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Sample records for beta sheet formation

  1. Slow formation of aggregation-resistant beta-sheet folding intermediates.

    PubMed

    Junker, Mirco; Clark, Patricia L

    2010-03-01

    Protein folding has been studied extensively for decades, yet our ability to predict how proteins reach their native state from a mechanistic perspective is still rudimentary at best, limiting our understanding of folding-related processes in vivo and our ability to manipulate proteins in vitro. Here, we investigate the in vitro refolding mechanism of a large beta-helix protein, pertactin, which has an extended, elongated shape. At 55 kDa, this single domain, all-beta-sheet protein allows detailed analysis of the formation of beta-sheet structure in larger proteins. Using a combination of fluorescence and far-UV circular dichroism spectroscopy, we show that the pertactin beta-helix refolds remarkably slowly, with multiexponential kinetics. Surprisingly, despite the slow refolding rates, large size, and beta-sheet-rich topology, pertactin refolding is reversible and not complicated by off-pathway aggregation. The slow pertactin refolding rate is not limited by proline isomerization, and 30% of secondary structure formation occurs within the rate-limiting step. Furthermore, site-specific labeling experiments indicate that the beta-helix refolds in a multistep but concerted process involving the entire protein, rather than via initial formation of the stable core substructure observed in equilibrium titrations. Hence pertactin provides a valuable system for studying the refolding properties of larger, beta-sheet-rich proteins, and raises intriguing questions regarding the prevention of aggregation during the prolonged population of partially folded, beta-sheet-rich refolding intermediates. Proteins 2010. (c) 2009 Wiley-Liss, Inc. PMID:19847915

  2. Conformational diversity in prion protein variants influences intermolecular [beta]-sheet formation

    SciTech Connect

    Lee, Seungjoo; Antony, Lizamma; Hartmann, Rune; Knaus, Karen J.; Surewicz, Krystyna; Surewicz, Witold K.; Yee, Vivien C.

    2010-04-19

    A conformational transition of normal cellular prion protein (PrP{sup C}) to its pathogenic form (PrP{sup Sc}) is believed to be a central event in the transmission of the devastating neurological diseases known as spongiform encephalopathies. The common methionine/valine polymorphism at residue 129 in the PrP influences disease susceptibility and phenotype. We report here seven crystal structures of human PrP variants: three of wild-type (WT) PrP containing V129, and four of the familial variants D178N and F198S, containing either M129 or V129. Comparison of these structures with each other and with previously published WT PrP structures containing M129 revealed that only WT PrPs were found to crystallize as domain-swapped dimers or closed monomers; the four mutant PrPs crystallized as non-swapped dimers. Three of the four mutant PrPs aligned to form intermolecular {beta}-sheets. Several regions of structural variability were identified, and analysis of their conformations provides an explanation for the structural features, which can influence the formation and conformation of intermolecular {beta}-sheets involving the M/V129 polymorphic residue.

  3. Conversion of alpha-helices into beta-sheets features in the formation of the scrapie prion proteins.

    PubMed Central

    Pan, K M; Baldwin, M; Nguyen, J; Gasset, M; Serban, A; Groth, D; Mehlhorn, I; Huang, Z; Fletterick, R J; Cohen, F E

    1993-01-01

    Prions are composed largely, if not entirely, of prion protein (PrPSc in the case of scrapie). Although the formation of PrPSc from the cellular prion protein (PrPC) is a post-translational process, no candidate chemical modification was identified, suggesting that a conformational change features in PrPSc synthesis. To assess this possibility, we purified both PrPC and PrPSc by using nondenaturing procedures and determined the secondary structure of each. Fourier-transform infrared (FTIR) spectroscopy demonstrated that PrPC has a high alpha-helix content (42%) and no beta-sheet (3%), findings that were confirmed by circular dichroism measurements. In contrast, the beta-sheet content of PrPSc was 43% and the alpha-helix 30% as measured by FTIR. As determined in earlier studies, N-terminally truncated PrPSc derived by limited proteolysis, designated PrP 27-30, has an even higher beta-sheet content (54%) and a lower alpha-helix content (21%). Neither PrPC nor PrPSc formed aggregates detectable by electron microscopy, while PrP 27-30 polymerized into rod-shaped amyloids. While the foregoing findings argue that the conversion of alpha-helices into beta-sheets underlies the formation of PrPSc, we cannot eliminate the possibility that an undetected chemical modification of a small fraction of PrPSc initiates this process. Since PrPSc seems to be the only component of the "infectious" prion particle, it is likely that this conformational transition is a fundamental event in the propagation of prions. Images Fig. 1 Fig. 4 PMID:7902575

  4. Liquid Crystal Based Sensor to Detect Beta-Sheet Formation of Peptides

    NASA Astrophysics Data System (ADS)

    Sadati, Monirosadat; Izmitli Apik, Aslin; Abbott, Nicholas L.; de Pablo, Juan J.

    2015-03-01

    Protein aggregation into amyloid fibrils is involved in the progression of Alzheimer's, typeII diabetes and Huntington's diseases. Although larger aggregates remain important for clinical determination, small oligomers are of great interest due to their potentially toxic nature. It is therefore crucial to develop methods that probe the aggregation process at early stages and in the vicinity of biological membranes. Here, we present a simple method that relies on liquid crystalline materials and a Langmuir monolayer at the aqueous-liquid crystal (LC) interface. The approach is based on the LC's specific response to β-sheet structures, which abound in amyloid fibrils. When the system is observed under polarized light, the fibrils formed by amyloidogenic peptides give rise to the formation of elongated and branched structures in the LCs. Moreover, the PolScope measurements prove that the LCs are predominantly aligned along the fibrils when exposed to a β-sheet forming peptide. In contrast, non-amyloidogenic peptides form ellipsoidal domains of irregularly tilted LCs. This method is capable of reporting aggregation at lipid-aqueous interfaces at nanomolar concentrations of the peptide, and much earlier than commonly used fluorescence-based techniques. We thank Prof. Oleg D. Levrentovich and Young-Ki Kim from the Liquid Crystal Institute of Kent State University for the use of their PolScope instrument. This work was partially supported by the Swiss National Science Foundation (P300P2_151342).

  5. Specific collapse followed by slow hydrogen-bond formation of beta-sheet in the folding of single-chain monellin.

    PubMed

    Kimura, Tetsunari; Uzawa, Takanori; Ishimori, Koichiro; Morishima, Isao; Takahashi, Satoshi; Konno, Takashi; Akiyama, Shuji; Fujisawa, Tetsuro

    2005-02-22

    Characterization of the conformational landscapes for proteins with different secondary structures is important in elucidating the mechanism of protein folding. The folding trajectory of single-chain monellin composed of a five-stranded beta-sheet and a helix was investigated by using a pH-jump from the alkaline unfolded to native state. The kinetic changes in the secondary structures and in the overall size and shape were measured by circular dichroism spectroscopy and small-angle x-ray scattering, respectively. The formation of the tertiary structure was monitored by intrinsic and extrinsic fluorescence. A significant collapse was observed within 300 micros after the pH-jump, leading to the intermediate with a small amount of secondary and tertiary structures but with an overall oblate shape. Subsequently, the stepwise formation of secondary and tertiary structures was detected. The current observation was consistent with the theoretical prediction that a more significant collapse precedes the formation of secondary structures in the folding of beta-sheet proteins than that of helical proteins [Shea, J. E., Onuchic, J. N. & Brooks, C. L., III (2002) Proc. Natl. Acad. Sci. USA 99, 16064-16068]. Furthermore, it was implied that the initial collapse was promoted by the formation of some specific structural elements, such as tight turns, to form the oblate shape. PMID:15710881

  6. Formation of intermolecular beta-sheet structures: a phenomenon relevant to protein film structure at oil-water interfaces of emulsions.

    PubMed

    Lefèvre, Thierry; Subirade, Muriel

    2003-07-01

    Oil-in-water emulsions stabilized with beta-lactoglobulin (beta-lg) were made using a homogenizer or a high-speed blender. The protein was studied by Fourier transform infrared (FTIR) spectroscopy in the raw emulsion, in the bulk phase, and at the interface, as a function of pH, oil content, and homogenizing pressure. Results show that the amount of adsorbed protein varies with the available interfacial area. The protein that remains in the aqueous phase exhibit no spectral change, which suggests that homogenization causes no conformational modification or reversible ones. Strong and irreversible changes were observed in the adsorbed protein. Our findings reveal the formation of intermolecular antiparallel beta-sheets upon adsorption due to the protein self-aggregation. As deduced from transmission electronic microscopy, this surface aggregation leads to the formation of continuous and homogeneous membranes coating the globules. The structure of the adsorbed proteins is unaffected by the homogenizing pressures used in our study and slightly modified by the pH. FTIR spectroscopy allows to characterize the type of aggregates formed at the interface. An analysis of the spectra of beta-lg heat-induced gels shows that the aggregates at the interface are very close at a molecular scale to those that constitute particulate gels near the protein's isoelectric point. Since the type of aggregates is similar when the emulsion water phase is pure D(2)O and D(2)O at pD 4.4, the interface not only seems to induce aggregation, but seems to determine the type of aggregation as well. The mechanism that drives the formation of particulate aggregates (rather than fine-stranded ones) may reside in strong protein-protein interactions that are promoted by adverse oil-protein interactions. PMID:12804885

  7. The Promiscuity of [beta]-Strand Pairing Allows for Rational Design of [beta]-Sheet Face Inversion

    SciTech Connect

    Makabe, Koki; Koide, Shohei

    2009-06-17

    Recent studies suggest the dominant role of main-chain H-bond formation in specifying {beta}-sheet topology. Its essentially sequence-independent nature implies a large degree of freedom in designing {beta}-sheet-based nanomaterials. Here we show rational design of {beta}-sheet face inversions by incremental deletions of {beta}-strands from the single-layer {beta}-sheet of Borrelia outer surface protein A. We show that a {beta}-sheet structure can be maintained when a large number of native contacts are removed and that one can design large-scale conformational transitions of a {beta}-sheet such as face inversion by exploiting the promiscuity of strand-strand interactions. High-resolution X-ray crystal structures confirmed the success of the design and supported the importance of main-chain H-bonds in determining {beta}-sheet topology. This work suggests a simple but effective strategy for designing and controlling nanomaterials based on {beta}-rich peptide self-assemblies.

  8. Amyloid Beta Mediates Memory Formation

    ERIC Educational Resources Information Center

    Garcia-Osta, Ana; Alberini, Cristina M.

    2009-01-01

    The amyloid precursor protein (APP) undergoes sequential cleavages to generate various polypeptides, including the amyloid [beta] (1-42) peptide (A[beta][1-42]), which is believed to play a major role in amyloid plaque formation in Alzheimer's disease (AD). Here we provide evidence that, in contrast with its pathological role when accumulated,…

  9. Structural principles for the propeller assembly of beta-sheets: the preference for seven-fold symmetry.

    PubMed

    Murzin, A G

    1992-10-01

    Twisted beta-sheets, packed face to face, may be arranged in circular formation like blades of a propeller or turbine. This beta-propeller fold has been found in three proteins: that in neuraminidase consists of six beta-sheets while those in methylamine dehydrogenase and galactose oxidase are composed of seven beta-sheets. A model for multisheet packing in the beta-propeller fold is proposed. This model gives both geometrical parameters of the beta-propellers composed of different numbers of sheets and patterns of residue packing at their sheet-to-sheet interfaces. All the known beta-propeller structures have been analyzed, and the observed geometries and residue packing are found to be in good agreement with those predicted by models. It is shown that unusual seven-fold symmetry is preferable to six- or eight-fold symmetry for propeller-like multi-sheet assembly. According to the model, a six-beta-sheet propeller has to have predominantly small residues in the beta-strands closed to its six-fold axis, but no strong sequence constraints are necessary for a seven-fold beta-propeller. PMID:1409568

  10. Current Sheet Formation and Reconnection at a Magnetic X Line

    NASA Astrophysics Data System (ADS)

    DeVore, C. Richard; Antiochos, S. K.

    2011-05-01

    Phenomena ranging from the quiescent heating of the ambient plasma to the highly explosive release of energy and acceleration of particles in flares are conjectured to result from magnetic reconnection at electric current sheets in the Sun's corona. We are investigating numerically the formation and eventual reconnection of a current sheet in an initially potential 2D magnetic field containing a null. Subjecting this simple configuration to unequal stresses in the four quadrants bounded by the X-line separatrix distorts the potential null into a double-Y-line current sheet. Although the gas pressure is finite in our simulations, so that the plasma beta is infinite at the null, we find that even small distortions of the magnetic field induce the formation of a tangential discontinuity there. This result is well known to occur in the zero-beta, force-free limit; surprisingly, it persists into the high-beta regime where, in principle, a small plasma pressure inhomogeneity could balance all of the magnetic stress. In addition to working to understand the dynamical details of this ideal process, we are examining the effect of resistive dissipation on the development of the current sheet and are seeking to determine the critical condition for fast-reconnection onset in the sheet. Our progress on understanding these issues, and the implications for the dynamic activity associated with current sheets in the solar corona, will be reported at the conference. We gratefully acknowledge NASA sponsorship of our research.

  11. Beating the Heat - Fast Scanning Melts Silk Beta Sheet Crystals

    PubMed Central

    Cebe, Peggy; Hu, Xiao; Kaplan, David L.; Zhuravlev, Evgeny; Wurm, Andreas; Arbeiter, Daniela; Schick, Christoph

    2013-01-01

    Beta-pleated-sheet crystals are among the most stable of protein secondary structures, and are responsible for the remarkable physical properties of many fibrous proteins, such as silk, or proteins forming plaques as in Alzheimer's disease. Previous thinking, and the accepted paradigm, was that beta-pleated-sheet crystals in the dry solid state were so stable they would not melt upon input of heat energy alone. Here we overturn that assumption and demonstrate that beta-pleated-sheet crystals melt directly from the solid state to become random coils, helices, and turns. We use fast scanning chip calorimetry at 2,000 K/s and report the first reversible thermal melting of protein beta-pleated-sheet crystals, exemplified by silk fibroin. The similarity between thermal melting behavior of lamellar crystals of synthetic polymers and beta-pleated-sheet crystals is confirmed. Significance for controlling beta-pleated-sheet content during thermal processing of biomaterials, as well as towards disease therapies, is envisioned based on these new findings. PMID:23350037

  12. Structure and dynamics of parallel beta-sheets, hydrophobic core, and loops in Alzheimer's A beta fibrils.

    PubMed

    Buchete, Nicolae-Viorel; Hummer, Gerhard

    2007-05-01

    We explore the relative contributions of different structural elements to the stability of Abeta fibrils by molecular-dynamics simulations performed over a broad range of temperatures (298 K to 398 K). Our fibril structures are based on solid-state nuclear magnetic resonance experiments of Abeta(1-40) peptides, with sheets of parallel beta-strands connected by loops and stabilized by interior salt bridges. We consider models with different interpeptide interfaces, and different staggering of the N- and C-terminal beta-strands along the fibril axis. Multiple 10-20 ns molecular-dynamics simulations show that fibril segments with 12 peptides are stable at ambient temperature. The different models converge toward an interdigitated side-chain packing, and present water channels solvating the interior D23/K28 salt bridges. At elevated temperatures, we observe the early phases of fibril dissociation as a loss of order in the hydrophilic loops connecting the two beta-strands, and in the solvent-exposed N-terminal beta-sheets. As the most dramatic structural change, we observe collective sliding of the N- and C-terminal beta-sheets on top of each other. The interior C-terminal beta-sheets in the hydrophobic core remain largely intact, indicating that their formation and stability is crucial to the dissociation/elongation and stability of Abeta fibrils. PMID:17293399

  13. Beating the Heat: Fast Scanning Melts Beta Sheet Crystals

    NASA Astrophysics Data System (ADS)

    Cebe, Peggy; Hu, Xiao; Kaplan, David; Zhuravlev, Evgeny; Wurm, Andreas; Arbeiter, Daniella; Schick, Christoph

    2014-03-01

    Beta-pleated-sheet crystals are among the most stable of protein secondary structures, and are responsible for the remarkable physical properties of many fibrous proteins, such as silk. Previous thinking was that beta-pleated-sheet crystals in the dry solid state would not melt upon input of heat energy alone. Indeed, at conventional heating rates (~1-50 °C/min), silk exhibits its glass transition (~175 °C), followed by cold crystallization, and then by immediate thermal degradation beginning at about 225 °C. Here we demonstrate that beta-pleated-sheet crystals can melt directly from the solid state to become random coils, helices, and turns. We use fast scanning chip calorimetry at 2,000 K/s to avoid thermal degradation, and report the first reversible thermal melting of protein beta-pleated-sheet crystals, exemplified by silk fibroin. The similarity between thermal melting behavior of lamellar crystals of synthetic polymers and beta-pleated-sheet crystals is confirmed. The authors acknowledge support from the National Science Foundation and German Academic Exchange Service DAAD; EZ acknowledges a European Union funded Marie Curie EST fellowship (ADVATEC); XH and DK acknowledge NIH P41 Tissue Engineering Resource Center.

  14. Enhancement of beta-sheet assembly by cooperative hydrogen bonds potential

    PubMed Central

    Levy-Moonshine, Ami; Amir, El-ad David; Keasar, Chen

    2009-01-01

    Motivation: The roughness of energy landscapes is a major obstacle to protein structure prediction, since it forces conformational searches to spend much time struggling to escape numerous traps. Specifically, beta-sheet formation is prone to stray, since many possible combinations of hydrogen bonds are dead ends in terms of beta-sheet assembly. It has been shown that cooperative terms for backbone hydrogen bonds ease this problem by augmenting hydrogen bond patterns that are consistent with beta sheets. Here, we present a novel cooperative hydrogen-bond term that is both effective in promoting beta sheets and computationally efficient. In addition, the new term is differentiable and operates on all-atom protein models. Results: Energy optimization of poly-alanine chains under the new term led to significantly more beta-sheet content than optimization under a non-cooperative term. Furthermore, the optimized structure included very few non-native patterns. Availability: The new term is implemented within the MESHI package and is freely available at http://cs.bgu.ac.il/∼meshi. Contact: chen.keasar@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19628506

  15. Continuum Theory of Beta-Sheet Ribbons.

    NASA Astrophysics Data System (ADS)

    Ghafouri, Rouzbeh

    2005-03-01

    We present a continuum description for the β-sheet ribbons encountered in amyloid fibrils, allowing both stretching and bending of the ribbon in response to chiral twist. The theory leads to a non-linear variant of the Worm-Like Chain (WLC). At a critical value of the ratio of the bending and stretching moduli, the Foppl-von K'arm'an Number, we encounter a continuous buckling transition from a straight Helicoid to a Spiral Ribbon. Two of the three persistence lengths of the ribbon become very short at the transition point indicating strong thermal shape fluctuations. The transition becomes discontinuous if the ribbon width is treated as a free thermodynamic variable.

  16. Laminated, Nontwisting Beta-Sheet Fibrils Constructed via Peptide Self-Assembly

    NASA Astrophysics Data System (ADS)

    Lamm, Matthew S.; Rajagopal, Karthikan; Schneider, Joel P.; Pochan, Darrin J.

    2006-03-01

    A de novo designed peptide has been characterized that self-assembles into beta-sheet fibrils exhibiting a nontwisted, laminated morphology. The laminated morphology is constituted by 2.5nm wide filaments that laterally associate to form flat fibril laminates exceeding 100nm in width and microns in length. The height of each fibril is determined by the length of exactly one peptide momomer in an extended beta-strand conformation, approximately 7nm. Once formed, these fibrils are highly stable over a range of temperatures and pH and exhibit characteristics similar to those of amyloid fibrils. Kinetic parameters of pH and temperature can be used to affect the rate of beta-sheet formation and, consequently, the degree of lamination. Finally, the importance of peptide sequence on the resultant fibril morphology is demonstrated via rational peptide design and discussed in the context of current theories of fibril twisting.

  17. Evidence for Novel [beta]-Sheet Structures in Iowa Mutant [beta]-Amyloid Fibrils

    SciTech Connect

    Tycko, Robert; Sciarretta, Kimberly L.; Orgel, Joseph P.R.O.; Meredith, Stephen C.

    2009-07-24

    Asp23-to-Asn mutation within the coding sequence of {beta}-amyloid, called the Iowa mutation, is associated with early onset, familial Alzheimer's disease and cerebral amyloid angiopathy, in which patients develop neuritic plaques and massive vascular deposition predominantly of the mutant peptide. We examined the mutant peptide, D23N-A{beta}40, by electron microscopy, X-ray diffraction, and solid-state NMR spectroscopy. D23N-A{beta}40 forms fibrils considerably faster than the wild-type peptide (k = 3.77 x 10{sup -3} min{sup -1} and 1.07 x 10{sup -4} min{sup -1} for D23N-A{beta}40 and the wild-type peptide WT-A{beta}40, respectively) and without a lag phase. Electron microscopy shows that D23N-A{beta}40 forms fibrils with multiple morphologies. X-ray fiber diffraction shows a cross-{beta} pattern, with a sharp reflection at 4.7 {angstrom} and a broad reflection at 9.4 {angstrom}, which is notably smaller than the value for WT-A{beta}40 fibrils (10.4 {angstrom}). Solid-state NMR measurements indicate molecular level polymorphism of the fibrils, with only a minority of D23N-A{beta}40 fibrils containing the in-register, parallel {beta}-sheet structure commonly found in WT-A{beta}40 fibrils and most other amyloid fibrils. Antiparallel {beta}-sheet structures in the majority of fibrils are indicated by measurements of intermolecular distances through 13C-13C and 15N-13C dipole-dipole couplings. An intriguing possibility exists that there is a relationship between the aberrant structure of D23N-A{beta}40 fibrils and the unusual vasculotropic clinical picture in these patients.

  18. Current Sheet Formation and Reconnection Dynamics in the Solar Corona

    NASA Astrophysics Data System (ADS)

    Edmondson, Justin K.; Antiochos, S. K.; DeVore, C.; Zurbuchen, T. H.

    2009-05-01

    Current sheet formation is a necessary consequence of the evolution of the multi-polar magnetic field topologies that are ubiquitous throughout the solar corona. We present a very high-resolution study of 3D MHD current sheet formation and the resulting reconnection dynamics in an environment appropriate for the corona. The initial field consists of a translationally invariant, potential field with a null-point topology (i.e., 4-flux systems) and a low-beta plasma. A finite-extent, 3D Syrovatskii-type current sheet forms as a result of stressing of this system by a uniform, incompressible flow applied at the line-tied photospheric boundary. The system is assumed to be ideal, except for the presence of numerical resistivity. The fully 3-D evolution is calculated with very high resolution (9x and 10x refinement across the full extent of the current sheet) using the Adaptively Refined MHD Solver (ARMS). The initial evolution of this computationally-intensive simulation results in a current sheet with a nearly 30-to-1 aspect ratio, a significant fraction of the system characteristic length, that unexpectedly appears to be stable. In addition, up to this point in the evolution any magnetic reconnection that we observe is of the slow Sweet-Parker type. We expect, however, that as we continue stressing the field, the current sheet will become unstable and develop explosive dynamics. We discuss the implications of our results on coronal structure and activity, such as heating and eruptions. This work has been supported, in part, by the NASA HTP and SR&T programs.

  19. Infrared spectroscopy of pyrrole-2-carboxaldehyde and its dimer: a planar beta-sheet peptide model?

    PubMed

    Rice, Corey A; Dauster, Ingo; Suhm, Martin A

    2007-04-01

    Intermolecular interactions relevant for antiparallel beta-sheet formation between peptide strands are studied by Fourier transform infrared spectroscopy of the low temperature, vacuum-isolated model compound pyrrole-2-carboxaldehyde and its dimer in the N-H and C=O stretching range. Comparison to quantum chemical predictions shows that even for some triple-zeta quality basis sets, hybrid density functionals and Møller-Plesset perturbation calculations fail to provide a consistent and fully satisfactory description of hydrogen bond induced frequency shifts and intensity ratios in the double-harmonic approximation. The latter approach even shows problems in reproducing the planar structure of the dimer and the correct sign of the C=O stretching shift for standard basis sets. The effect of matrix isolation is modeled by condensing layers of Ar atoms on the isolated monomer and dimer. The dimer structure is discussed in the context of the peptide beta-sheet motif. PMID:17430038

  20. Role of Polyalanine Domains in -Sheet Formation in Spider Silk Block Copolymers

    SciTech Connect

    Rabotyagova, O.; Cebe, P; Kaplan, D

    2010-01-01

    Genetically engineered spider silk-like block copolymers were studied to determine the influence of polyalanine domain size on secondary structure. The role of polyalanine block distribution on {beta}-sheet formation was explored using FT-IR and WAXS. The number of polyalanine blocks had a direct effect on the formation of crystalline {beta}-sheets, reflected in the change in crystallinity index as the blocks of polyalanines increased. WAXS analysis confirmed the crystalline nature of the sample with the largest number of polyalanine blocks. This approach provides a platform for further exploration of the role of specific amino acid chemistries in regulating the assembly of {beta}-sheet secondary structures, leading to options to regulate material properties through manipulation of this key component in spider silks.

  1. Formation of Sprays From Conical Liquid Sheets

    NASA Technical Reports Server (NTRS)

    Peck, Bill; Mansour, N. N.; Koga, Dennis (Technical Monitor)

    1999-01-01

    Our objective is to predict droplet size distributions created by fuel injector nozzles in Jet turbines. These results will be used to determine the initial conditions for numerical simulations of the combustion process in gas turbine combustors. To predict the droplet size distribution, we are currently constructing a numerical model to understand the instability and breakup of thin conical liquid sheets. This geometry serves as a simplified model of the liquid jet emerging from a real nozzle. The physics of this process is difficult to study experimentally as the time and length scales are very short. From existing photographic data, it does seem clear that three-dimensional effects such as the formation of streamwise ligaments and the pulling back of the sheet at its edges under the action of surface tension are important.

  2. Folding dynamics of a family of beta-sheet proteins

    NASA Astrophysics Data System (ADS)

    Rousseau, Denis

    2008-03-01

    Fatty acid binding proteins (FABP) consist of ten anti-parallel beta strands and two small alpha helices. The beta strands are arranged into two nearly orthogonal five-strand beta sheets that surround the interior cavity, which binds unsaturated long-chain fatty acids. In the brain isoform (BFABP), these are very important for the development of the central nervous system and neuron differentiation. Furthermore, BFABP is implicated in the pathogenesis of a variety of human diseases including cancer and neuronal degenerative disorders. In this work, site-directed spin labeling combined with EPR techniques have been used to study the folding mechanism of BFABP. In the first series of studies, we labeled the two Cys residues at position 5 and 80 in the wild type protein with an EPR spin marker; in addition, two singly labeled mutants at positions 5 and 80 in the C80A and C5A mutants, respectively, were also produced and used as controls. The changes in the distances between the two residues were examined by a pulsed EPR method, DEER (Double Electron Electron Resonance), as a function of guanidinium hydrochloride concentration. The results were compared with those from CW EPR, circular dichroism and fluorescence measurements, which provide the information regarding sidechain mobility, secondary structure and tertiary structure, respectively. The results will be discussed in the context of the folding mechanism of the family of fatty acid binding proteins.

  3. A recipe for designing water-soluble, beta-sheet-forming peptides.

    PubMed Central

    Mayo, K. H.; Ilyina, E.; Park, H.

