capable of forming pores in biomembranes that can cause changes in neuronal and endothelial cell membrane permeability. It has also been shown that Aβ peptides containing the “Arctic” mutation are more neurotoxic and aggregate more readily than the wild-type Aβ peptides at physiological conditions. Here, we propose that the extension of the helical structure of Leu17-Asn27 and a high aliphaticity (neutrality) of the C-terminal region in the Arctic Aβ peptides are consistent with the idea that formation of ion-permeable pores by Aβ oligomers may be one of prevailing mechanisms of a larger neuronal toxicity of the Arctic Aβ compared to the wild-type Aβ peptides, independent of oxidative damage and lipid peroxidation.

  19. Energy landscape, structure and rate effects on strength properties of alpha-helical proteins

    Bertaud, Jeremie; Hester, Joshua; Jimenez, Daniel D; Buehler, Markus J

    2010-01-01

    The strength of protein domains is crucial to identify the mechanical role of protein domains in biological processes such as mechanotransduction, tissue mechanics and tissue remodeling. Whereas the concept of strength has been widely investigated for engineered materials, the strength of fundamental protein material building blocks and how it depends on structural parameters such as the chemical bonding, the protein filament length and the timescale of observation or deformation velocity remains poorly understood. Here we report a systematic analysis of the influence of key parameters that define the energy landscape of the strength properties of alpha-helical protein domains, including energy barriers, unfolding and refolding distances, the locations of folded and unfolded states, as well as variations of the length and pulling velocity of alpha-helical protein filaments. The analysis is facilitated by the development of a double-well mesoscale potential formulation, utilized here to carry out a systematic numerical analysis of the behavior of alpha-helices. We compare the results against widely used protein strength models based on the Bell model, one of the simplest models used to characterize the strength of protein filaments. We find that, whereas Bell-type models are a reasonable approximation to describe the rupture of alpha-helical protein domains for a certain range of pulling speeds and values of energy barriers, the model ceases to hold for very large energy barriers and for very small pulling speeds, in agreement with earlier findings. We conclude with an application of our mesoscale model to investigate the effect of the length of alpha-helices on their mechanical strength. We find a weakening effect as the length of alpha-helical proteins increases, followed by an asymptotic regime in which the strength remains constant. We compare strand lengths found in biological proteins with the scaling law of strength versus alpha-helix filament length. The

  20. Conformations and orientations of a signal peptide interacting with phospholipid monolayers

    Cornell, D.G.; Dluhy, R.A.; Briggs, M.S.; McKnight, C.J.; Gierasch, L.M.

    1989-01-01

    The interaction of a chemically synthesized 25-residue signal peptide of LamB protein from Escherichia coli with phospholipids has been studied with a film balance technique. The conformation, orientation, and concentration of the peptides in lipid monolayers have been determined from polarized infrared spectroscopy, ultraviolet spectroscopy, and assay of 14 C-labeled peptide in transferred films. When the LamB signal peptide in injected into the subphase under a phosphatidylethanolamine-phosphatidylglycerol monolayer at low initial pressure, insertion of a portion of the peptide into the lipid film is evidenced by a rapid rise in film pressure. Spectroscopic results obtained on films transferred to quartz plates and Ge crystals show that the peptide is a mixture of α-helix and β-conformation where the long axis of the α-helix penetrates the monolayer plane and the β-structure which is coplanar with the film. By contrast, when peptide is injected under lipid at high initial pressure, no pressure rise is observed, and the spectroscopic results show the presence of only β-structure which is coplanar with the monolayer. The spectroscopic and radioassay results are all consistent with the picture of a peptide anchored to the monolayer through electrostatic binding with a helical portion inserted into the lipid region of the monolayer and a β-structure portion resident in the aqueous phase. The negative charges on the lipid molecules are roughly neutralized by the positive charges of the peptide

  1. Interplay of energetic ions and Alfven modes in helical plasmas

    Kolesnichenko, Ya.I.; Lutsenko, V.V.; Yakovenko, Yu.Y.; Yamazaki, K.; Nakajima, N.; Narushima, Y.; Toi, K.; Yamamoto, S.

    2003-08-01

    Alfven eigenmodes and their destabilization by energetic ions in stellarators, mainly, in the Large Helical Device (LHD) plasmas, are considered. A general expression for the instability growth rate is derived, which generalizes that obtained in Ref. [Ya.I. Kolesnichenko et al., Phys. Plasmas 9, 517 (2002)] by taking into account the finite magnitude of the perturbed longitudinal magnetic field. The structures of the Alfven continuum and Alfven eigenmodes, as well as the resonances of the wave-particle interaction, are studied. A numerical simulation of the destabilization of Alfven waves with low mode numbers during neutral-beam injection in a particular LHD shot is carried out. The obtained solutions represent even and odd core-localized Toroidicity-induced Alfven Eigenmodes, the calculated frequencies and the mode numbers being in agreement with experimental data. The growth rates of the instabilities are calculated. This work was done during the stay of Ya.I. Kolesnichenko in NIFS as a Guest Professor from January 26, 2003 to April 25, 2003. (author)

  2. Pumping Characteristics of a Helical Screw Agitator with a Draught Tube

    Hwang, Jung-Hoon; Kim, Youn-Jea

    In the use of helical type agitator, the mixing process is usually restricted to the laminar flow regime. Common examples of laminar mixing are found where the fluid has a very high viscosity, i.e., pseudoplastic fluids. It can be indicated that a helical type agitator is sufficiently suited to the creeping flow mixing. The pumping characteristic of a Helical Screw Agitator with a draught tube (HSA) is required to evaluate its capacity for the optimal configuration of the mixing chamber. It could be executed by changing some parameters such as the number of helix, the angular velocity and the rotating direction and so on. In this study, the numerical simulation was carried out with the Eulerian multiphase mixture model and the moving mesh approximation. Some of the optimum design parameters have been developed with the aid of numerical data from the Computational Fluid Dynamics (CFD) analysis. Using the commercial code, Fluent, the pumping characteristics in the HSA are investigated from the rheological properties, and the results are graphically depicted.

  3. The diversity and evolution of anuran skin peptides.

    König, Enrico; Bininda-Emonds, Olaf R P; Shaw, Chris

    2015-01-01

    Amphibians exhibit various, characteristic adaptations related to their "incomplete" shift from the aquatic to the terrestrial habitat. In particular, the integument was subject to a number of specialized modifications during the evolution of these animals. In this review, we place special emphasis on endogenous host-defence skin peptides from the cuteanous granular glands anuran amphibians (frogs and toads). The overview on the two broad groups of neuroactive and antimicrobial peptides (AMPs) goes beyond a simple itemization in that we provide a new perspective into the evolution and function of anuran AMPs. Briefly, these cationic, amphipathic and α-helical peptides are traditionally viewed as being part of the innate immune system, protecting the moist skin against invading microorganisms through their cytolytic action. However, the complete record of anuran species investigated to date suggests that AMPs are distributed sporadically (i.e., non-universally) across Anura. Together with the intriguing observation that virtually all anurans known to produce neuropeptides in their granular glands also co-secrete cytolytic peptides, we call the traditional role for AMPs as being purely antimicrobial into question and present an alternative scenario. We hypothesize AMPs to assist neuroactive peptides in their antipredator role through their cytolytic action increasing the delivery of the latter to the endocrine and nervous system of the predator. Thus, AMPs are more accurately viewed as cytolysins and their contribution to the immune system is better regarded as an accessory benefit. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. Structural Interplay - Tuning Mechanics in Peptide-Polyurea Hybrids

    Korley, Lashanda

    Utilizing cues from natural materials, we have been inspired to explore the hierarchical arrangement critical to energy absorption and mechanical enhancement in synthetic systems. Of particular interest is the soft domain ordering proposed as a contributing element to the observed toughness in spider silk. Multiblock copolymers, are ideal and dynamic systems in which to explore this approach via variations in secondary structure of nature's building blocks - peptides. We have designed a new class of polyurea hybrids that incorporate peptidic copolymers as the soft segment. The impact of hierarchical ordering on the thermal, mechanical, and morphological behavior of these bio-inspired polyurethanes with a siloxane-based, peptide soft segment was investigated. These peptide-polyurethane/urea hybrids were microphase segregated, and the beta-sheet secondary structure of the soft segment was preserved during polymerization and film casting. Toughness enhancement at low strains was achieved, but the overall extensibility of the peptide-incorporated systems was reduced due to the unique hard domain organization. To decouple the secondary structure influence in the siloxane-peptide soft segment from mechanics dominated by the hard domain, we also developed non-chain extended peptide-polyurea hybrids in which the secondary structure (beta sheet vs. alpha helix) was tuned via choice of peptide and peptide length. It was shown that this structural approach allowed tailoring of extensibility, toughness, and modulus. The sheet-dominant hybrid materials were typically tougher and more elastic due to intermolecular H-bonding facilitating load distribution, while the helical-prevalent systems generally exhibited higher stiffness. Recently, we have explored the impact of a molecular design strategy that overlays a covalent and physically crosslinked architecture in these peptide-polyurea hybrids, demonstrating that physical constraints in the network hybrids influences peptide

  5. General architecture of the alpha-helical globule.

    Murzin, A G; Finkelstein, A V

    1988-12-05

    A model is presented for the arrangement of alpha-helices in globular proteins. In the model, helices are placed on certain ribs of "quasi-spherical" polyhedra. The polyhedra are chosen so as to allow the close packing of helices around a hydrophobic core and to stress the collective interactions of the individual helices. The model predicts a small set of stable architectures for alpha-helices in globular proteins and describes the geometries of the helix packings. Some of the predicted helix arrangements have already been observed in known protein structures; others are new. An analysis of the three-dimensional structures of all proteins for which co-ordinates are available shows that the model closely approximates the arrangements and packing of helices actually observed. The average deviations of the real helix axes from those in the model polyhedra is +/- 20 degrees in orientation and +/- 2 A in position (1 A = 0.1 nm). We also show that for proteins that are not homologous, but whose helix arrangements are described by the same polyhedron, the root-mean-square difference in the position of the C alpha atoms in the helices is 1.6 to 3.0 A.

  6. MAGNETIC HELICITY FLUX IN THE PRESENCE OF SHEAR

    Hubbard, Alexander; Brandenburg, Axel

    2011-01-01

    Magnetic helicity has risen to be a major player in dynamo theory, with the helicity of the small-scale field being linked to the dynamo saturation process for the large-scale field. It is a nearly conserved quantity, which allows its evolution equation to be written in terms of production and flux terms. The flux term can be decomposed in a variety of fashions. One particular contribution that has been expected to play a significant role in dynamos in the presence of mean shear was isolated by Vishniac and Cho. Magnetic helicity fluxes are explicitly gauge dependent however, and the correlations that have come to be called the Vishniac-Cho flux were determined in the Coulomb gauge, which turns out to be fraught with complications in shearing systems. While the fluxes of small-scale helicity are explicitly gauge dependent, their divergences can be gauge independent. We use this property to investigate magnetic helicity fluxes of the small-scale field through direct numerical simulations in a shearing-box system and find that in a numerically usable gauge the divergence of the small-scale helicity flux vanishes, while the divergence of the Vishniac-Cho flux remains finite. We attribute this seeming contradiction to the existence of horizontal fluxes of small-scale magnetic helicity with finite divergences.

  7. Magnetic Helicity Flux in the Presence of Shear

    Hubbard, Alexander; Brandenburg, Axel

    2011-01-01

    Magnetic helicity has risen to be a major player in dynamo theory, with the helicity of the small-scale field being linked to the dynamo saturation process for the large-scale field. It is a nearly conserved quantity, which allows its evolution equation to be written in terms of production and flux terms. The flux term can be decomposed in a variety of fashions. One particular contribution that has been expected to play a significant role in dynamos in the presence of mean shear was isolated by Vishniac & Cho. Magnetic helicity fluxes are explicitly gauge dependent however, and the correlations that have come to be called the Vishniac-Cho flux were determined in the Coulomb gauge, which turns out to be fraught with complications in shearing systems. While the fluxes of small-scale helicity are explicitly gauge dependent, their divergences can be gauge independent. We use this property to investigate magnetic helicity fluxes of the small-scale field through direct numerical simulations in a shearing-box system and find that in a numerically usable gauge the divergence of the small-scale helicity flux vanishes, while the divergence of the Vishniac-Cho flux remains finite. We attribute this seeming contradiction to the existence of horizontal fluxes of small-scale magnetic helicity with finite divergences.

  8. Magnetic Helicities and Dynamo Action in Magneto-rotational Turbulence

    Bodo, G.; Rossi, P. [INAF/Osservatorio Astrofisico di Torino, Strada Osservatorio 20, I-10025 Pino Torinese (Italy); Cattaneo, F. [Department of Astronomy and Astrophysics, The University of Chicago, 5640 S. Ellis Avenue, Chicago IL 60637 (United States); Mignone, A., E-mail: bodo@oato.inaf.it [Dipartimento di Fisica, Università degli Studi di Torino, Via Pietro Giuria 1, 10125 Torino (Italy)

    2017-07-10

    We examine the relationship between magnetic flux generation, taken as an indicator of large-scale dynamo action, and magnetic helicity, computed as an integral over the dynamo volume, in a simple dynamo. We consider dynamo action driven by magneto-rotational turbulence (MRT) within the shearing-box approximation. We consider magnetically open boundary conditions that allow a flux of helicity in or out of the computational domain. We circumvent the problem of the lack of gauge invariance in open domains by choosing a particular gauge—the winding gauge—that provides a natural interpretation in terms of the average winding number of pairwise field lines. We use this gauge precisely to define and measure the helicity and the helicity flux for several realizations of dynamo action. We find in these cases that the system as a whole does not break reflectional symmetry and that the total helicity remains small even in cases when substantial magnetic flux is generated. We find no particular connection between the generation of magnetic flux and the helicity or the helicity flux through the boundaries. We suggest that this result may be due to the essentially nonlinear nature of the dynamo processes in MRT.

  9. Peptides in melanoma therapy.

    Mocellin, Simone

    2012-01-01

    Peptides derived from tumor associated antigens can be utilized to elicit a therapeutically effective immune response against melanoma in experimental models. However, patient vaccination with peptides - although it is often followed by the induction of melanoma- specific T lymphocytes - is rarely associated with tumor response of clinical relevance. In this review I summarize the principles of peptide design as well as the results so far obtained in the clinical setting while treating cutaneous melanoma by means of this active immunotherapy strategy. I also discuss some immunological and methodological issues that might be helpful for the successful development of peptide-based vaccines.

  10. Antimicrobial Peptides in Reptiles

    van Hoek, Monique L.

    2014-01-01

    Reptiles are among the oldest known amniotes and are highly diverse in their morphology and ecological niches. These animals have an evolutionarily ancient innate-immune system that is of great interest to scientists trying to identify new and useful antimicrobial peptides. Significant work in the last decade in the fields of biochemistry, proteomics and genomics has begun to reveal the complexity of reptilian antimicrobial peptides. Here, the current knowledge about antimicrobial peptides in reptiles is reviewed, with specific examples in each of the four orders: Testudines (turtles and tortosises), Sphenodontia (tuataras), Squamata (snakes and lizards), and Crocodilia (crocodilans). Examples are presented of the major classes of antimicrobial peptides expressed by reptiles including defensins, cathelicidins, liver-expressed peptides (hepcidin and LEAP-2), lysozyme, crotamine, and others. Some of these peptides have been identified and tested for their antibacterial or antiviral activity; others are only predicted as possible genes from genomic sequencing. Bioinformatic analysis of the reptile genomes is presented, revealing many predicted candidate antimicrobial peptides genes across this diverse class. The study of how these ancient creatures use antimicrobial peptides within their innate immune systems may reveal new understandings of our mammalian innate immune system and may also provide new and powerful antimicrobial peptides as scaffolds for potential therapeutic development. PMID:24918867

  11. High-n helicity-induced shear Alfven eigenmodes

    Nakajima, N.; Cheng, C.Z.; Okamoto, M.

    1992-05-01

    The high-n Helicity-induced shear Alfven Eigenmodes (HAE) are considered both analytically and numerically for the straight helical magnetic system, where n is the toroidal mode number. The eigenmode equation for the high-n HAE modes is derived along the field line and with the aid of the averaging method is shown to reduce to the Mathieu equation asymptotically. The discrete HAE modes are shown to exist inside the continuum spectrum gaps. The continuous spectrum gaps appear around ω 2 = ω A 2 [N(lι-m)/2] 2 for N = 1,2,.., where ω A is the toroidal Alfven transit frequency, and l, m, and ι are the polarity of helical coils, the toroidal pitch number of helical coils, and the rotational transform, respectively. For the same ω A and ι, the frequency of the helical continuum gap is larger than that of the continuum gap in tokamak plasmas by |l-ι -1 m|. The polarity of helical coils l plays a crucial role in determining the spectrum gaps and the properties of the high-n HAE modes. The spectrum gaps near the magnetic axis are created by the helical ripple with circular flux surfaces for l = 1, and ≥ 3 helicals. For l = 2 helical systems, the spectrum gaps are created by the ellipticity of the flux surfaces. These analytical results for the continuum gaps and the existence of the high-n HAE modes in the continuum gaps are confirmed numerically for the l = 2 case, and we find that the HAE modes exist for mode structures with the even and the odd parities. (author)

  12. Solution structures of the linear leaderless bacteriocins enterocin 7A and 7B resemble carnocyclin A, a circular antimicrobial peptide.