    1996-01-01

    Based on observations of solubility and folding properties of peptide 33-mers derived from the beta-sheet domains of platelet factor-4 (PF4), interleukin-8 (IL-8), and growth related protein (Gro-alpha), as well as other beta-sheet-forming peptides, general guidelines have been developed to aid in the design of water soluble, self-association-induced beta-sheet-forming peptides. CD, 1H-NMR, and pulsed field gradient NMR self-diffusion measurements have been used to assess the degree of folding and state of aggregation. PF4 peptide forms native-like beta-sheet tetramers and is sparingly soluble above pH 6. IL-8 peptide is insoluble between pH 4.5 and pH 7.5, yet forms stable, native-like beta-sheet dimers at higher pH. Gro-alpha peptide is soluble at all pH values, yet displays no discernable beta-sheet structure even when diffusion data indicate dimer-tetramer aggregation. A recipe used in the de novo design of water-soluble beta-sheet-forming peptides calls for the peptide to contain 40-50% hydrophobic residues, usually aliphatic ones (I, L, V, A, M) (appropriately paired and mostly but not always alternating with polar residues in the sheet sequence), a positively charged (K, R) to negatively charged (E, D) residue ratio between 4/2 and 6/2, and a noncharged polar residue (N, Q, T, S) composition of about 20% or less. Results on four de novo designed, 33-residue peptides are presented supporting this approach. Under near physiologic conditions, all four peptides are soluble, form beta-sheet structures to varying degrees, and self-associate. One peptide folds as a stable, compact beta-sheet tetramer, whereas the others are transient beta-sheet-containing aggregates. PMID:8819163

  4. Diffraction from the beta-sheet crystallites in spider silk.

    PubMed

    Ulrich, S; Glišović, A; Salditt, T; Zippelius, A

    2008-11-01

    We analyze the wide-angle X-ray scattering from oriented spider silk fibers in terms of a quantitative scattering model, including both structural and statistical parameters of the beta-sheet crystallites of spider silk in the amorphous matrix. The model is based on kinematic scattering theory and allows for rather general correlations of the positional and orientational degrees of freedom, including the crystallite's size, composition and dimension of the unit cell. The model is evaluated numerically and compared to experimental scattering intensities allowing us to extract the geometric and statistical parameters. We show explicitly that for the experimentally found mosaicity (width of the orientational distribution) intercrystallite effects are negligible and the data can be analyzed in terms of single-crystallite scattering, as is usually assumed in the literature. PMID:18843512

  5. Precise assembly of complex beta sheet topologies from de novo designed building blocks

    PubMed Central

    King, Indigo Chris; Gleixner, James; Doyle, Lindsey; Kuzin, Alexandre; Hunt, John F; Xiao, Rong; Montelione, Gaetano T; Stoddard, Barry L; DiMaio, Frank; Baker, David

    2015-01-01

    Design of complex alpha-beta protein topologies poses a challenge because of the large number of alternative packing arrangements. A similar challenge presumably limited the emergence of large and complex protein topologies in evolution. Here, we demonstrate that protein topologies with six and seven-stranded beta sheets can be designed by insertion of one de novo designed beta sheet containing protein into another such that the two beta sheets are merged to form a single extended sheet, followed by amino acid sequence optimization at the newly formed strand-strand, strand-helix, and helix-helix interfaces. Crystal structures of two such designs closely match the computational design models. Searches for similar structures in the SCOP protein domain database yield only weak matches with different beta sheet connectivities. A similar beta sheet fusion mechanism may have contributed to the emergence of complex beta sheets during natural protein evolution. DOI: http://dx.doi.org/10.7554/eLife.11012.001 PMID:26650357

  6. Propagating structure of alzheimer's {beta}-amyloid is parallel {beta}-sheet with residues in exact register.

    SciTech Connect

    Benzinger, T. L. S.; Gregory, D. M.; Burkoth, T. S.; Miller-Auer, H.; Lynn, D. G.; Botto, R. E.; Meredith, S. C.; Chemistry; Univ. of Chicago

    1998-11-10

    The pathognomonic plaques of Alzheimer's disease are composed primarily of the 39- to 43-aa {beta}-amyloid (A{beta}) peptide. Crosslinking of A{beta} peptides by tissue transglutaminase (tTg) indicates that Gln15 of one peptide is proximate to Lys16 of another in aggregated A{beta}. Here we report how the fibril structure is resolved by mapping interstrand distances in this core region of the A{beta} peptide chain with solid-state NMR. Isotopic substitution provides the source points for measuring distances in aggregated A{beta}. Peptides containing a single carbonyl 13C label at Gln15, Lys16, Leu17, or Val18 were synthesized and evaluated by NMR dipolar recoupling methods for the measurement of interpeptide distances to a resolution of 0.2 Angstrom. Analysis of these data establish that this central core of A{beta} consists of a parallel {beta}-sheet structure in which identical residues on adjacent chains are aligned directly, i.e., in register. Our data, in conjunction with existing structural data, establish that the A{beta} fibril is a hydrogen-bonded, parallel {beta}-sheet defining the long axis of the A{beta} fibril propagation.

  7. Formation and separation of merged liquid sheets developed from the mixing of coaxial swirling liquid sheets

    NASA Astrophysics Data System (ADS)

    Sivakumar, D.; Raghunandan, B. N.

    2003-11-01

    Liquid-liquid coaxial swirl atomizers are used in liquid rocket engines to achieve an efficient mixing between the fuel and oxidizer sprays. The characteristics of the mixed spray are mainly controlled by the flow behavior of merged liquid sheet originating at the contact point of inner and outer swirling liquid sheets. With an intention of identifying various flow regimes of merged liquid sheet at different conditions of inner and outer liquid sheets, we report here a fundamental experimental investigation on the characteristics of merged liquid sheets using water as the experimental liquid. The physical processes involved in the formation and separation of a merged liquid sheet are described from the experimental measurements. For a given outer liquid sheet condition, the merged liquid sheet forms and separates at specific inner liquid sheet flow conditions. At low outer liquid sheet flow conditions with Weber number less than 50, the merged liquid sheet exhibits a self-sustaining periodic separation process, whose frequency increases with increasing inner liquid sheet Weber number for a given outer liquid sheet Weber number. Experimental measurements are presented to show that the dynamics of the contact point plays a major role in governing the characteristics of merged liquid sheets.

  8. Conversion of non-fibrillar {beta}-sheet oligomers into amyloid fibrils in Alzheimer's disease amyloid peptide aggregation

    SciTech Connect

    Benseny-Cases, Nuria; Cocera, Mercedes; Cladera, Josep

    2007-10-05

    A{beta}(1-40) is one of the main components of the fibrils found in amyloid plaques, a hallmark of brains affected by Alzheimer's disease. It is known that prior to the formation of amyloid fibrils in which the peptide adopts a well-ordered intermolecular {beta}-sheet structure, peptide monomers associate forming low and high molecular weight oligomers. These oligomers have been previously described in electron microscopy, AFM, and exclusion chromatography studies. Their specific secondary structures however, have not yet been well established. A major problem when comparing aggregation and secondary structure determinations in concentration-dependent processes such as amyloid aggregation is the different concentration range required in each type of experiment. In the present study we used the dye Thioflavin T (ThT), Fourier-transform infrared spectroscopy, and electron microscopy in order to structurally characterize the different aggregated species which form during the A{beta}(1-40) fibril formation process. A unique sample containing 90 {mu}M peptide was used. The results show that oligomeric species which form during the lag phase of the aggregation kinetics are a mixture of unordered, helical, and intermolecular non-fibrillar {beta}-structures. The number of oligomers and the amount of non-fibrillar {beta}-structures grows throughout the lag phase and during the elongation phase these non-fibrillar {beta}-structures are transformed into fibrillar (amyloid) {beta}-structures, formed by association of high molecular weight intermediates.

  9. Structural characterization of adsorbed helical and beta-sheet peptides

    NASA Astrophysics Data System (ADS)

    Samuel, Newton Thangadurai

    Adsorbed peptides on surfaces have potential applications in the fields of biomaterials, tissue engineering, peptide microarrays and nanobiotechnology. The surface region, the "biomolecular interface" between a material and the biological environment, plays a crucial role in these applications. As a result, characterization of adsorbed peptide structure, especially with respect to identity, concentration, spatial distribution, conformation and orientation, is important. The present research employs NEXAFS (near-edge X-ray absorption fine structure spectroscopy) and SFG (sum frequency generation spectroscopy) to provide information about the adsorbed peptide structure. Soft X-ray NEXAFS is a synchrotron-based technique which typically utilizes polarized X-rays to interrogate surfaces under ultra-high vacuum conditions. SFG is a non-linear optical technique which utilizes a combination of a fixed visible and a tunable infrared laser beams to generate a surface-vibrational spectrum of surface species. SFG has the added advantage of being able to directly analyze the surface-structure at the solid-liquid interface. The main goals of the present research were twofold: characterize the structure of adsorbed peptides (1) ex situ using soft X-ray NEXAFS, and (2) in situ using non-linear laser spectroscopy (SFG). Achieving the former goal involved first developing a comprehensive characterization of the carbon, nitrogen and oxygen k-edge NEXAFS spectra for amino acids, and then using a series of helical and beta-sheet peptides to demonstrate the sensitivity of polarization-dependent NEXAFS to secondary structure of adsorbed peptides. Characterizing the structure of adsorbed peptides in situ using SFG involved developing a model system to probe the solid-liquid interface in situ; demonstrating the ability to probe the molecular interactions and adsorbed secondary structure; following the time-dependent ordering of the adsorbed peptides; and establishing the ability to obtain

  10. Thickness of mouthguard sheets after vacuum-pressure formation: influence of mouthguard sheet material.

    PubMed

    Takahashi, Mutsumi; Koide, Kaoru; Iwasaki, Shin-Ichi

    2016-06-01

    The aim of this study was to investigate the thickness of mouthguard sheet after vacuum-pressure formation based on the mouthguard sheet material. Three mouthguard sheet materials (4.0 mm thick) were compared: ethylene-vinyl acetate co-polymer (EVA), olefin co-polymer (OL), and polyolefin-polystyrene co-polymer (OS). The working model was made by hard gypsum that was trimmed to the height of 20 mm at the cutting edge of the maxillary central incisor and 15 mm at the mesiobuccal cusp of the maxillary first molar. Where the center of the softened sheet sagged 15 mm lower than the clamp, the sheet was pressed against the working model, followed by vacuum forming for 10 s and compression molding for 2 min. The thickness of mouthguard sheets after fabrication was determined for the incisal portion (incisal edge and labial surface) and molar portion (cusp and buccal surface), and dimensional measurements were obtained using a measuring device. Differences in the change in thickness due to sheet materials were analyzed by one-way analysis of variance (anova) followed by Bonferroni's multiple comparison tests. The OL sheet was thickest at all measurement points. At the incisal edge and cusp, thickness after formation was highest for OL, then EVA and finally OS. At the labial surface and buccal surface, the thickness after formation was highest for OL, then OS and finally EVA. This study suggested that post-fabrication mouthguard thickness differed according to sheet material, with the olefin co-polymer sheet having the smallest thickness reduction. PMID:26446242

  11. Magnetohydrodynamic Simulations of Current-Sheet Formation and Reconnection at a Magnetic X Line

    NASA Astrophysics Data System (ADS)

    DeVore, C. R.; Antiochos, S. K.; Karpen, J. T.; Black, C.

    2011-12-01

    Phenomena ranging from the quiescent heating of the ambient plasma to the highly explosive release of energy and acceleration of particles in flares are conjectured to result from magnetic reconnection at electric current sheets in the Sun's corona. We are investigating numerically, using a macroscopic magnetohydrodynamic (MHD) model with adaptive mesh refinement, the formation and reconnection of a current sheet in an initially potential 2D magnetic field containing a null. Subjecting this simple configuration to unequal stresses in the four quadrants bounded by the X-line separatrix distorts the potential null into a double-Y-line current sheet. We find that even small distortions of the magnetic field induce the formation of a tangential discontinuity in the high-beta region around the null. A continuously applied stress eventually leads to the onset of fast magnetic reconnection across the sheet, with copious production, merging, and ejection of magnetic islands. We compare the current-sheet development and evolution for three cases: quasi-ideal MHD with numerical resistivity only; uniformly resistive MHD; and MHD with an embedded kinetic reconnection model. Analogous kinetic simulations using particle-in-cell (PIC) methods to investigate the small-scale dynamics of the system also are being pursued (C. Black et al., this meeting). Our progress toward understanding this simple system will be reported, as will the implications of our results for the dynamic activity associated with coronal current sheets and for general multiscale modeling of magnetized plasmas in the Heliosphere. Our research was supported by NASA.

  12. Formation of current sheets in magnetic reconnection

    SciTech Connect

    Boozer, Allen H.

    2014-07-15

    An ideal evolution of magnetic fields in three spatial dimensions tends to cause neighboring field lines to increase their separation exponentially with distance ℓ along the lines, δ(ℓ)=δ(0)e{sup σ(ℓ)}. The non-ideal effects required to break magnetic field line connections scale as e{sup −σ}, so the breaking of connections is inevitable for σ sufficiently large—even though the current density need nowhere be large. When the changes in field line connections occur rapidly compared to an Alfvén transit time, the constancy of j{sub ||}/B along the magnetic field required for a force-free equilibrium is broken in the region where the change occurs, and an Alfvénic relaxation of j{sub ||}/B occurs. Independent of the original spatial distribution of j{sub ||}/B, the evolution is into a sheet current, which is stretched by a factor e{sup σ} in width and contracted by a factor e{sup σ} in thickness with the current density j{sub ||} increasing as e{sup σ}. The dissipation of these sheet currents and their associated vorticity sheets appears to be the mechanism for transferring energy from a reconnecting magnetic field to a plasma. Harris sheets, which are used in models of magnetic reconnection, are shown to break up in the direction of current flow when they have a finite width and are in a plasma in force equilibrium. The dependence of the longterm nature of magnetic reconnection in systems driven by footpoint motion can be studied in a model that allows qualitative variation in the nature of that motion: slow or fast motion compared to the Alfvén transit time and the neighboring footpoints either exponentially separating in time or not.

  13. Multi-layer Parallel Beta-Sheet Structure of Amyloid Beta peptide (1-40) aggregate observed by discrete molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Peng, Shouyong; Urbanc, Brigita; Ding, Feng; Cruz, Luis; Buldyrev, Sergey; Dokholyan, Nikolay; Stanley, H. E.

    2003-03-01

    New evidence shows that oligomeric forms of Amyloid-Beta are potent neurotoxins that play a major role in neurodegeneration of Alzheimer's disease. Detailed knowledge of the structure and assembly dynamics of Amyloid-Beta is important for the development of new therapeutic strategies. Here we apply a two-atom model with Go interactions to model aggregation of Amyloid-Beta (1-40) peptides using the discrete molecular dynamics simulation. At temperatures above the transition temperature from an alpha-helical to random coil, we obtain two types of parallel beta-sheet structures, (a) a helical beta-sheet structure at a lower temperature and (b) a parallel beta-sheet structure at a higher temperature, both with inter-sheet distance of 10 A and with free edges which possibly enable further fibrillar elongation.

  14. Characteristics of Amyloid-Related Oligomers Revealed by Crystal Structures of Macrocyclic [beta]-Sheet Mimics

    SciTech Connect

    Liu, Cong; Sawaya, Michael R.; Cheng, Pin-Nan; Zheng, Jing; Nowick, James S.; Eisenberg, David

    2011-09-20

    Protein amyloid oligomers have been strongly linked to amyloid diseases and can be intermediates to amyloid fibers. {beta}-Sheets have been identified in amyloid oligomers. However, because of their transient and highly polymorphic properties, the details of their self-association remain elusive. Here we explore oligomer structure using a model system: macrocyclic peptides. Key amyloidogenic sequences from A{beta} and tau were incorporated into macrocycles, thereby restraining them to {beta}-strands, but limiting the growth of the oligomers so they may crystallize and cannot fibrillate. We determined the atomic structures for four such oligomers, and all four reveal tetrameric interfaces in which {beta}-sheet dimers pair together by highly complementary, dry interfaces, analogous to steric zippers found in fibers, suggesting a common structure for amyloid oligomers and fibers. In amyloid fibers, the axes of the paired sheets are either parallel or antiparallel, whereas the oligomeric interfaces display a variety of sheet-to-sheet pairing angles, offering a structural explanation for the heterogeneity of amyloid oligomers.

  15. Dynamics of sheet nacre formation in bivalves.

    PubMed

    Rousseau, Marthe; Meibom, Anders; Gèze, Marc; Bourrat, Xavier; Angellier, Martine; Lopez, Evelyne

    2009-03-01

    Formation of nacre (mother-of-pearl) is a biomineralization process of fundamental scientific as well as industrial importance. However, the dynamics of the formation process is still not understood. Here, we use scanning electron microscopy and high spatial resolution ion microprobe depth-profiling to image the full three-dimensional distribution of organic materials around individual tablets in the top-most layer of forming nacre in bivalves. Nacre formation proceeds by lateral, symmetric growth of individual tablets mediated by a growth-ring rich in organics, in which aragonite crystallizes from amorphous precursors. The pivotal role in nacre formation played by the growth-ring structure documented in this study adds further complexity to a highly dynamical biomineralization process. PMID:19121399

  16. The molecular organization of the beta-sheet region in Corneous beta-proteins (beta-keratins) of sauropsids explains its stability and polymerization into filaments.

    PubMed

    Calvaresi, Matteo; Eckhart, Leopold; Alibardi, Lorenzo

    2016-06-01

    The hard corneous material of avian and reptilian scales, claws, beak and feathers is mainly derived from the presence of proteins formerly known as beta-keratins but now termed Corneous beta-proteins of sauropsids to distinguish them from keratins, which are members of the intermediate filament protein family. The modeling of the conserved 34 amino acid residues long central beta-sheet region of Corneous beta-proteins using an ab initio protein folding and structure prediction algorithm indicates that this region is formed by four antiparallel beta-sheets. Molecular dynamic simulations and Molecular Mechanics/Poisson Boltzmann Surface Area (MM-PBSA) analysis showed that the disposition of polar and apolar amino acids within the beta-region gives rise to an amphipathic core whose stability is further increased, especially in an aqueous environment, by the association into a dimer due to apolar interactions and specific amino-acid interactions. The dimers in turn polymerize into a 3nm thick linear beta-filament due to van der Waals and hydrogen-bond interactions. It is suggested that once this nuclear core of anti-parallel sheets evolved in the genome of a reptilian ancestor of the extant reptiles and birds about 300 millions years ago, new properties emerged in the corneous material forming scales, claws, beaks and feathers in these amniotes based on the tendency of these unique corneous proteins to form stable filaments different from keratin intermediate filaments or sterical structures formed by other corneous proteins so far known. PMID:26965557

  17. Metallopolymer-peptide conjugates: synthesis and self-assembly of polyferrocenylsilane graft and block copolymers containing a beta-sheet forming Gly-Ala-Gly-Ala tetrapeptide segment.

    PubMed

    Vandermeulen, Guido W M; Kim, Kyoung Taek; Wang, Zhuo; Manners, Ian

    2006-04-01

    We describe the synthesis and self-assembly of two beta-sheet forming metallopolymer-peptide conjugates. The ability of the oligotetrapeptide sequence Gly-Ala-Gly-Ala (GAGA) to form antiparallel beta-sheets was retained in PFS-b-AGAG (PFS = polyferrocenylsilane) and PFS-g-AGAG conjugates with block and graft architectures, respectively. In the solid state, DSC experiments suggest a phase separation between the peptide and PFS domains. In toluene, PFS-b-AGAG interestingly forms a fibrous network which consists of a core containing the self-assembled antiparallel beta-sheet peptide and a corona of organometallic PFS. The self-assembly of the peptide into antiparallel beta-sheets is the driving force for the fiber formation, whereas PFS prevents uncontrolled lateral aggregation of the fibers. The use of an oligopeptide to self-assemble an otherwise random coiled organometallic polymer may be a useful strategy to enhance nanostructure formation. In the cases described here, the conjugates may be used to create nanopatterned ceramics, and the redox properties of the resulting supramolecular aggregates are of significant interest. PMID:16602714

  18. Laminated Morphology of Nontwisting beta-Sheet Fibrilis Constructed via Peptide Self-Assembly

    SciTech Connect

    Lamm,M.; Rajagopal, K.; Schneider, J.; Pochan, D.

    2005-01-01

    A synthetic peptide has been de novo designed that self-assembles into {beta}-sheet fibrils exhibiting a nontwisted, stacked morphology. The stacked morphology is constituted by 2.5 nm wide filaments that laterally associate to form flat fibril laminates exceeding 50 nm in width and micrometers in length. The height of each fibril is limited to the length of exactly one peptide monomer in an extended {beta}-strand conformation, approximately 7 nm. Once assembled, these highly ordered, 2-D structures are stable over a wide range of pH and temperature and exhibit characteristics similar to those of amyloid fibrils. Furthermore, the rate of assembly and degree of fibril lamination can be controlled with kinetic parameters of pH and temperature. Finally, the presence of a diproline peptide between two {beta}-sheet-forming strands in the peptide sequence is demonstrated to be an important factor in promoting the nontwisting, laminated fibril morphology.

  19. On spontaneous formation of current sheets: Untwisted magnetic fields

    SciTech Connect

    Bhattacharyya, R.; Low, B. C.; Smolarkiewicz, P. K.

    2010-11-15

    This is a study of the spontaneous formation of electric current sheets in an incompressible viscous fluid with perfect electrical conductivity, governed by the magnetohydrodynamic Navier-Stokes equations. Numerical solutions to two initial value problems are presented for a three-dimensional, periodic, untwisted magnetic field evolving, with no change in magnetic topology under the frozen-in condition and at characteristic fluid Reynolds numbers of the order of 500, from a nonequilibrium initial state with the fluid at rest. The evolution converts magnetic free energy into kinetic energy to be all dissipated away by viscosity so that the field settles into a minimum-energy, static equilibrium. The solutions demonstrate that, as a consequence of the frozen-in condition, current sheets must form during the evolution despite the geometric simplicity of the prescribed initial fields. In addition to the current sheets associated with magnetic neutral points and field reversal layers, other sheets not associated with such magnetic features are also in evidence. These current sheets form on magnetic flux surfaces. This property is used to achieve a high degree of the frozen-in condition in the simulations, by describing the magnetic field entirely in terms of the advection of its flux surfaces and integrating the resulting governing equations with a customized version of a general-purpose high-resolution (viz., nonoscillatory) hydrodynamical simulation code EULAG [J. M. Prusa et al., Comput. Fluids 37, 1193 (2008)]. Incompressibility imposes the additional global constraint that the flux surfaces must evolve with no change in the spatial volumes they enclose. In this approach, current sheet formation is demonstrated graphically by the progressive pressing together of suitably selected flux surfaces until their separation has diminished below the minimal resolved distance on a fixed grid. The frozen-in condition then fails in the simulation as the field reconnects through

  20. Captides: Rigid Junctions between Beta Sheets and Small Molecules

    PubMed Central

    Kier, Brandon L.; Andersen, Niels H.

    2014-01-01

    An extensive series of covalently linked small molecule-peptide adducts based on a terminally capped beta hairpin motif is reported. The constructs can be prepared by standard solid-phase fmoc chemistry with 1 to 4 peptide chains linked to small molecule hubs bearing carboxylic acid moieties. The key feature of interest is the precise, buried environment of the small molecule, and its rigid orientation relative to one or more short, but fully structured peptide chain(s). Most of this study employs a minimalist 9 residue “captide”, a capped β-turn, but we illustrate general applicability to peptides which can terminate in a beta strand. The non-peptide portion of these adducts can include nearly any molecule bearing one or more carboxylic acid groups. Fold-dependent rigidity sets this strategy apart from currently available bioconjugation methods, which typically engender significant flexibility between peptide and tag. Applications to catalyst enhancement, drug design, higher-order assembly, and FRET calibration rulers are discussed. PMID:24909552

  1. Reversible transition between alpha-helix and beta-sheet conformation of a transmembrane domain.

    PubMed

    Yassine, Wissam; Taib, Nada; Federman, Silvina; Milochau, Alexandra; Castano, Sabine; Sbi, Walid; Manigand, Claude; Laguerre, Michel; Desbat, Bernard; Oda, Reiko; Lang, Jochen

    2009-09-01

    Despite the important functions of protein transmembrane domains, their structure and dynamics are often scarcely known. The SNARE proteins VAMP/synaptobrevin and syntaxin 1 are implicated in membrane fusion. Using different spectroscopic approaches we observed a marked sensitivity of their transmembrane domain structure in regard to the lipid/peptide ratio. In the dilute condition, peptides corresponding to the complete transmembrane domain fold into an alpha-helix inserted at approximately 35 degrees to the normal of the membranes, an observation in line with molecular simulations. Upon an increase in the peptide/lipid ratio, the peptides readily exhibited transition to beta-sheet structure. Moreover, the insertion angle of these beta-sheets increased to 54 degrees and was accompanied by a derangement of lipid acyl chains. For both proteins the transition from alpha-helix to beta-sheet was reversible under certain conditions by increasing the peptide/lipid ratio. This phenomenon was observed in different model systems including multibilayers and small unilamellar vesicles. In addition, differences in peptide structure and transitions were observed when using distinct lipids (DMPC, DPPC or DOPC) thus indicating parameters influencing transmembrane domain structure and conversion from helices to sheets. The putative functional consequences of this unprecedented dynamic behavior of a transmembrane domain are discussed. PMID:19482005

  2. Hydrophobic interactions and hydrogen bonds in β-sheet formation

    NASA Astrophysics Data System (ADS)

    Narayanan, Chitra; Dias, Cristiano L.

    2013-09-01

    In this study, we investigate interactions of extended conformations of homodimeric peptides made of small (glycine or alanine) and large hydrophobic (valine or leucine) sidechains using all-atom molecular dynamics simulations to decipher driving forces for β-sheet formation. We make use of a periodic boundary condition setup in which individual peptides are infinitely long and stretched. Dimers adopt β-sheet conformations at short interpeptide distances (ξ ˜ 0.5 nm) and at intermediate distances (˜0.8 nm), valine and leucine homodimers assume cross-β-like conformations with side chains interpenetrating each other. These two states are identified as minima in the potential of mean force. While the number of interpeptide hydrogen bonds increases with decreasing interpeptide distance, the total hydrogen bond number in the system does not change significantly, suggesting that formation of β-sheet structures from extended conformations is not driven by hydrogen bonds. This is supported by an increase in electrostatic energy at short interpeptide distances. A remarkable correlation between the volume of the system and the total electrostatic energy is observed, further reinforcing the idea that excluding water in proteins comes with an enthalpic penalty. We also discuss microscopic mechanisms accounting for β-sheet formation based on computed enthalpy and entropy and we show that they are different for peptides with small and large side chains.

  3. Possible participation of transient sheets of 1. -->. 4-. beta. -glucans in the biosynthesis of cellulose I. [Acetobacter xylinum

    SciTech Connect

    Colvin, J.R.

    1983-01-01

    It is suggested that a primary, essential stage in the biologic formation of a microfibril of cellulose I is an extracellular, lateral association of presynthesized (1..-->..4)-..beta..-D-glucans, by hydrogen bonding, to form long, thin sheets. These sheets then superimpose themselves nonenzymatically by London forces to form the nascent microfibril. The ends of the constituent glucans of the nascent microfibril may undergo extension or rearrangement of the type indicated by Maclachlan and colleagues. The formation of the metastable, native structure (cellulose I) may be deduced from the above suggestion as a natural consequence of closest packing of the sheets. The irreversibility of the change from cellulose I to cellulose II, either by mercerization or regeneration, also follows from the postulate. The suggestion also explains why cellulose microfibrils and chitin microfibrils may be formed contiguously in cell walls without interfering with each other. High-resolution electron micrographs of the tips of newly formed microfibrils of bacterial cellulose which had been very lightly negatively stained with sodium phosphotungstate are consistent with the suggestion. 33 references, 3 figures.

  4. Thermally Induced Alpha-Helix to Beta-Sheet Transition in Regenerated Silk Fibers and Films

    SciTech Connect

    Drummy,L.; Phillips, D.; Stone, M.; Farmer, B.; Naik, R.

    2005-01-01

    The structure of thin films cast from regenerated solutions of Bombyx mori cocoon silk in hexafluoroisopropyl alcohol (HFIP) was studied by synchrotron X-ray diffraction during heating. A solid-state conformational transition from an alpha-helical structure to the well-known beta-sheet silk II structure occurred at a temperature of approximately 140 degrees C. The transition appeared to be homogeneous, as both phases do not coexist within the resolution of the current study. Modulated differential scanning calorimetry (DSC) of the films showed an endothermic melting peak followed by an exothermic crystallization peak, both occurring near 140 degrees C. Oriented fibers were also produced that displayed this helical molecular conformation. Subsequent heating above the structural transition temperature produced oriented beta-sheet fibers very similar in structure to B. mori cocoon fibers. Heat treatment of silk films at temperatures well below their degradation temperature offers a controllable route to materials with well-defined structures and mechanical behavior.

  5. Design and biological activity of {beta}-sheet breaker peptide conjugates

    SciTech Connect

    Rocha, Sandra Cardoso, Isabel; Boerner, Hans; Pereira, Maria Carmo; Saraiva, Maria Joao; Coelho, Manuel

    2009-03-06

    The sequence LPFFD (iA{beta}{sub 5}) prevents amyloid-{beta} peptide (A{beta}) fibrillogenesis and neurotoxicity, hallmarks of Alzheimer's disease (AD), as previously demonstrated. In this study iA{beta}{sub 5} was covalently linked to poly(ethylene glycol) (PEG) and the activity of conjugates was assessed and compared to the activity of the peptide alone by in vitro studies. The conjugates were characterized by MALDI-TOF. Competition binding assays established that conjugates retained the ability to bind A{beta} with similar strength as iA{beta}{sub 5}. Transmission electron microscopy analysis showed that iA{beta}{sub 5} conjugates inhibited amyloid fibril formation, which is in agreement with binding properties observed for the conjugates towards A{beta}. The conjugates were also able to prevent amyloid-induced cell death, as evaluated by activation of caspase 3. These results demonstrated that the biological activity of iA{beta}{sub 5} is not affected by the pegylation process.

  6. Formation and dynamical history of the beta Pictoris system

    NASA Astrophysics Data System (ADS)

    Wyatt, M.

    2014-09-01

    The structure of the beta Pic disk holds many clues to its formation and dynamical history. In particular there is strong evidence for sculpting by the beta Pic-b planet. For example, a warp in the disk at 80au is thought to be driven by the secular perturbations of that planet, and scattering of comets by beta Pic-b is thought to be the origin of the Falling Evaporating Bodies. A clump in the disk coincident with the warp, also at ~80au, provides clues to the outer planetary system which for now is poorly constrained. One possible origin for the clump is in trapping of comets into resonance with an outer planet currently at ~60au, with an alternative scenario being a giant impact between planetary embryos. This talk will consider the various disk structures and what they tell us about the formation and dynamical history of the beta Pictoris system.

  7. Inhibition of aggregation of amyloid peptides by beta-sheet breaker peptides and their binding affinity.

    PubMed

    Viet, Man Hoang; Ngo, Son Tung; Lam, Nguyen Sy; Li, Mai Suan

    2011-06-01

    The effects of beta-sheet breaker peptides KLVFF and LPFFD on the oligomerization of amyloid peptides were studied by all-atom simulations. It was found that LPFFD interferes the aggregation of Aβ(16-22) peptides to a greater extent than does KLVFF. Using the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method, we found that the former binds more strongly to Aβ(16-22). Therefore, by simulations, we have clarified the relationship between aggregation rates and binding affinity: the stronger the ligand binding, the slower the oligomerization process. The binding affinity of pentapeptides to full-length peptide Aβ(1-40) and its mature fibrils has been considered using the Autodock and MM-PBSA methods. The hydrophobic interaction between ligands and receptors plays a more important role for association than does hydrogen bonding. The influence of beta-sheet breaker peptides on the secondary structures of monomer Aβ(1-40) was studied in detail, and it turns out that, in their presence, the total beta-sheet content can be enhanced. However, the aggregation can be slowed because the beta-content is reduced in fibril-prone regions. Both pentapeptides strongly bind to monomer Aβ(1-40), as well as to mature fibrils, but KLVFF displays a lower binding affinity than LPFFD. Our findings are in accord with earlier experiments that both of these peptides can serve as prominent inhibitors. In addition, we predict that LPFFD inhibits/degrades the fibrillogenesis of full-length amyloid peptides better than KLVFF. This is probably related to a difference in their total hydrophobicities in that the higher the hydrophobicity, the lower the inhibitory capacity. The GROMOS96 43a1 force field with explicit water and the force field proposed by Morris et al. (Morris et al. J. Comput. Chem. 1998, 19, 1639 ) were employed for all-atom molecular dynamics simulations and Autodock experiments, respectively. PMID:21563780

  8. The beta-sheet to alpha-helix transition of beta-lactoglobulin monitored in real time with a microfabricated IR mixer

    NASA Astrophysics Data System (ADS)

    Kauffmann, Ekkehard; Darton, Nick; Gerwert, Klaus; Austin, Robert

    2001-03-01

    The helix to sheet transition of proteins, a crucial step in amylogenic diseases, is investigated with a new diffusional IR mixer using time-resolved FTIR spectroscopy capable of 400 microsecond time resolution. We show that the beta to alpha transition of beta-lactoglobulin proceeds via a compact molten globule b-sheet intermediate with an unusually short lifetime of 7 ms. Because the protein does not have to unfold for the beta-sheet to alpha-helix transition the energy barrier seems to be unexpectedly low. The rough energy landscape of a protein includes not only the steep free energy funnel that guides the unfolded protein into its compact native state

  9. CURRENT SHEETS FORMATION IN TANGLED CORONAL MAGNETIC FIELDS

    SciTech Connect

    Rappazzo, A. F.; Parker, E. N. E-mail: parker@oddjob.uchicago.edu

    2013-08-10

    We investigate the dynamical evolution of magnetic fields in closed regions of solar and stellar coronae. To understand under which conditions current sheets form, we examine dissipative and ideal reduced magnetohydrodynamic models in Cartesian geometry, where two magnetic field components are present: the strong guide field B{sub 0}, extended along the axial direction, and the dynamical orthogonal field b. Magnetic field lines thread the system along the axial direction that spans the length L and are line-tied at the top and bottom plates. The magnetic field b initially has only large scales, with its gradient (current) length scale of the order of l{sub b}. We identify the magnetic intensity threshold b/B{sub 0} {approx} l{sub b}/L. For values of b below this threshold, field-line tension inhibits the formation of current sheets, while above the threshold they form quickly on fast ideal timescales. In the ideal case, above the magnetic threshold, we show that current sheets thickness decreases in time until it becomes smaller than the grid resolution, with the analyticity strip width {delta} decreasing at least exponentially, after which the simulations become underresolved.

  10. Current Sheets Formation in Tangled Coronal Magnetic Fields

    NASA Astrophysics Data System (ADS)

    Rappazzo, A. F.; Parker, E. N.

    2013-08-01

    We investigate the dynamical evolution of magnetic fields in closed regions of solar and stellar coronae. To understand under which conditions current sheets form, we examine dissipative and ideal reduced magnetohydrodynamic models in Cartesian geometry, where two magnetic field components are present: the strong guide field B 0, extended along the axial direction, and the dynamical orthogonal field b. Magnetic field lines thread the system along the axial direction that spans the length L and are line-tied at the top and bottom plates. The magnetic field b initially has only large scales, with its gradient (current) length scale of the order of l b . We identify the magnetic intensity threshold b/B 0 ~ l b /L. For values of b below this threshold, field-line tension inhibits the formation of current sheets, while above the threshold they form quickly on fast ideal timescales. In the ideal case, above the magnetic threshold, we show that current sheets thickness decreases in time until it becomes smaller than the grid resolution, with the analyticity strip width δ decreasing at least exponentially, after which the simulations become underresolved.

  11. Factors contributing to decreased protein stability when aspartic acid residues are in {beta}-sheet regions.

    SciTech Connect

    Pokkuluri, P. R.; Cai, X.; Raffen, R.; Gu, M.; Stevens, F. J.; Schiffer, M.

    2002-07-01

    Asp residues are significantly under represented in {beta}-sheet regions of proteins, especially in the middle of {beta}-strands, as found by a number of studies using statistical, modeling, or experimental methods. To further understand the reasons for this under representation of Asp, we prepared and analyzed mutants of a {beta}-domain. Two Gln residues of the immunoglobulin light-chain variable domain (V{sub L}) of protein Len were replaced with Asp, and then the effects of these changes on protein stability and protein structure were studied. The replacement of Q38D, located at the end of a {beta}-strand, and that of Q89D, located in the middle of a {beta}-strand, reduced the stability of the parent immunoglobulin VL domain by 2.0 kcal/mol and 5.3 kcal/mol, respectively. Because the Q89D mutant of the wild-type V{sub L}-Len domain was too unstable to be expressed as a soluble protein, we prepared the Q89D mutant in a triple mutant background, V{sub L}-Len M4L/Y27dD/T94H, which was 4.2 kcal/mol more stable than the wild-type V{sub L}-Len domain. The structures of mutants V{sub L}-Len Q38D and V{sub L}-Len Q89D/M4L/Y27dD/T94H were determined by X-ray diffraction at 1.6 A resolution. We found no major perturbances in the structures of these QD mutant proteins relative to structures of the parent proteins. The observed stability changes have to be accounted for by cumulative effects of the following several factors: (1) by changes in main-chain dihedral angles and in side-chain rotomers, (2) by close contacts between some atoms, and, most significantly, (3) by the unfavorable electrostatic interactions between the Asp side chain and the carbonyls of the main chain. We show that the Asn side chain, which is of similar size but neutral, is less destabilizing. The detrimental effect of Asp within a {beta}-sheet of an immunoglobulin-type domain can have very serious consequences. A somatic mutation of a {beta}-strand residue to Asp could prevent the expression of the

  12. An exact collisionless equilibrium for the Force-Free Harris Sheet with low plasma beta

    SciTech Connect

    Allanson, O. Neukirch, T. Wilson, F. Troscheit, S.

    2015-10-15

    We present a first discussion and analysis of the physical properties of a new exact collisionless equilibrium for a one-dimensional nonlinear force-free magnetic field, namely, the force-free Harris sheet. The solution allows any value of the plasma beta, and crucially below unity, which previous nonlinear force-free collisionless equilibria could not. The distribution function involves infinite series of Hermite polynomials in the canonical momenta, of which the important mathematical properties of convergence and non-negativity have recently been proven. Plots of the distribution function are presented for the plasma beta modestly below unity, and we compare the shape of the distribution function in two of the velocity directions to a Maxwellian distribution.

  13. sup 1 H NMR identification of a. beta. -sheet structure and description of folding topology in putidaredoxin

    SciTech Connect

    Pochapsky, T.C.; Ye, Xiao Mei )

    1991-04-23

    Putidaredoxin (Pdx), a 106-residue globular protein consisting of a single polypeptide chain and a (2Fe-2S) cluster, is the physiological reductant of P-450{sub cam}, which in turn catalyzes the monohydroxylation of camphor by molecular oxygen. No crystal structure has been obtained for Pdx or for any closely homologous protein. The application of two-dimensional {sup 1}H NMR methods to the problem of structure determination in Pdx is reported. A {beta}-sheet consisting of five short strands and one {beta}-turn has been identified from distinctive nuclear Overhauser effect patterns. All of the backbone resonances and a majority of the side-chain resonances corresponding to protons in the {beta}-sheet have been assigned sequence specifically. The sheet contains one parallel and three antiparallel strand orientations. Hydrophobic side chains in the {beta}-sheet face primarily toward the protein interior, except for a group of three valine side chains that are apparently solvent exposed. The potential significance of this hydrophobic patch in terms of biological activity is discussed. The folding topology, as determined by the constraints of the {beta}-sheet, is compared with that of other (2Fe-2S) proteins for which folding topologies are known.

  14. Moulin distribution and formation on the southwest Greenland ice sheet

    NASA Astrophysics Data System (ADS)

    Chu, V. W.; Smith, L. C.; Gleason, C. J.; Yang, K.; Poinar, K.; Joughin, I.; Pitcher, L. H.

    2015-12-01

    River moulins represent a significant connection between surface meltwater generated on the Greenland ice sheet and subglacial drainage networks, where increased meltwater can enhance ice sliding dynamics. In this study, a new high-resolution moulin map is created from WorldView-1/2 imagery acquired during the 2012 record melt year for a 12,500 km2 area near Russell Glacier in southwest Greenland. A total of 1,236 moulins are mapped and categorized as being located: in crevasse fields, along a single ice fracture, within drained lake basins, or having no visible formation mechanism. We find the presence of moulins up to 1787 m elevation, with 11% of moulins found above 1600 m elevation: higher than previously mapped moulins and where glaciological theory suggests few moulins should form. Our study observes moulins in both extensional and compressional ice flow regimes (28% of moulins are found in areas of high extensional strain rate >0.005 yr-1), suggesting that strain rates are not a strong indicator of the likelihood for moulin formation. Overall, moulin density tends to increase with higher bed elevation, thinner ice, lower surface slope, higher velocity, and higher strain rate. In sum, moulins are most common in crevassed, thinner ice near the ice sheet edge, but significant quantities also develop at high elevations. This indicates that future inland expansion of melting may create hydrologic connections between the surface and the bed at higher elevations than previously thought.

  15. Designing biomaterials exploiting beta-sheet forming peptides self-assembly

    NASA Astrophysics Data System (ADS)

    Saiani, Alberto

    2013-03-01

    The use of non-covalent self-assembly to construct materials has become a prominent strategy in material science offering practical routes for the construction of increasingly functional materials for a variety of applications ranging from electronic to biotechnology. A variety of molecular building blocks can be used for this purpose, one such block that has attracted considerable attention are de-novo designed peptides. The library of 20 natural amino acids offers the ability to play with the intrinsic properties of the peptide such as structure, hydrophobicity, charge and functionality allowing the design of materials with a wide range of properties. The beta-sheet motif is of particular interest as short peptides can be designed to form beta-sheet rich fibres that entangle and consequently form hydrogels. These hydrogels can be further functionalised using specific biological signals or drugs by synthesising functionalised peptides that are incorporated into the hydrogel network during the self-assembling process. This functionalisation approach is very attractive has it does not require any chemistry avoiding therefore the use of additional potentially toxic chemicals. It also offers the possibility to introduce multiple functionalities in a straightforward fashion. The hydrogels can also be made responsive through the use of enzymatic catalysis and/or conjugation with responsive polymers. In this presentation we will discuss the design opportunities offered by these peptides to create new functional biomaterials.

  16. Strength limit of entropic elasticity in beta-sheet protein domains

    NASA Astrophysics Data System (ADS)

    Keten, Sinan; Buehler, Markus J.

    2008-12-01

    Elasticity and strength of individual beta-sheet protein domains govern key biological functions and the mechanical properties of biopolymers including spider silk, amyloids, and muscle fibers. The worm-like-chain (WLC) model is commonly used to describe the entropic elasticity of polypeptides and other biomolecules. However, force spectroscopy experiments have shown pronounced deviations from the ideal WLC behavior, leading to controversial views about the appropriate elastic description of proteins at nanoscale. Here we report a simple model that explains the physical mechanism that leads to the breakdown of the WLC idealization in experiments by using only two generic parameters of the protein domain, the H-bond energy and the protein backbone’s persistence length. We show that a rupture initiation condition characterized by the free energy release rate of H-bonds characterizes the limit of WLC entropic elasticity of beta-sheet protein domains and the onset of rupture. Our findings reveal that strength and elasticity are coupled and cannot be treated separately. The predictions of the model are compared with atomic force microscopy experiments of protein rupture.

  17. Microphase Separation Controlled beta-Sheet Crystallization Kinetics in Fibrous Proteins

    SciTech Connect

    Hu, X.; Lu, Q; Kaplan, D; Cebe, P

    2009-01-01

    Silk is a naturally occurring fibrous protein with a multiblock chain architecture. As such, it has many similarities with synthetic block copolymers, including the possibility for e-sheet crystallization restricted within the crystallizable blocks. The mechanism of isothermal crystallization kinetics of e-sheet crystals in silk multiblock fibrous proteins is reported in this study. Kinetics theories, such as Avrami analysis which was established for studies of synthetic polymer crystal growth, are for the first time extended to investigate protein self-assembly in e-sheet rich Bombyx mori silk fibroin samples, using time-resolved Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC) and synchrotron real-time wide-angle X-ray scattering (WAXS). The Avrami exponent, n, was close to 2 for all methods and crystallization temperatures, indicating formation of e-sheet crystals in silk proteins is different from the 3-D spherulitic crystal growth found in synthetic polymers. Observations by scanning electron microscopy support the view that the protein structures vary during the different stages of crystal growth, and show a microphase separation pattern after chymotrypsin enzyme biodegradation. We present a model to explain the crystallization of the multiblock silk fibroin protein, by analogy to block copolymers: crystallization of e-sheets occurs under conditions of geometrical restriction caused by phase separation of the crystallizable and uncrystallizable blocks. This crystallization model could be widely applicable in other proteins with multiblock (i.e., crystallizable and noncrystallizable) domains.

  18. Current Sheet Formation, Equilibria and Heating in the Closed Corona

    NASA Astrophysics Data System (ADS)

    Rappazzo, A. F.

    2014-12-01

    Parker model for coronal heating is investigated within theframework of reduced magnetohydrodynamics (RMHD) in cartesian geometry. A popular hypothesis is that in response to slow photospheric motionsthe magnetic field evolves quasi-statically through a seriesof unstable equilibria. Instabilities, e.g., kink modes or else,allow the release of energy while the field relaxes to a new equilibrium.On the other hand it has long been suggested that the dynamics relevant to the basic heating of coronal loops may not entaila quasi-static evolution (Parker 1972, 1994), and recently it has beenshown that the relaxation of an initial configuration out of equilibriumdevelops current sheets without accessing intermediate equilibria (Rappazzo & Parker 2013).The properties of the equilibria are therefore key in understanding thedynamics of coronal heating both in the case of low-frequency photospheric motions (DC) and for propagating waves (AC).Equilibria and nonlinear dynamics are studied numerically and theoretically,explaining why dynamics are inhibited below a critical twist, while for highervalues of the fluctuations nonlinear dynamics lead to the formation of current sheets (and magnetic reconnection in the non ideal case), whose thickness istracked with the analiticity strip method and shown to decrease at least exponentiallydown to dissipative lenght-scales on fast ideal Alfvenic timescales. The impact onthe heating of solar and stellar coronae will be discussed.

  19. Helix versus sheet formation in a small peptide

    NASA Astrophysics Data System (ADS)

    Peng, Yong; Hansmann, Ulrich H.

    2003-10-01

    Segments with the amino acid sequence EKAYLRT (glutamine-lysine-alanine-tyrosine-leucine-arginine-threonine) appear in naturally occurring proteins both in α-helices and β-sheets. For this reason, we have used this peptide to study how secondary structure formation in proteins depends on the local environment. Our data rely on multicanonical Monte Carlo simulations where the interactions among all atoms are taken into account. Results in gas phase are compared with that in an implicit solvent. We find that both the solvated molecule and EKAYLRT in gas phase form an α-helix when not interacting with other molecules. However, in the vicinity of a β-strand, the peptide forms a β-strand. Because of this change in secondary structure our peptide may provide a simple model for the α→β transition that is supposedly related to the outbreak of prion diseases and similar illnesses.

  20. Protein unfolding at interfaces: slow dynamics of alpha-helix to beta-sheet transition.

    PubMed

    Sethuraman, Ananthakrishnan; Vedantham, Ganesh; Imoto, Taiji; Przybycien, Todd; Belfort, Georges

    2004-09-01

    A two-phase sequential dynamic change in the secondary structure of hen egg lysozyme (Lys) adsorbed on solid substrates was observed. The first phase involved fast conversion of alpha-helix to random/turns (within the first minute or at very low coverage or high substrate wettability) with no perceptible change in beta-sheet content. The second phase (1-1200 min), however, involved a relatively slow conversion from alpha-helix to beta-sheet without a noticeable change in random/turns. An important finding of this work is that the concentration of lysozyme in the adsorbed state has a substantial effect on the fractional content of secondary structures. Attenuated total reflection Fourier transform infrared (ATR/FTIR) spectroscopy, along with a newly-developed optimization algorithm for predicting the content of secondary structure motifs, was used to correlate the secondary structure and the amount of adsorbed lysozyme with the surface wettability of six different flat nanoporous substrates. Although three independent variables, surface wettability, solution concentration and time for adsorption, were used to follow the fractional structural changes of lysozyme, the results were all normalized onto a single plot with the amount adsorbed as the universal independent variable. Consequently, lateral interactions among proteins likely drive the transition process. Direct intermolecular force adhesion measurements between lysozyme and different functionalized self-assembled alkanethiol monolayers confirm that hydrophobic surfaces interact strongly with proteins. The lysozyme-unfolding pathway during early adsorption appears to be similar to that predicted by published molecular modeling results. PMID:15281120

  1. Reversible Hydrogel–Solution System of Silk with High Beta-Sheet Content

    PubMed Central

    2015-01-01

    Silkworm silk has been widely used as a textile fiber, as biomaterials and in optically functional materials due to its extraordinary properties. The β-sheet-rich natural nanofiber units of about 10–50 nm in diameter are often considered the origin of these properties, yet it remains unclear how silk self-assembles into these hierarchical structures. A new system composed of β-sheet-rich silk nanofibers about 10–20 nm in diameter is reported here, where these nanofibers formed into “flowing hydrogels” at 0.5–2% solutions and could be transformed back into the solution state at lower concentrations, even with a high β-sheet content. This is in contrast with other silk processed materials, where significant β-sheet content negates reversibility between solution and solid states. These fibers are formed by regulating the self-assembly process of silk in aqueous solution, which changes the distribution of negative charges while still supporting β-sheet formation in the structures. Mechanistically, there appears to be a shift toward negative charges along the outside of the silk nanofibers in our present study, resulting in a higher zeta potential (above −50 mV) than previous silk materials which tend to be below −30 mV. The higher negative charge on silk nanofibers resulted in electrostatic repulsion strong enough to negate further assembly of the nanofibers. Changing silk concentration changed the balance between hydrophobic interactions and electrostatic repulsion of β-sheet-rich silk nanofibers, resulting in reversible hydrogel–solution transitions. Furthermore, the silk nanofibers could be disassembled into shorter fibers and even nanoparticles upon ultrasonic treatment following the transition from hydrogel to solution due to the increased dispersion of hydrophobic smaller particles, without the loss of β-sheet content, and with retention of the ability to transition between hydrogel and solution states through reversion to longer nanofibers

  2. Reversible hydrogel-solution system of silk with high beta-sheet content.

    PubMed

    Bai, Shumeng; Zhang, Xiuli; Lu, Qiang; Sheng, Weiqin; Liu, Lijie; Dong, Boju; Kaplan, David L; Zhu, Hesun

    2014-08-11

    Silkworm silk has been widely used as a textile fiber, as biomaterials and in optically functional materials due to its extraordinary properties. The β-sheet-rich natural nanofiber units of about 10-50 nm in diameter are often considered the origin of these properties, yet it remains unclear how silk self-assembles into these hierarchical structures. A new system composed of β-sheet-rich silk nanofibers about 10-20 nm in diameter is reported here, where these nanofibers formed into "flowing hydrogels" at 0.5-2% solutions and could be transformed back into the solution state at lower concentrations, even with a high β-sheet content. This is in contrast with other silk processed materials, where significant β-sheet content negates reversibility between solution and solid states. These fibers are formed by regulating the self-assembly process of silk in aqueous solution, which changes the distribution of negative charges while still supporting β-sheet formation in the structures. Mechanistically, there appears to be a shift toward negative charges along the outside of the silk nanofibers in our present study, resulting in a higher zeta potential (above -50 mV) than previous silk materials which tend to be below -30 mV. The higher negative charge on silk nanofibers resulted in electrostatic repulsion strong enough to negate further assembly of the nanofibers. Changing silk concentration changed the balance between hydrophobic interactions and electrostatic repulsion of β-sheet-rich silk nanofibers, resulting in reversible hydrogel-solution transitions. Furthermore, the silk nanofibers could be disassembled into shorter fibers and even nanoparticles upon ultrasonic treatment following the transition from hydrogel to solution due to the increased dispersion of hydrophobic smaller particles, without the loss of β-sheet content, and with retention of the ability to transition between hydrogel and solution states through reversion to longer nanofibers during self

  3. Singularity formation and nonlinear evolution of a viscous vortex sheet model

    NASA Astrophysics Data System (ADS)

    Sohn, Sung-Ik

    2013-01-01

    We study Dhanak's model [J. Fluid Mech. 269, 265 (1994)], 10.1017/S0022112094001552 of a viscous vortex sheet in the sharp limit, to investigate singularity formations and present nonlinear evolutions of the sheets. The finite-time singularity does not disappear by giving viscosity to the vortex sheet, but is delayed. The singularity in the sharp viscous vortex sheet is found to be different from that of the inviscid sheet in several features. A discontinuity in the curvature is formed in the viscous sheet, similarly as the inviscid sheet, but a cusp in the vortex sheet strength is less sharpened by viscosity. Exponential decay of the Fourier amplitudes is lost by the formation of the singularity, and the amplitudes of high wavenumbers exhibit an algebraic decay, while in the inviscid vortex sheet, the algebraic decay of the Fourier amplitudes is valid from fairly small wavenumbers. The algebraic decay rate of the viscous vortex sheet is approximately -2.5, independent of viscosity, which is the same rate as the asymptotic analysis of the inviscid sheet. Results for evolutions of the regularized vortex sheets show that the roll-up is weakened by viscosity, and the regularization parameter has more significant effects on the fine-structure of the core than does viscosity.

  4. Network formation through active migration of human vascular endothelial cells in a multilayered skeletal myoblast sheet.

    PubMed

    Nagamori, Eiji; Ngo, Trung Xuan; Takezawa, Yasunori; Saito, Atsuhiro; Sawa, Yoshiki; Shimizu, Tatsuya; Okano, Teruo; Taya, Masahito; Kino-oka, Masahiro

    2013-01-01

    Autologous transplantation of myoblast sheet has attracted attention as a new technique for curing myocardial infarction. Myoblast sheet has the ability to secret cytokines that improve heart function via the facilitation of angiogenesis on affected part. To mimic the in vivo angiogenesis in the myoblast sheet after transplantation, a five-layered cell sheet of human skeletal muscle myoblasts (HSMMs) was overlaid on human umbilical vein endothelial cells (HUVECs) which enables evaluation of dynamic HUVEC behavior. HUVECs existing initially at the bottom of the sheet changed to be a stretched shape and migrated upward compared with the surrounding HSMMs in the sheet. Prolonged incubation resulted in network formation of HUVECs in the middle of the sheet, although non-networked HUVECs continued to migrate to the top of the sheet, which meant the spatial habitation of HUVECs in the cell sheet. Image processing was performed to determine the variation in the extent of network formation at different HUVEC densities. It was found that the extent of formed network depended on the frequency of encounters among HUVECs in the middle of the sheet. The present system, which can evaluate network formation, is considered to be a promising in vitro angiogenesis model. PMID:23117213

  5. New insights regarding protein folding as learned from beta-sheets

    PubMed Central

    Zhang, Ning; Feng, Yuanming; Gao, Shan; Ruan, Jishou; Zhang, Tao

    2012-01-01

    The folding of denatured proteins into their native conformations is called Anfinsen's dogma, and is the rationale for predicting protein structures based on primary sequences. Through the last 40 years of study, all available algorithms which either predict 3D or 2D protein structures, or predict the rate of protein folding based on the amino acid sequence alone, are limited in accuracy (80 %). This fact has led some researchers to look for the lost information, from mRNA to protein sequences, and it encourages us to rethink the rationale of Anfinsen's dogma. In this study, we focus on the relationship between the strand and its partners. We find two rules based on a non-redundant dataset taken from the PDB database. We refer to these two rules as the “first coming first pairing” rule and the “loveless” rule. The first coming first pairing rule indicates that a given strand prefers to pair with the next strand, if the connected region is flexible enough. The loveless rule means that the affinities between a given strand and another strand are comparable to the affinity between the given strand and its partner. Of course, the affinities between the given strand and a helix/coil peptide are significantly less than the affinity between the given strand and its partner. These two rules suggest that in protein folding, we have folding taking place during translation, and suggest also that a denatured protein is not the same as its primary sequence. Rechecking the original Anfinsen experiments, we find that the method used to denature protein in the experiment simply breaks the disulfide bonds, while the helices and sheets remain intact. In other words, denatured proteins still retain all helices and beta sheets, while the primary sequence does not. Although further verification via biological experiments is needed, our results as shown in this study may reveal a new insight for studying protein folding.

  6. Membrane Pore Formation by Amyloid beta (25-35) Peptide

    NASA Astrophysics Data System (ADS)

    Kandel, Nabin; Tatulian, Suren

    Amyloid (A β) peptide contributes to Alzheimer's disease by a yet unidentified mechanism. One of the possible mechanisms of A β toxicity is formation of pores in cellular membranes. We have characterized the formation of pores in phospholipid membranes by the Aβ25 - 35 peptide (GSNKGAIIGLM) using fluorescence, Fourier transform infrared spectroscopy (FTIR) and circular dichroism (CD) techniques. CD and FTIR identified formation of β-sheet structure upon incubation of the peptide in aqueous buffer for 2 hours. Unilamellar vesicles composed of a zwitterionic lipid, 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC), and 70 % POPC plus 30 % of an acidic lipid, 1-palmitoyl-2-oleoyl-phosphatidylglycerol (POPG), are made in 30 mM CaCl2. Quin-2, a fluorophore that displays increased fluorescence upon Ca2+ binding, is added to the vesicles externally. Peptide addition results in increased Quin-2 fluorescence, which is interpreted by binding of the peptide to the vesicles, pore formation, and Ca2+ leakage. The positive and negative control measurements involve addition of a detergent, Triton X-100, which causes vesicle rupture and release of total calcium, and blank buffer, respectively.