    Lohans, Christopher T; Towle, Kaitlyn M; Miskolzie, Mark; McKay, Ryan T; van Belkum, Marco J; McMullen, Lynn M; Vederas, John C

    2013-06-11

    Leaderless bacteriocins are a class of ribosomally synthesized antimicrobial peptides that are produced by certain Gram-positive bacteria without an N-terminal leader section. These bacteriocins are of great interest due to their potent inhibition of many Gram-positive organisms, including food-borne pathogens such as Listeria and Clostridium spp. We now report the NMR solution structures of enterocins 7A and 7B, leaderless bacteriocins recently isolated from Enterococcus faecalis 710C. These are the first three-dimensional structures to be reported for bacteriocins of this class. Unlike most other linear Gram-positive bacteriocins, enterocins 7A and 7B are highly structured in aqueous conditions. Both peptides are primarily α-helical, adopting a similar overall fold. The structures can be divided into three separate α-helical regions: the N- and C-termini are both α-helical, separated by a central kinked α-helix. The overall structures bear an unexpected resemblance to carnocyclin A, a 60-residue peptide that is cyclized via an amide bond between the C- and N-termini and has a saposin fold. Because of synergism observed for other two-peptide leaderless bacteriocins, it was of interest to probe possible binding interactions between enterocins 7A and 7B. However, despite synergistic activity observed between these peptides, no significant binding interaction was observed based on NMR and isothermal calorimetry.

  13. Theoretical modeling of transport barriers in helical plasmas

    Toda, S.; Itoh, K.; Ohyabu, N.

    2008-10-01

    A unified transport modelling to explain electron Internal Transport Barriers (e-ITB) in helical plasmas and Internal Diffusion Barriers (IDB) observed in Large Helical Device (LHD) is proposed. The e-ITB can be predicted with the effect of zonal flows to obtain the e-ITB in the low collisional regime when the radial variation of the particle anomalous diffusivity is included. Transport analysis in this article can newly show that the particle fuelling induces the IDB formation when this unified transport modelling is used in the high collisional regime. The density limit for the IDB in helical plasmas is also examined including the effect of the radiation loss. (author)

  14. Drift mode calculations for the Large Helical Device

    Rewoldt, G.; Ku, L.-P.; Tang, W.M.; Sugama, H.; Nakajima, N.; Watanabe, K.Y.; Murakami, S.; Yamada, H.; Cooper, W.A.

    2000-01-01

    A fully kinetic assessment of the stability properties of toroidal drift modes has been obtained for a case for the Large Helical Device (LHD) [A.Iiyoshi, et al., Plasma Physics and Controlled Nuclear Fusion Research, 1998, Nucl.Fusion 39, 1245 (1999)]. This calculation retains the important effects in the linearized gyrokinetic equation, using the lowest-order ''ballooning representation'' for high toroidal mode number instabilities in the electrostatic limit. Results for toroidal drift waves destabilized by trapped particle dynamics and ion temperature gradients are presented, using three-dimensional magnetohydrodynamics equilibria reconstructed from experimental measurements. The effects of helically-trapped particles and helical curvature are investigated

  15. Experimental Evidence of Helical Flow in Porous Media

    Ye, Yu; Chiogna, Gabriele; Cirpka, Olaf A.

    2015-01-01

    Helical flow leads to deformation of solute plumes and enhances transverse mixing in porous media. We present experiments in which macroscopic helical flow is created by arranging different materials to obtain an anisotropic macroscopic permeability tensor with spatially variable orientation....... The resulting helical flow entails twisting streamlines which cause a significant increase in lateral mass exchange and thus a large enhancement of plume dilution (up to 235%) compared to transport in homogenous media. The setup may be used to effectively mix solutes in parallel streams similarly to static...... mixers, but in porous media....

  16. Linear local stability of electrostatic drift modes in helical systems

    Yamagishi, O.; Nakajima, N.; Sugama, H.; Nakamura, Y.

    2003-01-01

    We investigate the stability of the drift wave in helical systems. For this purpose, we solve the linear local gyrokinetic-Poisson equation, in the electrostatic regime. As a model of helical plasmas, Large helical Device (LHD) is considered. The equation we apply is rather exact in the framework of linear gyrokinetic theory, where only the approximation is the ballooning representation. In this paper, we consider only collisionless cases. All the frequency regime can be naturally reated without any assumptions, and in such cases, ion temperature gradient modes (ITG), trapped electron modes (TEM), and electron temperature gradient modes (ETG) are expected to become unstable linearly independently. (orig.)

  17. Magnetic Helical Micro- and Nanorobots: Toward Their Biomedical Applications

    Famin Qiu

    2015-03-01

    Full Text Available Magnetic helical micro- and nanorobots can perform 3D navigation in various liquids with a sub-micrometer precision under low-strength rotating magnetic fields (<10 mT. Since magnetic fields with low strengths are harmless to cells and tissues, magnetic helical micro/nanorobots are promising tools for biomedical applications, such as minimally invasive surgery, cell manipulation and analysis, and targeted therapy. This review provides general information on magnetic helical micro/nanorobots, including their fabrication, motion control, and further functionalization for biomedical applications.

  18. Insulin C-peptide test

    C-peptide ... the test depends on the reason for the C-peptide measurement. Ask your health care provider if ... C-peptide is measured to tell the difference between insulin the body produces and insulin someone injects ...

  19. Peptide Vaccines for Leishmaniasis

    Rory C. F. De Brito

    2018-05-01

    Full Text Available Due to an increase in the incidence of leishmaniases worldwide, the development of new strategies such as prophylactic vaccines to prevent infection and decrease the disease have become a high priority. Classic vaccines against leishmaniases were based on live or attenuated parasites or their subunits. Nevertheless, the use of whole parasite or their subunits for vaccine production has numerous disadvantages. Therefore, the use of Leishmania peptides to design more specific vaccines against leishmaniases seems promising. Moreover, peptides have several benefits in comparison with other kinds of antigens, for instance, good stability, absence of potentially damaging materials, antigen low complexity, and low-cost to scale up. By contrast, peptides are poor immunogenic alone, and they need to be delivered correctly. In this context, several approaches described in this review are useful to solve these drawbacks. Approaches, such as, peptides in combination with potent adjuvants, cellular vaccinations, adenovirus, polyepitopes, or DNA vaccines have been used to develop peptide-based vaccines. Recent advancements in peptide vaccine design, chimeric, or polypeptide vaccines and nanovaccines based on particles attached or formulated with antigenic components or peptides have been increasingly employed to drive a specific immune response. In this review, we briefly summarize the old, current, and future stands on peptide-based vaccines, describing the disadvantages and benefits associated with them. We also propose possible approaches to overcome the related weaknesses of synthetic vaccines and suggest future guidelines for their development.

  20. Peptide Vaccines for Leishmaniasis.

    De Brito, Rory C F; Cardoso, Jamille M De O; Reis, Levi E S; Vieira, Joao F; Mathias, Fernando A S; Roatt, Bruno M; Aguiar-Soares, Rodrigo Dian D O; Ruiz, Jeronimo C; Resende, Daniela de M; Reis, Alexandre B

    2018-01-01

    Due to an increase in the incidence of leishmaniases worldwide, the development of new strategies such as prophylactic vaccines to prevent infection and decrease the disease have become a high priority. Classic vaccines against leishmaniases were based on live or attenuated parasites or their subunits. Nevertheless, the use of whole parasite or their subunits for vaccine production has numerous disadvantages. Therefore, the use of Leishmania peptides to design more specific vaccines against leishmaniases seems promising. Moreover, peptides have several benefits in comparison with other kinds of antigens, for instance, good stability, absence of potentially damaging materials, antigen low complexity, and low-cost to scale up. By contrast, peptides are poor immunogenic alone, and they need to be delivered correctly. In this context, several approaches described in this review are useful to solve these drawbacks. Approaches, such as, peptides in combination with potent adjuvants, cellular vaccinations, adenovirus, polyepitopes, or DNA vaccines have been used to develop peptide-based vaccines. Recent advancements in peptide vaccine design, chimeric, or polypeptide vaccines and nanovaccines based on particles attached or formulated with antigenic components or peptides have been increasingly employed to drive a specific immune response. In this review, we briefly summarize the old, current, and future stands on peptide-based vaccines, describing the disadvantages and benefits associated with them. We also propose possible approaches to overcome the related weaknesses of synthetic vaccines and suggest future guidelines for their development.

  1. Peptide Nucleic Acids

    2004-01-01

    A novel class of compounds known as peptide nucleic acids, bind complementary DNA and RNA strands, and generally do so more strongly than the corresponding DNA or RNA strands while exhibiting increased sequence specificity and solubility. The peptide nucleic acids comprise ligands selected from...

  2. Peptide-based biosensors: From self-assembled interfaces to molecular probes in electrochemical assays.

    Puiu, Mihaela; Bala, Camelia

    2018-04-01

    Redox-tagged peptides have emerged as functional materials with multiple applications in the area of sensing and biosensing applications due to their high stability, excellent redox properties and versatility of biomolecular interactions. They allow direct observation of molecular interactions in a wide range of affinity and enzymatic assays and act as electron mediators. Short helical peptides possess the ability to self-assemble in specific configurations with the possibility to develop in highly-ordered, stable 1D, 2D and 3D architectures in a hierarchical controlled manner. We provide here a brief overview of the electrochemical techniques available to study the electron transfer in peptide films with particular interest in developing biosensors with immobilized peptide motifs, for biological and clinical applications. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Design study of a normal conducting helical snake for AGS

    Takano, Junpei; Okamura, Masahiro; Roser, Thomas; MacKay, William W; Luccio, Alfredo U; Takano, Koji

    2004-01-01

    A new normal conducting snake magnet is being fabricated for the Alternate Gradient Synchrotron (AGS) at Brookhaven National Laboratory (BNL). In the Relativistic Heavy Ion Collider (RHIC) project, a superconducting type helical dipole magnets had been developed and it performed successfully in high-energy polarized proton acceleration. The new AGS helical snake has the same basic magnetic structure but is more complicated. To achieve no beam shift and no beam deflection in one magnetic device, helical pitches and rotating angles were carefully calculated. Compared to a superconducting magnet, a normal warm magnet must have a large cross- sectional area of conductors which make it difficult to design a magnet with large helical pitch. We developed a modified window frame structure to accommodate the large number of conductors. Its three dimensional magnetic field was simulated by using OPERA3D/TOSCA. 3 Refs.

  4. A 3D printed helical antenna with integrated lens

    Farooqui, Muhammad Fahad; Shamim, Atif

    2015-01-01

    A novel antenna configuration comprising a helical antenna with an integrated lens is demonstrated in this work. The antenna is manufactured by a unique combination of 3D printing of plastic material (ABS) and inkjet printing of silver nano

  5. Particle orbit analysis for LHD helical axis configurations

    Guasp, J.; Yamazaki, K.; Motojima, O.

    1993-04-01

    Fast ion orbits for helical magnetic axis configurations in LHD (Large Helical Device) are analyzed and compared with the standard circular axis case. Boundaries between passing and helically trapped particle regions show clear differences: in the non-planar axis case the helically trapped region spreads, near the magnetic axis, over a much wider band across the 90deg pitch angle value and shows a very marked asymmetry. The locally trapped particle region is also wider than in the standard case. The differences in the loss cone boundaries of the two cases are rather small, however, the effects of re-entering criteria are very important in both cases. On the contrary, effects of finite coil size are not significant. (author)

  6. Metallic and 3D-printed dielectric helical terahertz waveguides.

    Vogt, Dominik Walter; Anthony, Jessienta; Leonhardt, Rainer

    2015-12-28

    We investigate guidance of Terahertz (THz) radiation in metallic and 3D-printed dielectric helical waveguides in the frequency range from 0.2 to 1 THz. Our experimental results obtained from THz time-domain spectroscopy (THz-TDS) measurements are in very good agreement with finite-difference time-domain (FDTD) simulations. We observe single-mode, low loss and low dispersive propagation of THz radiation in metallic helical waveguides over a broad bandwidth. The 3D-printed dielectric helical waveguides have substantially extended the bandwidth of a low loss dielectric tube waveguide as observed from the experimental and simulation results. The high flexibility of the helical design allows an easy incorporation into bench top THz devices.

  7. Helical-axis stellarators with noninterlocking planar coils

    Reiman, A.; Boozer, A.

    1983-08-01

    The properties of helical axis stellarator fields generated by unlinked, planar coils are described. It is shown that such fields can have a magnetic well and large rotational transform, implying large equilibrium and stability beta limits

  8. Helical-axis stellarators with noninterlocking planar coils

    Reiman, A.; Boozer, A.

    1983-08-01

    The properties of helical axis stellarator fields generated by unlinked, planar coils are described. It is shown that such fields can have a magnetic well and large rotational transform, implying large equilibrium and stability beta limits.

  9. Energy and helicity of magnetic torus knots and braids

    Oberti, Chiara; Ricca, Renzo L.

    2018-02-01

    By considering steady magnetic fields in the shape of torus knots and unknots in ideal magnetohydrodynamics, we compute some fundamental geometric and physical properties to provide estimates for magnetic energy and helicity. By making use of an appropriate parametrization, we show that knots with dominant toroidal coils that are a good model for solar coronal loops have negligible total torsion contribution to magnetic helicity while writhing number provides a good proxy. Hence, by the algebraic definition of writhe based on crossing numbers, we show that the estimated values of writhe based on image analysis provide reliable information for the exact values of helicity. We also show that magnetic energy is linearly related to helicity, and the effect of the confinement of magnetic field can be expressed in terms of geometric information. These results can find useful application in solar and plasma physics, where braided structures are often present.

  10. Investigation into the heat transfer performance of helically ribbed surfaces

    Firth, R.J.

    1981-12-01

    The first part of an investigation into flow and heat transfer in annular channels and seven pin clusters is described. One of the main aims of the project is to improve cluster heat transfer prediction codes for helically ribbed surfaces. A study is made of the heat transfer and flow characteristics of a helically ribbed pin in an annular channel. It is shown that the swirling flow, which is induced by the helical ribs, gives rise to substantially enhanced diffusivity levels. This phenomenon had not been taken into account by previous analysis techniques. The methods for analysing heat transfer and pressure drop data from annular channels which were originally developed for non-swirling flow are generalised to accommodate swirling flow. The new methods are shown to be consistent with empirical data. Roughness parameter data is presented for helically ribbed surfaces with an axial rib pitch into height ratio of about 7. (author)

  11. Energy fluxes in helical magnetohydrodynamics and dynamo action

    Kinetic and magnetic helicities do not affect the renormalized parameters, ... Generation of magnetic field in plasma, usually referred to as 'dynamo', is one of the ..... energy fluxes for the inertial-range wave numbers where the same power.

  12. Consumerism and the Sister Carrie's American Dream%Consumerism and the Sister Carrie''s American Dream

    卢亚丽

    2017-01-01

    From the aspect of consumerism to this text analyze Sister Carrie's"American dream"destruction. The author wholly and deeply analyzes the embodiment of consumerism in Dreiser's Sister Carrie and Dreiser's outlook and values under the effect of consumerism. To prove that the reason for destruction of Carrie's American dream is consumerism.

  13. Novel short antibacterial and antifungal peptides with low cytotoxicity: Efficacy and action mechanisms

    Qi, Xiaobao; Zhou, Chuncai; Li, Peng [School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 Singapore (Singapore); Xu, Weixin [School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore (Singapore); Cao, Ye; Ling, Hua; Ning Chen, Wei; Ming Li, Chang; Xu, Rong [School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 Singapore (Singapore); Lamrani, Mouad [Menicon Co., Ltd. Immeuble Espace Cordeliers, 2, rue President Carnot, 69002 Lyon (France); Mu, Yuguang, E-mail: ygmu@ntu.edu.sg [School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore (Singapore); Leong, Susanna Su Jan [School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 Singapore (Singapore); Wook Chang, Matthew, E-mail: matthewchang@ntu.edu.sg [School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 Singapore (Singapore); Chan-Park, Mary B., E-mail: mbechan@ntu.edu.sg [School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 Singapore (Singapore)

    2010-07-30

    Research highlights: {yields} Short antimicrobial peptides with nine and eleven residues were developed. {yields} These peptides show strong bactericidal activity against clinically important bacterial and fungal pathogens. {yields} These peptides exhibit high stability in the presence of salts, and low cytotoxicity. {yields} These peptides exert their action by disrupting membrane lipids. -- Abstract: Short antimicrobial peptides with nine and eleven residues were developed against several clinically important bacterial and fungal pathogens (specifically Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Candida albicans, and Fusarium solani). Twelve analogues of previously reported peptides BP76 (KKLFKKILKFL) and Pac-525 (KWRRWVRWI) were designed, synthesized, and tested for their antimicrobial activities. Two of our eleven amino acid peptides, P11-5 (GKLFKKILKIL) and P11-6 (KKLIKKILKIL), have very low MICs of 3.1-12.5 {mu}g ml{sup -1} against all five pathogens. The MICs of these two peptides against S. aureus, C. albicans and F. solani are four to ten times lower than the corresponding MICs of the reference peptide BP76. P9-4 (KWRRWIRWL), our newly designed nine-amino acid analogue, also has particularly low MICs of 3.1-6.2 {mu}g ml{sup -1} against four of the tested pathogens; these MICs are two to eight times lower than those reported for Pac-525 (6.2-50 {mu}g ml{sup -1}).These new peptides (P11-5, P11-6 and P9-4) also exhibit improved stability in the presence of salts, and have low cytotoxicity as shown by the hemolysis and MTT assays. From the results of field-emission scanning electron microscopy, membrane depolarization and dye-leakage assays, we propose that these peptides exert their action by disrupting membrane lipids. Molecular dynamics simulation studies confirm that P11-6 peptide maintains relatively stable helical structure and exerts more perturbation action on the order of acyl tail of lipid bilayer.

  14. The Cyclic Antibacterial Peptide Enterocin AS-48: Isolation, Mode of Action, and Possible Food Applications

    Grande Burgos, Mar?a Jos?; P?rez Pulido, Rub?n; L?pez Aguayo, Mar?a del Carmen; G?lvez, Antonio; Lucas, Rosario

    2014-01-01

    Enterocin AS-48 is a circular bacteriocin produced by Enterococcus. It contains a 70 amino acid-residue chain circularized by a head-to-tail peptide bond. The conformation of enterocin AS-48 is arranged into five alpha-helices with a compact globular structure. Enterocin AS-48 has a wide inhibitory spectrum on Gram-positive bacteria. Sensitivity of Gram-negative bacteria increases in combination with outer-membrane permeabilizing treatments. Eukaryotic cells are bacteriocin-resistant. This ...

  15. Acute pulmonary embolism in helical computed tomography

    Paslawski, M.

    2005-01-01

    Pulmonary embolism is a common condition in which diagnostic and therapeutic delays contribute to substantial morbidity and mortality. Clinical diagnosis is difficult because the signs and symptoms re unspecific, and a differential diagnosis is extensive, including pneumonia or bronchitis, asthma, myocardial infraction, pulmonary edema, anxiety, dissection of the aorta, pericardial tamponade, lung cancer, primary pulmonary hypertension, rib fracture, and pneumothorax. The purpose of the study was to present the use of CT in diagnosing acute pulmonary embolism. A group of 23 patients with clinically suspected pulmonary embolism underwent CT examination with a helical CT scanner (Somatom Emotion, Siemens) before and after administration of 150 ml of Ultravist. Pulmonary embolism was found in the CT examinations of 13 patients. In two of these it was a central filling defect. Amputation of the artery was found in one. Parietal filling defect in three patients formed an acute angle with the vessel walls. Saddle emboli appearing as filling defects in the contrast column that hung over vessel bifurcations was found in two patients. In five patients,emboli were found in small segmental arteries. CT provides information not only on the pulmonary arteries, but also on the lung parenchyma, hila, mediastinum, and the heart. Alternative findings may be identified by CT chest examination, stablishing alternative diagnoses, including pulmonary disorders (such as pneumonia or fibrosis), pleural abnormalities, and cardiovascular disease (such as aortic dissection or pericardial tamponade). Another advantage of the CT is its widespread availability.(author)

  16. Polymer dynamics driven by a helical filament

    Balin, Andrew; Shendruk, Tyler; Zoettl, Andreas; Yeomans, Julia

    Microbial flagellates typically inhabit complex suspensions of extracellular polymeric material which can impact the swimming speed of motile microbes, filter-feeding of sessile cells, and the generation of biofilms. There is currently a need to better understand how the fundamental dynamics of polymers near active cells or flagella impacts these various phenomena. We study the hydrodynamic and steric influence of a rotating helical filament on suspended polymers using Stokesian Dynamics simulations. Our results show that as a stationary rotating helix pumps fluid along its long axis, nearby polymers migrate radially inwards and are elongated in the process. We observe that the actuation of the helix tends to increase the probability of finding polymeric material within its pervaded volume. At larger Weissenberg numbers, this accumulation of polymers within the vicinity of the helix is greater. Further, we have analysed the stochastic work performed by the helix on the polymers and we show that this quantity is positive on average and increases with polymer contour length. Our results provide a basis for understanding the microscopic interactions that govern cell dynamics in complex media. This work was supported through funding from the ERC Advanced Grant 291234 MiCE and we acknowledge EMBO funding to TNS (ALTF181-2013).

  17. Electronic Band Structure of Helical Polyisocyanides.

    Champagne, Benoît; Liégeois, Vincent; Fripiat, Joseph G; Harris, Frank E

    2017-10-19

    Restricted Hartree-Fock computations are reported for a methyl isocyanide polymer (repeating unit -C═N-CH 3 ), whose most stable conformation is expected to be a helical chain. The computations used a standard contracted Gaussian orbital set at the computational levels STO-3G, 3-21G, 6-31G, and 6-31G**, and studies were made for two line-group configurations motivated by earlier work and by studies of space-filling molecular models: (1) A structure of line-group symmetry L9 5 , containing a 9-fold screw axis with atoms displaced in the axial direction by 5/9 times the lattice constant, and (2) a structure of symmetry L4 1 that had been proposed, containing a 4-fold screw axis with translation by 1/4 of the lattice constant. Full use of the line-group symmetry was employed to cause most of the computational complexity to depend only on the size of the asymmetric repeating unit. Data reported include computed bond properties, atomic charge distribution, longitudinal polarizability, band structure, and the convoluted density of states. Most features of the description were found to be insensitive to the level of computational approximation. The work also illustrates the importance of exploiting line-group symmetry to extend the range of polymer structural problems that can be treated computationally.

  18. Energetics of load carrying in Nepalese porters.

    Bastien, Guillaume J; Schepens, Bénédicte; Willems, Patrick A; Heglund, Norman C

    2005-06-17

    Nepalese porters routinely carry head-supported loads equal to 100 to 200% of their body weight (Mb) for many days up and down steep mountain footpaths at high altitudes. Previous studies have shown that African women carry head-supported loads of up to 60% of their Mb far more economically than army recruits carrying equivalent loads in backpacks. Here we show that Nepalese porters carry heavier loads even more economically than African women. Female Nepalese porters, for example, carry on average loads that are 10% of their Mb heavier than the maximum loads carried by the African women, yet do so at a 25% smaller metabolic cost.

  19. Pulmonary artery aneurysm in Bechcet's disease: helical computed tomography study

    Munoz, J.; Caballero, P.; Olivera, M. J.; Cajal, M. L.; Caniego, J. L.

    2000-01-01

    Behcet's disease is a vasculitis of unknown etiology that affects arteries and veins of different sizes and can be associated with pulmonary artery aneurysms. We report the case of a patient with Behcet's disease and a pulmonary artery aneurysm who was studied by means of plain chest X ray, helical computed tomography and pulmonary arteriography. Helical computed tomography is a reliable technique for the diagnosis and follow-up of these patients. (Author) 9 refs

  20. ADDITIVE SELF-HELICITY AS A KINK MODE THRESHOLD

    Malanushenko, A.; Longcope, D. W.; Fan, Y.; Gibson, S. E.

    2009-01-01

    In this paper, we propose that additive self-helicity, introduced by Longcope and Malanushenko, plays a role in the kink instability for complex equilibria, similar to twist helicity for thin flux tubes. We support this hypothesis by a calculation of additive self-helicity of a twisted flux tube from the simulation of Fan and Gibson. As more twist gets introduced, the additive self-helicity increases, and the kink instability of the tube coincides with the drop of additive self-helicity, after the latter reaches the value of H A /Φ 2 ∼ 1.5 (where Φ is the flux of the tube and H A is the additive self-helicity). We compare the additive self-helicity to twist for a thin subportion of the tube to illustrate that H A /Φ 2 is equal to the twist number, studied by Berger and Field, when the thin flux tube approximation is applicable. We suggest that the quantity H A /Φ 2 could be treated as a generalization of a twist number, when the thin flux tube approximation is not applicable. A threshold on a generalized twist number might prove extremely useful studying complex equilibria, just as the twist number itself has proven useful studying idealized thin flux tubes. We explicitly describe a numerical method for calculating additive self-helicity, which includes an algorithm for identifying a domain occupied by a flux bundle and a method of calculating potential magnetic field confined to this domain. We also describe a numerical method to calculate twist of a thin flux tube, using a frame parallelly transported along the axis of the tube.

  1. Tokamak startup using point-source dc helicity injection.

    Battaglia, D J; Bongard, M W; Fonck, R J; Redd, A J; Sontag, A C

    2009-06-05

    Startup of a 0.1 MA tokamak plasma is demonstrated on the ultralow aspect ratio Pegasus Toroidal Experiment using three localized, high-current density sources mounted near the outboard midplane. The injected open field current relaxes via helicity-conserving magnetic turbulence into a tokamaklike magnetic topology where the maximum sustained plasma current is determined by helicity balance and the requirements for magnetic relaxation.

  2. Comparison between helical computed tomography angiography and intraoperative findings

    Abijit Shetty

    2014-01-01

    Conclusions: Helical CT is important in delineating the arterial, venous, and ureteral anatomy and can show the important incidental findings. Left renal donors and males have more variations in their renal anatomy. Technically challenging laparoscopic nephrectomy on the multiple-vessel-side donor is possible with the aid of helical CT. The importance of the CT in evaluating donor renal anatomy for a technically challenging laparoscopic donor nephrectomy is commendable.

  3. Scale Dependence of Magnetic Helicity in the Solar Wind

    Brandenburg, Axel; Subramanian, Kandaswamy; Balogh, Andre; Goldstein, Melvyn L.

    2011-01-01

    We determine the magnetic helicity, along with the magnetic energy, at high latitudes using data from the Ulysses mission. The data set spans the time period from 1993 to 1996. The basic assumption of the analysis is that the solar wind is homogeneous. Because the solar wind speed is high, we follow the approach first pioneered by Matthaeus et al. by which, under the assumption of spatial homogeneity, one can use Fourier transforms of the magnetic field time series to construct one-dimensional spectra of the magnetic energy and magnetic helicity under the assumption that the Taylor frozen-in-flow hypothesis is valid. That is a well-satisfied assumption for the data used in this study. The magnetic helicity derives from the skew-symmetric terms of the three-dimensional magnetic correlation tensor, while the symmetric terms of the tensor are used to determine the magnetic energy spectrum. Our results show a sign change of magnetic helicity at wavenumber k approximately equal to 2AU(sup -1) (or frequency nu approximately equal to 2 microHz) at distances below 2.8AU and at k approximately equal to 30AU(sup -1) (or nu approximately equal to 25 microHz) at larger distances. At small scales the magnetic helicity is positive at northern heliographic latitudes and negative at southern latitudes. The positive magnetic helicity at small scales is argued to be the result of turbulent diffusion reversing the sign relative to what is seen at small scales at the solar surface. Furthermore, the magnetic helicity declines toward solar minimum in 1996. The magnetic helicity flux integrated separately over one hemisphere amounts to about 10(sup 45) Mx(sup 2) cycle(sup -1) at large scales and to a three times lower value at smaller scales.

  4. Concept and development of measurement method of time sensitivity profile (TSP) in X-ray CT. Comparison of non-helical, single-slice helical, and multi-slice helical scans

    Tsujioka, Katsumi; Ida, Yoshihiro; Ohtsubo, Hironori; Takahashi, Yasukata; Niwa, Masayoshi

    2000-01-01

    We focused on the time element contained in a single CT image, and devised the concept of a time-sensitivity profile (TSP) describing how the time element is translated into an image. We calculated the data collection time range when the helical pitch is changed in non helical scans, single slice helical scans, and multi slice helical scans. We then calculated the time sensitivity profile (TSP) from the weighting applied when the data collection time range is translated into an image. TSP was also measured for each scanning method using our self-made moving phantom. TSPs obtained from the calculation and the experiments were very close. TSP showed interesting characteristics with each scanning method, especially in the case of multi slice helical scanning, in which TSP became shorter as helical pitch increased. We referred to the TSP's FWHM as the effective scanning time. When we conducted multi slice helical scanning at helical pitch 3, the effective scanning time increased to about 24% longer than that of a non helical scan. When we conducted multi slice helical scanning at helical pitch 5 or 6, the effective scanning time was about half that of a non helical scan. The time sensitivity profile (TSP) is a totally new concept that we consider an important element in discussing the time resolution of a CT scanner. The results of this review will provide significant data in determining the scanning parameters when scanning a moving object. (author)

  5. Predicting Three-Dimensional Conformations of Peptides Constructed of Only Glycine, Alanine, Aspartic Acid, and Valine

    Oda, Akifumi; Fukuyoshi, Shuichi

    2015-06-01

    The GADV hypothesis is a form of the protein world hypothesis, which suggests that life originated from proteins (Lacey et al. 1999; Ikehara 2002; Andras 2006). In the GADV hypothesis, life is thought to have originated from primitive proteins constructed of only glycine, alanine, aspartic acid, and valine ([GADV]-proteins). In this study, the three-dimensional (3D) conformations of randomly generated short [GADV]-peptides were computationally investigated using replica-exchange molecular dynamics (REMD) simulations (Sugita and Okamoto 1999). Because the peptides used in this study consisted of only 20 residues each, they could not form certain 3D structures. However, the conformational tendencies of the peptides were elucidated by analyzing the conformational ensembles generated by REMD simulations. The results indicate that secondary structures can be formed in several randomly generated [GADV]-peptides. A long helical structure was found in one of the hydrophobic peptides, supporting the conjecture of the GADV hypothesis that many peptides aggregated to form peptide multimers with enzymatic activity in the primordial soup. In addition, these results indicate that REMD simulations can be used for the structural investigation of short peptides.

  6. Interactions of photoactive DNAs with terminal deoxynucleotidyl transferase: Identification of peptides in the DNA binding domain

    Farrar, Y.J.K.; Evans, R.K.; Beach, C.M.; Coleman, M.S.

    1991-01-01

    Terminal deoxynucleotidyl transferase (terminal transferase) was specifically modified in the DNA binding site by a photoactive DNA substrate (hetero-40-mer duplex containing eight 5-azido-dUMP residues at one 3' end). Under optimal photolabeling conditions, 27-40% of the DNA was covalently cross-linked to terminal transferase. The specificity of the DNA and protein interaction was demonstrated by protection of photolabeling at the DNA binding domain with natural DNA substrates. In order to recover high yields of modified peptides from limited amounts of starting material, protein modified with 32 P-labeled photoactive DNA and digested with trypsin was extracted 4 times with phenol followed by gel filtration chromatography. All peptides not cross-linked to DNA were extracted into the phenol phase while the photolyzed DNA and the covalently cross-linked peptides remained in the aqueous phase. The 32 P-containing peptide-DNA fraction was subjected to amino acid sequence analysis. Two sequences, Asp 221 -Lys 231 (peptide B8) and Cys 234 -Lys 249 (peptide B10), present in similar yield, were identified. Structure predictions placed the two peptides in an α-helical array of 39 angstrom which would accommodate a DNA helix span of 11 nucleotides. These peptides share sequence similarity with a region in DNA polymerase β that has been implicated in the binding of DNA template

  7. Cell-penetrating recombinant peptides for potential use in agricultural pest control applications.

    Hughes, Stephen R; Dowd, Patrick F; Johnson, Eric T

    2012-09-28

    Several important areas of interest intersect in a class of peptides characterized by their highly cationic and partly hydrophobic structure. These molecules have been called cell-penetrating peptides (CPPs) because they possess the ability to translocate across cell membranes. This ability makes these peptides attractive candidates for delivery of therapeutic compounds, especially to the interior of cells. Compounds with characteristics similar to CPPs and that, in addition, have antimicrobial properties are being investigated as antibiotics with a reduced risk of causing resistance. These CPP-like membrane-acting antimicrobial peptides (MAMPs) are α-helical amphipathic peptides that interact with and perturb cell membranes to produce their antimicrobial effects. One source of MAMPs is spider venom. Because these compounds are toxic to insects, they also show promise for development as biological agents for control of insecticide-resistant agricultural pests. Spider venom is a potential source of novel insect-specific peptide toxins. One example is the small amphipathic α-helical peptide lycotoxin-1 (Lyt-1 or LCTX) from the wolf spider (Lycosa carolinensis). One side of the α-helix has mostly hydrophilic and the other mainly hydrophobic amino acid residues. The positive charge of the hydrophilic side interacts with negatively charged prokaryotic membranes and the hydrophobic side associates with the membrane lipid bilayer to permeabilize it. Because the surface of the exoskeleton, or cuticle, of an insect is highly hydrophobic, to repel water and dirt, it would be expected that amphipathic compounds could permeabilize it. Mutagenized lycotoxin 1 peptides were produced and expressed in yeast cultures that were fed to fall armyworm (Spodoptera frugiperda) larvae to identify the most lethal mutants. Transgenic expression of spider venom toxins such as lycotoxin-1 in plants could provide durable insect resistance.