  7. Collective oscillations and the linear and two-dimensional infrared spectra of inhomogeneous beta-sheets.

    PubMed

    Dijkstra, Arend G; Knoester, Jasper

    2005-05-19

    We numerically calculate the collective amide I oscillations and the associated linear and two-dimensional infrared (2DIR) spectra for model antiparallel beta-sheets and study the effect of inhomogeneity. To visualize the collective vibrational exciton states, a new method is introduced, which proves very useful in classifying the optically dominant states with respect to their symmetry properties and phase relations, even in the absence of exact symmetries. We find that energy (diagonal) and interaction (off-diagonal) disorder may have profoundly different effects on the main peaks in the linear spectrum. We also show that in the 2DIR spectra energy disorder leads to diagonal stretching of the diagonal peaks, while the cross-peaks are typically stretched more horizontally. This offers an explanation for the recently observed overall Z-shape in experimental spectra. Finally, we find that the anharmonic splitting between associated positive and negative features in the 2DIR spectra scales inversely proportionally with the exciton delocalization size imposed by the disorder, thus offering a spectroscopic ruler for this size. PMID:16852179

  8. A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA.

    PubMed Central

    Allen, M D; Yamasaki, K; Ohme-Takagi, M; Tateno, M; Suzuki, M

    1998-01-01

    The 3D solution structure of the GCC-box binding domain of a protein from Arabidopsis thaliana in complex with its target DNA fragment has been determined by heteronuclear multidimensional NMR in combination with simulated annealing and restrained molecular dynamic calculation. The domain consists of a three-stranded anti-parallel beta-sheet and an alpha-helix packed approximately parallel to the beta-sheet. Arginine and tryptophan residues in the beta-sheet are identified to contact eight of the nine consecutive base pairs in the major groove, and at the same time bind to the sugar phosphate backbones. The target DNA bends slightly at the central CG step, thereby allowing the DNA to follow the curvature of the beta-sheet. PMID:9736626

  9. The crystal structure of human glycosylation-inhibiting factor is a trimeric barrel with three 6-stranded beta-sheets.

    PubMed

    Kato, Y; Muto, T; Tomura, T; Tsumura, H; Watarai, H; Mikayama, T; Ishizaka, K; Kuroki, R

    1996-04-01

    Glycosylation-inhibiting factor (GIF) is a cytokine that is involved in the regulation of IgE synthesis. The crystal structure of recombinant human GIF was determined by the multiple isomorphous replacement method. The structure was refined to an R factor of 0.168 at 1.9 angstrom resolution. The overall structure is seen to consist of three interconnected subunits forming a barrel with three 6-stranded beta-sheets on the inside and six alpha-helices on the outside. There is a 5-angstrom-diameter "hole" through the middle of the barrel. The barrel structure of GIF in part resembles other "trefoil" cytokines such as interleukin 1 and fibroblast growth factor. Each subunit has a new class of alpha + beta sandwich structure consisting of two beta-alpha-beta motifs. These beta-alpha-beta motifs are related by a pseudo-twofold axis and resemble both interleukin 8 and the peptide binding domain of major histocompatibility complex protein, although the topology of the polypeptide chain is quite different. PMID:8610159

  10. The crystal structure of human glycosylation-inhibiting factor is a trimeric barrel with three 6-stranded beta-sheets.

    PubMed Central

    Kato, Y; Muto, T; Tomura, T; Tsumura, H; Watarai, H; Mikayama, T; Ishizaka, K; Kuroki, R

    1996-01-01

    Glycosylation-inhibiting factor (GIF) is a cytokine that is involved in the regulation of IgE synthesis. The crystal structure of recombinant human GIF was determined by the multiple isomorphous replacement method. The structure was refined to an R factor of 0.168 at 1.9 angstrom resolution. The overall structure is seen to consist of three interconnected subunits forming a barrel with three 6-stranded beta-sheets on the inside and six alpha-helices on the outside. There is a 5-angstrom-diameter "hole" through the middle of the barrel. The barrel structure of GIF in part resembles other "trefoil" cytokines such as interleukin 1 and fibroblast growth factor. Each subunit has a new class of alpha + beta sandwich structure consisting of two beta-alpha-beta motifs. These beta-alpha-beta motifs are related by a pseudo-twofold axis and resemble both interleukin 8 and the peptide binding domain of major histocompatibility complex protein, although the topology of the polypeptide chain is quite different. Images Fig. 1 Fig. 3 PMID:8610159

  11. [Neutralization of static electricity charged on running vinyl chloride sheet by the use of soft beta-ray sources (author's transl)].

    PubMed

    Itakura, K; Wada, N

    1978-04-01

    The feasibility of 147Pm and 3H beta-ray sources as static eliminator was experimentally investigated. A sheet of vinyl chloride of 0.1 mm in thickness was used as an example of electrified materials. Its surface charge densities before and after beta-ray neutralization were measured as the function of electrostatic charge changing the speed of the sheet and the distance between the beta-ray source and the sheet. With a 147Pm beta-ray source of 200mCi in effective activity, almost complete neutralization was found for the sheet with the charge density less than 6 X 10(-6) C/m2 running at the speed of 0.18 m/s. In the case of the running speed of 0.5 m/s frequently used in industry, the electrostatic charge below 3 X 10(6) C/m2, where corona discharger is not so effective, was also perfectly eliminated. It was found that the optimal distance between the beta-ray source and the sheet was 10 cm in the case of 147Pm. The use of 3H beta-ray source of 1 Ci was not satisfactory. These results demonstrate that 147 Pm beta-ray source operates most efficiently as static eliminator when the charge density of material and/or its moving speed is not high. PMID:663315

  12. Current Sheet Formation in a Conical Theta Pinch Faraday Accelerator with Radio-frequency Assisted Discharge

    NASA Technical Reports Server (NTRS)

    Polzin, Kurt A.; Hallock, Ashley K.; Choueiri, Edgar Y.

    2008-01-01

    Data from an inductive conical theta pinch accelerator are presented to gain insight into the process of inductive current sheet formation in the presence of a preionized background gas produced by a steady-state RF-discharge. The presence of a preionized plasma has been previously shown to allow for current sheet formation at lower discharge voltages and energies than those found in other pulsed inductive accelerator concepts, leading to greater accelerator efficiencies at lower power levels. Time-resolved magnetic probe measurements are obtained for different background pressures and pulse energies to characterize the effects of these parameters on current sheet formation. Indices are defined that describe time-resolved current sheet characteristics, such as the total current owing in the current sheet, the time-integrated total current ('strength'), and current sheet velocity. It is found that for a given electric field strength, maximums in total current, strength, and velocity occur for one particular background pressure. At other pressures, these current sheet indices are considerably smaller. The trends observed in these indices are explained in terms of the principles behind Townsend breakdown that lead to a dependence on the ratio of the electric field to the background pressure. Time-integrated photographic data are also obtained at the same experimental conditions, and qualitatively they compare quite favorably with the time-resolved magnetic field data.

  13. The peculiarities of formation of thin current sheet in the Earth's magnetotail

    NASA Astrophysics Data System (ADS)

    Kropotkin, Alexey; Artemyev, Anton; Malova, Helmi; Domrin, Vladimir

    We investigate the process of self-consistent thinning of magnetotail current sheet in the presence of the evolving magnetic field normal component Bz, which usually decreases during the substorm growth phase. Using PIC codes to describe plasma processes with ions becoming demagnetized and electrons being considered as the cold neutralizing background, we show that the appearance of the self-consistent electric field component inside CS can lead to the current sheet thinning and to the appearance of an extremely thin current sheet with thickness close to the ion gyroradius. Due to particle [ExB] drift during the current sheet evolution, the enhanced trapping of ions near the current sheet central plane takes place. It is shown that the density of quasi-trapped particles around current sheet at the final stage depends on both the value of the initial magnetic field normal component Bz, and the speed of the Bz decrease. If the initial magnetic field normal component is less than about 0.14 of the tangential field at the edges, the trapped plasma density near the current sheet is small. As a result, the above mentioned extremely thin current sheet is formed. In the opposite case, when the initial normal component related to the tangential field is larger than 0.14, the density of trapped particles is much higher, which produces effective thickening of the current sheet. In both cases transient (Speiser) ions are the main current carriers, but in the second case local diamagnetic currents of the trapped plasma perturb the сurrent sheet profile making it thicker. Also trapped particles can be responsible for intense negative currents at the current sheet edges. During the Bz decrease, an additional effect of ion polarization drifts in the Y direction can compete with these negative diamagnetic fields of quasi-trapped ions. Therefore the ion dynamics is probably the general mechanism which contributes to the formation of thin current sheet and its fine structure.

  14. Spontaneous formation of electric current sheets and the origin of solar flares

    NASA Technical Reports Server (NTRS)

    Low, B. C.; Wolfson, R.

    1988-01-01

    It is demonstrated that the continuous boundary motion of a sheared magnetic field in a tenuous plasma with an infinite electrical conductivity can induce the formation of multiple electric current sheets in the interior plasma. In response to specific footpoint displacements, the quadrupolar magnetic field considered is shown to require the formation of multiple electric current sheets as it achieves a force-free state. Some of the current sheets are found to be of finite length, running along separatrix lines of force which separate lobes of magnetic flux. It is suggested that current sheets in the form of infinitely thin magnetic shear layers may be unstable to resistive tearing, a process which may have application to solar flares.

  15. Ballooning Instability Induced Plasmoid Formation in Near-Earth Plasma Sheet*

    NASA Astrophysics Data System (ADS)

    Zhu, P.; Raeder, J.

    2013-12-01

    The formation of plasmoids in the near-Earth magnetotail is believed to be a key element of the substorm onset process. The physical mechanism of plasmoid formation in the plasma sheet has remained a subject of considerable interests and investigations. Previous work has identified a new scenario in MHD simulations where the nonlinear evolution of a ballooning instability is able to induce the formation of plasmoids in a generalized Harris sheet with finite normal magnetic component [1]. In present work, we further examine this novel mechanism for plasmoid formation and explore its implications in the context of substorm onset trigger problem. For that purpose, we adopt the generalized Harris sheet as a model proxy to the near-Earth region of magnetotail during the substorm growth phase. In this region the magnetic component normal to the neutral sheet Bn is weak but nonzero. The magnetic field lines are closed and there are no X-lines. Simulation results indicate that in the higher Lundquist number regime, the linear axial tail mode, which is also known as ``two-dimensional resistive tearing mode'', is stabilized by the finite Bn, hence cannot give rise to the formation of X-lines or plasmoids by itself. On the other hand, the linear ballooning mode is unstable in the same regime, and in its nonlinear stage, the tailward stretching of the plasma sheet in the closed field line region due to the growing ballooning finger structures tends to accelerate the thinning of the near-Earth current sheet. This eventually leads to the formation of a series of plasmoid structures in the near-Earth and middle magnetotail regions of plasma sheet. This new scenario of plasmoid formation suggests a critical role of ballooning instability in the near-Earth plasma sheet in triggering the onset of a substorm expansion. [1] P. Zhu and J. Raeder, Plasmoid formation in current sheet with finite normal magnetic component, Phys. Rev. Lett. 110, 235005 (2013). *Supported by NSF grants AGS

  16. [Effect of synthetic beta-carotene on the formation of cytolytic T-lymphocytes].

    PubMed

    Efimov, S A; Vakulova, L A; Rytenko, A N; Samokhvalov, G I; Sergeev, I M

    1984-06-01

    The effect of intraperitoneal injection of beta-carotene in different doses on the formation of cytolytic T lymphocytes (CTL) in a one-way mixed lymphocyte culture (MLC) of allogeneic mice was studied. The maximal cytotoxic activity of lymphocytes was attained in the MLC with splenocytes of mice which received 10 mg/kg beta-carotene 6 days before experimentation. The correlation was studied between the beta-carotene ability to stimulate CTL formation and antineoplastic activity. It was discovered that injection of beta-carotene in doses and times provoking maximal CTL induction had no effect on the animals' lifespan and the size of transplanted sarcoma 180. PMID:6234949

  17. Engineering of betabellin-15D: a 64 residue beta sheet protein that forms long narrow multimeric fibrils.

    PubMed Central

    Lim, A.; Saderholm, M. J.; Makhov, A. M.; Kroll, M.; Yan, Y.; Perera, L.; Griffith, J. D.; Erickson, B. W.

    1998-01-01

    The betabellin target structure is a beta-sandwich protein consisting of two 32 residue beta-sheets packed against one another by interaction of their hydrophobic faces. The 32 residue chain of betabellin-15S (HSLTAKIpkLTFSIAphTYTCAV pkYTAKVSH, where p=DPro, k=DLys, and h=DHis) did not fold in water at pH 6.5. Air oxidation of betabellin-15S provided betabellin-15D, the 64 residue disulfide bridged two-chain molecule, which also remained unfolded in water at pH 6.5. By circular dichroic spectropolarimetry, the extent of beta structure observed for betabellin-15D increased with the pH and ionic strength of the solution and the betabellin-15D concentration. By electron microscopy, in 5.0 mM MOPS and 0.25 M NaCl at pH 6.9, betabellin-15D formed long narrow multimeric fibrils. A molecular model was constructed to show that the dimensions of these betabellin-15D fibrils are consistent with a single row of beta-sandwich molecules joined by multiple intersheet H-bonds. PMID:9684887

  18. The formation of wrinkles in single-layer graphene sheets under nanoindentation

    NASA Astrophysics Data System (ADS)

    Gil, A. J.; Adhikari, S.; Scarpa, F.; Bonet, J.

    2010-04-01

    We investigate the formation of wrinkles and bulging in single-layer graphene sheets using an equivalent atomistic continuum nonlinear hyperelastic theory for nanoindentation and nanopressurization. We show that nonlinear geometrical effects play a key role in the development of wrinkles. Without abandoning the classical tension field membrane theory, we develop an enhanced model based upon the minimization of a relaxed energy functional in conjunction with nonlinear finite hyperelasticity. Formation of wrinkles are observed in rectangular graphene sheets due to the combination of induced membrane tension and edge effects under external pressure.

  19. Relating thin current sheet formation and tail reconnection to substorm development

    SciTech Connect

    Birn, J.; Schindler, K.

    2002-01-01

    Observations and simulations have demonstrated the important role of thin current sheet formation and magnetic reconnection in the course of substorms. We discuss new results on the formation of thin current sheets, obtained both within MHD and kinetic theory. They demonstrate when kinetic effects become important and indicate the possibility of a catastrophic onset of substorm dynamics and the potential association with arc brightening. MHD simulations show the role of reconnection in the buildup of the substorm current wedge and the influence of the underlying configuration on the quasi-static and dynamic evolution.

  20. Beta-D-Allose inhibits fruiting body formation and sporulation in Myxococcus xanthus.

    PubMed

    Chavira, Marielena; Cao, Nga; Le, Karen; Riar, Tanveer; Moradshahi, Navid; McBride, Melinda; Lux, Renate; Shi, Wenyuan

    2007-01-01

    Myxococcus xanthus, a gram-negative soil bacterium, responds to amino acid starvation by entering a process of multicellular development which culminates in the assembly of spore-filled fruiting bodies. Previous studies utilizing developmental inhibitors (such as methionine, lysine, or threonine) have revealed important clues about the mechanisms involved in fruiting body formation. We used Biolog phenotype microarrays to screen 384 chemicals for complete inhibition of fruiting body development in M. xanthus. Here, we report the identification of a novel inhibitor of fruiting body formation and sporulation, beta-d-allose. beta-d-Allose, a rare sugar, is a member of the aldohexose family and a C3 epimer of glucose. Our studies show that beta-d-allose does not affect cell growth, viability, agglutination, or motility. However, beta-galactosidase reporters demonstrate that genes activated between 4 and 14 h of development show significantly lower expression levels in the presence of beta-d-allose. Furthermore, inhibition of fruiting body formation occurs only when beta-d-allose is added to submerged cultures before 12 h of development. In competition studies, high concentrations of galactose and xylose antagonize the nonfruiting response to beta-d-allose, while glucose is capable of partial antagonism. Finally, a magellan-4 transposon mutagenesis screen identified glcK, a putative glucokinase gene, required for beta-d-allose-mediated inhibition of fruiting body formation. Subsequent glucokinase activity assays of the glcK mutant further supported the role of this protein in glucose phosphorylation. PMID:17056749

  1. Formation and function of the Rbl2p-beta-tubulin complex.

    PubMed

    Archer, J E; Magendantz, M; Vega, L R; Solomon, F

    1998-03-01

    The yeast protein Rbl2p suppresses the deleterious effects of excess beta-tubulin as efficiently as does alpha-tubulin. Both in vivo and in vitro, Rbl2p forms a complex with beta-tubulin that does not contain alpha-tubulin, thus defining a second pool of beta-tubulin in the cell. Formation of the complex depends upon the conformation of beta-tubulin. Newly synthesized beta-tubulin can bind to Rbl2p before it binds to alpha-tubulin. Rbl2p can also bind beta-tubulin from the alpha/beta-tubulin heterodimer, apparently by competing with alpha-tubulin. The Rbl2p-beta-tubulin complex has a half-life of approximately 2.5 h and is less stable than the alpha/beta-tubulin heterodimer. The results of our experiments explain both how excess Rbl2p can rescue cells overexpressing beta-tubulin and how it can be deleterious in a wild-type background. They also suggest that the Rbl2p-beta-tubulin complex is part of a cellular mechanism for regulating the levels and dimerization of tubulin chains. PMID:9488492

  2. Magnetic quadrupole formation of low-voltage sheet electron beams for high-power microwave devices

    SciTech Connect

    Basten, M.A.; Booske, J.H.; Anderson, J.; Joe, J.; Scharer, J.E.

    1995-12-31

    Sheet electron beams have the potential to make possible higher power sources of microwave radiation due to their ability to transport high currents, at reduced current densities, through a single narrow RF interaction circuit. Possible microwave device applications using sheet electron beams include sheet-beam klystrons, grating TWT`s, and planar FELs. One difficulty with the experimental investigation and implementation of sheet beams is the lack of a satisfactory source for large aspect-ratio beams. An attractive solution is the use of magnetic quadrupoles to transform an initially round beam from a conventional Pierce gun into a highly eccentric elliptical beam. Both 2-D envelope simulations and 3-D envelope and PIC code simulations indicate that this is a viable method of sheet beam formation, particularly for experimental investigations where flexibility and low-cost fabrication is desired. The authors are currently constructing a system to experimentally test this method. Features of the experiment include a low-cost commercially available Pierce gun, a four quadrupole sheet beam-forming system, and a highly elliptical output beam. Results of the 3-D PIC simulations of the beam and 3-D magnetostatic finite-element simulations of the quadrupole fringe fields will be discussed. Details of the experimental design and initial experimental measurements are presented.

  3. The palladium assisted transfer reduction of. alpha. ,. beta. -unsaturated nitroalkenes to oximes using ammonium formate

    SciTech Connect

    Kabalka, G.W.; Pace, R.D.; Wadgaonkar, P.P. )

    1990-01-01

    {alpha},{beta}-Unsaturated nitroalkenes are readily reduced to the corresponding oximes in good yields using ammonium formate in the presence of palladium. The reactions occur rapidly at room temperature in a solvent system of methanol and tetrahydrofuran.

  4. Most of the structural elements of the globular domain of murine prion protein form fibrils with predominant beta-sheet structure.

    PubMed

    Jamin, Nadège; Coïc, Yves-Marie; Landon, Céline; Ovtracht, Ludmila; Baleux, Françoise; Neumann, Jean-Michel; Sanson, Alain

    2002-10-01

    The conversion of the cellular prion protein into the beta-sheet-rich scrapie prion protein is thought to be the key step in the pathogenesis of prion diseases. To gain insight into this structural conversion, we analyzed the intrinsic structural propensity of the amino acid sequence of the murine prion C-terminal domain. For that purpose, this globular domain was dissected into its secondary structural elements and the structural propensity of the protein fragments was determined. Our results show that all these fragments, excepted that strictly encompassing helix 1, have a very high propensity to form structured aggregates with a dominant content of beta-sheet structures. PMID:12372610

  5. Bond formation in ultrasonically welded aluminum sheet metal

    NASA Astrophysics Data System (ADS)

    Wilkosz, Daniel Edward

    Ultrasonic welding (USW), a solid state joining technology, has been used to bond aluminum alloys commonly used in the automotive industry. Bonding occurs due to USW's high frequency (˜20 kHz) in-plane vibration of sample interfaces while being held under moderate clamp pressure normal to the plane of vibration. Vibration and clamp pressure are transmitted into bond formation via contact with a weld-tip. To better understand how weld-tip geometry affected bond formation, experiments were conducted to quantify how tip geometry influenced plastic deformation characteristics between fully welded coupons of 0.9mm thick AA6111-T4 aluminum alloy. Weld-interface microstructure features were documented by optical microscopy and features quantified in a 19 point matrix. Correlation between microstructure features, such as rolling-wakes, and resulting weld bond strengths of more than 3.0kN is made. Weld zone microstructure features appear to result from deformation at and severe migration of the original weld interface during USW. To confirm this hypothesis, intrinsic and extrinsic markers were employed to monitor weld interface deformation characteristics. Various physical and analytical techniques were used in conjunction with these markers to show that joining of "like" and "dislike" aluminum samples is achieved through mechanical mixing of mating interfaces and not by elemental diffusion. It is also hypothesized that severe deformation of the original interface would result in areas of high residual strain within a formed weld zone. To investigate this and the influence that tip geometry may have on residual strain, fully welded samples were annealed at 500°C for a controlled period of time and recovery, recrystallization and grain growth characteristics were monitored. In all welds, initial recrystallization and grain growth occurred at the outer ends of weld zones and along weld interfaces where the most turbulent mixing and grain size reduction was observed

  6. The imidazole role in strontium beta-diketonate complexes formation.

    PubMed

    Marchetti, Fabio; Pettinari, Claudio; Pettinari, Riccardo; Cingolani, Augusto; Gobetto, Roberto; Chierotti, Michele R; Drozdov, Andrei; Troyanov, Sergey I

    2006-04-01

    A selection of new strontium beta-diketonate derivatives (imH2)2[Sr2(beta-dike)6] [where imH = imidazole and beta-dike = tfac (tfacH = 1,1,1-trifluoro-2,4-pentanedione), tfbz (tfbzH = 1,1,1-trifluoro-4-phenyl-2,4-butanedione), or hfac (hfacH = 1,1,1,5,5,5-hexafluoro-2,4-pentanedione)], [Sr2(tfac)4(Meim)2(H2O)2], (MeimH)2[Sr(beta-dike)4] (where Meim = 1-methylimidazole and beta-dike = tfbz or hfac), [Sr2(thd)4(imH)2(EtOH)], and [Sr2(thd)4(Meim)2(EtOH)] (where thdH = 2,2,6,6-tetramethyl-3,5-heptanedione) have been synthesized and fully characterized. (imH2)2[Sr2(beta-dike)6] and (MeimH)2[Sr(beta-dike)4] are di- and mononuclear Sr anionic complexes, respectively, while [Sr2(tfac)4(Meim)2(H2O)2], [Sr2(thd)4(imH)2(EtOH)], and [Sr2(thd)4(Meim)2(EtOH)] are neutral dinuclear molecular derivatives. The derivative (imH2)2[Sr2(hfac)6] slowly decomposes in solution under aerobic conditions, giving (imH2)2[Sr(H2O)2(tfa)3](tfa) (tfaH = trifluoroacetic acid), which is an ionic compound containing polynuclear anionic chains composed of Sr(H2O)2(tfa)3 units. When a deficiency of imH is employed, the thdH proligand forms not only the dinuclear derivative [Sr2(thd)4(imH)2(EtOH)] but also an additional product with the formula [Sr(thd)2(H2O)2(EtOH)], in which the Sr atom is seven-coordinated. A complete solid-state characterization has been accomplished by comparing X-ray and solid-state 13C NMR data. Elucidation of the H-bond interaction between the heterocyclic rings and metal complexes by cross-polarization magic-angle-spinning 15N NMR is also reported. PMID:16562964

  7. EGCG Inhibited Lipofuscin Formation Based on Intercepting Amyloidogenic β-Sheet-Rich Structure Conversion

    PubMed Central

    Cai, Shuxian; Yang, Heng; Zeng, Kewu; Zhang, Jing; Zhong, Ni; Wang, Yingzi; Ye, Jing; Tu, Pengfei; Liu, Zhonghua

    2016-01-01

    Background Lipofuscin (LF) is formed during lipid peroxidation and sugar glycosylation by carbonyl-amino crosslinks with biomacrolecules, and accumulates slowly within postmitotic cells. The environmental pollution, modern dietary culture and lifestyle changes have been found to be the major sources of reactive carbonyl compounds in vivo. Irreversible carbonyl-amino crosslinks induced by carbonyl stress are essentially toxiferous for aging-related functional losses in modern society. Results show that (-)-epigallocatechin gallate (EGCG), the main polyphenol in green tea, can neutralize the carbonyl-amino cross-linking reaction and inhibit LF formation, but the underlying mechanism is unknown. Methods and Results We explored the mechanism of the neutralization process from protein, cell, and animal levels using spectrofluorometry, infrared spectroscopy, conformation antibodies, and electron microscopy. LF demonstrated an amyloidogenic β-sheet-rich with antiparallel structure, which accelerated the carbonyl-amino crosslinks formation and disrupted proteolysis in both PC12 cells and D-galactose (D-gal)-induced brain aging mice models. Additionally, EGCG effectively inhibited the formation of the amyloidogenic β-sheet-rich structure of LF, and prevented its conversion into toxic and on-pathway aggregation intermediates, thereby cutting off the carbonyl-amino crosslinks. Conclusions Our study indicated that the amyloidogenic β-sheet structure of LF may be the core driving force for carbonyl-amino crosslinks further formation, which mediates the formation of amyloid fibrils from native state of biomacrolecules. That EGCG exhibits anti-amyloidogenic β-sheet-rich structure properties to prevent the LF formation represents a novel strategy to impede the development of degenerative processes caused by ageing or stress-induced premature senescence in modern environments. PMID:27030967

  8. Designed α-sheet peptides inhibit amyloid formation by targeting toxic oligomers

    PubMed Central

    Hopping, Gene; Kellock, Jackson; Barnwal, Ravi Pratap; Law, Peter; Bryers, James; Varani, Gabriele; Caughey, Byron; Daggett, Valerie

    2014-01-01

    Previous studies suggest that the toxic soluble-oligomeric form of different amyloid proteins share a common backbone conformation, but the amorphous nature of this oligomer prevents its structural characterization by experiment. Based on molecular dynamics simulations we proposed that toxic intermediates of different amyloid proteins adopt a common, nonstandard secondary structure, called α-sheet. Here we report the experimental characterization of peptides designed to be complementary to the α-sheet conformation observed in the simulations. We demonstrate inhibition of aggregation in two different amyloid systems, β-amyloid peptide (Aβ) and transthyretin, by these designed α-sheet peptides. When immobilized the α-sheet designs preferentially bind species from solutions enriched in the toxic conformer compared with non-aggregated, nontoxic species or mature fibrils. The designs display characteristic spectroscopic signatures distinguishing them from conventional secondary structures, supporting α-sheet as a structure involved in the toxic oligomer stage of amyloid formation and paving the way for novel therapeutics and diagnostics. DOI: http://dx.doi.org/10.7554/eLife.01681.001 PMID:25027691

  9. Self-organization in space plasma: formation of magnetic shear in current sheets

    NASA Astrophysics Data System (ADS)

    Zelenyi, Lev; Delcourt, Dominique; Mingalev, Oleg; Malova, Helmi; Popov, Victor; Grigorenko, Elena; Petrukovich, Anatoli

    2016-07-01

    Thin current sheets are plasma structures that usually appear near reconnection regions. The presence of the shear magnetic field is characteristic for these structures. Self-consistent kinetic model of magnetotail thin current sheet (TCS) is used to understand the mechanisms of self-organization of sheared thin current sheets in a space plasma. It is shown that these configurations appear as a result of self-consistent evolution of some initial magnetic perturbation at current sheet center. Two general shapes of shear TCS components are found as a function of the transverse coordinate: symmetric and antisymmetric. We show that TCS formation goes together with the emergence of field-aligned currents in the center of the current sheet, as a result of north-south asymmetry of quasi-adiabatic ion motions. Ion drift currents can also contribute to the magnetic shear evolution, but their role is much less significant, their contribution depending upon the normal component Bz and the amplitude of the initial perturbation in TCS. Parametric maps illustrating different types of TCS equilibria are presented.

  10. Probing the Nanosecond Dynamics of a Designed Three-Stranded Beta-Sheet with a Massively Parallel Molecular Dynamics Simulation

    PubMed Central

    Voelz, Vincent A.; Luttmann, Edgar; Bowman, Gregory R.; Pande, Vijay S.

    2009-01-01

    Recently a temperature-jump FTIR study of a designed three-stranded sheet showing a fast relaxation time of ~140 ± 20 ns was published. We performed massively parallel molecular dynamics simulations in explicit solvent to probe the structural events involved in this relaxation. While our simulations produce similar relaxation rates, the structural ensemble is broad. We observe the formation of turn structure, but only very weak interaction in the strand regions, which is consistent with the lack of strong backbone-backbone NOEs in previous structural NMR studies. These results suggest that either DPDP-II folds at time scales longer than 240 ns, or that DPDP-II is not a well-defined three-stranded β-sheet. This work also provides an opportunity to compare the performance of several popular forcefield models against one another. PMID:19399235

  11. Formation and Reconnection of Three-Dimensional Current Sheets in the Solar Corona

    NASA Technical Reports Server (NTRS)

    Edmondson, J. K.; Antiochos, S. K.; DeVore, C. R.; Zurbuchen, T. H.