  8. Radio peptide imaging and therapy

    Buscombe, Jonh

    1997-01-01

    Full text. The concept of the magic bullet retains its attraction to us. If only we could take a drug or radioisotope and inject this intravenously and then will attach to the target cancer. This may allow imaging if labelled with a radio pharmaceutical or possibly even effective therapy. Initially work was started using antibodies of mouse origin. These have shown some utility in targeting tumors but there are problems in that these are essentially non-human proteins, often derived from mice. This leads to the formation of antibodies against that antibody so that repeat administrations lead to reduced efficacy and possibly may carry a risk anaphylaxis for the patient. Two different methods have evolved to deal with this situation. Either make antibodies more human or use smaller fragments, so that they are less likely to cause allergic reactions. The second method is to try and use a synthetic peptide. This will contain a series of amino acids which recognize a certain cell receptor. For example the somatostatin analogue Octreotide is an 8 amino acid peptide which has the same biological actions as natural somatostatin but an increased plasma half life. To this is added a linker a good example being DTPA and then radioisotope for example In-111. There we can have the complex In-111-DTPA-Octreotide which can be used to image somatostatin receptors in vivo. The main advantage over antibodies is that the cost production is less and many different variation of peptides for a particular receptor can be manufactured and assessed to find which is the optimal agent tumour imaging at a fraction of the cost of antibody production. There are two main approaches. Firstly to take a natural peptide hormone such as insulin or VIP and label by a simple method such as iodination with I-123. A group in Vienna have done it and shown good uptake of I-123 Insulin in primary hepatomas and of I-123 VIP in pancreatic cancers. Many natural peptide hormones however have a short plasma half

  9. Common and divergent structural features of a series of corticotropin releasing factor-related peptides.

    Grace, Christy Rani R; Perrin, Marilyn H; Cantle, Jeffrey P; Vale, Wylie W; Rivier, Jean E; Riek, Roland

    2007-12-26

    Members of the corticoliberin family include the corticotropin releasing factors (CRFs), sauvagine, the urotensins, and urocortin 1 (Ucn1), which bind to both the CRF receptors CRF-R1 and CRF-R2, and the urocortins 2 (Ucn2) and 3 (Ucn3), which are selective agonists of CRF-R2. Structure activity relationship studies led to several potent and long-acting analogues with selective binding to either one of the receptors. NMR structures of six ligands of this family (the antagonists astressin B and astressin2-B, the agonists stressin1, and the natural ligands human Ucn1, Ucn2, and Ucn3) were determined in DMSO. These six peptides show differences in binding affinities, receptor-selectivity, and NMR structure. Overall, their backbones are alpha-helical, with a small kink or a turn around residues 25-27, resulting in a helix-loop-helix motif. The C-terminal helices are of amphipathic nature, whereas the N-terminal helices vary in their amphipathicity. The C-terminal helices thereby assume a conformation very similar to that of astressin bound to the ECD1 of CRF-R2 recently reported by our group.1 On the basis of an analysis of the observed 3D structures and relative potencies of [Ala]-substituted analogues, it is proposed that both helices could play a crucial role in receptor binding and selectivity. In conclusion, the C-terminal helices may interact along their hydrophobic faces with the ECD1, whereas the entire N-terminal helical surface may be involved in receptor activation. On the basis of the common and divergent features observed in the 3D structures of these ligands, multiple binding models are proposed that may explain their plurality of actions.

  10. Designer lipid-like peptides: a class of detergents for studying functional olfactory receptors using commercial cell-free systems.

    Corin, Karolina; Baaske, Philipp; Ravel, Deepali B; Song, Junyao; Brown, Emily; Wang, Xiaoqiang; Wienken, Christoph J; Jerabek-Willemsen, Moran; Duhr, Stefan; Luo, Yuan; Braun, Dieter; Zhang, Shuguang

    2011-01-01

    A crucial bottleneck in membrane protein studies, particularly G-protein coupled receptors, is the notorious difficulty of finding an optimal detergent that can solubilize them and maintain their stability and function. Here we report rapid production of 12 unique mammalian olfactory receptors using short designer lipid-like peptides as detergents. The peptides were able to solubilize and stabilize each receptor. Circular dichroism showed that the purified olfactory receptors had alpha-helical secondary structures. Microscale thermophoresis suggested that the receptors were functional and bound their odorants. Blot intensity measurements indicated that milligram quantities of each olfactory receptor could be produced with at least one peptide detergent. The peptide detergents' capability was comparable to that of the detergent Brij-35. The ability of 10 peptide detergents to functionally solubilize 12 olfactory receptors demonstrates their usefulness as a new class of detergents for olfactory receptors, and possibly other G-protein coupled receptors and membrane proteins.

  11. Designer lipid-like peptides: a class of detergents for studying functional olfactory receptors using commercial cell-free systems.

    Karolina Corin

    Full Text Available A crucial bottleneck in membrane protein studies, particularly G-protein coupled receptors, is the notorious difficulty of finding an optimal detergent that can solubilize them and maintain their stability and function. Here we report rapid production of 12 unique mammalian olfactory receptors using short designer lipid-like peptides as detergents. The peptides were able to solubilize and stabilize each receptor. Circular dichroism showed that the purified olfactory receptors had alpha-helical secondary structures. Microscale thermophoresis suggested that the receptors were functional and bound their odorants. Blot intensity measurements indicated that milligram quantities of each olfactory receptor could be produced with at least one peptide detergent. The peptide detergents' capability was comparable to that of the detergent Brij-35. The ability of 10 peptide detergents to functionally solubilize 12 olfactory receptors demonstrates their usefulness as a new class of detergents for olfactory receptors, and possibly other G-protein coupled receptors and membrane proteins.

  12. Plural three-wave resonances of space charge wave harmonics in transit section of klystron-type two-stream FEL with helical electron beam

    Lysenko, Alexander; Volk, Iurii; Serozhko, Anastasia

    2017-01-01

    We have carried out the research of plural three-wave resonances of space charge wave (SCW) harmonics in the transit section of the klystron type two-stream superheterodyne free-electron laser (TSFEL) with helical electron beam in cubic non-linear approximation. We have found out that two...

  13. Consumerism and the Sister Carrie's American Dream

    卢亚丽

    2017-01-01

    From the aspect of consumerism to this text analyze Sister Carrie's"American dream"destruction. The author wholly and deeply analyzes the embodiment of consumerism in Dreiser's Sister Carrie and Dreiser's outlook and values under the effect of consumerism. To prove that the reason for destruction of Carrie's American dream is consumerism.

  14. Local Dynamic Stability Associated with Load Carrying

    Jian Liu

    2013-03-01

    Conclusion: Current study confirmed the sensitivity of local dynamic stability measure in load carrying situation. It was concluded that load carrying tasks were associated with declined local dynamic stability, which may result in increased risk of fall accident. This finding has implications in preventing fall accidents associated with occupational load carrying.

  15. Divertor Heat Flux Reduction by Resonant Magnetic Perturbations in the LHD-Type Helical DEMO Reactor

    Yanagi, N.; Sagara, A.; Goto, T.; Masuzaki, S.; Miyazawa, J., E-mail: yanagi@lhd.nifs.ac.jp [National Institute for Fusion Science, Toki (Japan)

    2012-09-15

    Full text: The conceptual design studies of the LHD-type helical fusion DEMO reactor, FFHR-d1, are progressing steadfastly. The LHD-type heliotron magnetic configuration equipped with the built- in helical divertors has a potential to realize low divertor heat flux in spatial average. However, the toroidal asymmetry may give more than a couple of times higher peak heat flux at some locations, as has been experimentally observed in LHD and confirmed by magnetic field-line tracing. By providing radiation dispersion accompanied with a plasma detachment, the heat flux may decrease significantly though the compatibility with a good core plasma confinement is an important issue to be explored. Whereas the engineering difficulties for developing materials to be used under the neutron environment require even further decrease of the heat flux (even though the heliotron is a unique configuration that divertor plates be largely shielded from the direct irradiation of neutrons by breeder blankets). In this respect, we proposed, in the last IAEA FEC, a new strike point sweeping scheme using a set of auxiliary helical coils, termed helical divertor (HD) coils. The HD coils carrying a few percent of the current amplitude of the main helical coils sweep the divertor strike points without altering the core plasma. Though this scheme is effective in dispersing the heat flux in the poloidal direction, the toroidal asymmetry still remains. The AC operation may also give unforeseen engineering difficulties. We here propose that the peak heat flux be mitigated using RMP fields in steady-state. The magnetic field-lines are numerically traced in the vacuum configuration and their footprints coming to the divertor regions are counted. Their fraction plotted as a function of the toroidal angle indicates that the peak heat flux be mitigated to {approx} 20 MW per square meters at 3 GW fusion power generation without having radiation dispersion when an RMP field is applied. We note that the

  16. Helical Birods: An Elastic Model of Helically Wound Double-Stranded Rods

    Prior, Christopher

    2014-03-11

    © 2014, Springer Science+Business Media Dordrecht. We consider a geometrically accurate model for a helically wound rope constructed from two intertwined elastic rods. The line of contact has an arbitrary smooth shape which is obtained under the action of an arbitrary set of applied forces and moments. We discuss the general form the theory should take along with an insight into the necessary geometric or constitutive laws which must be detailed in order for the system to be complete. This includes a number of contact laws for the interaction of the two rods, in order to fit various relevant physical scenarios. This discussion also extends to the boundary and how this composite system can be acted upon by a single moment and force pair. A second strand of inquiry concerns the linear response of an initially helical rope to an arbitrary set of forces and moments. In particular we show that if the rope has the dimensions assumed of a rod in the Kirchhoff rod theory then it can be accurately treated as an isotropic inextensible elastic rod. An important consideration in this demonstration is the possible effect of varying the geometric boundary constraints; it is shown the effect of this choice becomes negligible in this limit in which the rope has dimensions similar to those of a Kirchhoff rod. Finally we derive the bending and twisting coefficients of this effective rod.

  17. Recent Results of Helical Nonneutral Plasmas on Compact Helical System (CHS)

    Himura, H.; Yamamoto, Y.; Sanpei, A.; Masamune, S.; Wakabayashi, H.; Isobe, M.

    2006-01-01

    First of all, non-constant space potential φs and electron density ne on magnetic surfaces of helical nonneutral plasmas are verified experimentally. The difference in φs enlarges significantly at the outer region inside the closed magnetic surfaces, and the corresponding equipotential surfaces are inferred to shift upward vertically with respect to magnetic surfaces. Meanwhile, larger value of ne is clearly observed in the downward region (z < 0) of magnetic surfaces, which seems to be consistent with the φs measurement. These results are the first evidence which strongly suggests the equilibrium proposed for nonneutral plasmas confined in closed magnetic surfaces. Secondly, in order to investigate the mechanism of the multiple disruption of helical nonneutral plasmas observed in experiments, space and time evolutions of electron flux are measured carefully inside the magnetic surfaces, when the plasma disruption occurs. Surprisingly, a set of data show that the observed disruption is at first happened at ρ ∼ 0.8, where ρ is the normalized minor radius, and then, it seems to propagate inside magnetic surfaces

  18. Electrohydrodynamic (EHD) vortices in helical turbulence

    Kikuchi, H.

    1996-01-01

    The study of large-scale coherent hydrodynamic (HD) vortex generation has been extended to electrified charged dusty vortices to be termed as electrohydrodynamic (EHD) vortices, incorporating helical turbulence in electric and magnetic fields into that in fluid velocity, which are all created by an external DC electric field on the background. A new equation of EHD vortices is introduced on the basis of a set of EHD or electromagnetohydrodynamic (EMHD) equations, including equations of state and a full set of Maxwell's equations by using functional techniques for estimating equations for an ensemble average, turbulent background, and additional random field. In fact, EHD vortices for a charged dusty fluid can be more explosive with larger instabilities than HD vortices. In addition, it is inferred that an external DC electric field could provide the origin of additional self-organization to a coalescence of fluid vortex and electric field lines as a manifestation of a new frozen-in field concept for electric fields when the electric Reynolds number is sufficiently high. This is discussed on the basis of a set of general transport equations for fluid vorticity, magnetic and electric fields that are rederived concisely. In particular, a novel concept of electric field line merging-reconnection is developed in close relation to fluid vortex line merging, indicating a coalescence of fluid vortex breakdown or merging point and electric field line reconnection point, X-type or O-type with possible application to tornadic thunderstorms. In fact, a thundercloud charge distribution so as to provide a coalescence of fluid vortex and electric field lines is quite possible without theoretical inconsistency, and is thought most likely to occur from observations available so far. (orig.)

  19. Usefulness of helical computed tomography in the acute diverticulitis

    Rossini, S.A.; Gonzalez Villaveiran, R.F.; Merola, S.

    2009-01-01

    Objective: The evaluation of the usefulness of helical computed tomography (HCT) in the diagnosis and therapeutic management of the acute diverticulitis. Materials and methods: Six months retrospective cohort study of 100 patient population clinically suspected of diverticulitis was carried out. The exams were made with oral and intravenous contrast unless the patient presented contraindications. A correlation of these studies with the therapeutic response and clinical follow up was done with surgery and histopathology. Results: From a total of 100 patients studied, 62 presented tomographic diagnosis of diverticulitis, 41 were classified as simple diverticulitis and 21 were complicated cases (abscess, phlegmon, plastron, free perforation, vesicocolonic fistula and intestinal obstruction). In 24 patients an alternative diagnosis was made (appendicitis, appendagitis, urethral litiasis, colitis, salpingitis, pancreatitis, uraco cyst complication, colonic mechanical obstruction, colonic perforation with foreign body): 14 patients did not present tomographic findings to support the clinical symptoms, two of them were false-negative by the clinic and by the response to treatment. These data represented a sensibility of 96,87%, specificity of 100%, PPV of 100% and NPV of 94,7% and a certainty of 98 for the tomography diagnosis of acute diverticulitis. Of the 41 patients with tomographic diagnostic of not complicated diverticulitis, 37 received medical outpatient treatment and only 4 medical treatment with placement; of the 21 patients diagnosed with complicated diverticulitis, 18 were hospitalised with medical treatment and the other 3 patients needed surgery; of the 14 patients without tomographic findings of diverticulitis, in 12 outpatients an expectant conduct was followed and the other 2 received medical outpatient treatment. Conclusion: HCT is very useful and effective in diagnosis, evaluation and management of patients with clinical suspicion of diverticulitis

  20. Antimicrobial Peptide from the Wild Bee Hylaeus signatus Venom and Its Analogues: Structure-Activity Study and Synergistic Effect with Antibiotics

    Nešuta, Ondřej; Hexnerová, Rozálie; Buděšínský, Miloš; Slaninová, Jiřina; Bednárová, Lucie; Hadravová, Romana; Straka, J.; Veverka, Václav; Čeřovský, Václav

    2016-01-01

    Roč. 79, č. 4 (2016), s. 1073-1083 ISSN 0163-3864 R&D Projects: GA TA ČR(CZ) TA04010638; GA MŠk(CZ) LO1304 Institutional support: RVO:61388963 Keywords : alpha-helical peptides * in vitro activity * Pseudomonas aeruginosa Subject RIV: CC - Organic Chemistry Impact factor: 3.281, year: 2016

  1. Control of phospholipid flip-flop by transmembrane peptides

    Kaihara, Masanori; Nakao, Hiroyuki; Yokoyama, Hirokazu; Endo, Hitoshi; Ishihama, Yasushi; Handa, Tetsurou; Nakano, Minoru

    2013-01-01

    Highlights: ► Phospholipid flip-flop in transmembrane peptide-containing vesicles was investigated. ► Peptides that contained polar residues in the center of the transmembrane region promoted phospholipid flip-flop. ► A bioinformatics approach revealed the presence of polar residues in the transmembrane region of ER membrane proteins. ► Polar residues in ER membrane proteins possibly provide flippase-like activity. - Abstract: We designed three types of transmembrane model peptides whose sequence originates from a frequently used model peptide KALP23, and we investigated their effects on phospholipid flip-flop. Time-resolved small-angle neutron scattering and a dithionite fluorescent quenching assay demonstrated that TMP-L, which has a fully hydrophobic transmembrane region, did not enhance phospholipid flip-flop, whereas TMP-K and TMP-E, which have Lys and Glu, respectively, in the center of their transmembrane regions, enhanced phospholipid flip-flop. Introduction of polar residues in the membrane-spanning helices is considered to produce a locally polar region and enable the lipid head group to interact with the polar side-chain inside the bilayers, thereby reducing the activation energy for the flip-flop. A bioinformatics approach revealed that acidic and basic residues account for 4.5% of the central region of the transmembrane domain in human ER membrane proteins. Therefore, polar residues in ER membrane proteins are considered to provide flippase-like activity

  2. Selection of peptides interfering with protein-protein interaction.

    Gaida, Annette; Hagemann, Urs B; Mattay, Dinah; Räuber, Christina; Müller, Kristian M; Arndt, Katja M

    2009-01-01

    Cell physiology depends on a fine-tuned network of protein-protein interactions, and misguided interactions are often associated with various diseases. Consequently, peptides, which are able to specifically interfere with such adventitious interactions, are of high interest for analytical as well as medical purposes. One of the most abundant protein interaction domains is the coiled-coil motif, and thus provides a premier target. Coiled coils, which consist of two or more alpha-helices wrapped around each other, have one of the simplest interaction interfaces, yet they are able to confer highly specific homo- and heterotypic interactions involved in virtually any cellular process. While there are several ways to generate interfering peptides, the combination of library design with a powerful selection system seems to be one of the most effective and promising approaches. This chapter guides through all steps of such a process, starting with library options and cloning, detailing suitable selection techniques and ending with purification for further down-stream characterization. Such generated peptides will function as versatile tools to interfere with the natural function of their targets thereby illuminating their down-stream signaling and, in general, promoting understanding of factors leading to specificity and stability in protein-protein interactions. Furthermore, peptides interfering with medically relevant proteins might become important diagnostics and therapeutics.

  3. Folding and insertion thermodynamics of the transmembrane WALP peptide

    Bereau, Tristan, E-mail: bereau@mpip-mainz.mpg.de [Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany); Bennett, W. F. Drew [Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1 (Canada); Pfaendtner, Jim [Department of Chemical Engineering, University of Washington, Seattle, Washington 98195 (United States); Deserno, Markus [Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States); Karttunen, Mikko [Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, MetaForum, 5600 MB Eindhoven (Netherlands)

    2015-12-28

    The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA){sub n} (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide’s insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum—in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence.

  4. Folding and insertion thermodynamics of the transmembrane WALP peptide

    Bereau, Tristan; Bennett, W. F. Drew; Pfaendtner, Jim; Deserno, Markus; Karttunen, Mikko

    2015-01-01

    The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA) n (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide’s insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum—in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence

  5. Formation and electrochemical investigation of ordered cobalt coordinated peptide monolayers on gold substrates

    Wang Xinxin; Nagata, Kenji; Higuchi, Masahiro

    2012-01-01

    The monolayers composed of cobalt coordinated peptides were prepared on gold substrates by two different approaches. One was the self-assembly method, which was used to prepare a peptide monolayer on the gold substrate via the spontaneous attachment of peptides owing to the interaction between gold and sulfur at the N-terminal of the peptide. The other one was the stepwise polymerization method that was utilized to fabricate the unidirectionally arranged peptide monolayer by the stepwise condensation of amino acids from the initiator fixed on the gold substrate. Leu 2 Ala(4-Pyri)Leu 6 Ala(4-Pyri)Leu 6 sequence was chosen as the cobalt coordinated peptide. The 4-pyridyl alanines, Ala(4-Pyri)s, were introduced as ligands for cobalt to the leucine-rich sequential peptide. The complexation between cobalt and pyridyl groups of the peptide induced the formation of a stable α-helical bundle, which oriented perpendicularly to the substrate surface. In the case of the monolayer fabricated by the stepwise polymerization method, the direction of the peptide macro-dipole moment aligned unidirectionally, and the cobalt complexes were fixed in the monolayer to form the ordered arrangement. On the other hand, the peptides prepared by the self-assembly method formed the mixture of parallel and antiparallel packing owing to the dipole-dipole interaction. The spatial location of the cobalt complexes in the monolayer prepared by the self-assembly method was distorted, compared with that in the monolayer fabricated by the stepwise polymerization method. The vectorial electron flow through the peptide monolayer was achieved by the regular alignment of the peptide macro-dipole moment and the cobalt complexes in the monolayer fabricated by the stepwise polymerization method. - Highlights: ► We fabricated ordered Co coordinated peptide monolayers on the gold substrates. ► The Co complexes in peptide monolayer formed an ordered arrangement of the peptide. ► The peptide macro

  6. Diversity-oriented peptide stapling

    Tran, Thu Phuong; Larsen, Christian Ørnbøl; Røndbjerg, Tobias

    2017-01-01

    as a powerful method for peptide stapling. However, to date CuAAC stapling has not provided a simple method for obtaining peptides that are easily diversified further. In the present study, we report a new diversity-oriented peptide stapling (DOPS) methodology based on CuAAC chemistry. Stapling of peptides...

  7. Ripple transport in helical-axis advanced stellarators - a comparison with classical stellarator/torsatrons

    Beidler, C.D.; Hitchon, W.N.G.

    1993-08-01

    Calculations of the neoclassical transport rates due to particles trapped in the helical ripples of a stellarator's magnetic field are carried out, based on solutions of the bounce-averaged kinetic equation. These calculations employ a model for the magnetic field strength, B, which is an accurate approximation to the actual B for a wide variety of stellarator-type devices, among which are Helical-Axis Advanced Stellarators (Helias) as well as conventional stellarators and torsatrons. Comparisons are carried out in which it is shown that the Helias concept leads to significant reductions in neoclassical transport rates throughout the entire long-mean-free-path regime, with the reduction being particularly dramatic in the ν -1 regime. These findings are confirmed by numerical simulations. Further, it is shown that the behavior of deeply trapped particles in Helias can be fundamentally different from that in classical stellarator/torsatrons; as a consequence, the beneficial effects of a radial electric field on the transport make themselves felt at lower collision frequency than is usual. (orig.)

  8. Reversible pH-controlled DNA-binding peptide nanotweezers: An in-silico study

    Gaurav Sharma

    2008-11-01

    Full Text Available Gaurav Sharma1, Kaushal Rege2,3, David E Budil4, Martin L Yarmush2,5, Constantinos Mavroidis11Department of Mechanical and Industrial Engineering; 4Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA; 2The Center for Engineering in Medicine (CEM, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; 3Department of Chemical Engineering, Arizona State University, Tempe, AZ, USA; 5Department of Biomedical Engineering, Rutgers University, NJ, USAAbstract: We describe the molecular dynamics (MD-aided engineering design of mutant peptides based on the α-helical coiled-coil GCN4 leucine zipper peptide (GCN4-p1 in order to obtain environmentally-responsive nanotweezers. The actuation mechanism of the nanotweezers depends on the modification of electrostatic charges on the residues along the length of the coiled coil. Modulating the solution pH between neutral and acidic values results in the reversible movement of helices toward and away from each other and creates a complete closed-open-closed transition cycle between the helices. Our results indicate that the mutants show a reversible opening of up to 15 Å (1.5 nm; approximately 150% of the initial separation upon pH actuation. Investigation on the physicochemical phenomena that influence conformational properties, structural stability, and reversibility of the coiled-coil peptide-based nanotweezers revealed that a rationale- and design-based approach is needed to engineer stable peptide or macromolecules into stimuli-responsive devices. The efficacy of the mutant that demonstrated the most significant reversible actuation for environmentally responsive modulation of DNA-binding activity was also demonstrated. Our results have significant implications in bioseparations and in the engineering of novel transcription factors.Keywords: bionanotechnology, nanotweezers, coiled-coil, GCN4, leucine zipper, molecular dynamics, environmentally

  9. PNA Peptide chimerae

    Koch, T.; Næsby, M.; Wittung, P.

    1995-01-01

    Radioactive labelling of PNA has been performed try linking a peptide segment to the PNA which is substrate for protein kinase A. The enzymatic phosphorylation proceeds in almost quantitative yields....

  10. A three-dimensional-weighted cone beam filtered backprojection (CB-FBP) algorithm for image reconstruction in volumetric CT-helical scanning

    Tang Xiangyang; Hsieh Jiang; Nilsen, Roy A; Dutta, Sandeep; Samsonov, Dmitry; Hagiwara, Akira

    2006-01-01

    Based on the structure of the original helical FDK algorithm, a three-dimensional (3D)-weighted cone beam filtered backprojection (CB-FBP) algorithm is proposed for image reconstruction in volumetric CT under helical source trajectory. In addition to its dependence on view and fan angles, the 3D weighting utilizes the cone angle dependency of a ray to improve reconstruction accuracy. The 3D weighting is ray-dependent and the underlying mechanism is to give a favourable weight to the ray with the smaller cone angle out of a pair of conjugate rays but an unfavourable weight to the ray with the larger cone angle out of the conjugate ray pair. The proposed 3D-weighted helical CB-FBP reconstruction algorithm is implemented in the cone-parallel geometry that can improve noise uniformity and image generation speed significantly. Under the cone-parallel geometry, the filtering is naturally carried out along the tangential direction of the helical source trajectory. By exploring the 3D weighting's dependence on cone angle, the proposed helical 3D-weighted CB-FBP reconstruction algorithm can provide significantly improved reconstruction accuracy at moderate cone angle and high helical pitches. The 3D-weighted CB-FBP algorithm is experimentally evaluated by computer-simulated phantoms and phantoms scanned by a diagnostic volumetric CT system with a detector dimension of 64 x 0.625 mm over various helical pitches. The computer simulation study shows that the 3D weighting enables the proposed algorithm to reach reconstruction accuracy comparable to that of exact CB reconstruction algorithms, such as the Katsevich algorithm, under a moderate cone angle (4 deg.) and various helical pitches. Meanwhile, the experimental evaluation using the phantoms scanned by a volumetric CT system shows that the spatial resolution along the z-direction and noise characteristics of the proposed 3D-weighted helical CB-FBP reconstruction algorithm are maintained very well in comparison to the FDK

  11. Structural studies of polypeptides: Mechanism of immunoglobin catalysis and helix propagation in hybrid sequence, disulfide containing peptides

    Storrs, Richard Wood [Univ. of California, Berkeley, CA (United States)

    1992-08-01

    Catalytic immunoglobin fragments were studied Nuclear Magnetic Resonance spectroscopy to identify amino acid residues responsible for the catalytic activity. Small, hybrid sequence peptides were analyzed for helix propagation following covalent initiation and for activity related to the protein from which the helical sequence was derived. Hydrolysis of p-nitrophenyl carbonates and esters by specific immunoglobins is thought to involve charge complementarity. The pK of the transition state analog P-nitrophenyl phosphate bound to the immunoglobin fragment was determined by 31P-NMR to verify the juxtaposition of a positively charged amino acid to the binding/catalytic site. Optical studies of immunoglobin mediated photoreversal of cis, syn cyclobutane thymine dimers implicated tryptophan as the photosensitizing chromophore. Research shows the chemical environment of a single tryptophan residue is altered upon binding of the thymine dimer. This tryptophan residue was localized to within 20 Å of the binding site through the use of a nitroxide paramagnetic species covalently attached to the thymine dimer. A hybrid sequence peptide was synthesized based on the bee venom peptide apamin in which the helical residues of apamin were replaced with those from the recognition helix of the bacteriophage 434 repressor protein. Oxidation of the disufide bonds occured uniformly in the proper 1-11, 3-15 orientation, stabilizing the 434 sequence in an α-helix. The glycine residue stopped helix propagation. Helix propagation in 2,2,2-trifluoroethanol mixtures was investigated in a second hybrid sequence peptide using the apamin-derived disulfide scaffold and the S-peptide sequence. The helix-stop signal previously observed was not observed in the NMR NOESY spectrum. Helical connectivities were seen throughout the S-peptide sequence. The apamin/S-peptide hybrid binded to the S-protein (residues 21-166 of ribonuclease A) and reconstituted enzymatic activity.

  12. Structural studies of polypeptides: Mechanism of immunoglobin catalysis and helix propagation in hybrid sequence, disulfide containing peptides

    Storrs, R.W.

    1992-08-01

    Catalytic immunoglobin fragments were studied Nuclear Magnetic Resonance spectroscopy to identify amino acid residues responsible for the catalytic activity. Small, hybrid sequence peptides were analyzed for helix propagation following covalent initiation and for activity related to the protein from which the helical sequence was derived. Hydrolysis of p-nitrophenyl carbonates and esters by specific immunoglobins is thought to involve charge complementarity. The pK of the transition state analog P-nitrophenyl phosphate bound to the immunoglobin fragment was determined by [sup 31]P-NMR to verify the juxtaposition of a positively charged amino acid to the binding/catalytic site. Optical studies of immunoglobin mediated photoreversal of cis, syn cyclobutane thymine dimers implicated tryptophan as the photosensitizing chromophore. Research shows the chemical environment of a single tryptophan residue is altered upon binding of the thymine dimer. This tryptophan residue was localized to within 20 [Angstrom] of the binding site through the use of a nitroxide paramagnetic species covalently attached to the thymine dimer. A hybrid sequence peptide was synthesized based on the bee venom peptide apamin in which the helical residues of apamin were replaced with those from the recognition helix of the bacteriophage 434 repressor protein. Oxidation of the disufide bonds occured uniformly in the proper 1-11, 3-15 orientation, stabilizing the 434 sequence in an [alpha]-helix. The glycine residue stopped helix propagation. Helix propagation in 2,2,2-trifluoroethanol mixtures was investigated in a second hybrid sequence peptide using the apamin-derived disulfide scaffold and the S-peptide sequence. The helix-stop signal previously observed was not observed in the NMR NOESY spectrum. Helical connectivities were seen throughout the S-peptide sequence. The apamin/S-peptide hybrid binded to the S-protein (residues 21-166 of ribonuclease A) and reconstituted enzymatic activity.

  13. Handling data redundancy in helical cone beam reconstruction with a cone-angle-based window function and its asymptotic approximation

    Tang Xiangyang; Hsieh Jiang

    2007-01-01

    A cone-angle-based window function is defined in this manuscript for image reconstruction using helical cone beam filtered backprojection (CB-FBP) algorithms. Rather than defining the window boundaries in a two-dimensional detector acquiring projection data for computed tomographic imaging, the cone-angle-based window function deals with data redundancy by selecting rays with the smallest cone angle relative to the reconstruction plane. To be computationally efficient, an asymptotic approximation of the cone-angle-based window function is also given and analyzed in this paper. The benefit of using such an asymptotic approximation also includes the avoidance of functional discontinuities that cause artifacts in reconstructed tomographic images. The cone-angle-based window function and its asymptotic approximation provide a way, equivalent to the Tam-Danielsson-window, for helical CB-FBP reconstruction algorithms to deal with data redundancy, regardless of where the helical pitch is constant or dynamically variable during a scan. By taking the cone-parallel geometry as an example, a computer simulation study is conducted to evaluate the proposed window function and its asymptotic approximation for helical CB-FBP reconstruction algorithm to handle data redundancy. The computer simulated Forbild head and thorax phantoms are utilized in the performance evaluation, showing that the proposed cone-angle-based window function and its asymptotic approximation can deal with data redundancy very well in cone beam image reconstruction from projection data acquired along helical source trajectories. Moreover, a numerical study carried out in this paper reveals that the proposed cone-angle-based window function is actually equivalent to the Tam-Danielsson-window, and rigorous mathematical proofs are being investigated

  14. Tumor penetrating peptides

    Tambet eTeesalu

    2013-08-01

    Full Text Available Tumor-homing peptides can be used to deliver drugs into tumors. Phage library screening in live mice has recently identified homing peptides that specifically recognize the endothelium of tumor vessels, extravasate, and penetrate deep into the extravascular tumor tissue. The prototypic peptide of this class, iRGD (CRGDKGPDC, contains the integrin-binding RGD motif. RGD mediates tumor homing through binding to αv integrins, which are selectively expressed on various cells in tumors, including tumor endothelial cells. The tumor-penetrating properties of iRGD are mediated by a second sequence motif, R/KXXR/K. This C-end Rule (or CendR motif is active only when the second basic residue is exposed at the C-terminus of the peptide. Proteolytic processing of iRGD in tumors activates the cryptic CendR motif, which then binds to neuropilin-1 activating an endocytic bulk transport pathway through tumor tissue. Phage screening has also yielded tumor-penetrating peptides that function like iRGD in activating the CendR pathway, but bind to a different primary receptor. Moreover, novel tumor-homing peptides can be constructed from tumor-homing motifs, CendR elements and protease cleavage sites. Pathologies other than tumors can be targeted with tissue-penetrating peptides, and the primary receptor can also be a vascular zip code of a normal tissue. The CendR technology provides a solution to a major problem in tumor therapy, poor penetration of drugs into tumors. The tumor-penetrating peptides are capable of taking a payload deep into tumor tissue in mice, and they also penetrate into human tumors ex vivo. Targeting with these peptides specifically increases the accumulation in tumors of a variety of drugs and contrast agents, such as doxorubicin, antibodies and nanoparticle-based compounds. Remarkably the drug to be targeted does not have to be coupled to the peptide; the bulk transport system activated by the peptide sweeps along any compound that is

  15. Helical Polyacetylenes Induced via Noncovalent Chiral Interactions and Their Applications as Chiral Materials.

    Maeda, Katsuhiro; Yashima, Eiji

    2017-08-01

    Construction of predominantly one-handed helical polyacetylenes with a desired helix sense utilizing noncovalent chiral interactions with nonracemic chiral guest compounds based on a supramolecular approach is described. As with the conventional dynamic helical polymers possessing optically active pendant groups covalently bonded to the polymer chains, this noncovalent helicity induction system can show significant chiral amplification phenomena, in which the chiral information of the nonracemic guests can transfer with high cooperativity through noncovalent bonding interactions to induce an almost single-handed helical conformation in the polymer backbone. An intriguing "memory effect" of the induced macromolecular helicity is observed for some polyacetylenes, which means that the helical conformations induced in dynamic helical polyacetylene can be transformed into metastable static ones by tuning their helix-inversion barriers. Potential applications of helical polyacetylenes with controlled helix sense constructed by the "noncovalent helicity induction and/or memory effect" as chiral materials are also described.