    2010-01-01

    Current-sheet formation and magnetic reconnection are believed to be the basic physical processes responsible for much of the activity observed in astrophysical plasmas, such as the Sun s corona. We investigate these processes for a magnetic configuration consisting of a uniform background field and an embedded line dipole, a topology that is expected to be ubiquitous in the corona. This magnetic system is driven by a uniform horizontal flow applied at the line-tied photosphere. Although both the initial field and the driver are translationally symmetric, the resulting evolution is calculated using a fully three-dimensional magnetohydrodynamic (3D MHD) simulation with adaptive mesh refinement that resolves the current sheet and reconnection dynamics in detail. The advantage of our approach is that it allows us to apply directly the vast body of knowledge gained from the many studies of 2D reconnection to the fully 3D case. We find that a current sheet forms in close analogy to the classic Syrovatskii 2D mechanism, but the resulting evolution is different than expected. The current sheet is globally stable, showing no evidence for a disruption or a secondary instability even for aspect ratios as high as 80:1. The global evolution generally follows the standard Sweet- Parker 2D reconnection model except for an accelerated reconnection rate at a very thin current sheet, due to the tearing instability and the formation of magnetic islands. An interesting conclusion is that despite the formation of fully 3D structures at small scales, the system remains close to 2D at global scales. We discuss the implications of our results for observations of the solar corona. Subject Headings: Sun: corona Sun: magnetic fields Sun: reconnection

  12. FORMATION AND RECONNECTION OF THREE-DIMENSIONAL CURRENT SHEETS IN THE SOLAR CORONA

    SciTech Connect

    Edmondson, J. K.; Antiochos, S. K.; DeVore, C. R.; Zurbuchen, T. H.

    2010-07-20

    Current-sheet formation and magnetic reconnection are believed to be the basic physical processes responsible for much of the activity observed in astrophysical plasmas, such as the Sun's corona. We investigate these processes for a magnetic configuration consisting of a uniform background field and an embedded line dipole, a topology that is expected to be ubiquitous in the corona. This magnetic system is driven by a uniform horizontal flow applied at the line-tied photosphere. Although both the initial field and the driver are translationally symmetric, the resulting evolution is calculated using a fully three-dimensional (3D) magnetohydrodynamic simulation with adaptive mesh refinement that resolves the current sheet and reconnection dynamics in detail. The advantage of our approach is that it allows us to directly apply the vast body of knowledge gained from the many studies of two-dimensional (2D) reconnection to the fully 3D case. We find that a current sheet forms in close analogy to the classic Syrovatskii 2D mechanism, but the resulting evolution is different than expected. The current sheet is globally stable, showing no evidence for a disruption or a secondary instability even for aspect ratios as high as 80:1. The global evolution generally follows the standard Sweet-Parker 2D reconnection model except for an accelerated reconnection rate at a very thin current sheet, due to the tearing instability and the formation of magnetic islands. An interesting conclusion is that despite the formation of fully 3D structures at small scales, the system remains close to 2D at global scales. We discuss the implications of our results for observations of the solar corona.

  13. Nature of Axial Tail Instability and Bubble-Blob Formation in Near-Earth Plasma Sheet*

    NASA Astrophysics Data System (ADS)

    Zhu, P.; Raeder, J.; Hegna, C. C.; Sovinec, C. R.

    2011-12-01

    Previous global MHD simulations of substorm events have identified the dynamic presence of an axial tail instability with dawn-dusk symmetry in the near-Earth plasma sheet as a major cause of the initial loss of MHD equilibrium on closed field lines prior to the subsequent magnetic reconnection and substorm expansion onset processes [Raeder et al. 2010; Siscoe et al. 2009]. In this work, energy principle analysis indicates that a two-dimensional thin current sheet configuration in the magnetotail is typically stable to the axial mode within the framework of ideal MHD model. Linear resistive MHD calculations find axial tail instabilities on closed field lines in the generalized Harris sheet configurations. The properties of these instabilities are similar to the axial tail modes observed in the global MHD simulations. The axial tail mode is unstable in regimes of low Lundquist number and regions with small normal component of magnetic field. Mode growth and structure show both similarities and differences in comparison to the linear resistive tearing mode of a one-dimensional Harris sheet. Unlike the conventional tearing mode of Harris sheet, the linear axial tail instability does not involve any reconnection process. Instead, the nature of the mode is dominantly an interchange or slippage process among neighboring flux tubes as facilitated by dissipations such as resistivity. The formation of bubble-blob pairs in pressure and entropy distributions in the near-Earth plasma sheet is shown to be a natural component as well as consequence of this axial instability process. *Supported by NSF grants AGS-0902360 and PHY-0821899. REFERENCES: Raeder, J., P. Zhu, Y. Ge, and G. Siscoe (2010), Open Geospace General Circulation Model simulation of a substorm: Axial tail instability and ballooning mode preceding substorm onset, J. Geophys. Res., 115, A00I16, doi:10.1029/2010JA015876. Siscoe, G. L., M. M. Kuznetsova, and J. Raeder (2009), Search for an onset mechanism that

  14. Formation and Degradation of Beta-casomorphins in Dairy Processing

    PubMed Central

    Nguyen, Duc Doan; Johnson, Stuart Keith; Busetti, Francesco; Solah, Vicky Ann

    2015-01-01

    Milk proteins including casein are sources of peptides with bioactivity. One of these peptides is beta-casomorphin (BCM) which belongs to a group of opioid peptides formed from β-casein variants. Beta-casomorphin 7 (BCM7) has been demonstrated to be enzymatically released from the A1 or B β-casein variant. Epidemiological evidence suggests the peptide BCM 7 is a risk factor for development of human diseases, including increased risk of type 1 diabetes and cardiovascular diseases but this has not been thoroughly substantiated by research studies. High performance liquid chromatography coupled to UV-Vis and mass spectrometry detection as well as enzyme–linked immunosorbent assay (ELISA) has been used to analyze BCMs in dairy products. BCMs have been detected in raw cow's milk and human milk and a variety of commercial cheeses, but their presence has yet to be confirmed in commercial yoghurts. The finding that BCMs are present in cheese suggests they could also form in yoghurt, but be degraded during yoghurt processing. Whether BCMs do form in yoghurt and the amount of BCM forming or degrading at different processing steps needs further investigation and possibly will depend on the heat treatment and fermentation process used, but it remains an intriguing unknown. PMID:25077377

  15. Radical Formation Initiates Solvent-Dependent Unfolding and β-sheet Formation in a Model Helical Peptide.

    PubMed

    Owen, Michael C; Strodel, Birgit; Csizmadia, Imre G; Viskolcz, Béla

    2016-06-01

    We examined the effects of Cα-centered radical formation on the stability of a model helical peptide, N-Ac-KK(AL)10KK-NH2. Three, 100 ns molecular dynamics simulations using the OPLS-AA force field were carried out on each α-helical peptide in six distinct binary TIP4P water/2,2,2-trifluoroethanol (TFE) mixtures. The α-helicity was at a maximum in 20% TFE, which was inversely proportional to the number of H-bonds between water molecules and the peptide backbone. The radial distribution of TFE around the peptide backbone was highest in 20% TFE, which enhanced helix stability. The Cα-centered radical initiated the formation of a turn within 5 ns, which was a smaller kink at high TFE concentrations, and a loop at lower TFE concentrations. The highest helicity of the peptide radical was measured in 100% TFE. The formation of hydrogen bonds between the peptide backbone and water destabilized the helix, whereas the clustering of TFE molecules around the radical center stabilized the helix. Following radical termination, the once helical structure converted to a β-sheet rich state in 100% water only, and this transition did not occur in the nonradical control peptide. This study gives evidence on how the formation of peptide radicals can initiate α-helical to β-sheet transitions under oxidative stress conditions. PMID:27169334

  16. Landscape formation by past continental ice sheets: insights into the subglacial environment

    NASA Astrophysics Data System (ADS)

    Piotrowski, Jan A.

    2014-05-01

    Glaciers and ice sheets are known as most powerful, climatically driven agents of large-scale sediment redistribution and landscape formation in the Earth system. During the Quaternary, repeated waxing and waning of continental ice sheets contributed to profound reshaping of the Earth surface and set the scene for the development of ecosystems in the post-glacial time. Despite the well-established impact of glaciers on the upper lithosphere the specific processes of glacial erosion, transport and deposition and the formation landforms at the ice-bed interface are contentious. In particular, the relative importance of direct ice impact versus the impact of glacial meltwater is highly controversial. Here, we focus on the southern peripheral area of the Scandinavian Ice Sheet hosting thick successions of soft, deformable sediments and examine some spectacular sediment/landform assemblages found nowadays in both terrestrial and marine settings to illustrate the nature of the subglacial processes. In order to decipher the past ice sheet behavior field, experimental and numerical approaches are combined. It is shown that the strength of the coupling between the ice and the bed that controls the response of the substratum to ice overriding and stress propagation depends primarily on the ability of the glacial system to evacuate meltwater from ice-bed interface. Strong coupling, locally enhanced by subglacial permafrost resulted in deeply rooted (100's of meters) glaciotectonic deformation reflected on the surface as ice-shoved hills whereas weak coupling promoted by water accumulating under the ice triggered the formation of deep (100's of meters) tunnel valley networks. Under the arteries of fast-flowing ice known as palaeo-ice streams, remoulding of soft sediments generated mega-scale glacial lineations and drumlins that hold the key to understanding glacier dynamics. The subglacial environment is envisaged as a four-dimensional mosaic of stable and deforming spots

  17. Magnetic quadrupole formation of elliptical sheet electron beams for high-power microwave devices

    SciTech Connect

    Basten, M.A.; Booske, J.H.; Anderson, J. . Electrical and Computer Engineering Dept.)

    1994-10-01

    Sheet electron beams are attractive for high-power microwave sources due to their ability to transport high current, at reduced current density, through thin clearance apertures and in close proximity to walls or RF structures. This paper reports on the theoretical investigation of magnetic quadrupole formation of elliptical sheet electron beams for use in high-power microwave devices. The beam envelope equations for an initially round beam passing through a physical non-symmetric quadrupole pair in the presence of space-charge, finite beam emittance, and under the effects of third-order field components and longitudinal velocity variations are presented. The presence of space-charge compensates for over-focusing in the thin beam-dimension and allows for the formation of highly elliptic sheet electron beams. As an example, the results of the study were applied to an existing Pierce gun source with a beam radius of 0.6 cm, beam energy of 10 keV and current density of 2.0 A/cm[sup 2]. The authors find that an elliptical beam with major radius r[sub a] = 3.61 cm, minor radius r[sub b] = 0.16 cm and ellipticity (r[sub a]/r[sub b]) of 22.5 can be produced with only modest quadrupole gradients of 64 G/cm and 18 G/cm. Quadrupole formation of elliptical sheet-beams may be particularly suited for experimental research applications since existing round-beam electron guns may be used and changes in beam ellipticity may be made without breaking the vacuum system.

  18. Current sheet Formation in a Conical Theta Pinch Faraday Accelerator with Radio-Frequency Assisted Discharge

    NASA Technical Reports Server (NTRS)

    Hallock, Ashley K.; Choueiri, Edgar Y.; Polzin, Kurt A.

    2007-01-01

    The inductive formation of current sheets in a conical theta pinch FARAD (Faraday Accelerator with Radio-frequency Assisted Discharge) thruster is investigated experimentally with time-integrated photography. The goal is to help in understanding the mechanisms and conditions controlling the strength and extent of the current sheet, which are two indices important for FARAD as a propulsion concept. The profiles of these two indices along the inside walls of the conical acceleration coil are assumed to be related to the profiles of the strength and extent of the luminosity pattern derived from photographs of the discharge. The variations of these profiles as a function of uniform back-fill neutral pressure (with no background magnetic field and all parameters held constant) provided the first clues on the nature and qualitative dependencies of current sheet formation. It was found that there is an optimal pressure for which both indices reach a maximum and that the rate of change in these indices with pressure differs on either side of this optimal pressure. This allowed the inference that current sheet formation follows a Townsend-like breakdown mechanism modified by the existence of a finite pressure-dependent radio-frequency-generated electron density background. The observation that the effective location of the luminosity pattern favors the exit-half of the conical coil is explained as the result of the tendency of the inductive discharge circuit to operate near its minimal self-inductance. Movement of the peak in the luminosity pattern towards the upstream side of the cone with increasing pressure is believed to result from the need of the circuit to compensate for the increase in background plasma resistivity due to increasing pressure.

  19. In Search of the Attributes Responsible for Sliver Formation in Cold Rolled Steel Sheets

    NASA Astrophysics Data System (ADS)

    Mohanty, Itishree; Das, Prasun; Bhattacharjee, Debashish; Datta, Shubhabrata

    2016-06-01

    Surface quality is one of the most important characteristics of cold rolled (CR) steel sheets for its application in consumer goods industries. The actual cause of sliver formation is very difficult to determine, as it is revealed only after the final cold rolling of the steel. A thorough investigation on searching the root cause of sliver formation in CR steel is done here using several statistical tools towards mining the industrial data for extraction of knowledge. As the complex interactions between the variables make it difficult to identify the cause, it is seen that findings from different techniques differed to a certain extent. Still it is revealed that 21 variables could be short listed as major contributor for sliver formation, but those are found to be from all the areas of the processing. This leads to the conclusion that no particular process variable or particular processing could be held responsible for sliver formation.

  20. Conditions for the formation of nongyrotropic current sheets in slowly evolving plasmas

    NASA Astrophysics Data System (ADS)

    Schindler, Karl; Hesse, Michael

    2010-08-01

    This paper addresses the formation of nongyrotropic current sheets resulting from slow external driving. The medium is a collisionless plasma with one spatial dimension and a three-dimensional velocity space. The study is based on particle simulation and an analytical approach. Earlier results that apply to compression of an initial Harris sheet are generalized in several ways. In a first step a general sufficient criterion for the presence of extra ion and electron currents due to nongyrotropic plasma conditions is derived. Then cases with antisymmetric magnetic and electric fields are considered. After establishing consistency of the criterion with the earlier case, the usefulness of this concept is illustrated in detail by two further particle simulations. The results indicate that the formation of nongyrotropic current sheets is a ubiquitous phenomenon for plasmas with antisymmetric fields that have evolved slowly from initial gyrotropic states. A fourth case concerns a plasma with a unidirectional magnetic field. Consistent with the general criterion, the observed final state is fluidlike in that it is approximately gyrotropic. Momentum balance is shown to include a contribution that results from accumulation of an off-diagonal pressure tensor component during the evolution. Heat flux also plays an important role.

  1. Addition of Adipose-Derived Stem Cells to Mesenchymal Stem Cell Sheets Improves Bone Formation at an Ectopic Site

    PubMed Central

    Wang, Zhifa; Li, Zhijin; Dai, Taiqiang; Zong, Chunlin; Liu, Yanpu; Liu, Bin

    2016-01-01

    To determine the effect of adipose-derived stem cells (ADSCs) added to bone marrow-derived mesenchymal stem cell (MSC) sheets on bone formation at an ectopic site. We isolated MSCs and ADSCs from the same rabbits. We then prepared MSC sheets for implantation with or without ADSCs subcutaneously in the backs of severe combined immunodeficiency (SCID) mice. We assessed bone formation at eight weeks after implantation by micro-computed tomography and histological analysis. In osteogenic medium, MSCs grew to form multilayer sheets containing many calcium nodules. MSC sheets without ADSCs formed bone-like tissue; although neo-bone and cartilage-like tissues were sparse and unevenly distributed by eight weeks after implantation. In comparison, MSC sheets with ADSCs promoted better bone regeneration as evidenced by the greater density of bone, increased mineral deposition, obvious formation of blood vessels, large number of interconnected ossified trabeculae and woven bone structures, and greater bone volume/total volume within the composite constructs. Our results indicate that although sheets of only MSCs have the potential to form tissue engineered bone at an ectopic site, the addition of ADSCs can significantly increase the osteogenic potential of MSC sheets. Thus, the combination of MSC sheets with ADSCs may be regarded as a promising therapeutic strategy to stimulate bone regeneration. PMID:26848656

  2. Interactive property of large thrust sheets with footwall rocks—the Sub thrust interactive duplex hypothesis: A mechanism of dome formation in thrust sheets

    NASA Astrophysics Data System (ADS)

    Hatcher, Robert D.

    1991-06-01

    Recently acquired Appalachian Ultradeep Core Hole (ADCOH) Project site investigation seismic reflection data and geologic data from the Appalachians and several other orogenic belts suggest an important mutually interdependent relationship exists between emplacement of large crystalline thrust sheets and the deforming foreland rocks beneath. This relationship suggests isolated domes beneath crystalline thrust sheets may be produced by passive folding of the sheet as a result of formation of an antiformal stack duplex in the platform sedimentary sequence beneath. Suggestions that domes in crystalline thrust sheets formed by interference of late open folds is doubtlessly still valid in places, but the platform duplex mechanism is probably also valid to explain the late doming of many crystalline and other large thrust sheets. The dome beneath the Shooting Creek and Brasstown Bald windows in the ADCOH site region is imaged as an antiformal stack duplex at depth. The Tallulah Falls dome, Grandfather Mountain and Mountain City windows, and Smokies Foothills duplex in the site region and elsewhere in the southern Blue Ridge are all late isolated domes and all are probably or demonstrably underlain by antiformal stack duplexes beneath the Blue Ridge-Piedmont composite crystalline thrust sheet. The Assynt window and footwall duplex benath the Arnabol and Moine thrusts in Scotland, and the Engadine window in the Alps may be similar structures.

  3. Beta-Sheet-Forming, Self-Assembled Peptide Nanomaterials towards Optical, Energy, and Healthcare Applications.

    PubMed

    Kim, Sungjin; Kim, Jae Hong; Lee, Joon Seok; Park, Chan Beum

    2015-08-12

    Peptide self-assembly is an attractive route for the synthesis of intricate organic nanostructures that possess remarkable structural variety and biocompatibility. Recent studies on peptide-based, self-assembled materials have expanded beyond the construction of high-order architectures; they are now reporting new functional materials that have application in the emerging fields such as artificial photosynthesis and rechargeable batteries. Nevertheless, there have been few reviews particularly concentrating on such versatile, emerging applications. Herein, recent advances in the synthesis of self-assembled peptide nanomaterials (e.g., cross β-sheet-based amyloid nanostructures, peptide amphiphiles) are selectively reviewed and their new applications in diverse, interdisciplinary fields are described, ranging from optics and energy storage/conversion to healthcare. The applications of peptide-based self-assembled materials in unconventional fields are also highlighted, such as photoluminescent peptide nanostructures, artificial photosynthetic peptide nanomaterials, and lithium-ion battery components. The relation of such functional materials to the rapidly progressing biomedical applications of peptide self-assembly, which include biosensors/chips and regenerative medicine, are discussed. The combination of strategies shown in these applications would further promote the discovery of novel, functional, small materials. PMID:25929870

  4. Calcofluor fluorescence assay for wort beta-glucan in a microplate format

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The widely-used fluorescent (Calcofluor) flow injection analysis method for determining the concentrations of beta-glucans in Congress worts from barley malts is adapted to microplate format. Adaptation of the Calcofluor assay to use widely available fluorescent microplate readers makes the assay m...

  5. Low cost fabrication of sheet structure using a new beta titanium alloy, Ti-15V-3Cr-3Al-3Sn

    NASA Technical Reports Server (NTRS)

    Kaneko, R. S.; Davis, G. W.; Woods, C. A.; Royster, D. M.

    1982-01-01

    Development efforts have been undertaken to improve the processing and structural efficiencies of advanced cold-formable beta Ti alloys, using the standard, hot-formed and rivetted construction of Ti-6Al-4V sheet structures as a basis for comparison. Ti-15V-3Cr-3Al-3Sn (Ti-15-3) beta alloy is formable, brazable and weldable in the solution-treated condition, and after aging displays mechanical properties suitable for postulated service in the -65 to 600 F temperature range. A novel methodology using cold-formed Ti-15-3 stringers and Ti-6Al-4V face sheets that are joined by means of an out-of-furnace isothermal brazing process, followed by low temperature aging, can reduce production costs by as much as 28 per cent. Structural efficiency has been demonstrated in room and elevated temperature crippling tests of small skin-stringer assemblies.

  6. Circularly permuted monomeric red fluorescent proteins with new termini in the beta-sheet.

    PubMed

    Carlson, Haley J; Cotton, Darrel W; Campbell, Robert E

    2010-08-01

    Circularly permuted fluorescent proteins (FPs) have a growing number of uses in live cell fluorescence biosensing applications. Most notably, they enable the construction of single fluorescent protein-based biosensors for Ca(2+) and other analytes of interest. Circularly permuted FPs are also of great utility in the optimization of fluorescence resonance energy transfer (FRET)-based biosensors by providing a means for varying the critical dipole-dipole orientation. We have previously reported on our efforts to create circularly permuted variants of a monomeric red FP (RFP) known as mCherry. In our previous work, we had identified six distinct locations within mCherry that tolerated the insertion of a short peptide sequence. Creation of circularly permuted variants with new termini at the locations corresponding to the sites of insertion led to the discovery of three permuted variants that retained no more than 18% of the brightness of mCherry. We now report the extensive directed evolution of the variant with new termini at position 193 of the protein sequence for improved fluorescent brightness. The resulting variant, known as cp193g7, has 61% of the intrinsic brightness of mCherry and was found to be highly tolerant of circular permutation at other locations within the sequence. We have exploited this property to engineer an expanded series of circularly permuted variants with new termini located along the length of the 10th beta-strand of mCherry. These new variants may ultimately prove useful for the creation of single FP-based Ca(2+) biosensors. PMID:20521333

  7. Phosphoinositide 3-kinase p85beta regulates invadopodium formation

    PubMed Central

    Cariaga-Martínez, Ariel E.; Cortés, Isabel; García, Esther; Pérez-García, Vicente; Pajares, María J.; Idoate, Miguel A.; Redondo-Muñóz, Javier; Antón, Inés M.; Carrera, Ana C.

    2014-01-01

    ABSTRACT The acquisition of invasiveness is characteristic of tumor progression. Numerous genetic changes are associated with metastasis, but the mechanism by which a cell becomes invasive remains unclear. Expression of p85β, a regulatory subunit of phosphoinositide-3-kinase, markedly increases in advanced carcinoma, but its mode of action is unknown. We postulated that p85β might facilitate cell invasion. We show that p85β localized at cell adhesions in complex with focal adhesion kinase and enhanced stability and maturation of cell adhesions. In addition, p85β induced development at cell adhesions of an F-actin core that extended several microns into the cell z-axis resembling the skeleton of invadopodia. p85β lead to F-actin polymerization at cell adhesions by recruiting active Cdc42/Rac at these structures. In accordance with p85β function in invadopodium-like formation, p85β levels increased in metastatic melanoma and p85β depletion reduced invadopodium formation and invasion. These results show that p85β enhances invasion by inducing cell adhesion development into invadopodia-like structures explaining the metastatic potential of tumors with increased p85β levels. PMID:25217619

  8. Numerical modeling of Tibetan Plateau formation: Thin-sheet versus fully 3D models

    NASA Astrophysics Data System (ADS)

    Lechmann, S. M.; Schmalholz, S. M.; Kaus, B. J. P.

    2009-04-01

    Knowledge about the tectonic evolution of the Tibetan Plateau is still incomplete and many open questions remain concerning the deformation style of the crustal thickening, causing the abnormally high elevation of the Tibetan Plateau. Different models have been suggested explaining the crustal thickening by (1) homogeneous, continuous deformation using thin-sheet models, (2) discrete movement along thrusts developing crustal wedges and (3) lateral crustal flow due to pressure gradients resulting from topography. Most existing models are not fully three-dimensional (3D) models (e.g. thin-sheet models) and assume a certain deformation style a priori, which makes it difficult to judge the applicability of such constrained models to the formation of the Tibetan Plateau. We present a comparison of deformation styles during continent indentation resulting from a fully 3D numerical model and a thin-sheet model. The rheology for both models is power-law. The 3D model consists of four layers representing a simplified lithosphere: strong upper crust, weak lower crust, strong upper mantle and weak lower mantle. From the effective viscosity distribution of the 3D model a vertically averaged effective viscosity is calculated and used for the thin-sheet model to make direct comparisons between the two models. Simulating indentation is achieved by assigning free slip at one lateral side of the model, and fixing two other sides. The boundary at which indentation is taking place, exhibits a tripartite velocity profile: Next to the free slip side a section with constant horizontal velocity is applied. The velocity then gradually decreases towards zero, applying a cosine-function. The last section of the indenting boundary next to the fixed side is also fixed. The 3D model additionally exhibits a free surface and a bottom boundary allowing free slip. The 3D code employs the finite element method with a mixed velocity-pressure formulation to simulate incompressible flow. A Lagrangian

  9. Beta-catenin and BMP-2 synergize to promote osteoblast differentiation and new bone formation.

    PubMed

    Mbalaviele, Gabriel; Sheikh, Sharmin; Stains, Joseph P; Salazar, Valerie S; Cheng, Su-Li; Chen, Di; Civitelli, Roberto

    2005-02-01

    Mutations of critical components of the Wnt pathway profoundly affect skeletal development and maintenance, probably via modulation of beta-catenin signaling. We tested the hypothesis that beta-catenin is involved in mesenchymal lineage allocation to osteogenic cells using a beta-catenin mutant with constitutive transcriptional activity (DeltaN151). Although this stable beta-catenin had no effects by itself on osteogenic differentiation of multipotent embryonic cell lines, it synergized with bone morphogenetic protein-2 (BMP-2) resulting in dramatic stimulation of alkaline phosphatase activity, osteocalcin gene expression, and matrix mineralization. Likewise, DeltaN151 and BMP-2 synergistically stimulated new bone formation after subperiosteal injection in mouse calvaria in vivo. Conversely, DeltaN151 prevented adipogenic differentiation from pre-adipocytic or uncommitted mesenchymal cells in vitro. Intriguingly, the synergism with BMP-2 on gene transcription occurred without altering expression of Cbfa1/Runx2, suggesting actions independent or downstream of this osteoblast-specific transcription factor. Thus, beta-catenin directs osteogenic lineage allocation by enhancing mesenchymal cell responsiveness to osteogenic factors, such as BMP-2, in part via Tcf/Lef dependent mechanisms. In vivo, this synergism leads to increased new bone formation. PMID:15526274

  10. Effect of secondary structure on the potential of mean force for poly-L-lysine in the alpha-Helix and beta-sheet conformations

    SciTech Connect

    Grigsby, J.J.; Blanch, H.W.; Prausnitz, J.M.

    2001-10-30

    Because poly-L-lysine (PLL) can exist in the {alpha}-helix or {beta}-sheet conformation depending on solution preparation and solution conditions, PLL is a suitable candidate to probe the dependence of protein interactions on secondary structure. The osmotic second virial coefficient and weight-average molecular weight are reported from low-angle laser-light scattering measurements for PLL as a function of NaCl concentration, pH, and {alpha}-helix or {beta}-sheet content. Interactions between PLL molecules become more attractive as salt concentration increases due to screening of PLL charge by salt ions and at low salt concentration become more attractive as pH increases due to decreased net charge on PLL. The experimental results show that interactions are stronger for the {beta}-sheet conformation than for the {alpha}-helix conformation. A spherically-symmetric model for the potential of mean force is used to account for specific interactions not described by DLVO theory and to show how differences in secondary structure affect PLL interactions.

  11. A common structural motif incorporating a cystine knot and a triple-stranded beta-sheet in toxic and inhibitory polypeptides.

    PubMed Central

    Pallaghy, P. K.; Nielsen, K. J.; Craik, D. J.; Norton, R. S.

    1994-01-01

    A common structural motif consisting of a cystine knot and a small triple-stranded beta-sheet has been defined from comparison of the 3-dimensional structures of the polypeptides omega-conotoxin GVIA (Conus geographus), kalata BI (Oldenlandia affinis DC), and CMTI-I (Curcurbita maxima). These 3 polypeptides have diverse biological activities and negligible amino acid sequence identity, but each contains 3 disulfide bonds that give rise to a cystine knot. This knot consists of a ring formed by the first 2 bonds (1-4 and 2-5) and the intervening polypeptide backbone, through which the third disulfide (3-6) passes. The other component of this motif is a triple-stranded, anti-parallel beta-sheet containing a minimum of 10 residues, XXC2, XC5X, XXC6X (where the numbers on the half-cysteine residues refer to their positions in the disulfide pattern). The presence in these polypeptides of both the cysteine knot and antiparallel beta-sheet suggests that both structural features are required for the stability of the motif. This structural motif is also present in other protease inhibitors and a spider toxin. It appears to be one of the smallest stable globular domains found in proteins and is commonly used in toxins and inhibitors that act by blocking the function of larger protein receptors such as ion channels or proteases. PMID:7849598

  12. Formation and transport of sheet electron beams and multi-beam configurations for high-power microwave devices

    SciTech Connect

    Basten, M.A.; Booske, J.H.; Anderson, J.; Scharer, J.E.