  16. Measuring Social carrying Capacity: An Exploratory Study

    López-Bonilla, Jesús Manuel; López-Bonilla, Luis Miguel

    2007-01-01

    The tourist carrying capacity commands a growing interest given that it is closely linked with sustainable tourist development. The justification of the utility of this concept is given by means of a simple and efficient methodological proposal, by analysing the social carrying capacity. To this end, an empirical application is carried out in the Western Andalusia. In some of the cases analysed, the satisfaction of the tourist is found to decline when the levels of the tourist use are higher ...

  17. Peptide aldehyde inhibitors of bacterial peptide deformylases.

    Durand, D J; Gordon Green, B; O'Connell, J F; Grant, S K

    1999-07-15

    Bacterial peptide deformylases (PDF, EC 3.5.1.27) are metalloenzymes that cleave the N-formyl groups from N-blocked methionine polypeptides. Peptide aldehydes containing a methional or norleucinal inhibited recombinant peptide deformylase from gram-negative Escherichia coli and gram-positive Bacillus subtilis. The most potent inhibitor was calpeptin, N-CBZ-Leu-norleucinal, which was a competitive inhibitor of the zinc-containing metalloenzymes, E. coli and B. subtilis PDF with Ki values of 26.0 and 55.6 microM, respectively. Cobalt-substituted E. coli and B. subtilis deformylases were also inhibited by these aldehydes with Ki values for calpeptin of 9.5 and 12.4 microM, respectively. Distinct spectral changes were observed upon binding of calpeptin to the Co(II)-deformylases, consistent with the noncovalent binding of the inhibitor rather than the formation of a covalent complex. In contrast, the chelator 1,10-phenanthroline caused the time-dependent inhibition of B. subtilis Co(II)-PDF activity with the loss of the active site metal. The fact that calpeptin was nearly equipotent against deformylases from both gram-negative and gram-positive bacterial sources lends further support to the idea that a single deformylase inhibitor might have broad-spectrum antibacterial activity. Copyright 1999 Academic Press.

  18. Structural and pharmacological characteristics of chimeric peptides derived from peptide E and beta-endorphin reveal the crucial role of the C-terminal YGGFL and YKKGE motifs in their analgesic properties.

    Condamine, Eric; Courchay, Karine; Rego, Jean-Claude Do; Leprince, Jérôme; Mayer, Catherine; Davoust, Daniel; Costentin, Jean; Vaudry, Hubert

    2010-05-01

    Peptide E (a 25-amino acid peptide derived from proenkephalin A) and beta-endorphin (a 31-amino acid peptide derived from proopiomelanocortin) bind with high affinity to opioid receptors and share structural similarities but induce analgesic effects of very different intensity. Indeed, whereas they possess the same N-terminus Met-enkephalin message sequence linked to a helix by a flexible spacer and a C-terminal part in random coil conformation, in contrast with peptide E, beta-endorphin produces a profound analgesia. To determine the key structural elements explaining this very divergent opioid activity, we have compared the structural and pharmacological characteristics of several chimeric peptides derived from peptide E and beta-endorphin. Structures were obtained under the same experimental conditions using circular dichroism, computational estimation of helical content and/or nuclear magnetic resonance spectroscopy (NMR) and NMR-restrained molecular modeling. The hot-plate and writhing tests were used in mice to evaluate the antinociceptive effects of the peptides. Our results indicate that neither the length nor the physicochemical profile of the spacer plays a fundamental role in analgesia. On the other hand, while the functional importance of the helix cannot be excluded, the last 5 residues in the C-terminal part seem to be crucial for the expression or absence of the analgesic activity of these peptides. These data raise the question of the true function of peptides E in opioidergic systems. Copyright (c) 2010 Elsevier Inc. All rights reserved.

  19. Helical CT in evaluation of the bronchial tree

    Perhomaa, M.; Laehde, S.; Rossi, O.; Suramo, I.

    1997-01-01

    Purpose: To establish a protocol for and to assess the value of helical CT in the imaging of the bronchial tree. Material and Methods: Noncontrast helical CT was performed in 30 patients undergoing fiberoptic bronchoscopy for different reasons. Different protocols were compared; they included overlapping 10 mm, 5 mm, or 3 mm slices and non-tilted, cephalad or caudal tilted images. Ordinary cross-sectional and multiplanar 2D reformats were applied for visualization of the bronchial branches. The effect of increasing the helical pitch was tested in one patient. Results: A total of 92.1-100% of the segmental bronchi present in the helical acquisitions were identified by the different protocols. The collimation had no significant impact on the identification of the bronchial branches, but utilization of 3-mm overlapping slices made it easier to distinguish the nearby branches and provided better longitudinal visualization of the bronchi in 2D reformats. The tilted scans illustrated the disadvantage of not covering all segmental bronchi in one breath-hold. An increase of the pitch from 1 to 1.5 did not cause noticeable blurring of the images. CT and bronchoscopic findings correlated well in the area accessible to bronchoscopy, but CT detected 5 additional pathological lesions (including 2 cancers) in the peripheral lung. Conclusion: Helical CT supplemented with bronchography-like 2D reformats provides an effective method complementary to bronchoscopy in the examination of the bronchial tree. (orig.)

  20. Relativistic helicity and link in Minkowski space-time

    Yoshida, Z.; Kawazura, Y.; Yokoyama, T.

    2014-01-01

    A relativistic helicity has been formulated in the four-dimensional Minkowski space-time. Whereas the relativistic distortion of space-time violates the conservation of the conventional helicity, the newly defined relativistic helicity conserves in a barotropic fluid or plasma, dictating a fundamental topological constraint. The relation between the helicity and the vortex-line topology has been delineated by analyzing the linking number of vortex filaments which are singular differential forms representing the pure states of Banach algebra. While the dimension of space-time is four, vortex filaments link, because vorticities are primarily 2-forms and the corresponding 2-chains link in four dimension; the relativistic helicity measures the linking number of vortex filaments that are proper-time cross-sections of the vorticity 2-chains. A thermodynamic force yields an additional term in the vorticity, by which the vortex filaments on a reference-time plane are no longer pure states. However, the vortex filaments on a proper-time plane remain to be pure states, if the thermodynamic force is exact (barotropic), thus, the linking number of vortex filaments conserves

  1. Chirality of Intermediate Filaments and Magnetic Helicity of Active Regions

    Lim, Eun-Kyung; Chae, J.

    2009-05-01

    Filaments that form either between or around active regions (ARs) are called intermediate filaments. Even though there have been many theoretical studies, the origin of the chirality of filaments is still unknown. We investigated how intermediate filaments are related to their associated ARs, especially from the point of view of magnetic helicity and the orientation of polarity inversion lines (PILs). The chirality of filaments has been determined based on the orientations of barbs observed in the full-disk Hα images taken at Big Bear Solar Observatory during the rising phase of solar cycle 23. The sign of magnetic helicity of ARs has been determined using S/inverse-S shaped sigmoids from Yohkoh SXT images. As a result, we have found a good correlation between the chirality of filaments and the magnetic helicity sign of ARs. Among 45 filaments, 42 filaments have shown the same sign as helicity sign of nearby ARs. It has been also confirmed that the role of both the orientation and the relative direction of PILs to ARs in determining the chirality of filaments is not significant, against a theoretical prediction. These results suggest that the chirality of intermediate filaments may originate from magnetic helicity of their associated ARs.

  2. Gynecological applications of helical CT using SmartPrep

    Sakurada, Akira; Kakizaki, Dai; Abe, Kimihiko [Tokyo Medical Coll. (Japan)

    1999-11-01

    SmartPrep is software program for scanning a given region of interest (ROI) at optimal contrast density. An operator can arbitrarily define ROI and preset the CT value at which scanning should be started. After the injection of a contrast medium, system conducts continuous monitoring of the ROI and the operator starts helical scanning of the planned region when the present CT value has been reached. In comparison with conventional helical CT that requires a period of time from the beginning of contrast medium injection to the beginning of scanning, SmartPrep minimizes personal error and better depicts the artery-predominant phase under optimal conditions. In this study we examine the usefulness of contrast-enhanced helical CT using SmartPrep in the evaluation of gynecological disease. When the contrast medium was injected into the dorsal vein of the hand at a rate of 3 ml/sec, strong staining of pelvic arteries was observed in the CT images started at 17 to 23 sec after injection. The early-phase helical CT obtained under these conditions provided good depiction of lesions in cases of placenta accreta and invasive mole, as well as clear demonstration of tumor angiogenesis and evaluation of laterality in cases of cervical cancer. Comparison of the early and delayed phase also facilitated easier evaluation of lymph nodes than conventional comparison of simple and contrast-enhanced CT. The results thus suggest the usefulness of contrast-enhanced helical CT using SmartPrep in gynecology. (author)

  3. Structural analysis of compression helical spring used in suspension system

    Jain, Akshat; Misra, Sheelam; Jindal, Arun; Lakhian, Prateek

    2017-07-01

    The main aim of this work has to develop a helical spring for shock absorber used in suspension system which is designed to reduce shock impulse and liberate kinetic energy. In a vehicle, it increases comfort by decreasing amplitude of disturbances and it improves ride quality by absorbing and dissipating energy. When a vehicle is in motion on a road and strikes a bump, spring comes into action quickly. After compression, spring will attempt to come to its equilibrium state which is on level road. Helical springs can be made lighter with more strength by reducing number of coils and increasing the area. In this research work, a helical spring is modeled and analyzed to substitute the existing steel spring which is used in suspension. By using different materials, stress and deflection of helical spring can be varied. Comparability between existing spring and newly replaced spring is used to verify the results. For finding detailed stress distribution, finite element analysis is used to find stresses and deflection in both the helical springs. Finite element analysis is a method which is used to find proximate solutions of a physical problem defined in a finite domain. In this research work, modeling of spring is accomplished using Solid Works and analysis on Ansys.

  4. Kinetic theory of rf current drive and helicity injection

    Mett, R.R.

    1992-01-01

    Current drive and helicity injection by plasma waves are examined with the use of kinetic theory. The Vlasov equation yields a general current drive formula that contains resonant and nonresonant (ponderomotivelike) contributions. Standard quasilinear current drive is described by the former, while helicity current drive may be contained in the latter. Since direct analytical comparison of the sizes of the two terms is, in general, difficult, a new approach is taken. Solution of the drift-kinetic equation shows that the standard Landau damping/transit time magnetic pumping quasilinear diffusion coefficient is the only contribution to steady-state current drive to leading order in ε=ρ L /l, where ρ L is the Larmor radius and l is the inhomogeneity scale length. All nonresonant contributions, including the helicity, appear at higher order, after averages are taken over a flux surface, over azimuth, and over time. Consequently, at wave frequencies well below the electron cyclotron frequency, a wave helicity flux perpendicular to the magnetic field does not influence the parallel motion of electrons to leading order and therefore will not drive a significant current. Any current associated with a wave helicity flux is then either ion current (and thus inefficient) or electron current stemming from effects not included in the drift-kinetic treatment, such as cyclotron, collisional, or nonlinear (i.e., not quasilinear)

  5. Reduced bispectrum seeded by helical primordial magnetic fields

    Hortúa, Héctor Javier [Universidad Nacional de Colombia-Bogotá, Facultad de Ciencias, Departamento de Física, Carrera 30 Calle 45-03, C.P. 111321 Bogotá (Colombia); Castañeda, Leonardo, E-mail: hjhortuao@unal.edu.co, E-mail: lcastanedac@unal.edu.co [Grupo de Gravitación y Cosmología, Observatorio Astronómico Nacional, Universidad Nacional de Colombia, cra 45 No 26-85, Edificio Uriel Gutierréz, Bogotá, D.C. (Colombia)

    2017-06-01

    In this paper, we investigate the effects of helical primordial magnetic fields (PMFs) on the cosmic microwave background (CMB) reduced bispectrum. We derive the full three-point statistics of helical magnetic fields and numerically calculate the even contribution in the collinear configuration. We then numerically compute the CMB reduced bispectrum induced by passive and compensated PMF modes on large angular scales. There is a negative signal on the bispectrum due to the helical terms of the fields and we also observe that the biggest contribution to the bispectrum comes from the non-zero IR cut-off for causal fields, unlike the two-point correlation case. For negative spectral indices, the reduced bispectrum is enhanced by the passive modes. This gives a lower value of the upper limit for the mean amplitude of the magnetic field on a given characteristic scale. However, high values of IR cut-off in the bispectrum, and the helical terms of the magnetic field relaxes this bound. This demonstrates the importance of the IR cut-off and helicity in the study of the nature of PMFs from CMB observations.

  6. l=1 helical axis heliotron device in Kyoto university

    Nagasaki, K.; Sano, F.; Mizuuchi, T.; Hanatani, K.; Okada, H.; Obiki, T.

    1999-01-01

    Helical systems are an attractive candidate for magnetic fusion reactor. Recently, there has been great progress in theoretical research of three dimensional magnetic field structures, resulting in several kinds of confinement optimization being proposed for toroidal magnetic confinement system. For example, some sophisticated ideas have appeared on stage such as quasi-helical symmetry and quasi-isodynamic system. To find experimentally which way is the best Optimisation, a new helical axis heliotron device, so called 'Heliotron J', is under construction in the Institute of Advanced Energy, Kyoto University, Japan. In this conference, the basic concept and the present status will be presented. In the conventional plane axis helical system, it was difficult to have both good particle confinement and good MHD stability simultaneously. The goal of Heliotron J project is to clarify their compatibility in the spatial axis toroidal device. The best way for Optimising the helical magnetic field configuration will be explored by investigating the plasma response to the change in the field components. The main subjects for plasma experiment are: demonstration of the existence of good magnetic flux surfaces, reduction of neoclassical transport in collisionless regime, MHD Stabilisation in high β plasma, controllability of bootstrap current, good confinement of high energy particles

  7. Controllable helical deformations on printed anisotropic composite soft actuators

    Wang, Dong; Li, Ling; Serjouei, Ahmad; Dong, Longteng; Weeger, Oliver; Gu, Guoying; Ge, Qi

    2018-04-01

    Helical shapes are ubiquitous in both nature and engineering. However, the development of soft actuators and robots that mimic helical motions has been hindered primarily due to the lack of efficient modeling approaches that take into account the material anisotropy and the directional change of the external loading point. In this work, we present a theoretical framework for modeling controllable helical deformations of cable-driven, anisotropic, soft composite actuators. The framework is based on the minimum potential energy method, and its model predictions are validated by experiments, where the microarchitectures of the soft composite actuators can be precisely defined by 3D printing. We use the developed framework to investigate the effects of material and geometric parameters on helical deformations. The results show that material stiffness, volume fraction, layer thickness, and fiber orientation can be used to control the helical deformation of a soft actuator. In particular, we found that a critical fiber orientation angle exists at which the twist of the actuator changes the direction. Thus, this work can be of great importance for the design and fabrication of soft actuators with tailored deformation behavior.

  8. Double Helical Gear Performance Results in High Speed Gear Trains

    Handschuh, Robert F.; Ehinger, Ryan; Sinusas, Eric; Kilmain, Charles

    2010-01-01

    The operation of high speed gearing systems in the transmissions of tiltrotor aircraft has an effect on overall propulsion system efficiency. Recent work has focused on many aspects of high-speed helical gear trains as would be used in tiltrotor aircraft such as operational characteristics, comparison of analytical predictions to experimental data and the affect of superfinishing on transmission performance. Baseline tests of an aerospace quality system have been conducted in the NASA Glenn High-Speed Helical Gear Train Test Facility and have been described in earlier studies. These earlier tests had utilized single helical gears. The results that will be described in this study are those attained using double helical gears. This type of gear mesh can be configured in this facility to either pump the air-oil environment from the center gap between the meshing gears to the outside of tooth ends or in the reverse direction. Tests were conducted with both inward and outward air-oil pumping directions. Results are compared to the earlier baseline results of single helical gears.

  9. Heat transfer characteristics of a helical heat exchanger

    San, Jung-Yang; Hsu, Chih-Hsiang; Chen, Shih-Hao

    2012-01-01

    Heat transfer performance of a helical heat exchanger was investigated. The heat exchanger is composed of a helical tube with rectangular cross section and two cover plates. The ε–Ntu relation of the heat exchanger was obtained using a numerical method. In the analysis, the flow in the tube (helical flow) was considered to be mixed and the flow outside the tube (radial flow) was unmixed. In the experiment, the Darcy friction factor (f) and convective heat transfer coefficient (h) of the radial flow were measured. The radial flow was air and the helical flow was water. Four different channel spacing (0.5, 0.8, 1.2 and 1.6 mm) were individually considered. The Reynolds numbers were in the range 307–2547. Two correlations, one for the Darcy friction factor and the other for the Nusselt number, were proposed. - Highlights: ► We analyze the heat transfer characteristics of a helical heat exchanger and examine the effectiveness–Ntu relation. ► Increasing number of turns of the heat exchanger would slightly increase the effectiveness. ► There is an optimum Ntu value corresponding to a maximum effectiveness. ► We measure the Darcy friction factor and Nusselt number of the radial flow and examine the correlations.