    1995-11-01

    Sheet electron beams and configurations with multiple electron beams have the potential to make possible higher power sources of microwave radiation due to their ability to transport high currents, at reduced current densities, through a single RF interaction circuit. Possible microwave device applications using sheet electron beams include sheet-beam klystrons, rectangular grating circuits, and planar FELS. Historically, implementation of sheet beams in microwave devices has been discouraged by their susceptibility to the diocotron instability in solenoidal focusing systems. However, recent theoretical and numerical studies have shown that stable transport of sheet beams is possible, in periodically cusped magnetic (PCM) fields. The use of an offset-pole PCM configuration has been shown analytically to provide side-fields for 2-D focusing of the beam, and this has been recently verified with PIC code simulations. The authors will present further theoretical studies of sheet and multi-beam transport and discuss results from an experimental investigation of the formation, stability and transport of PCM-focused sheet electron beams. This includes a laboratory method of forming an elliptical sheet beam using a magnetic quadrupole pair and a round-beam Pierce gun.

  13. Biosynthesis of streptothricin F. 5. Formation of. beta. -lysine by Streptomyces L-1689-23

    SciTech Connect

    Thiruvengadam, T.K.; Gould, S.J.; Aberhart, D.J.; Lin, H.J.

    1983-08-10

    The formation of the ..beta..-lysine moiety of streptothricin F has been studied by feeding to Streptomyces L-1689-23 ..cap alpha..-(3-/sup 13/C,/sup 15/N)-, ..cap alpha..-((3RS)-/sup 2/H/sub 2/)-, ..cap alpha..-((3R)-/sup 2/H)-, and ..cap alpha..-((3S)-/sup 2/H)lysine and ..beta..-((2S)-/sup 2/H)lysine. From the analysis of either the /sup 13/C NMR or /sup 2/H NMR spectrum of the derived antibiotics, it has been determined that the ..cap alpha..-nitrogen migrates to C-3 with inversion of configuration by an intramolecular process, and the 3-pro-R hydrogen migrates to C-2 with inversion of configuration by a process that is substantially or completely intermolecular. The very high degree of incorporation of labeled ..beta..-lysine indicates it is probably an intermediate in the biosynthesis of streptothricin F.

  14. High-Resolution Structure of a Self-Assembly-Competent Form of a Hydrophobic Peptide Captured in a Soluble [beta]-Sheet Scaffold

    SciTech Connect

    Makabe, Koki; Biancalana, Matthew; Yan, Shude; Tereshko, Valentina; Gawlak, Grzegorz; Miller-Auer, Hélène; Meredith, Stephen C.; Koide, Shohei

    2010-02-08

    {beta}-Rich self-assembly is a major structural class of polypeptides, but still little is known about its atomic structures and biophysical properties. Major impediments for structural and biophysical studies of peptide self-assemblies include their insolubility and heterogeneous composition. We have developed a model system, termed peptide self-assembly mimic (PSAM), based on the single-layer {beta}-sheet of Borrelia outer surface protein A. PSAM allows for the capture of a defined number of self-assembly-like peptide repeats within a water-soluble protein, making structural and energetic studies possible. In this work, we extend our PSAM approach to a highly hydrophobic peptide sequence. We show that a penta-Ile peptide (Ile{sub 5}), which is insoluble and forms {beta}-rich self-assemblies in aqueous solution, can be captured within the PSAM scaffold in a form capable of self-assembly. The 1.1-{angstrom} crystal structure revealed that the Ile{sub 5} stretch forms a highly regular {beta}-strand within this flat {beta}-sheet. Self-assembly models built with multiple copies of the crystal structure of the Ile5 peptide segment showed no steric conflict, indicating that this conformation represents an assembly-competent form. The PSAM retained high conformational stability, suggesting that the flat {beta}-strand of the Ile{sub 5} stretch primed for self-assembly is a low-energy conformation of the Ile{sub 5} stretch and rationalizing its high propensity for self-assembly. The ability of the PSAM to 'solubilize' an otherwise insoluble peptide stretch suggests the potential of the PSAM approach to the characterization of self-assembling peptides.

  15. Amyloid formation and inhibition of an all-beta protein: A study on fungal polygalacturonase

    NASA Astrophysics Data System (ADS)

    Chinisaz, Maryam; Ghasemi, Atiyeh; Larijani, Bagher; Ebrahim-Habibi, Azadeh

    2014-02-01

    Theoretically, all proteins can adopt the nanofibrillar structures known as amyloid, which contain cross-beta structures. The all-beta folded proteins are particularly interesting in this regard, since they appear to be naturally more predisposed toward this structural arrangement. In this study, methanol has been used to drive the beta-helix protein polygalacturonase (PG), toward amyloid fibril formation. Congo red absorbance, thioflavin T fluorescence, circular dichroism (CD) and transmission electron microscopy have been used to characterize this process. Similar to other all-beta proteins, PG shows a non-cooperative fibrillation mechanism, but the structural changes that are monitored by CD indicate a different pattern. Furthermore, several compounds containing aromatic components were tested as potential inhibitors of amyloid formation. Another protein predominantly composed of alpha-helices (human serum albumin) was also targeted by these ligands, in order to get an insight into their potential anti-aggregation property toward structurally different proteins. Among tested compounds, silibinin and chlorpropamide were able to considerably affect both proteins fibrillation process.

  16. Enzyme-catalyzed formation of beta-peptides: beta-peptidyl aminopeptidases BapA and DmpA acting as beta-peptide-synthesizing enzymes.

    PubMed

    Heck, Tobias; Kohler, Hans-Peter E; Limbach, Michael; Flögel, Oliver; Seebach, Dieter; Geueke, Birgit

    2007-09-01

    In recent studies, we discovered that the three beta-peptidyl aminopeptidases, BapA from Sphingosinicella xenopeptidilytica 3-2W4, BapA from S. microcystinivorans Y2, and DmpA from Ochrobactrum anthropi LMG7991, possess the unique feature of cleaving N-terminal beta-amino acid residues from beta- and alpha/beta-peptides. Herein, we investigated the use of the same three enzymes for the reverse reaction catalyzing the oligomerization of beta-amino acids and the synthesis of mixed peptides with N-terminal beta-amino acid residues. As substrates, we employed the beta-homoamino acid derivatives H-beta hGly-pNA, H-beta3 hAla-pNA, H-(R)-beta3 hAla-pNA, H-beta3 hPhe-pNA, H-(R)-beta3 hPhe-pNA, and H-beta3 hLeu-pNA. All three enzymes were capable of coupling the six beta-amino acids to oligomers with chain lengths of up to eight amino acid residues. With the enzyme DmpA as the catalyst, we observed very high conversion rates, which correspond to dimer yields of up to 76%. The beta-dipeptide H-beta3 hAla-beta3 hLeu-OH and the beta/alpha-dipeptide H-beta hGly-His-OH (carnosine) were formed with almost 50% conversion, when a five-fold excess of beta3-homoleucine or histidine was incubated with H-beta3 hAla-pNA and H-beta hGly-pNA, respectively, in the presence of the enzyme BapA from S. microcystinivorans Y2. BapA from S. xenopeptidilytica 3-2W4 turned out to be a versatile catalyst capable of coupling various beta-amino acid residues to the free N-termini of beta- and alpha-amino acids and even to an alpha-tripeptide. Thus, these aminopeptidases might be useful to introduce a beta-amino acid residue as an N-terminal protecting group into a 'natural' alpha-peptide, thereby stabilizing the peptide against degradation by other proteolytic enzymes. PMID:17886858

  17. Observations of magnetic merging and the formation of the plasma sheet in the earth's magnetotail

    NASA Technical Reports Server (NTRS)

    Lin, R. P.; Anderson, K. A.; Mccoy, J. E.; Russell, C. T.

    1977-01-01

    Particle and magnetic field observations of the field line merging process in the earth's magnetotail are presented. By analyzing the lunar shadow pattern of electron fluxes detected by the lunar-orbiting Apollo 16 subsatellite it has been possible to identify the topology and to measure the velocity of the magnetotail field lines. The observations reported here were made as the moon crossed the separatrix between premerging and merged field lines. The measured field line velocities toward the merging region were 30-60 km/s, and the thickness of the separatrix was estimated to be about 2000 km. Most of the magnetic energy released in the merging process appears to go into the energization of particles. The length and the thickness of the merging region are inferred to be of the order of about 10 earth radii and about 4000 km, respectively. The energized particles travel away from the merging region along the separatrix. Those headed earthward may form the plasma sheet by being trapped on closed field lines. The rate of energization and the energy spectrum of those particles are consistent with those required for formation of the plasma sheet.

  18. 2D 1H and 3D 1H-15N NMR of zinc-rubredoxins: contributions of the beta-sheet to thermostability.

    PubMed Central

    Richie, K. A.; Teng, Q.; Elkin, C. J.; Kurtz, D. M.

    1996-01-01

    Based on 2D 1H-1H and 2D and 3D 1H-15N NMR spectroscopies, complete 1H NMR assignments are reported for zinc-containing Clostridium pasteurianum rubredoxin (Cp ZnRd). Complete 1H NMR assignments are also reported for a mutated Cp ZnRd, in which residues near the N-terminus, namely, Met 1, Lys 2, and Pro 15, have been changed to their counterparts, (-), Ala and Glu, respectively, in rubredoxin from the hyperthermophilic archaeon, Pyrococcus furiosus (Pf Rd). The secondary structure of both wild-type and mutated Cp ZnRds, as determined by NMR methods, is essentially the same. However, the NMR data indicate an extension of the three-stranded beta-sheet in the mutated Cp ZnRd to include the N-terminal Ala residue and Glu 15, as occurs in Pf Rd. The mutated Cp Rd also shows more intense NOE cross peaks, indicating stronger interactions between the strands of the beta-sheet and, in fact, throughout the mutated Rd. However, these stronger interactions do not lead to any significant increase in thermostability, and both the mutated and wild-type Cp Rds are much less thermostable than Pf Rd. These correlations strongly suggest that, contrary to a previous proposal [Blake PR et al., 1992, Protein Sci 1:1508-1521], the thermostabilization mechanism of Pf Rd is not dominated by a unique set of hydrogen bonds or electrostatic interactions involving the N-terminal strand of the beta-sheet. The NMR results also suggest that an overall tighter protein structure does not necessarily lead to increased thermostability. PMID:8732760

  19. Nonlinear evolution of three-dimensional instabilities of thin and thick electron scale current sheets: Plasmoid formation and current filamentation

    SciTech Connect

    Jain, Neeraj; Büchner, Jörg

    2014-07-15

    Nonlinear evolution of three dimensional electron shear flow instabilities of an electron current sheet (ECS) is studied using electron-magnetohydrodynamic simulations. The dependence of the evolution on current sheet thickness is examined. For thin current sheets (half thickness =d{sub e}=c/ω{sub pe}), tearing mode instability dominates. In its nonlinear evolution, it leads to the formation of oblique current channels. Magnetic field lines form 3-D magnetic spirals. Even in the absence of initial guide field, the out-of-reconnection-plane magnetic field generated by the tearing instability itself may play the role of guide field in the growth of secondary finite-guide-field instabilities. For thicker current sheets (half thickness ∼5 d{sub e}), both tearing and non-tearing modes grow. Due to the non-tearing mode, current sheet becomes corrugated in the beginning of the evolution. In this case, tearing mode lets the magnetic field reconnect in the corrugated ECS. Later thick ECS develops filamentary structures and turbulence in which reconnection occurs. This evolution of thick ECS provides an example of reconnection in self-generated turbulence. The power spectra for both the thin and thick current sheets are anisotropic with respect to the electron flow direction. The cascade towards shorter scales occurs preferentially in the direction perpendicular to the electron flow.

  20. Formation and transport of low-voltage, space-charge dominated sheet electron beams for high-power microwave devices

    SciTech Connect

    Basten, M.A.; Booske, J.H.; Louis, L.J.; Joe, J.; Scharer, J.E.

    1996-12-31

    Sheet electron beams have the potential to make possible higher power sources of microwave radiation due to their ability to transport high currents, at reduced current densities, through a single narrow RF interaction circuit. The authors will discuss experimental investigations of the formation of an elliptical sheet beam using magnet quadrupoles and a round-beam electron gun. Features of this configuration include a low-cost, commercially available Pierce gun and a lens system consisting of four tunable magnetic quadrupoles with modest field gradients. Three-dimensional envelope and particle-in-cell simulations indicate that this method can generate highly elliptic output beams, with variability in final beam size, for laboratory experiments on sheet beam transport. They also will present the results of particle-in-cell simulations of the transport of sheet beams in long-period offset-pole periodic magnet arrays. While the stability of sheet beams in short-period arrays has previously been established, the extension to longer magnet periods indicate that side-focusing of space-charge dominated sheet beams is more problematic than beam stability. However, long-term (> 20 periods) stable transport is demonstrated for {lambda}{sub m} = 1 cm for a 2 A, 10 kV elliptical beam with a = 2.7 cm and b = 0.05 cm.

  1. The three-dimensional structural surface of two beta-sheet scorpion toxins mimics that of an alpha-helical dihydropyridine receptor segment.

    PubMed Central

    Green, Daniel; Pace, Suzi; Curtis, Suzanne M; Sakowska, Magdalena; Lamb, Graham D; Dulhunty, Angela F; Casarotto, Marco G

    2003-01-01

    An alpha-helical II-III loop segment of the dihydropyridine receptor activates the ryanodine receptor calcium-release channel. We describe a novel manipulation in which this agonist's activity is increased by modifying its surface structure to resemble that of a toxin molecule. In a unique system, native beta-sheet scorpion toxins have been reported to activate skeletal muscle ryanodine receptor calcium channels with high affinity by binding to the same site as the lower-affinity alpha-helical dihydropyridine receptor segment. We increased the alignment of basic residues in the alpha-helical peptide to mimic the spatial orientation of active residues in the scorpion toxin, with a consequent 2-20-fold increase in the activity of the alpha-helical peptide. We hypothesized that, like the native peptide, the modified peptide and the scorpion toxin may bind to a common site. This was supported by (i) similar changes in ryanodine receptor channel gating induced by the native or modified alpha-helical peptide and the beta-sheet toxin, a 10-100-fold reduction in channel closed time, with a < or = 2-fold increase in open dwell time and (ii) a failure of the toxin to further activate channels activated by the peptides. These results suggest that diverse structural scaffolds can present similar conformational surface properties to target common receptor sites. PMID:12429019

  2. Protein Secondary Structures (alpha-helix and beta-sheet) at a Cellular Levle and Protein Fractions in Relation to Rumen Degradation Behaviours of Protein: A New Approach

    SciTech Connect

    Yu,P.

    2007-01-01

    Studying the secondary structure of proteins leads to an understanding of the components that make up a whole protein, and such an understanding of the structure of the whole protein is often vital to understanding its digestive behaviour and nutritive value in animals. The main protein secondary structures are the {alpha}-helix and {beta}-sheet. The percentage of these two structures in protein secondary structures influences protein nutritive value, quality and digestive behaviour. A high percentage of {beta}-sheet structure may partly cause a low access to gastrointestinal digestive enzymes, which results in a low protein value. The objectives of the present study were to use advanced synchrotron-based Fourier transform IR (S-FTIR) microspectroscopy as a new approach to reveal the molecular chemistry of the protein secondary structures of feed tissues affected by heat-processing within intact tissue at a cellular level, and to quantify protein secondary structures using multicomponent peak modelling Gaussian and Lorentzian methods, in relation to protein digestive behaviours and nutritive value in the rumen, which was determined using the Cornell Net Carbohydrate Protein System. The synchrotron-based molecular chemistry research experiment was performed at the National Synchrotron Light Source at Brookhaven National Laboratory, US Department of Energy. The results showed that, with S-FTIR microspectroscopy, the molecular chemistry, ultrastructural chemical make-up and nutritive characteristics could be revealed at a high ultraspatial resolution ({approx}10 {mu}m). S-FTIR microspectroscopy revealed that the secondary structure of protein differed between raw and roasted golden flaxseeds in terms of the percentages and ratio of {alpha}-helixes and {beta}-sheets in the mid-IR range at the cellular level. By using multicomponent peak modelling, the results show that the roasting reduced (P <0.05) the percentage of {alpha}-helixes (from 47.1% to 36.1%: S

  3. Formation of a very thin current sheet in the near-earth magnetotail and the explosive growth phase of substorms

    NASA Technical Reports Server (NTRS)

    Lee, L. C.; Zhang, L.; Choe, G. S.; Cai, H. J.

    1995-01-01

    A magnetofricional method is used to construct two-dimensional MHD equilibria of the Earth's magnetosphere for a given distribution of entropy functions(S = pV(exp gamma), where p is the plasma pressure and V is the tube volume per unit magnetic flux. It is found that a very thin current sheet with B (sub zeta) is less than 0.5 nu T and thickness less than 1000 km can be formed in the near-earth magnetotail (x is approximately -8 to -20R(sub e) during the growth phase of substorm. The tail current sheets are found to become thinner as the entropy or the entropy gradient increases. It is suggested that the new entropy anti-diffusion instability associated with plasma transport across field lines leads to magnetic field dipolarization and accelerates the formation of thin current sheet, which may explain the observed explosive growth phase of substorms.

  4. Optimal heating condition of mouthguard sheet in vacuum-pressure formation: part 2 Olefin-based thermoplastic elastomer.

    PubMed

    Takahashi, Mutsumi; Koide, Kaoru

    2016-04-01

    The purposes of this study were to clarify the suitable heating conditions during vacuum-pressure formation of olefin copolymer sheets and to examine the sheet temperature at molding and the thickness of the molded mouthguard. Mouthguards were fabricated using 4.0-mm-thick olefin copolymer sheets utilizing a vacuum-pressure forming device, and then, 10 s of vacuum forming and 2 min of compression molding were applied. Three heating conditions were investigated. They were, defined by the degree of sagging observed at the center of the softened sheet (10, 15, or 20 mm lower than the clamp (H-10, H-15, or H-20, respectively)). The working model was trimmed to the height of 20 mm at the maxillary central incisor and 15 mm at the mesiobuccal cusp of the maxillary first molar. The temperature on both the directly heated and the non-heated surfaces of the mouthguard sheet was measured by the radiation thermometer for each condition. The thickness of mouthguard sheets after fabrication was determined for the incisal portion (incisal edge and labial surface) and molar portion (cusp and buccal surface), and dimensional measurements were obtained using a measuring device. Differences in the thickness due to the heating condition of the sheets were analyzed by one-way analysis of variance and Bonferroni's multiple comparison tests. The temperature difference between the heated and non-heated surfaces was highest under H-10. Sheet temperature under H-15 and H-20 was almost the same. The thickness differences were noted at incisal edge, cusp, and buccal surface, and H-15 was the greatest. This study demonstrated that heating of the sheet resulting in sag of 15 mm or more was necessary for sufficient softening of the sheet and that the mouthguard thickness decreased with increased sag. In conclusion, sag of 15 mm can be recommended as a good indicator of appropriate molding timing for this material. PMID:26341504

  5. Repetitive formation and decay of current sheets in magnetic loops: An origin of diverse magnetic structures

    SciTech Connect

    Kumar, Dinesh; Bhattacharyya, R.; Smolarkiewicz, P. K.

    2015-01-15

    In this work, evolution of an incompressible, thermally homogeneous, infinitely conducting, viscous magnetofluid is numerically explored as the fluid undergoes repeated events of magnetic reconnection. The initial magnetic field is constructed by a superposition of two linear force-free fields and has similar morphology as the magnetic loops observed in the solar corona. The results are presented for computations with three distinct sets of footpoint geometries. To onset reconnection, we rely on numerical model magnetic diffusivity, in the spirit of implicit large eddy simulation. It is generally expected that in a high Lundquist number fluid, repeated magnetic reconnections are ubiquitous and hence can lead to a host of magnetic structures with considerable observational importance. In particular, the simulations presented here illustrate formations of magnetic islands, rotating magnetic helices and rising flux ropes—depending on the initial footpoint geometry but through the common process of repeated magnetic reconnections. Further, we observe the development of extended current sheets in two case studies, where the footpoint reconnections generate favorable dynamics.

  6. Interactive desktop analysis of high resolution simulations: application to turbulent plume dynamics and current sheet formation

    NASA Astrophysics Data System (ADS)

    Clyne, John; Mininni, Pablo; Norton, Alan; Rast, Mark

    2007-08-01

    The ever increasing processing capabilities of the supercomputers available to computational scientists today, combined with the need for higher and higher resolution computational grids, has resulted in deluges of simulation data. Yet the computational resources and tools required to make sense of these vast numerical outputs through subsequent analysis are often far from adequate, making such analysis of the data a painstaking, if not a hopeless, task. In this paper, we describe a new tool for the scientific investigation of massive computational datasets. This tool (VAPOR) employs data reduction, advanced visualization, and quantitative analysis operations to permit the interactive exploration of vast datasets using only a desktop PC equipped with a commodity graphics card. We describe VAPORs use in the study of two problems. The first, motivated by stellar envelope convection, investigates the hydrodynamic stability of compressible thermal starting plumes as they descend through a stratified layer of increasing density with depth. The second looks at current sheet formation in an incompressible helical magnetohydrodynamic flow to understand the early spontaneous development of quasi two-dimensional (2D) structures embedded within the 3D solution. Both of the problems were studied at sufficiently high spatial resolution, a grid of 5042 by 2048 points for the first and 15363 points for the second, to overwhelm the interactive capabilities of typically available analysis resources.

  7. Different roles of protein kinase C-beta and -delta in arachidonic acid cascade, superoxide formation and phosphoinositide hydrolysis.

    PubMed Central

    Duyster, J; Schwende, H; Fitzke, E; Hidaka, H; Dieter, P

    1993-01-01

    In contrast with protein kinase C (PKC)-beta, PKC-delta is exclusively detectable in the membrane fraction of liver macrophages. After long-term treatment with phorbol 12-myristate 13-acetate (PMA) PKC-beta is depleted faster (within 3 h) than PKC-delta (> 7h). Simultaneously, pretreatment with PMA for 3 h inhibits the PMA- and zymosan-induced generation of superoxide and the PMA-induced formation of prostaglandin (PG) E2, whereas a preincubation of more than 7 h is required to affect the zymosan-induced release of PGE2 and inositol phosphates. These results support an involvement of PKC-beta in the PMA-induced activation of the arachidonic acid cascade and in superoxide formation and imply an involvement of PKC-delta in zymosan-induced phosphoinositide hydrolysis and PGE2 formation. Two phorbol ester derivates, sapintoxin A (SAPA) and 12-deoxyphorbol 13-phenylacetate 20-acetate (DOPPA), which have been previously reported to activate preferentially PLC-beta but not PKC-delta in vitro [Ryves, Evans, Olivier, Parker and Evans (1992) FEBS Lett. 288, 5-9], induce the formation of PGE2 and superoxide, down-regulate PKC-delta and potentiate inositol phosphate formation in parallel SAPA, but not DOPPA, down-regulates PKC-beta and inhibits the PMA-induced formation of eicosanoids and superoxide. Images Figure 1 Figure 2 Figure 5 PMID:8389125

  8. Targets of TGF-beta signaling in Caenorhabditis elegans dauer formation.

    PubMed

    Inoue, T; Thomas, J H

    2000-01-01

    Caenorhabditis elegans dauer formation is controlled by multiple environmental factors. The chemosensory neuron ASI regulates dauer formation by secretion of DAF-7/TGF-beta, but the molecular targets of the DAF-7 ligand are incompletely defined and the cellular targets are unknown. We genetically characterized and cloned a putative transducer of DAF-7 signaling called daf-14 and found that it encodes a Smad protein. DAF-14 Smad has a highly unusual structure completely lacking the N-terminal domain found in all other Smad proteins known to date. daf-14 genetically interacts with daf-8, which encodes another Smad, and the interaction suggests partial functional redundancy between these two Smad proteins. We also studied the cellular targets of DAF-7 signaling by studying the sites of action of daf-14 and daf-4, the putative receptor for DAF-7. daf-14::gfp is expressed in multiple tissues that are remodeled during dauer formation. However, analysis of mosaics generated by free duplication loss and tissue-specific expression constructs indicate cell-nonautonomous function of daf-4, arguing against direct DAF-7 signaling to tissues throughout the animal. Instead, these experiments suggest the nervous system as a target of DAF-7 signaling and that the nervous system in turn regulates dauer formation by other tissues. PMID:10625546

  9. Spontaneous formation of stringlike clusters and smectic sheets for colloidal rods confined in thin wedgelike gaps.

    PubMed

    Maeda, Hideatsu; Maeda, Yoshiko

    2013-08-20

    Monodispersed colloidal rods of β-FeOOH with sizes ranging from 270 to 580 nm in length and 50 to 80 nm in width were synthesized. Narrow wedgelike gaps (0 to 700 nm in height) were formed around the inner bottom edge of the suspension glass cells. Optical microscopic observations revealed the formation of stringlike clusters of the rods and smectic sheets (by spontaneous side-by-side clustering of the strings) in the isotropic phase of the rod suspensions confined in narrow gaps; the electrolyte (HCl) concentrations of the suspensions are 5-40 mM, at which inter-rod interactions are attractive. The strings exhibit different colors that were used to investigate the structures of the strings with the help of interference color theory for thin films. The results are as follows. (1) The rods, lying flat on the gap bottom, are connected side-by-side and stacked upward to form stringlike clusters with different thicknesses depending on the gap height. (2) The stacking numbers (N(sr)) of the rods are estimated to be 1-5. With N(sr) increasing from 2 to 5, the volume fractions (ϕ) of the rods in the strings increased typically from 0.25-0.3 to 0.35-0.42 to reach limiting values (close to the ϕ values of the rods in the bulk smectic phase). (3) Unexpected low-ϕ strings are found in regions with an intermediate height in the gaps. These behaviors of ϕ may be caused by thermal fluctuations of the strings. PMID:23876087

  10. The effect of low levels of dopants upon the formation and properties of beta-phase molybdenum nitride

    SciTech Connect

    Cairns, A.G.; Gallagher, J.G.; Hargreaves, J.S.J.; Mckay, D.; Rico, J.L.; Wilson, K.

    2010-03-15

    The addition of 1 wt% Pd, Au, Ni and Cu dopants has been demonstrated to strongly alter the morphology of beta-phase molybdenum nitride prepared by treatment of MoO{sub 3} with a 3/1 H{sub 2}/N{sub 2} mixture at 750 deg. C. Furthermore, the addition of Pd significantly enhances the surface area and the formation of the nitride phase. It is proposed that the facile formation of molybdenum bronzes in this system is important in this respect. The dopants have also been observed to modify the denitridation characteristics of the beta-phase, with an overall reduction of the proportion of NH{sub 3} formed upon using a 3/1 H{sub 2}/Ar mixture with respect to the undoped sample. - Graphical abstract: Low levels of Pd, Au, Ni and Cu dopant have significant effects upon the morphology, formation and dentitridation characteristics of beta-phase molybdenum nitride.

  11. A study of the formation and dynamics of the Earth's plasma sheet using ion composition data

    NASA Technical Reports Server (NTRS)

    Lennartsson, O. W.

    1994-01-01

    Over two years of data from the Lockheed Plasma Composition Experiment on the ISEE 1 spacecraft, covering ion energies between 100 eV/e and about 16 keV/e, have been analyzed in an attempt to extract new information about three geophysical issues: (1) solar wind penetration of the Earth's magnetic tail; (2) relationship between plasma sheet and tail lobe ion composition; and (3) possible effects of heavy terrestrial ions on plasma sheet stability.

  12. Differential mode of interaction of ThioflavinT with native β structural motif in human α 1-acid glycoprotein and cross beta sheet of its amyloid: Biophysical and molecular docking approach

    NASA Astrophysics Data System (ADS)

    Ajmal, Mohammad Rehan; Nusrat, Saima; Alam, Parvez; Zaidi, Nida; Badr, Gamal; Mahmoud, Mohamed H.; Rajpoot, Ravi Kant; Khan, Rizwan Hasan

    2016-08-01

    The present study details the interaction mechanism of Thioflavin T (ThT) to Human α1-acid glycoprotein (AAG) applying various spectroscopic and molecular docking methods. Fluorescence quenching data revealed the binding constant in the order of 104 M-1 and the standard Gibbs free energy change value, ΔG = -6.78 kcal mol-1 for the interaction between ThT and AAG indicating process is spontaneous. There is increase in absorbance of AAG upon the interaction of ThT that may be due to ground state complex formation between ThT and AAG. ThT impelled rise in β-sheet structure in AAG as observed from far-UV CD spectra while there are minimal changes in tertiary structure of the protein. DLS results suggested the reduction in AAG molecular size, ligand entry into the central binding pocket of AAG may have persuaded the molecular compaction in AAG. Isothermal titration calorimetric (ITC) results showed the interaction process to be endothermic with the values of standard enthalpy change ΔH0 = 4.11 kcal mol-1 and entropy change TΔS0 = 10.82 kcal.mol- 1. Moreover, docking results suggested hydrophobic interactions and hydrogen bonding played the important role in the binding process of ThT with F1S and A forms of AAG. ThT fluorescence emission at 485 nm was measured for properly folded native form and for thermally induced amyloid state of AAG. ThT fluorescence with native AAG was very low, while on the other hand with amyloid induced state of the protein AAG showed a positive emission peak at 485 nm upon the excitation at 440 nm, although it binds to native state as well. These results confirmed that ThT binding alone is not responsible for enhancement of ThT fluorescence but it also required beta stacked sheet structure found in protein amyloid to give proper signature signal for amyloid. This study gives the mechanistic insight into the differential interaction of ThT with beta structures found in native state of the proteins and amyloid forms, this study reinforce

  13. Crystal Structures of IAPP Amyloidogenic Segments Reveal a Novel Packing Motif of Out-of-Register Beta Sheets.

    PubMed

    Soriaga, Angela B; Sangwan, Smriti; Macdonald, Ramsay; Sawaya, Michael R; Eisenberg, David

    2016-07-01

    Structural studies of amyloidogenic segments by X-ray crystallography have revealed a novel packing motif, consisting of out-of-register β sheets, which may constitute one of the toxic species in aggregation related diseases. Here we sought to determine the presence of such a motif in islet amyloid polypeptide (IAPP), whose amyloidogenic properties are associated with type 2 diabetes. We determined four new crystal structures of segments within IAPP, all forming steric zippers. Most interestingly, one of the segments in the fibril core of IAPP forms an out-of-register steric zipper. Analysis of this structure reveals several commonalities with previously solved out-of-register fibrils. Our results provide additional evidence of out-of-register β sheets as a common structural motif in amyloid aggregates. PMID:26629790

  14. Diagnostics of basal conditions - the formation of extensive zones of surface ribs in ice-sheets and streams

    NASA Astrophysics Data System (ADS)

    Hindmarsh, Richard C. A.; Sergienko, Olga V.; Creyts, Timothy T.

    2015-04-01

    Most if not all current predictions of the evolution of ice-streams to changes induced by global change assume static basal conditions. This is a result of current restrictions in the remote sensing of the ice-sheet basal physical environment, which cannot resolve the small-scale phenomena believed to control the basal traction. The search therefore is on for observable structures or features that are the result of the operation of basal processes. Any successful theory of ice-sheet basal processes would need to be able to explain such phenomena associated with or caused by special properties of the basal environment. We present one class of these phenomena, and also present tentative hypotheses as to their formation. Using recent high-resolution observations of the Antarctic and Greenland ice sheets topography, the computed driving stress and the inferred basal traction reveal broad-scale organization in 5-20 km band-like patterns in both quantities. The similarity of patterns on the Greenland and Antarctic ice sheets suggests that the flow of ice sheets is controlled by the same fundamental processes operating at their base, which control ice sheet sliding and are highly variable on relatively short spatial and temporal scales. The formation mechanism for these bands contains information about the operation of the sub-glacial system. There are three possible, non-exclusive causes of these ribs which we examine from a theoretical and evidential point-of-view (i) They are the surface response to similar bands in the basal topography, whose regularity would equally require an explanation in terms of basal processes. (ii) They are translating surface waves in the ice, supported by membrane stress gradients rather than by gradients in the basal resistance. (iii) The ribs are due to the development of a band-like structure in the basal shear stress distribution that is the result of a pattern-forming instability in sub-glacial till and water flow, perhaps related to

  15. The formation of ice rises, their dynamics and role in the deglaciation of the Antarctic ice sheet

    NASA Astrophysics Data System (ADS)

    Favier, Lionel; Pattyn, Frank

    2015-04-01

    Numerous underwater mountains emerge from the edge of the continental shelf around the Antarctic ice sheet. During the last deglaciation, those features gave birth to ice rises, each being small scale copies of a continental ice sheet characterised by an ice divide and a local flow going outwards embedded within the fringing ice shelves. The well-known millenium-scale stability of ice rises can be strong indicators for the past deglaciation termination. However, the interpretation of physical measurements of an ice rise is not straightforward due to unknown past ice dynamics. Here, using the Bisicles ice-sheet model, we investigate for the first time the formation of an ice rise on top of an underwater mountain during the retreat of an ideal Antarctic-like ice sheet (i.e., including both grounded and floating ice flow). Prior to the retreat, the underwater mountain is barely detectable from the ice surface geometry and velocity. During the ice sheet retreat, induced by an increase of the sea level, an ice divide develops quickly above the underwater mountain. Within a short period of hundreds of years, the ice rise adopts a thousand years stability along with two main features: (i) a shifted upstream position of the ice rise compared to the mountain underneath and (ii) a geometrical asymmetry of the ice rise showing a gentle slope upstream and a steep slope downstream. We also investigate the influence of a non uniform surface mass balance on the migration of the ice divide. Our results provide additional ice dynamical constraints to facilitate numerical reconstructions of the last deglacial history in Antarctica as we demonstrate that ice rises are stable, but transient features of the ice shelf, stabilizing fast outlet flow. The timing of pinning and unpinning therefore becomes crucial in simulating the episodes of slow and fast grounding line retreat, respectively.

  16. Inhibition of bacterial cell wall-induced leukocyte recruitment and hepatic granuloma formation by TGF-beta gene transfer.

    PubMed

    Song, X; Zeng, L; Pilo, C M; Zagorski, J; Wahl, S M

    1999-10-01

    Intraperitoneal injection of streptococcal cell walls (SCW) into Lewis rats results in dissemination of SCW to the liver, spleen, bone marrow, and peripheral joints. The uptake of SCW by Kupffer cells in the liver initiates a chain of events largely mediated by T lymphocytes and macrophages. Local synthesis and secretion of cytokines and growth factors in response to the persistent SCW lead to the evolution and maintenance of a chronic T cell-dependent granulomatous response and result in granuloma formation and irreversible hepatic fibrosis. In an attempt to impede the development of the chronic granulomatous lesions in the liver, we injected a plasmid DNA encoding TGF-beta 1 i.m. to the SCW animals to determine the effect of TGF-beta 1 gene transfer on the course of liver inflammation and fibrosis. A single injection of plasmid DNA encoding TGF-beta 1 resulted in virtual abolition of the development of the SCW-induced hepatic granuloma formation and matrix expansion. TGF-beta 1 DNA not only reduced key proinflammatory cytokines including TNF-alpha, IL-1 beta, IFN-gamma, and IL-18, but also inhibited both CXC and CC chemokine production, thereby blocking inflammatory cell recruitment and accumulation in the liver. Moreover, TGF-beta 1 gene delivery inhibited its own expression in the liver tissue, which is otherwise up-regulated in SCW-injected animals. Our study suggests that TGF-beta 1 gene transfer suppresses hepatic granuloma formation by blocking the recruitment of inflammatory cells to the liver, and thus may provide a new approach to the control of hepatic granulomatous and fibrotic diseases. PMID:10491005

  17. Effects of Transforming Growth Factor Beta 1 in Cerebellar Development: Role in Synapse Formation

    PubMed Central

    Araujo, Ana P. B.; Diniz, Luan P.; Eller, Cristiane M.; de Matos, Beatriz G.; Martinez, Rodrigo; Gomes, Flávia C. A.

    2016-01-01

    Granule cells (GC) are the most numerous glutamatergic neurons in the cerebellar cortex and represent almost half of the neurons of the central nervous system. Despite recent advances, the mechanisms of how the glutamatergic synapses are formed in the cerebellum remain unclear. Among the TGF-β family, TGF-beta 1 (TGF-β1) has been described as a synaptogenic molecule in invertebrates and in the vertebrate peripheral nervous system. A recent paper from our group demonstrated that TGF-β1 increases the excitatory synapse formation in cortical neurons. Here, we investigated the role of TGF-β1 in glutamatergic cerebellar neurons. We showed that the expression profile of TGF-β1 and its receptor, TβRII, in the cerebellum is consistent with a role in synapse formation in vitro and in vivo. It is low in the early postnatal days (P1–P9), increases after postnatal day 12 (P12), and remains high until adulthood (P30). We also found that granule neurons express the TGF-β receptor mRNA and protein, suggesting that they may be responsive to the synaptogenic effect of TGF-β1. Treatment of granular cell cultures with TGF-β1 increased the number of glutamatergic excitatory synapses by 100%, as shown by immunocytochemistry assays for presynaptic (synaptophysin) and post-synaptic (PSD-95) proteins. This effect was dependent on TβRI activation because addition of a pharmacological inhibitor of TGF-β, SB-431542, impaired the formation of synapses between granular neurons. Together, these findings suggest that TGF-β1 has a specific key function in the cerebellum through regulation of excitatory synapse formation between granule neurons. PMID:27199658

  18. Study of Benzyl Salicylate/beta-Cyclodextrin Inclusion Complex Formation by Positron Annihilation

    NASA Astrophysics Data System (ADS)

    Bellitto, V. J.; Hsu Hadley, F. H., Jr.; Trinh, T.

    1996-11-01

    Results of positron annihilation lifetime spectra of beta-cyclodextrin and beta-cyclodextrin complexed with benzyl salicylate,benzyl acetate, or ethyl salicylate in air and vacuum were used to determine the fraction of beta-cyclodextrin which remains uncomplexed in the benzyl salicylate/beta-cyclodextrin 1:2 molar ratio inclusion complex. The intensity of the longest-lived component in vacuum was shown to decrease when the beta-cyclodextrin cavity was filled with benzyl salicylate, benzyl acetate, or ethyl salicylate guest molecules. Comparison of the intensity for beta-cyclodextrin, benzyl salicylate/beta-cyclodextrin 1:2 molar ratio, and 1:1 molar ratio indicated that the benzyl and salicylate moieties each formed an inclusion complex with a molecule of beta-cyclodextrin in the benzyl salicylate/beta-cyclodextrin 1:2 complex. It was determined that the benzyl moiety of the benzyl salicylate molecule is preferred by the beta-cyclodextrin "host" and that only 34of the salicylate moieties are complexed in the benzyl salicylate/beta-cyclodextrin 1:2 sample.

  19. Beta Cell Formation in vivo Through Cellular Networking, Integration and Processing (CNIP) in Wild Type Adult Mice.

    PubMed

    Doiron, Bruno; Hu, Wenchao; DeFronzo, Ralph A

    2016-01-01

    Insulin replacement therapy is essential in type 1 diabetic individuals and is required in ~40- 50% of type 2 diabetics during their lifetime. Prior attempts at beta cell regeneration have relied upon pancreatic injury to induce beta cell proliferation, dedifferentiation and activation of the embryonic pathway, or stem cell replacement. We report an alternative method to transform adult non-stem (somatic) cells into pancreatic beta cells. The Cellular Networking, Integration and Processing (CNIP) approach targets cellular mechanisms involved in pancreatic function in the organ's adult state and utilizes a synergistic mechanism that integrates three important levels of cellular regulation to induce beta cell formation: (i) glucose metabolism, (ii) membrane receptor function, and (iii) gene transcription. The aim of the present study was to induce pancreatic beta cell formation in vivo in adult animals without stem cells and without dedifferentiating cells to recapitulate the embryonic pathway as previously published (1-3). Our results employing CNIP demonstrate that: (i) insulin secreting cells can be generated in adult pancreatic tissue in vivo and circumvent the problem of generating endocrine (glucagon and somatostatin) cells that exert deleterious effects on glucose homeostasis, and (ii) longterm normalization of glucose tolerance and insulin secretion can be achieved in a wild type diabetic mouse model. The CNIP cocktail has the potential to be used as a preventative or therapeutic treatment or cure for both type 1 and type 2 diabetes. PMID:26696016

  20. Role of the von Hippel-Lindau tumor suppressor gene in the formation of beta1-integrin fibrillar adhesions.

    PubMed

    Esteban-Barragán, Miguel A; Avila, Pilar; Alvarez-Tejado, Miguel; Gutiérrez, M Dolores; García-Pardo, Angeles; Sánchez-Madrid, Francisco; Landázuri, Manuel O

    2002-05-15

    The von Hippel-Lindau tumor suppressor gene (VHL) is absent or inactivated in the VHLcancer syndrome and in most sporadic renal cancers. VHL is requiredfor the assembly of a proper extracellular fibronectin matrix, although the exact mechanism remains unknown. In this report, we demonstrate that 786-O renal cancer cells are unable to organize an adequate matrix even in the presence of an excess of exogenous fibronectin. Because the formation of integrin fibrillar adhesions plays a pivotal role in the organization of extracellular fibronectin, we next examined the expression and subcellular distribution of integrins in VHL- cells and their wild-type VHL stably transfected counterparts. The levels of beta1 and alphav integrins were increased in VHL- cells when compared with VHL+ transfectants. Early after plating, both VHL+ and VHL- cells were capable of assembling classic "patch-like" alphav focal contacts. As the culture advanced and cells became confluent, alphav integrins partly relocated to the intercellular junctions in VHL+ transfectants, which then developed large beta1 fibrillar-type adhesions and anchored firmly to the substrate. In contrast, confluent VHL- cells were unable to assemble beta1 fibrillar adhesions, and alphav focal contacts remained unchanged at all stages of the culture. Exogenous activation of beta1 integrins with either divalent cations or activating antibodies partly restored the capability of VHL- cells to assemble beta1 fibrillar adhesions and fibronectin fibers. Finally, pulse-chase studies of metabolically labeled 786-O cells revealed that the maturation of the common beta1-integrin chain was delayed in VHL- cells when compared with VHL+ cells. Our results show that VHL is an important regulator of integrins and is essential for the formation of beta1 fibrillar adhesions. These findings help to explain the abnormal extracellular matrix organization and increased motility of VHL- renal cancer cells. PMID:12019174

  1. Efficiently engineered cell sheet using a complex of polyethylenimine–alginate nanocomposites plus bone morphogenetic protein 2 gene to promote new bone formation

    PubMed Central

    Jin, Han; Zhang, Kai; Qiao, Chunyan; Yuan, Anliang; Li, Daowei; Zhao, Liang; Shi, Ce; Xu, Xiaowei; Ni, Shilei; Zheng, Changyu; Liu, Xiaohua; Yang, Bai; Sun, Hongchen

    2014-01-01

    Regeneration of large bone defects is a common clinical problem. Recently, stem cell sheet has been an emerging strategy in bone tissue engineering. To enhance the osteogenic potential of stem cell sheet, we fabricated bone morphogenetic protein 2 (BMP-2) gene-engineered cell sheet using a complex of polyethylenimine–alginate (PEI–al) nanocomposites plus human BMP-2 complementary(c)DNA plasmid, and studied its osteogenesis in vitro and in vivo. PEI–al nanocomposites carrying BMP-2 gene could efficiently transfect bone marrow mesenchymal stem cells. The cell sheet was made by culturing the cells in medium containing vitamin C for 10 days. Assays on the cell culture showed that the genetically engineered cells released the BMP-2 for at least 14 days. The expression of osteogenesis-related gene was increased, which demonstrated that released BMP-2 could effectively induce the cell sheet osteogenic differentiation in vitro. To further test the osteogenic potential of the cell sheet in vivo, enhanced green fluorescent protein or BMP-2-producing cell sheets were treated on the cranial bone defects. The results indicated that the BMP-2-producing cell sheet group was more efficient than other groups in promoting bone formation in the defect area. Our results suggested that PEI–al nanocomposites efficiently deliver the BMP-2 gene to bone marrow mesenchymal stem cells and that BMP-2 gene-engineered cell sheet is an effective way for promoting bone regeneration. PMID:24855355

  2. Observation of Depolarized ZnO(0001) Monolayers: Formation of Unreconstructed Planar Sheets

    SciTech Connect

    Tusche, C.; Meyerheim, H. L.; Kirschner, J.

    2007-07-13

    A novel nonpolar structure of 2 monolayer (ML) thick ZnO(0001) films grown on Ag(111) has been revealed, using surface x-ray diffraction and scanning tunneling microscopy. Zn and O atoms are arranged in planar sheets like in the hexagonal boron-nitride prototype structure. The observed depolarization is accompanied by a significant lateral 1.6% expansion of the lattice parameter and a 3% reduced Zn-O bond length within the sheets. The nonpolar structure stabilizes an atomically flat surface morphology unseen for ZnO surfaces thus far. The transition to the bulk wurtzite structure occurs in the 3-4 ML coverage range, connected to considerable roughening.

  3. Focal adhesion kinase (FAK) phosphorylation is not required for genistein-induced FAK-beta-1-integrin complex formation.

    PubMed

    Liu, Y; Kyle, E; Lieberman, R; Crowell, J; Kellof, G; Bergan, R C

    2000-01-01

    It has previously been shown that changes in the activity of focal adhesion kinase (FAK), and its binding to beta-1-integrin, accompany genistein-induced adhesion of prostate cells. Consumption of genistein world wide is associated with a lower incidence of metastatic prostate cancer. Early human clinical trials of genistein are under way to evaluate genistein's potential causal role in this regard. Though an important cell adhesion-associated signaling molecule, FAK's role in regulating prostate cell adhesion was not clear. Elucidation of this process would provide important information relating to both biology and potential clinical endpoints. It was hypothesized that FAK activation and complex formation are temporally related in prostate cells, and can thus be separated. Significant activation of FAK was demonstrated when cells adhered to fibronectin, as compared to poly-L-lysine, thus demonstrating that beta-1-integrin plays a significant role in activating FAK. Neither FAK activation, nor FAK-integrin complex formation, required beta-1-integrin ligand. However, disruption of the cellular cytoskeleton by cytochalasin D prevented FAK activation, but did not block genistein-induced complex formation. In the face of a disrupted cytoskeleton, signaling through FAK could not be restored through either integrin cross linking, or re-establishment of tensile forces via attachment to solid matrix. These studies demonstrate that FAK-beta-1-integrin complex formation does not require FAK activation, suggesting that it is an early event in prostate cell adhesion. An intact cytoskeleton is necessary for FAK activation. The functional importance of beta-1-integrin in prostate cells is demonstrated. Current findings support plans to test genistein in prostate cancer. PMID:11315093

  4. Formation and evolution of flapping and ballooning waves in magnetospheric plasma sheet

    NASA Astrophysics Data System (ADS)

    Ma, J. Z. G.; Hirose, A.

    2016-05-01

    By adopting Lembége & Pellat's 2D plasma-sheet model, we investigate the flankward flapping motion and Sunward ballooning propagation driven by an external source (e.g., magnetic reconnection) produced initially at the sheet center. Within the ideal MHD framework, we adopt the WKB approximation to obtain the Taylor-Goldstein equation of magnetic perturbations. Fourier spectral method and Runge-Kutta method are employed in numerical simulations, respectively, under the flapping and ballooning conditions. Studies expose that the magnetic shears in the sheet are responsible for the flapping waves, while the magnetic curvature and the plasma gradient are responsible for the ballooning waves. In addition, the flapping motion has three phases in its temporal development: fast damping phase, slow recovery phase, and quasi-stabilized phase; it is also characterized by two patterns in space: propagating wave pattern and standing wave pattern. Moreover, the ballooning modes are gradually damped toward the Earth, with a wavelength in a scale size of magnetic curvature or plasma inhomogeneity, only 1-7% of the flapping one; the envelops of the ballooning waves are similar to that of the observed bursty bulk flows moving toward the Earth.

  5. Folding into a beta-hairpin can prevent amyloid fibril formation.

    PubMed

    Hosia, Waltteri; Bark, Niklas; Liepinsh, Edvards; Tjernberg, Agneta; Persson, Bengt; Hallén, Dan; Thyberg, Johan; Johansson, Jan; Tjernberg, Lars

    2004-04-27

    The tetrapeptide KFFE is one of the shortest amyloid fibril-forming peptides described. Herein, we have investigated how the structural environment of this motif affects polymerization. Using a turn motif (YNGK) or a less rigid sequence (AAAK) to fuse two KFFE tetrapeptides, we show by several biophysical methods that the amyloidogenic properties are strongly dependent on the structural environment. The dodecapeptide KFFEAAAKKFFE forms abundant thick fibril bundles. Freshly dissolved KFFEAAAKKFFE is monomeric and shows mainly disordered secondary structure, as evidenced by circular dichroism, NMR spectroscopy, hydrogen/deuterium exchange measurements, and molecular modeling studies. In sharp contrast, the dodecapeptide KFFEYNGKKFFE does not form fibrils but folds into a stable beta-hairpin. This structure can oligomerize into a stable 12-mer and multiples thereof, as shown by size exclusion chromatography, sedimentation analysis, and electrospray mass spectrometry. These data indicate that the structural context in which a potential fibril forming sequence is present can prevent fibril formation by favoring self-limiting oligomerization over polymerization. PMID:15096033

  6. Formation of lobate debris aprons on Mars: Assessment of regional ice sheet collapse and debris-cover armoring

    NASA Astrophysics Data System (ADS)

    Fastook, James L.; Head, James W.; Marchant, David R.

    2014-01-01

    Lobate debris aprons (LDA) are lobate-shaped aprons surrounding scarps and isolated massifs that are concentrated in the vicinity of the northern Dichotomy Boundary on Mars. LDAs have been interpreted as (1) ice-cemented talus aprons undergoing viscous flow, (2) local debris-covered alpine-like glaciers, or (3) remnants of the collapse of a regional retreating ice sheet. We investigate the plausibility that LDAs are remnants of a more extensive regional ice sheet by modeling this process. We find that as a regional ice sheet collapses, the surface drops below cliff and massif bedrock margins, exposing bedrock and regolith, and initiating debris deposition on the surface of a cold-based glacier. Reduced sublimation due to debris-cover armoring of the proto-LDA surface produces a surface slope and consequent ice flow that carries the armoring debris away from the rock outcrops. As collapse and ice retreat continue the debris train eventually reaches the substrate surface at the front of the glacier, leaving the entire LDA armored by debris cover. Using a simplified ice flow model we are able to characterize the temperature and sublimation rate that would be necessary to produce LDAs with a wide range of specified lateral extents and thicknesses. We then apply this method to a database of documented LDA parameters (height, lateral extent) from the Dichotomy Boundary region, and assess the implications for predicted climate conditions during their formation and the range of formation times implied by the model. We find that for the population examined here, typical temperatures are in the range of -85 to -40 °C and typical sublimation rates lie in the range of 6-14 mm/a. Lobate debris apron formation times (from the point of bedrock exposure to complete debris cover) cluster near 400-500 ka. These results show that LDA length and thickness characteristics are consistent with climate conditions and a formation scenario typical of the collapse of a regional retreating

  7. Molecular cloning and characterization of beta-expansin gene related to root hair formation in barley.

    PubMed

    Kwasniewski, Miroslaw; Szarejko, Iwona

    2006-07-01

    Root hairs are specialized epidermal cells that play a role in the uptake of water and nutrients from the rhizosphere and serve as a site of interaction with soil microorganisms. The process of root hair formation is well characterized in Arabidopsis (Arabidopsis thaliana); however, there is a very little information about the genetic and molecular basis of root hair development in monocots. Here, we report on isolation and cloning of the beta-expansin (EXPB) gene HvEXPB1, tightly related to root hair initiation in barley (Hordeum vulgare). Using root transcriptome differentiation in the wild-type/root-hairless mutant system, a cDNA fragment present in roots of wild-type plants only was identified. After cloning of full-length cDNA and genomic sequences flanking the identified fragment, the subsequent bioinformatics analyses revealed homology of the protein coded by the identified gene to the EXPB family. Reverse transcription-PCR showed that expression of HvEXPB1 cosegregated with the root hair phenotype in F2 progeny of the cross between the hairless mutant rhl1.a and the wild-type Karat parent variety. Expression of the HvEXPB1 gene was root specific; it was expressed in roots of wild-type forms, but not in coleoptiles, leaves, tillers, and spikes. The identified gene was active in roots of two other analyzed root hair mutants: rhp1.a developing root hair primordia only and rhs1.a with very short root hairs. Contrary to this, a complete lack of HvEXPB1 expression was observed in roots of the spontaneous root-hairless mutant bald root barley. All these observations suggest a role of the HvEXPB1 gene in the process of root hair formation in barley. PMID:16679418

  8. Origin of life. Primordial genetics: Information transfer in a pre-RNA world based on self-replicating beta-sheet amyloid conformers.

    PubMed

    Maury, Carl Peter J

    2015-10-01

    The question of the origin of life on Earth can largely be reduced to the question of what was the first molecular replicator system that was able to replicate and evolve under the presumably very harsh conditions on the early Earth. It is unlikely that a functional RNA could have existed under such conditions and it is generally assumed that some other kind of information system preceded the RNA world. Here, I present an informational molecular system that is stable, self-replicative, environmentally responsive, and evolvable under conditions characterized by high temperatures, ultraviolet and cosmic radiation. This postulated pregenetic system is based on the amyloid fold, a functionally unique polypeptide fold characterized by a cross beta-sheet structure in which the beta strands are arranged perpendicular to the fiber axis. Beside an extraordinary structural robustness, the amyloid fold possesses a unique ability to transmit information by a three-dimensional templating mechanism. In amyloidogenesis short peptide monomers are added one by one to the growing end of the fiber. From the same monomeric subunits several structural variants of amyloid may be formed. Then, in a self-replicative mode, a specific amyloid conformer can act as a template and confer its spatially encoded information to daughter molecular entities in a repetitive way. In this process, the specific conformational information, the spatially changed organization, is transmitted; the coding element is the steric zipper structure, and recognition occurs by amino acid side chain complementarity. The amyloid information system fulfills several basic requirements of a primordial evolvable replicator system: (i) it is stable under the presumed primitive Earth conditions, (ii) the monomeric building blocks of the informational polymer can be formed from available prebiotic compounds, (iii) the system is self-assembling and self-replicative and (iv) it is adaptive to changes in the environment and

  9. Exogenous transforming growth factor-beta amplifies its own expression and induces scar formation in a model of human fetal skin repair.

    PubMed Central

    Lin, R Y; Sullivan, K M; Argenta, P A; Meuli, M; Lorenz, H P; Adzick, N S

    1995-01-01

    OBJECTIVE: Fetal skin wounds heal without scarring. To determine the role of TGF-beta 1 in fetal wound healing, mRNA expression of TGF-beta 1 was analyzed in human fetal and adult skin wounds. METHODS: Human fetal skin transplanted to a subcutaneous location on an adult athymic mouse that was subsequently wounded heals without scar, whereas human adult skin heals with scar formation in that location. In situ hybridization for TGF-beta 1 mRNA expression and species-specific immunohistochemistry for fibroblasts, macrophages, and neutrophils were performed in human adult wounds, fetal wounds, and fetal wounds treated with a TGF-beta 1 slow release disk. RESULTS: Transforming growth factor-beta 1 mRNA expression was induced by wounding adult skin. No TGF-beta 1 mRNA upregulation was detected in human fetal skin after wounding. However, when exogenous TGF-beta 1 was added to human fetal skin, induction of TGF-beta 1 mRNA expression in human fetal fibroblasts occurred, an adult-like inflammatory response was detected, and the skin healed with scar formation. CONCLUSIONS: Transforming growth factor-beta 1 is an important modulator in scar formation. Anti-TGF-beta 1 strategies may promote scarless healing in adult wounds. Images Figure 1. Figure 2. Figure 3. Figure 5. Figure 6. PMID:7639582

  10. Design study of the geometry of the blanking tool to predict the burr formation of Zircaloy-4 sheet

    SciTech Connect

    Ha, Jisun Lee, Hyungyil Kim, Dongchul Kim, Naksoo

    2013-12-16

    In this work, we investigated factors that influence burr formation for zircaloy-4 sheet used for spacer grids of nuclear fuel roads. Factors we considered are geometric factors of punch. We changed clearance and velocity in order to consider the failure parameters, and we changed shearing angle and corner radius of L-shaped punch in order to consider geometric factors of punch. First, we carried out blanking test with failure parameter of GTN model using L-shaped punch. The tendency of failure parameters and geometric factors that affect burr formation by analyzing sheared edges is investigated. Consequently, geometric factor's influencing on the burr formation is also high as failure parameters. Then, the sheared edges and burr formation with failure parameters and geometric factors is investigated using FE analysis model. As a result of analyzing sheared edges with the variables, we checked geometric factors more affect burr formation than failure parameters. To check the reliability of the FE model, the blanking force and the sheared edges obtained from experiments are compared with the computations considering heat transfer.

  11. The Growth of Magma Bodies by Amalgamation of Discrete Sheet Intrusions: Implications for the Formation of Magma Chambers

    NASA Astrophysics Data System (ADS)

    Annen, C.