  10. Coexistence of a two-states organization for a cell-penetrating peptide in lipid bilayer.

    Plénat, Thomas; Boichot, Sylvie; Dosset, Patrice; Milhiet, Pierre-Emmanuel; Le Grimellec, Christian

    2005-12-01

    Primary amphipathic cell-penetrating peptides transport cargoes across cell membranes with high efficiency and low lytic activity. These primary amphipathic peptides were previously shown to form aggregates or supramolecular structures in mixed lipid-peptide monolayers, but their behavior in lipid bilayers remains to be characterized. Using atomic force microscopy, we have examined the interactions of P(alpha), a primary amphipathic cell-penetrating peptide which remains alpha-helical whatever the environment, with dipalmitoylphosphatidylcholine (DPPC) bilayers. Addition of P(alpha) at concentrations up to 5 mol % markedly modified the supported bilayers topography. Long and thin filaments lying flat at the membrane surface coexisted with deeply embedded peptides which induced a local thinning of the bilayer. On the other hand, addition of P(alpha) only exerted very limited effects on the corresponding liposome's bilayer physical state, as estimated from differential scanning calorimetry and diphenylhexatriene fluorescence anisotropy experiments. The use of a gel-fluid phase separated supported bilayers made of a dioleoylphosphatidylcholine/dipalmitoylphosphatidylcholine mixture confirmed both the existence of long filaments, which at low peptide concentration were preferentially localized in the fluid phase domains and the membrane disorganizing effects of 5 mol % P(alpha). The simultaneous two-states organization of P(alpha), at the membrane surface and deeply embedded in the bilayer, may be involved in the transmembrane carrier function of this primary amphipathic peptide.

  11. Folding and membrane insertion of the pore-forming peptide gramicidin occur as a concerted process.

    Hicks, Matthew R; Damianoglou, Angeliki; Rodger, Alison; Dafforn, Timothy R

    2008-11-07

    Many antibiotic peptides function by binding and inserting into membranes. Understanding this process provides an insight into the fundamentals of both membrane protein folding and antibiotic peptide function. For the first time, in this work, flow-aligned linear dichroism (LD) is used to study the folding of the antibiotic peptide gramicidin. LD provides insight into the combined processes of peptide folding and insertion and has the advantage over other similar techniques of being insensitive to off-membrane aggregation events. By combining LD data with conventional measurements of protein fluorescence and circular dichroism, the mechanism of gramicidin insertion is elucidated. The mechanism consists of five separately assignable steps that include formation of a water-insoluble gramicidin aggregate, dissociation from the aggregate, partitioning of peptide to the membrane surface, oligomerisation on the surface and concerted insertion and folding of the peptide to the double-helical form of gramicidin. Measurement of the rates of each step shows that although changes in the fluorescence signal cease 10 s after the initiation of the process, the insertion of the peptide into the membrane is actually not complete for a further 60 min. This last membrane insertion phase is only apparent by measurement of LD and circular dichroism signal changes. In summary, this study demonstrates the importance of multi-technique approaches, including LD, in studies of membrane protein folding.

  12. Non-inductive current drive via helicity injection by Alfven waves in low-aspect-ratio tokamaks

    Cuperman, S.; Bruma, C.; Komoshvili, K. [Tel Aviv Univ. (Israel). Sackler Faculty of Exact Sciences

    1996-08-01

    A theoretical investigation of radio-frequency (RF) current drive via helicity injection in low aspect ratio tokamaks is carried out. A current-carrying cylindrical plasma surrounded by a helical sheet-current antenna and situated inside a perfectly conducting shell is considered. Toroidal features of low-aspect-ratio tokamaks are simulated by incorporating the following effects: (i) arbitrarily small aspect ratio, R{sub O}/a ``identical to`` 1/{epsilon}; (ii) strongly sheared equilibrium magnetic field; and (iii) relatively large poloidal component of the equilibrium magnetic field. This study concentrates on the Alfven continuum, i.e. the case in which the wave frequency satisfies the condition {l_brace}{omega}{sub Alf}({tau}){r_brace}{sub min}{r_brace} {<=} {omega} {<=} {l_brace}{omega}{sub Alf}({tau}){r_brace}{sub max}, where {omega}{sub Alf}({tau}) ``identical to`` {omega}{sub Alf}[n({tau}), B{sub O}({tau})] is an eigenfrequency of the shear Alfven wave (SAW). Thus, using low-{beta} magnetohydrodynamics, the wave equation with correct boundary (matching) conditions is solved, the RF field components are found, and subsequently current drive, power deposition and efficiency are computed. The results of our investigation clearly demonstrate the possibility of generation of RF-driven currents via helicity injection by Alfven waves in low-aspect-ratio tokamaks, in the SAW mode. A special algorithm is developed that enables one to select the antenna parameters providing optimal current drive efficiency. (Author).

  13. Stable single helical C- and I-chains inside single-walled carbon nanotubes

    Yao Z; Li Y; Jing X D; Meng F S; Zhao X; Li J H; Qiu Z Y; Yuan Q; Wang W X; Bi L; Liu H; Zhang Y P; Liu C J; Zheng S P; Liu B B

    2016-01-01

    The helicity of stable single helical carbon chains and iodine chains inside single-walled carbon nanotubes (SWCNTs) is studied by calculating the systematic van der Waals interaction energy. The results show that the optimal helical radius increases linearly with increasing tube radius, which produces a constant separation between the chain structure and the tube wall. The helical angle exhibits a ladder-like decrease with increasing tube radius, indicating that a large tube can produce a small helicity in the helical structures. (paper)

  14. The Concept of Carrying Capacity in Tourism

    Josef Zelenka

    2014-05-01

    Full Text Available Carrying capacity is often pragmatically, theoretically as well as purely intuitively considered as a concept in the context of tourism sustainability. The carrying capacity application has the greatest potential in protected areas, in frequently visited cultural and natural attractions, and in relation to sustaining of the lifestyle of the local community and tourism destination potential in general. Despite its importance, partial applications, determination of basic theoretical principles, and specifying connection to the other theoretical concepts in tourism (particularly destination life cycle, LAC concept, visitors management, there still is a rightful opinion of some authors suggesting that there is no consistent theory of tourism carrying capacity. This theory would be the base for sophisticated practical carrying capacity applications. This paper is therefore focused on introduction of the theoretical concept of carrying capacity, which can be discussed and possibly further elaborated.

  15. Antimicrobial activity of GN peptides and their mode of action

    Mojsoska, Biljana; Nielsen, Hanne Mørck; Jenssen, Håvard

    2016-01-01

    peptides due to their characteristics as naturally derived compounds with antimicrobial activity. In this study, we aimed at characterizing the mechanism of action of a small set of in silico optimized peptides. Following determination of peptide activity against E. coli, S. aureus, and P. aeruginosa......Increasing prevalence of bacteria that carries resistance towards conventional antibiotics has prompted the investigation into new compounds for bacterial intervention to ensure efficient infection control in the future. One group of potential lead structures for antibiotics is antimicrobial...

  16. New reconstruction algorithm in helical-volume CT

    Toki, Y.; Rifu, T.; Aradate, H.; Hirao, Y.; Ohyama, N.

    1990-01-01

    This paper reports on helical scanning that is an application of continuous scanning CT to acquire volume data in a short time for three-dimensional study. In a helical scan, the patient couch sustains movement during continuous-rotation scanning and then the acquired data is processed to synthesize a projection data set of vertical section by interpolation. But the synthesized section is not thin enough; also, the image may have artifacts caused by couch movement. A new reconstruction algorithm that helps resolve such problems has been developed and compared with the ordinary algorithm. The authors constructed a helical scan system based on TCT-900S, which can perform 1-second rotation continuously for 30 seconds. The authors measured section thickness using both algorithms on an AAPM phantom, and we also compared degree of artifacts on clinical data

  17. Geometric scalings for the electrostatically driven helical plasma state

    Akçay, Cihan; Finn, John M.; Nebel, Richard A.; Barnes, Daniel C.

    2017-12-01

    A new plasma state has been investigated [Akcay et al., Phys. Plasmas 24, 052503 (2017)], with a uniform applied axial magnetic field in a periodic cylinder of length L = 2 π R , driven by helical electrodes. The drive is single helicity, depending on m θ + k z = m θ - n ζ , where ζ = z / R and k = - n / R . For strong ( m , n ) = ( 1 , 1 ) drive, the state was found to have a strong axial mean current density, with a mean-field safety factor q 0 ( r ) just above the pitch of the electrodes m / n = 1 in the interior. This state has possible applications to DC electrical transformers and tailoring of the current profile in tokamaks. We study two geometric issues of interest for these applications: (i) scaling of properties with the plasma length or aspect ratio and (ii) behavior for different helicities, specifically ( m , n ) = ( 1 , n ) for n > 1 and ( m , n ) = ( 2 , 1 ) .

  18. Effect of loss cone on confinement in toroidal helical device

    Itoh, K.; Itoh, S.-I.; Fukuyama, A.; Hanatani, K.

    1988-12-01

    Analytical estimation is given on the loss cone in the toroidal helical devices in the presence of the radial electric field and the modulation of the helical ripple. The minimum energy of particles entering the loss cone is calculated. The modulation is not always effective in reducing the loss in the presence of the radial electric field. The plasma loss due to the loss cone is estimated in the collisionless limit. The radial electric field is estimated in the presence of the loss cone. It is found that the transition to the solution with positive radial electric field, which is necessary to achieve the high-ion-temperature mode, becomes difficult. This difficulty is large for the systems with the small helical ripple. (author)

  19. Imploding to equilibrium of helically symmetric theta pinches

    Sharky, N.N.

    1978-01-01

    The time-dependent, single-fluid, dissipative magnetohydrodynamic equations are solved in helical coordinates (r,phi), where phi = THETA-kz, k = 2π/L and L is the periodicity length in the z-direction. The two-dimensional numerical calculations simulate theta pinches which have an l = 1 helical field added to them. Given the applied magnetic fields and the initial state of the plasma, we study the time evolution of the system. The plasma is found to experience two kinds of oscillations, occurring on different time scales. These are the radial compression oscillations, and the slower helical oscillations of the plasma column. The plasma motion is followed until these oscillations disappear and an equilibrium is nearly reached. Hence given the amplitude and the rise time of the applied magnetic fields, the calculations allow one to relate the initial state of a cold, homogeneous plasma to its final equilibrium state where it is heated and compressed

  20. Theory of dynamics in long pulse helical plasmas

    Itoh, K.; Sanuki, H.; Toda, S.; Yokoyama, M.; Itoh, S.-I.; Yagi, M.; Fukuyama, A.

    2001-01-01

    Self-organized dynamics of toroidal helical plasma, which is induced by the nonlinear transport property, is discussed. Neoclassical ripple diffusion is a dominant mechanism that drives the radial electric field. The bifurcation nature of the electric field generation gives rise to the electric field domain interface, across which the electric field changes strongly. This domain interface is an origin of internal transport barrier in helical systems. This nonlinearity gives rise to the self-organized oscillations; the electric field pulsation is one of the examples. Based on the model of density limit, in which the competition between the transport loss and radiation loss is analyzed, dynamics near the density limit of helical systems is also discussed. (author)

  1. Helicity amplitudes and electromagnetic decays of hyperon resonances

    Cauteren, T. van; Ryckebusch, J.; Metsch, B.; Petry, H.R.

    2005-01-01

    We present results for the helicity amplitudes of the lowest-lying hyperon resonances Y * , computed within the framework of the Bonn Constituent-Quark model, which is based on the Bethe-Salpeter approach. The seven parameters entering the model were fitted to the best-known baryon masses. Accordingly, the results for the helicity amplitudes are genuine predictions. Some hyperon resonances are seen to couple more strongly to a virtual photon with finite Q 2 than to a real photon. Other Y * 's, such as the S 01 (1670) Λ-resonance or the S 11 (1620) Σ-resonance, couple very strongly to real photons. We present a qualitative argument for predicting the behaviour of the helicity asymmetries of baryon resonances at high Q 2 . (orig.)

  2. Tandem MS Analysis of Selenamide-Derivatized Peptide Ions

    Zhang, Yun; Zhang, Hao; Cui, Weidong; Chen, Hao

    2011-09-01

    Our previous study showed that selenamide reagents such as ebselen and N-(phenylseleno)phthalimide (NPSP) can be used for selective and rapid derivatization of protein/peptide thiols in high conversion yield. This paper reports the systematic investigation of MS/MS dissociation behaviors of selenamide-derivatized peptide ions upon collision induced dissociation (CID) and electron transfer dissociation (ETD). In the positive ion mode, derivatized peptide ions exhibit tag-dependent CID dissociation pathways. For instance, ebselen-derivatized peptide ions preferentially undergo Se-S bond cleavage upon CID to produce a characteristic fragment ion, the protonated ebselen ( m/z 276), which allows selective identification of thiol peptides from protein digest as well as selective detection of thiol proteins from protein mixture using precursor ion scan (PIS). In contrast, NPSP-derivatized peptide ions retain their phenylselenenyl tags during CID, which is useful in sequencing peptides and locating cysteine residues. In the negative ion CID mode, both types of tags are preferentially lost via the Se-S cleavage, analogous to the S-S bond cleavage during CID of disulfide-containing peptide anions. In consideration of the convenience in preparing selenamide-derivatized peptides and the similarity of Se-S of the tag to the S-S bond, we also examined ETD of the derivatized peptide ions to probe the mechanism for electron-based ion dissociation. Interestingly, facile cleavage of Se-S bond occurs to the peptide ions carrying either protons or alkali metal ions, while backbone cleavage to form c/z ions is severely inhibited. These results are in agreement with the Utah-Washington mechanism proposed for depicting electron-based ion dissociation processes.

  3. Dynamic analysis of a liquid droplet and optimization of helical angles for vortex drainage gas recovery

    Xiaodong Wu

    2016-10-01

    Full Text Available Downhole vortex drainage gas recovery is a new gas production technology. So far, however, the forces and motions of liquid phase in the swirling flow field of wellbores during its field application have not been figured out. In this paper, the forces of liquid droplets in the swirling flow field of wellbores were analyzed on the basis of two-phase fluid dynamics theories. Then, the motion equations of fluid droplets along axial and radical directions were established. Magnitude comparison was performed on several typical acting forces, including Basset force, virtual mass force, Magnus force, Saffman force and Stokes force. Besides, the formula for calculating the optimal helical angle of vortex tools was established according to the principle that the vertical resultant force on fluid droplets should be the maximum. And afterwards, each acting force was comprehensively analyzed in terms of its origin, characteristics and direction based on the established force analysis model. Magnitude comparison indicates that the forces with less effect can be neglected, including virtual mass force, Basset force and convection volume force. Moreover, the vertically upward centrifugal force component occurs on the fluid droplets in swirling flow field instead of those in the conventional flow field of wellbores, which is favorable for the fluid droplets to move upward. The reliability of optimal helical angle calculation formula was verified by means of case analysis. It is demonstrated that with the decrease of well depth, the fluid-carrying capability of gas and the optimal helical angle increase. The research results in this paper have a guiding significance to the optimization design of downhole vortex tools and the field application of downhole vortex drainage gas recovery technology.

  4. Three-dimensional helical (spiral) CT angiography. Visualization of vessels in the maxillofacial regions

    Hanawa, Shigeo; Sakamoto, Hidetomo; Mori, Shin-ichiro; Kagawa, Toyohiro; Seze, Ryosuke; Ishioka, Hisakazu; Tashiro, Himiko; Ogawa, Kazuhisa; Wada, Tadako

    1998-01-01

    Authors performed the contrast helical CT for tumors on the maxillofacial regions, and reconstituted these data into the three-dimensional helical (spiral) CT angiography (CTA). Furthermore the conditions of photographing and the clinical significance of CTA were discussed. The subjects were 24 cases (including 13 of malignant tumors, 4 of benign tumors, 4 of inflammation and 3 of malformations), to which the contrast helical CT was performed transvenously. The photographing condition was set in principal to 140 kV of the tube voltage, 160 (200) mA of the tube current, 3 mm of the X-ray beam width, 3 mm/sec (pitch=1) of the turn-table moving speed. The relationship between the beam width and the pitch was determined by the phantom experiments. The scanning was carried out maximally for continuous 60 sec as the scanning time of a turn/sec. Of all cases, CTA visualized three-dimensionally vessels, but it was hard in the total carotid arteries and the internal-external carotid arteries. Authors analyzed the axial and the multiplanar reconstitution (MPR) images as the two-dimensional display, and the surface rendering (SR), the volume rendering and the maximum intensity projections (MIP) as the three-dimensional display. The axial and MPR image of the facial arteries and the lingual arteries as the branched vessels from the external carotid arteries were recognized easily. By SR, it was easily to understand the anatomical relationship among vessels, gnathic bone and cervical vertebrae, and by MIP sufficiently observe the concentration dependent calcification of the vessel walls. Three-dimensional CTA is very useful to get the three-dimensional visual information about the anatomical structures of the maxillofacial regions which is necessary for oral surgeons to plan the pre-operational strategies. (K.H.)

  5. Conformal avoidance helical tomotherapy for dogs with nasopharyngeal tumors

    Welsh, J.S.; Turek, M.; Mackie, T.R.; Miller, P.; Mehta, M.P.; Forrest, L.J.

    2003-01-01

    Helical tomotherapy provides a unique means of delivering intensity-modulated radiation therapy (IMRT) using a novel treatment unit, which merges features of a linear accelerator with a helical CT scanner. Thanks to the CT imaging capacity, targeted regions can be visualized prior to, during, or immediately after each treatment. Such image-guidance through megavoltage CT will allow the realization and refinement of the concept of adaptive radiotherapy - the reconstruction of the actually delivered daily dose (as opposed to planned dose) accompanied by prescription adjustments when appropriate. In addition to this unique feature, helical tomotherapy promises further improvements in the specific avoidance of critical normal structures, i.e. conformal avoidance, the counterpart of conformal therapy. The first definitive treatment protocol using helical tomotherapy is presently underway for dogs with nasopharyngeal tumors. In general, such tumors can be treated with conventional external beam radiation therapy but at the cost of severe ocular toxicity due to the anatomy of the canine head. These are readily measurable toxicities and are almost universal in incidence; therefore, the canine nasopharyngeal tumor presents an ideal model to assess the ability to conformally avoid critical structures. It is hoped that conformal avoidance helical tomotherapy will improve tumor control via dose-escalation while reducing ocular toxicity in these veterinary patients. A total of 10 fractions are scheduled for these patients; the first 3 dogs have all received at least 7 fractions delivered via helical tomotherapy. Although preliminary, the first 3 dogs treated have not shown any evidence of ocular toxicity in this ongoing study

  6. Divertors for Helical Devices: Concepts, Plans, Results, and Problems

    Koenig, R.; Grigull, P.; McCormick, K.

    2004-01-01

    With Large Helical Device (LHD) and Wendelstein 7-X (W7-X), the development of helical devices is now taking a large step forward on the path to a steady-state fusion reactor. Important issues that need to be settled in these machines are particle flux and heat control and the impact of divertors on plasma performance in future continuously burning fusion plasmas. The divertor concepts that will initially be explored in these large machines were prepared in smaller-scale devices like Heliotron E, Compact Helical System (CHS), and Wendelstein 7-AS (W7-AS). While advanced divertor scenarios relevant for W7-X were already studied in W7-AS, other smaller-scale experiments like Heliotron-J, CHS, and National Compact Stellarator Experiment will be used for the further development of divertor concepts. The two divertor configurations that are being investigated are the helical and the island divertor, as well as the local island divertor, which was successfully demonstrated on CHS and just went into operation on LHD. At present, on its route to a fully closed helical divertor, LHD operates in an open helical divertor configuration. W7-X will be equipped right from the start with an actively cooled discrete island divertor that will allow quasi-continuous operation. The divertor design is very similar to the one explored on W7-AS. For sufficiently large island sizes and not too long field line connection lengths, this divertor gives access to a partially detached quasi-steady-state operating scenario in a newly found high-density H-mode operating regime, which benefits from high energy and low impurity confinement times, with edge radiation levels of up to 90% and sufficient neutral compression in the subdivertor region (>10) for active pumping. The basic physics of the different divertor concepts and associated implementation problems, like asymmetries due to drifts, accessibility of essential operating scenarios, toroidal asymmetries due to symmetry breaking error fields

  7. Variation in the helical structure of native collagen.

    Joseph P R O Orgel

    Full Text Available The structure of collagen has been a matter of curiosity, investigation, and debate for the better part of a century. There has been a particularly productive period recently, during which much progress has been made in better describing all aspects of collagen structure. However, there remain some questions regarding its helical symmetry and its persistence within the triple-helix. Previous considerations of this symmetry have sometimes confused the picture by not fully recognizing that collagen structure is a highly complex and large hierarchical entity, and this affects and is effected by the super-coiled molecules that make it. Nevertheless, the symmetry question is not trite, but of some significance as it relates to extracellular matrix organization and cellular integration. The correlation between helical structure in the context of the molecular packing arrangement determines which parts of the amino acid sequence of the collagen fibril are buried or accessible to the extracellular matrix or the cell. In this study, we concentrate primarily on the triple-helical structure of fibrillar collagens I and II, the two most predominant types. By comparing X-ray diffraction data collected from type I and type II containing tissues, we point to evidence for a range of triple-helical symmetries being extant in the molecules native environment. The possible significance of helical instability, local helix dissociation and molecular packing of the triple-helices is discussed in the context of collagen's supramolecular organization, all of which must affect the symmetry of the collagen triple-helix.

  8. Point contacts and localization in generic helical liquids

    Orth, Christoph P.; Strübi, Grégory; Schmidt, Thomas L.

    2013-10-01

    We consider two helical liquids on opposite edges of a two-dimensional topological insulator, which are connected by one or several local tunnel junctions. In the presence of spatially inhomogeneous Rashba spin-orbit coupling, the spin of the helical edge states is momentum dependent, and this spin texture can be different on opposite edges. We demonstrate that this has a strong impact on the electron transport between the edges. In particular, in the case of many random tunnel contacts, the localization length depends strongly on the spin textures of the edge states.

  9. Helical coil alignment in the advanced toroidal facility

    Taylor, D.J.; Cole, M.J.; Johnson, R.L.; Nelson, B.E.; Warwick, J.E.; Whitson, J.C.

    1985-01-01

    This paper presents a brief overview of the helical coil design concept, detailed descriptions of the method for installation and alignment, and discussions of segment installation and alignment equipment. Alignment is accomplished by optical methods using electronic theodolites connected to a microcomputer to form a coordinate measurement system. The coordinate measurement system is described in detail, along with target selection and fixturing for manipulation of the helical coil segments during installation. In addition, software is described including vendor-supplied software used in the coordinate measurement system and in-house-developed software used to calibrate segment and positioning fixture motion. 2 refs., 8 figs

  10. Effects of different rod spacers (helical types) on coolant crossmixing

    Zhukov, A.V.; Sviridenko, E.Ya.; Matyukhin, N.M.; Rymkevich, K.S.; Ushakov, P.A.

    1981-11-01

    The results of investigations (electromagnetic measuring method) on coolant cross mixing in rod clusters with spiral wire spacers with different winding directions, with alternating unfinned and finned rods (case 'fin to rod'), as well as in rod clusters with much space between the rods, (case 'fin to fin') are reported. The local fluid dynamics parameters (distribution of the transversal and longitudinal velocity component) that define the physical processes of the coolant exchange in the rod clusters with helical spacers are explained. The investigation results for different helical spacer types are compared with each other. (orig.) [de

  11. Demonstration of a helical armature for a superconducting generator

    Conley, P.L.; Kirtley, J.L. Jr.; Hagman, W.H.; Ula, A.H.M.S.

    1979-01-01

    This is a report on the design, construction and testing of an experimental helical armature for a superconducting geneator. Rated at 60 kVA, this armature was built to be operated in conjunction with the rotor of the first experimental superconducting machine built at MIT. It incorporates, in addition to the helical winding form, a high density edge-brazed end turn geometry, molded bar groups, and silicone fluid coolant and insulation impregnant. Tests showed that the thermal performance of the armature was within reasonable limits, magnetic analyses leading to the computation of reactance and voltage geneation were approximately correct. No abnormal cheating was observed. 9 refs

  12. Helically symmetric equilibria with pressure anisotropy and incompressible plasma flow

    Evangelias, A.; Kuiroukidis, A.; Throumoulopoulos, G. N.

    2018-02-01

    We derive a generalized Grad-Shafranov equation governing helically symmetric equilibria with pressure anisotropy and incompressible flow of arbitrary direction. Through the most general linearizing ansatz for the various free surface functions involved therein, we construct equilibrium solutions and study their properties. It turns out that pressure anisotropy can act either paramegnetically or diamagnetically, the parallel flow has a paramagnetic effect, while the non-parallel component of the flow associated with the electric field has a diamagnetic one. Also, pressure anisotropy and flow affect noticeably the helical current density.

  13. Synthesis, model and stability of helically coiled carbon nanotubes

    Fejes, Dora; Raffai, Manuella; Hernadi, Klara

    2013-01-01

    . Our experiments focused on the production and development of catalysts for the synthesis of helically coiled CNTs (carbon nanotubes). The catalysts were tested in the decomposition of acetylene by CCVD (Catalytic Chemical Vapor Deposition) method. The carbon deposit was imaged by TEM (Transmission......Structural model of helically coiled carbon nanotubes is proposed. It is constructed by means of topological coordinate method. Relaxation and cohesive energy calculation are performed by molecular mechanics, using second-generation bond order potential for hydrocarbons introduced by D. W. Brenner...

  14. Peptide Integrated Optics.

    Handelman, Amir; Lapshina, Nadezda; Apter, Boris; Rosenman, Gil

    2018-02-01

    Bio-nanophotonics is a wide field in which advanced optical materials, biomedicine, fundamental optics, and nanotechnology are combined and result in the development of biomedical optical chips. Silk fibers or synthetic bioabsorbable polymers are the main light-guiding components. In this work, an advanced concept of integrated bio-optics is proposed, which is based on bioinspired peptide optical materials exhibiting wide optical transparency, nonlinear and electrooptical properties, and effective passive and active waveguiding. Developed new technology combining bottom-up controlled deposition of peptide planar wafers of a large area and top-down focus ion beam lithography provides direct fabrication of peptide optical integrated circuits. Finding a deep modification of peptide optical properties by reconformation of biological secondary structure from native phase to β-sheet architecture is followed by the appearance of visible fluorescence and unexpected transition from a native passive optical waveguiding to an active one. Original biocompatibility, switchable regimes of waveguiding, and multifunctional nonlinear optical properties make these new peptide planar optical materials attractive for application in emerging technology of lab-on-biochips, combining biomedical photonic and electronic circuits toward medical diagnosis, light-activated therapy, and health monitoring. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Antimicrobial Peptides from Plants

    James P. Tam

    2015-11-01

    Full Text Available Plant antimicrobial peptides (AMPs have evolved differently from AMPs from other life forms. They are generally rich in cysteine residues which form multiple disulfides. In turn, the disulfides cross-braced plant AMPs as cystine-rich peptides to confer them with extraordinary high chemical, thermal and proteolytic stability. The cystine-rich or commonly known as cysteine-rich peptides (CRPs of plant AMPs are classified into families based on their sequence similarity, cysteine motifs that determine their distinctive disulfide bond patterns and tertiary structure fold. Cystine-rich plant AMP families include thionins, defensins, hevein-like peptides, knottin-type peptides (linear and cyclic, lipid transfer proteins, α-hairpinin and snakins family. In addition, there are AMPs which are rich in other amino acids. The ability of plant AMPs to organize into specific families with conserved structural folds that enable sequence variation of non-Cys residues encased in the same scaffold within a particular family to play multiple functions. Furthermore, the ability of plant AMPs to tolerate hypervariable sequences using a conserved scaffold provides diversity to recognize different targets by varying the sequence of the non-cysteine residues. These properties bode well for developing plant AMPs as potential therapeutics and for protection of crops through transgenic methods. This review provides an overview of the major families of plant AMPs, including their structures, functions, and putative mechanisms.

  16. One Peptide Reveals the Two Faces of α-Helix Unfolding-Folding Dynamics.

    Jesus, Catarina S H; Cruz, Pedro F; Arnaut, Luis G; Brito, Rui M M; Serpa, Carlos

    2018-04-12

    The understanding of fast folding dynamics of single α-helices comes mostly from studies on rationally designed peptides displaying sequences with high helical propensity. The folding/unfolding dynamics and energetics of α-helix conformations in naturally occurring peptides remains largely unexplored. Here we report the study of a protein fragment analogue of the C-peptide from bovine pancreatic ribonuclease-A, RN80, a 13-amino acid residue peptide that adopts a highly populated helical conformation in aqueous solution. 1 H NMR and CD structural studies of RN80 showed that α-helix formation displays a pH-dependent bell-shaped curve, with a maximum near pH 5, and a large decrease in helical content in alkaline pH. The main forces stabilizing this short α-helix were identified as a salt bridge formed between Glu-2 and Arg-10 and the cation-π interaction involving Tyr-8 and His-12. Thus, deprotonation of Glu-2 or protonation of His-12 are essential for the RN80 α-helix stability. In the present study, RN80 folding and unfolding were triggered by laser-induced pH jumps and detected by time-resolved photoacoustic calorimetry (PAC). The photoacid proton release, amino acid residue protonation, and unfolding/folding events occur at different time scales and were clearly distinguished using time-resolved PAC. The partial unfolding of the RN80 α-helix, due to protonation of Glu-2 and consequent breaking of the stabilizing salt bridge between Glu-2 and Arg-10, is characterized by a concentration-independent volume expansion in the sub-microsecond time range (0.8 mL mol -1 , 369 ns). This small volume expansion reports the cost of peptide backbone rehydration upon disruption of a solvent-exposed salt bridge, as well as backbone intrinsic expansion. On the other hand, RN80 α-helix folding triggered by His-12 protonation and subsequent formation of a cation-π interaction leads to a microsecond volume contraction (-6.0 mL mol -1 , ∼1.7 μs). The essential role of two

  17. Parallelization of Reversible Ripple-carry Adders

    Thomsen, Michael Kirkedal; Axelsen, Holger Bock

    2009-01-01

    The design of fast arithmetic logic circuits is an important research topic for reversible and quantum computing. A special challenge in this setting is the computation of standard arithmetical functions without the generation of \\emph{garbage}. Here, we present a novel parallelization scheme...... wherein $m$ parallel $k$-bit reversible ripple-carry adders are combined to form a reversible $mk$-bit \\emph{ripple-block carry adder} with logic depth $\\mathcal{O}(m+k)$ for a \\emph{minimal} logic depth $\\mathcal{O}(\\sqrt{mk})$, thus improving on the $mk$-bit ripple-carry adder logic depth $\\mathcal...

  18. Gun Carrying by High School Students in Boston, MA: Does Overestimation of Peer Gun Carrying Matter?

    Hemenway, David; Vriniotis, Mary; Johnson, Renee M.; Miller, Matthew; Azrael, Deborah

    2011-01-01

    This paper investigates: (1) whether high school students overestimate gun carrying by their peers, and (2) whether those students who overestimate peer gun carrying are more likely to carry firearms. Data come from a randomly sampled survey conducted in 2008 of over 1700 high school students in Boston, MA. Over 5% of students reported carrying a…

  19. Helical CT of traumatic injuries of the thoracic aorta

    Mengozzi, E.; Burzi, M.; Miceli, M.; Lipparini, M.; Sartoni Galloni, S.

    2000-01-01

    Acute thoracic aortic injuries account for up to 10-20% of fatalities in high-speed deceleration road accidents and have an estimated immediate fatality rate of 80-90%. Untreated survivors to acute trauma (10-20%) have a dismal prognosis: 30% of them die within 6 hours, 40-50% die within 24 hours, and 90% within 4 months. It was investigated the diagnostic accuracy of Helical Computed Tomography (Helical CT) in acute traumatic injuries of the thoracic aorta, and the role of this technique in the diagnostic management of trauma patients with a strong suspicion of aortic rupture. It was compared retrospectively the chest Helical CT findings of 256 trauma patients examined June 1995 through August 1999. Chest Helical CT examinations were performed according to trauma score, to associated traumatic lesions and to plain chest radiographic findings. All the examinations were performed with no intravenous contrast agent administration and the pitch 2 technique. After a previous baseline study, contrast-enhanced scans were acquired with pitch 1 in 87 patients. Helical CT showed aortic lesions in 9 of 256 patients examined. In all the 9 cases it was found a mediastinal hematoma and all of them had positive plain chest radiographic findings of mediastinal enlargement. Moreover, in 6 cases aortic knob blurring was also evident on plain chest film and in 5 cases depressed left mainstem bronchus and trachea deviation rightwards were observed. All aortic lesions were identified on axial scans and located at the isthmus of level. Aortic rupture was always depicted as pseudo diverticulum of the proximal descending tract and intimal flap. It was also found that periaortic hematoma in 6 cases and intramural hematoma in 1 case. There were non false positive results in the series: 7 patients with Helical CT diagnosis of aortic rupture were submitted to conventional aortography that confirmed both type and extension of the lesions as detected by Helical CT, and all findings were

  20. Acylation of Therapeutic Peptides

    Trier, Sofie; Henriksen, Jonas Rosager; Jensen, Simon Bjerregaard

    ) , which promotes intestinal growth and is used to treat bowel disorders such as inflammatory bowel diseases and short bowel syndrome, and the 32 amino acid salmon calcitonin (sCT), which lowers blood calcium and is employed in the treatment of post-menopausal osteoporosis and hypercalcemia. The two...... peptides are similar in size and structure, but oppositely charged at physiological pH. Both peptides were acylated with linear acyl chains of systematically increasing length, where sCT was furthermore acylated at two different positions on the peptide backbone. For GLP-2, we found that increasing acyl...... remained optimal overall. The results indicate that rational acylation of GLP-2 can increase its in vitro intestinal absorption, alone or in combination with permeation enhancers, and are consistent with the initial project hypothesis. For sCT, an unpredicted effect of acylation largely superseded...