    2007-12-01

    Until recently, igneous bodies (plutons and magma chambers) were commonly considered to be approximately spherical bodies, rapidly emplaced into the crust. However, field, structural, geophysical, and geochronological studies indicate that many plutons are low aspect-ratio tabular bodies (sills) that are formed by the amalgamation of successive discrete magma pulses. The thermal evolution of an igneous body that grows by accretion of thin magma sheets is fundamentally different from the evolution of a rapidly emplaced magma sphere or of a single thick magma sill. In thin sheet intrusions, the heat loss is through the walls of the sheets and the temperatures within the intrusions do not depend on the volumes injected but on the one-dimension sheets emplacement rate. The first sheets injected in a cold crust rapidly cool down and solidify. The ability of successive intrusions to stay at high temperature and eventually build up a long-lived magma chamber is controlled by the emplacement rate. Heat transfer modeling applied in the context of a volcanic arc shows that average emplacement rates of at least several centimeters per year and an incubation time of tens thousands of years are needed for a persistent magma chamber to form. During the incubation time, the intrusions solidify and when a chamber of high melt fraction magma eventually grows, the volume of eruptible magma only form a small part of the total intruded volume. The emplacement rate of plutons is controversial. Geochronological data suggest that some plutons may be emplaced over millions years. For a pluton that is assembled at a slow rate of a few millimeters per year, millions of years are needed, over which kilometric thicknesses are intruded, before a volume of magma larger than the size of a single intrusion becomes mobile and eruptible. In many cases, volcanic products may come from a deep source without being associated with a long-lived upper crust magma chamber. If volcanism is associated with

  12. Formation of sheet plumes, current coils, and helical magnetic fields in a spherical magnetohydrodynamic dynamo

    NASA Astrophysics Data System (ADS)

    Miyagoshi, Takehiro; Kageyama, Akira; Sato, Tetsuya

    2011-07-01

    Aiming at understanding of magnetic field generation process in rapidly rotating stars and planets represented by the Earth, computer simulations of magnetohydrodynamic (MHD) dynamo were performed in a rotating spherical shell geometry. Thermal convection and dynamo process with Ekman number of the order of 10-7 were studied. New structures of convection motion, dynamo-generated electrical current, and magnetic field are found. The flow is organized as a set of thin, sheet-like plumes. The current is made of small-scale coil structure with magnetic flux tubes within each of the coil. These flux tubes are connected each other to form a large scale helical magnetic field structure.

  13. Constraining the Late Pleistocene history of the Laurentide Ice Sheet by dating the Missinaibi Formation, Hudson Bay Lowlands, Canada

    NASA Astrophysics Data System (ADS)

    Dalton, April S.; Finkelstein, Sarah A.; Barnett, Peter J.; Forman, Steven L.

    2016-08-01

    Well-dated paleorecords from periods prior to the Last Glacial Maximum (LGM) are important for validating models of ice sheet build-up and growth. However, owing to glacial erosion, most Late Pleistocene records lie outside of the previously glaciated region, which limits their ability to inform about the dynamics of paleo-ice sheets. Here, we evaluate new and previously published chronology data from the Missinaibi Formation, a Pleistocene-aged deposit in the Hudson Bay Lowlands (HBL), Canada, located near the geographic center of the Laurentide Ice Sheet (LIS). Available radiocarbon (AMS = 44, conventional = 36), amino acid (n = 13), uranium-thorium (U-Th, n = 14), thermoluminescence (TL, n = 15) and optically stimulated luminescence (OSL, n = 5) data suggest that an ice-free HBL may have been possible during parts of Marine Isotope Stage 7 (MIS 7; ca. 243,000 to ca. 190,000 yr BP), MIS 5 (ca. 130,000 to ca. 71,000 yr BP) and MIS 3 (ca. 29,000 to ca. 57,000). While MIS 7 and MIS 5 are well-documented interglacial periods, the development of peat, forest bed and fluvial deposits dating to MIS 3 (n = 20 radiocarbon dates; 4 TL dates, 3 OSL dates), suggests that the LIS retreated and remained beyond, or somewhere within, the boundaries of the HBL during this interstadial. Ice sheet models approximate the margin of the LIS to Southern Ontario during this time, which is 700 km south of the HBL. Therefore, if correct, our data help constrain a significantly different configuration and dynamicity for the LIS than previously modelled. We can find no chronological basis to discount the MIS 3 age assignments. However, since most data originate from radiocarbon dates lying close to the reliable limit of this geochronometer, future work on dating the Missinaibi Formation using other geochronological methods (e.g. U-Th, OSL) is necessary in order to confirm the age estimates and strengthen the boundaries of the LIS during this period.

  14. Beta4 integrin-dependent formation of polarized three-dimensionalarchitecture confers resistance to apoptosis in normal and malignantmammary epithelium

    SciTech Connect

    Weaver, Valerie M.; Lelievre, Sophie; Lakins, Johnathon N.; Chrenek, Micah A.; Jones, Jonathan C.R.; Giancotti, Filippo; Werb, Zena; Bissell, Mina J.

    2002-08-27

    Tumor cells can evade chemotherapy by acquiring resistanceto apoptosis. We investigated the molecular mechanism whereby malignantand nonmalignant mammary epithelial cells become insensitive toapoptosis. We show that regardless of growth status formation ofpolarized, three-dimensional structures driven by basement membraneconfers protection to apoptosis in both nonmalignant and malignantmammary epithelial cells. By contrast, irrespective of their malignantstatus, nonpolarized structures are sensitive to induction of apoptosis.Resistance to apoptosis requires ligation of beta4 integrins, whichregulates tissue polarity, hemidesmosome formation and NFkB activation.Expression of beta4 integrin that lacks the hemidesmosome targetingdomain interferes with tissue polarity and NFkB activation and permitsapoptosis. These results indicate that integrin-induced polarity maydrive tumor cell resistance to apoptosis-inducing agents via effects onNFkB.

  15. Magnetic relaxation, current sheets, and structure formation in an extremely Tenuous fluid medium

    SciTech Connect

    Bajer, K.; Moffatt, H. K.

    2013-12-20

    The process of relaxation of a unidirectional magnetic field in a highly conducting tenuous fluid medium is considered. Null points of the field play a critical role in this process. During an initial stage of relaxation, variations in magnetic pressure are eliminated, and current sheets build up in the immediate neighborhood of null points. This initial phase is followed by a long diffusive phase of slow algebraic decay of the field, during which fluid is continuously sucked into the current sheets, leading to exponential growth of fluid density and concentration of mass around the null points, which show a tendency to cluster. Ultimately, this second phase of algebraic decay gives way to a final period of exponential decay of the field. The peaks of density at the null points survive as a fossil relic of the decay process. Numerical solution of the governing equations provides convincing confirmation of this three-stage scenario. Generalizations to two- and three-dimensional fields are briefly considered.

  16. Lactate adversely affects the in vitro formation of endothelial cell tubular structures through the action of TGF-{beta}1

    SciTech Connect

    Schmid, Stephan A. . E-mail: leoni.kunz-schughart@oncoray.de; Gaumann, Andreas; Wondrak, Marit; Eckermann, Christoph; Schulte, Stephanie; Mueller-Klieser, Wolfgang; Wheatley, Denys N.; Kunz-Schughart, Leoni A.

    2007-07-15

    When lactate accumulation in a tumor microenvironment reaches an average concentration of 10-20 mM, it tends to reflect a high degree of malignancy. However, the hypothesis that tumor-derived lactate has a number of partially adverse biological effects on malignant and tumor-associated host cells requires further evidence. The present study attempted to evaluate the impact of lactate on the process of angiogenesis, in particular on the formation of tubular structures. The endothelial cell (EC) network in desmoplastic breast tumors is primarily located in areas of reactive fibroblastic stroma. We employed a fibroblast-endothelial cell co-culture model as in vitro angiogenesis system normally producing florid in vitro tubule formation to analyze this situation. In contrast to previous studies, we found that lactate significantly reduces EC network formation in a dose-dependent manner as quantified by semi-automated morphometric analyses following immunohistochemical staining. The decrease in CD31-positive tubular structures and the number of intersections was independent of VEGF supplementation and became more pronounced in the presence of protons. The number of cells, primarily of the fibroblast population, was reduced but cell loss could not be attributed to a decrease in proliferative activity or pronounced apoptotic cell death. Treatment with 10 mM lactate was accompanied by enhanced mRNA expression and release of TGF-{beta}1, which also shows anti-angiogenic activity in the model. Both TGF-{beta}1 and lactate induced myofibroblastic differentiation adjacent to the EC tubular structures. The lactate response on the EC network was diminished by TGF-{beta}1 neutralization, indicating a causal relationship between lactate and TGF-{beta}1 in the finely tuned processes of vessel formation and maturation which may also occur in vivo within tumor tissue.

  17. Thymosin beta4 regulates cardiac valve formation via endothelial-mesenchymal transformation in zebrafish embryos.

    PubMed

    Shin, Sun-Hye; Lee, Sangkyu; Bae, Jong-Sup; Jee, Jun-Goo; Cha, Hee-Jae; Lee, You Mie

    2014-04-01

    Thymosin beta4 (TB4) has multiple functions in cellular response in processes as diverse as embryonic organ development and the pathogeneses of disease, especially those associated with cardiac coronary vessels. However, the specific roles played by TB4 during heart valve development in vertebrates are largely unknown. Here, we identified a novel function of TB4 in endothelialmesenchymal transformation (EMT) in cardiac valve endocardial cushions in zebrafish. The expressions of thymosin family members in developing zebrafish embryos were determined by whole mount in situ hybridization. Of the thymosin family members only zTB4 was expressed in the developing heart region. Cardiac valve development at 48 h post fertilization was defected in zebrafish TB4 (zTB4) morpholino-injected embryos (morphants). In zTB4 morphants, abnormal linear heart tube development was observed. The expressions of bone morphogenetic protein (BMP) 4, notch1b, and hyaluronic acid synthase (HAS) 2 genes were also markedly reduced in atrio-ventricular canal (AVC). Endocardial cells in the AVC region were stained with anti-Zn5 antibody reactive against Dm-grasp (an EMT marker) to observe EMT in developing cardiac valves in zTB4 morphants. EMT marker expression in valve endothelial cells was confirmed after transfection with TB4 siRNA in the presence of transforming growth factor β (TGFβ) by RT-PCR and immunofluorescent assay. Zn5-positive endocardial AVC cells were not observed in zTB4 morphants, and knockdown of TB4 suppressed TGF-β-induced EMT in ovine valve endothelial cells. Taken together, our results demonstrate that TB4 plays a pivotal role in cardiac valve formation by increasing EMT.1. PMID:24732964

  18. Formation of beta-methylmalate and its conversion to citramalate in Rhodospirillum rubrum.

    PubMed

    Osumi, T; Ebisuno, T; Nakano, H; Katsuki, H

    1975-10-01

    Using a cell-free extract of Rhodospirillum rubrum, studies were made of the condensation reaction between propionyl-CoA and glyoxylate. When [14C]propionate was incubated with the extract in the presence of glyoxylate, ATP, CoA, Mg2+, and Mn2+, radioactivity was incorporated into several compounds. Two of the main products were characterized as citramalate (CMA) and erythro-beta-methylmalate (erythro-MMA) on the basis of their behavior compared with authentic samples of CMA and erythro-MMA in the following three analyses: (i) paper chromatography using two solvent systems, (ii) radio-gas chromatography on their methyl esters, and (iii) chemical conversion to readily crystallizable derivatives, that is, citramalyl chloralide for CMA, and thymine for MMA. The CMA was thought to be of L(+)-form based on the results of optical resolution with brucine and also its susceptibility to L(+)-citramalate lyase of Clostridium tetanomorphum. When the reaction was carried out with lower concentrations of the enzyme, only MMA was accumulated. However, when the reaction was allowed to proceed further after addition of higher concentrations of the enzyme and of excess semicarbazide to prevent further condensation, the amount of accumulated MMA was decreased and CMA was formed instead. Furthermore, the time course of MMA and CMA formation exhibited a pattern typical of a precursor-product relationship. From these results, it was concluded that MMA was formed by alpha-condensation between propionyl-CoA and glyoxylate, and that CMA was derived from MMA, possibly from its CoA derivative. PMID:814116

  19. Morphological properties of tunnel valleys of the southern sector of the Laurentide Ice Sheet and implications for their formation

    NASA Astrophysics Data System (ADS)

    Livingstone, Stephen J.; Clark, Chris D.

    2016-07-01

    Tunnel valleys have been widely reported on the bed of former ice sheets and are considered an important expression of subglacial meltwater drainage. Although known to have been cut by erosive meltwater flow, the water source and development of channels has been widely debated; ranging between outburst flood events through to gradually occurring channel propagation. We have mapped and analysed the spatial pattern and morphometry of tunnel valleys and associated glacial landforms along the southern sector of the former Laurentide Ice Sheet from high-resolution digital elevation models. Around 2000 tunnel valleys have been mapped, revealing an organised pattern of sub-parallel, semi-regularly spaced valleys that form in distinctive clusters. The tunnel valleys are typically < 20 km long, and 0.5-3 km wide, although their width varies considerably down-valley. They preferentially terminate at moraines, which suggests that formation is time dependent; while we also observe some tunnel valleys that have grown headwards out of hill-hole pairs. Analysis of cross-cutting relationships between tunnel valleys, moraines and outwash fans permits reconstruction of channel development in relation to the retreating ice margin. This palaeo-drainage reconstruction demonstrates incremental growth of most valleys, with some used repeatedly or for long periods, during deglaciation, while others were abandoned shortly after their formation. Our data and interpretation support gradual (rather than a single-event) formation of most tunnel valleys with secondary contributions from flood drainage of subglacial and or supraglacially stored water down individual tunnel valleys. The distribution and morphology of tunnel valleys is shown to be sensitive to regional factors such as basal thermal regime, ice and bed topography, timing and climate.

  20. Formation of silicon hydride using hyperthermal negative hydrogen ions (H -) extracted from an argon-seeded hydrogen sheet plasma source

    NASA Astrophysics Data System (ADS)

    Fernandez, Marcedon S.; Blantocas, Gene Q.; Ramos, Henry J.

    2008-12-01

    An E × B probe (a modified Wien filter) is constructed to function both as a mass spectrometer and ion implanter. The device, given the acronym EXBII selects negative hydrogen ions (H -) from a premixed 10% argon-seeded hydrogen sheet plasma. With a vacuum background of 1.0 × 10 -6 Torr, H - extraction ensues at a total gas feed of 1.8 mTorr, 0.5 A plasma discharge. The EXBII is positioned 3 cm distance from the sheet core as this is the region densely populated by cold electrons ( Te ˜ 2 eV, Ne ˜ 3.4 × 10 11 cm -3) best suited for H - formation. The extracted H - ions of flux density ˜0.26 A/m 2 are segregated, accelerated to hyperthermal range (<100 eV) and subsequently deposited into a palladium-coated 1.1 × 1.1 cm 2, n-type Si (1 0 0) substrate held at the rear end of the EXBII, placed in lieu of its Faraday cup. The palladium membrane plays the role of a catalyst initiating the reaction between Si atoms and H - ions simultaneously capping the sample from oxidation and other undesirable adsorbents. AFM and FTIR characterization tests confirm the formation of SiH 2. Absorbance peaks between 900-970 cm -1 (bending modes) and 2050-2260 cm -1 (stretching modes) are observed in the FTIR spectra of the processed samples. It is found that varying hydrogen exposure time results in the shifting of wavenumbers which may be interpreted as changes in the frequencies of vibration for SiH 2. These are manifestations of chemical changes accompanying alterations in the force constant of the molecule. The sample with longer exposure time exhibits an additional peak at 2036 cm -1 which are hydrides of nano-crystalline silicon.

  1. β-sheet-like formation during the mechanical unfolding of prion protein.

    PubMed

    Tao, Weiwei; Yoon, Gwonchan; Cao, Penghui; Eom, Kilho; Park, Harold S

    2015-09-28

    Single molecule experiments and simulations have been widely used to characterize the unfolding and folding pathways of different proteins. However, with few exceptions, these tools have not been applied to study prion protein, PrP(C), whose misfolded form PrP(Sc) can induce a group of fatal neurodegenerative diseases. Here, we apply novel atomistic modeling based on potential energy surface exploration to study the constant force unfolding of human PrP at time scales inaccessible with standard molecular dynamics. We demonstrate for forces around 100 pN, prion forms a stable, three-stranded β-sheet-like intermediate configuration containing residues 155-214 with a lifetime exceeding hundreds of nanoseconds. A mutant without the disulfide bridge shows lower stability during the unfolding process but still forms the three-stranded structure. The simulations thus not only show the atomistic details of the mechanically induced structural conversion from the native α-helical structure to the β-rich-like form but also lend support to the structural theory that there is a core of the recombinant PrP amyloid, a misfolded form reported to induce transmissible disease, mapping to C-terminal residues ≈160-220. PMID:26429042

  2. β-sheet-like formation during the mechanical unfolding of prion protein

    NASA Astrophysics Data System (ADS)

    Tao, Weiwei; Yoon, Gwonchan; Cao, Penghui; Eom, Kilho; Park, Harold S.

    2015-09-01

    Single molecule experiments and simulations have been widely used to characterize the unfolding and folding pathways of different proteins. However, with few exceptions, these tools have not been applied to study prion protein, PrPC, whose misfolded form PrPSc can induce a group of fatal neurodegenerative diseases. Here, we apply novel atomistic modeling based on potential energy surface exploration to study the constant force unfolding of human PrP at time scales inaccessible with standard molecular dynamics. We demonstrate for forces around 100 pN, prion forms a stable, three-stranded β-sheet-like intermediate configuration containing residues 155-214 with a lifetime exceeding hundreds of nanoseconds. A mutant without the disulfide bridge shows lower stability during the unfolding process but still forms the three-stranded structure. The simulations thus not only show the atomistic details of the mechanically induced structural conversion from the native α-helical structure to the β-rich-like form but also lend support to the structural theory that there is a core of the recombinant PrP amyloid, a misfolded form reported to induce transmissible disease, mapping to C-terminal residues ≈160-220.

  3. β-sheet-like formation during the mechanical unfolding of prion protein

    SciTech Connect

    Tao, Weiwei; Cao, Penghui; Park, Harold S.; Yoon, Gwonchan; Eom, Kilho

    2015-09-28

    Single molecule experiments and simulations have been widely used to characterize the unfolding and folding pathways of different proteins. However, with few exceptions, these tools have not been applied to study prion protein, PrP{sup C}, whose misfolded form PrP{sup Sc} can induce a group of fatal neurodegenerative diseases. Here, we apply novel atomistic modeling based on potential energy surface exploration to study the constant force unfolding of human PrP at time scales inaccessible with standard molecular dynamics. We demonstrate for forces around 100 pN, prion forms a stable, three-stranded β-sheet-like intermediate configuration containing residues 155-214 with a lifetime exceeding hundreds of nanoseconds. A mutant without the disulfide bridge shows lower stability during the unfolding process but still forms the three-stranded structure. The simulations thus not only show the atomistic details of the mechanically induced structural conversion from the native α-helical structure to the β-rich-like form but also lend support to the structural theory that there is a core of the recombinant PrP amyloid, a misfolded form reported to induce transmissible disease, mapping to C-terminal residues ≈160-220.

  4. Investigating beta-hydroxyenduracididine formation in the biosynthesis of the mannopeptimycins.

    PubMed

    Haltli, Brad; Tan, Ying; Magarvey, Nathan A; Wagenaar, Melissa; Yin, Xihou; Greenstein, Michael; Hucul, John A; Zabriskie, T Mark

    2005-11-01

    The mannopeptimycins (MPPs) are potent glycopeptide antibiotics that contain both D and L forms of the unique, arginine-derived amino acid beta-hydroxyenduracididine (betahEnd). The product of the mppO gene in the MPP biosynthetic cluster resembles several non-heme iron, alpha-ketoglutarate-dependent oxygenases, such as VioC and clavaminate synthase. The role of MppO in betahEnd biosynthesis was confirmed through inactivation of mppO, which yielded a strain that produced dideoxy-MPPs, indicating that mppO is essential for generating the beta-hydroxy functionality for both betahEnd residues. Characterization in vitro of recombinant His6-MppO expressed in E. coli revealed that MppO selectively hydroxylates the beta carbon of free L-enduracididine. PMID:16298295

  5. Inhibition of amyloid fibril formation of human amylin by N-alkylated amino acid and alpha-hydroxy acid residue containing peptides.

    PubMed

    Rijkers, Dirk T S; Höppener, Jo W M; Posthuma, George; Lips, Cornelis J M; Liskamp, Rob M J

    2002-09-16

    Amyloid deposits are formed as a result of uncontrolled aggregation of (poly)peptides or proteins. Today several diseases are known, for example Alzheimer's disease, Creutzfeldt-Jakob disease, mad cow disease, in which amyloid formation is involved. Amyloid fibrils are large aggregates of beta-pleated sheets and here a general method is described to introduce molecular mutations in order to achieve disruption of beta-sheet formation. Eight backbone-modified amylin derivatives, an amyloidogenic peptide involved in maturity onset diabetes, were synthesized. Their beta-sheet forming properties were studied by IR spectroscopy and electron microscopy. Modification of a crucial amide NH by an alkyl chain led to a complete loss of the beta-sheet forming capacity of amylin. The resulting molecular mutated amylin derivative could be used to break the beta-sheet thus retarding beta-sheet formation of unmodified amylin. Moreover, it was found that the replacement of this amide bond by an ester moiety suppressed fibrillogenesis significantly. Introduction of N-alkylated amino acids and/or ester functionalities-leading to depsipeptides-into amyloidogenic peptides opens new avenues towards novel peptidic beta-sheet breakers for inhibition of beta-amyloid aggregation. PMID:12298020

  6. Systemic administration of transforming growth factor-beta 2 prevents the impaired bone formation and osteopenia induced by unloading in rats.

    PubMed Central

    Machwate, M; Zerath, E; Holy, X; Hott, M; Godet, D; Lomri, A; Marie, P J

    1995-01-01

    We investigated the effect of recombinant human transforming growth factor beta 2 (rhTGF-beta 2) administration on trabecular bone loss induced by unloading in rats. Hind limb suspension for 14 d inhibited bone formation and induced osteopenia as shown by decreased bone volume, calcium and protein contents in long bone metaphysis. Systemic infusion of rhTFG-beta 2 (2 micrograms/kg per day) maintained normal bone formation rate, and prevented the decrease in bone volume, bone mineral content, trabecular thickness and number induced by unloading. In vitro analysis of tibial marrow stromal cells showed that rhTGF-beta 2 infusion in unloaded rats increased the proliferation of osteoblast precursor cells, but did not affect alkaline phosphatase activity or osteocalcin production. Northern blot analysis of RNA extracted from the femoral metaphysis showed that rhTGF-beta 2 infusion in unloaded rats increased steady-state levels of type I collagen mRNA but not alkaline phosphatase mRNA levels. rhTGF-beta 2 infusion at the dose used had no effect on metaphyseal bone volume and formation, osteoblast proliferation or collagen expression in control rats. The results show that systemic administration of rhTGF-beta 2 enhances osteoblast precursor cell proliferation and type I collagen expression by osteoblasts, and prevents the impaired bone formation and osteopenia induced by unloading. Images PMID:7657798

  7. Separation of drug stereoisomers by the formation of. beta. -cyclodextrin inclusion complexes

    SciTech Connect

    Armstrong, D.W.; Ward, T.J.; Armstrong, R.D.; Beesley, T.E.

    1986-05-30

    For many drugs, only racemic mixtures are available for clinical use. Because different stereoisomers of drugs often cause different physiological responses, the use of pure isomers could elicit more exact therapeutic effects. Differential complexation of a variety of drug stereoisomers by immobilized ..beta..-cyclodextrin was investigated. Chiral recognition and racemic resolution were observed with a number of compounds from such clinically useful classes as ..beta..-blockers, calcium-channel blockers, sedative hypnotics, antihistamines, anticonvulsants, diuretics, and synthetic opiates. Separation of the diastereomers of the cardioactive and antimalarial cinchona alkaloids and of two antiestrogens was demonstrated as well. Three dimensional projections of ..beta..-cyclodextrin complexes of propanol, which is resolved by this technique, and warfarin, which is not, are compared. These studies have improved the understanding and application of the chiral interactions of ..beta..-cyclodextrin, and they have demonstrated a means to measure optical purity and to isolate or produce pure enantiomers of drugs. In addition, this highly specific technique could also be used in the pharmacological evaluation of enantiometric drugs. 27 references, 3 figures, 2 tables.

  8. Unfolding Simulations of Holomyoglobin from Four Mammals: Identification of Intermediates and β-Sheet Formation from Partially Unfolded States

    PubMed Central

    Dasmeh, Pouria; Kepp, Kasper P.

    2013-01-01

    Myoglobin (Mb) is a centrally important, widely studied mammalian protein. While much work has investigated multi-step unfolding of apoMb using acid or denaturant, holomyoglobin unfolding is poorly understood despite its biological relevance. We present here the first systematic unfolding simulations of holoMb and the first comparative study of unfolding of protein orthologs from different species (sperm whale, pig, horse, and harbor seal). We also provide new interpretations of experimental mean molecular ellipticities of myoglobin intermediates, notably correcting for random coil and number of helices in intermediates. The simulated holoproteins at 310 K displayed structures and dynamics in agreement with crystal structures (Rg ∼1.48–1.51 nm, helicity ∼75%). At 400 K, heme was not lost, but some helix loss was observed in pig and horse, suggesting that these helices are less stable in terrestrial species. At 500 K, heme was lost within 1.0–3.7 ns. All four proteins displayed exponentially decaying helix structure within 20 ns. The C- and F-helices were lost quickly in all cases. Heme delayed helix loss, and sperm whale myoglobin exhibited highest retention of heme and D/E helices. Persistence of conformation (RMSD), secondary structure, and ellipticity between 2–11 ns was interpreted as intermediates of holoMb unfolding in all four species. The intermediates resemble those of apoMb notably in A and H helices, but differ substantially in the D-, E- and F-helices, which interact with heme. The identified mechanisms cast light on the role of metal/cofactor in poorly understood holoMb unfolding. We also observed β-sheet formation of several myoglobins at 500 K as seen experimentally, occurring after disruption of helices to a partially unfolded, globally disordered state; heme reduced this tendency and sperm-whale did not display any sheet propensity during the simulations. PMID:24386077

  9. In vitro inhibition of beta-haematin formation, DNA interactions, antiplasmodial activity, and cytotoxicity of synthetic neocryptolepine derivatives.

    PubMed

    Van Miert, Sabine; Jonckers, Tim; Cimanga, Kanyanga; Maes, Louis; Maes, Bert; Lemière, Guy; Dommisse, Roger; Vlietinck, Arnold; Pieters, Luc

    2004-01-01

    Neocryptolepine, a minor alkaloid of Cryptolepis sanguinolenta, was investigated as a lead for new antiplasmodial agents, because of its lower cytotoxicity than cryptolepine, the major alkaloid. Synthetic 2- or 3-substituted neocryptolepine derivatives were evaluated for their biological activity. In addition to the antiplasmodial activity (Plasmodium falciparum chloroquine-sensitive and -resistant) also the cytotoxicity (MRC-5 cells) was determined. Several compounds such as 2-bromoneocryptolepine showing higher and more selective antiplasmodial activity than neocryptolepine were obtained. Several functional assays and in vitro tests were used to obtain additional information on the mechanism of action, i.e., the beta-haematin formation inhibitory assay (detoxification of haem) and the DNA-methylgreen displacement assay (interaction with DNA). It could be demonstrated that the 2- or 3-substituted neocryptolepine derivatives investigated here have about the same potency to inhibit the beta-haematin formation as chloroquine, indicating that inhibition of haemozoin formation makes at least an important contribution to their antiplasmodial activity, although their in vitro antiplasmodial activity is still less than chloroquine. PMID:15582513

  10. Reactions of OOH radical with beta-carotene, lycopene, and torulene: hydrogen atom transfer and adduct formation mechanisms.

    PubMed

    Galano, Annia; Francisco-Marquez, Misaela

    2009-08-13

    The relative free radical scavenging activity of beta-carotene, lycopene, and torulene toward OOH radicals has been studied using density functional theory. Hydrogen atom transfer (HAT) and radical adduct formation (RAF) mechanisms have been considered. All the possible reaction sites have been included in the modeling, and detailed branching ratios are reported for the first time. The reactions of hydrocarbon carotenoids (Car) with peroxyl radicals, in both polar and nonpolar environments, are predicted to proceed via RAF mechanism, with contributions higher than 98% to the overall OOH + Car reactions. Lycopene and torulene were found to be more reactive than beta-carotene. In nonpolar environments the reactivity of the studied carotenoids toward peroxyl radical follows the trend LYC > TOR > BC, whereas in aqueous solutions it is TOR > LYC > BC. OOH adducts are predicted to be formed mainly at the terminal sites of the conjugated polyene chains. The main addition sites were found to be C5 for beta-carotene and lycopene and C30 for torulene. The general agreement between the calculated magnitudes and the available experimental data supports the predictions from this work. PMID:19627101

  11. Non-linear Tearing and Flux rope Formation in 3D Null Current Sheets

    NASA Astrophysics Data System (ADS)

    Wyper, P. F.; Pontin, D. I.

    2014-12-01

    The manner in which small scale structure affects the large scale reconnection process in realistic 3D geometries is still an unsolved problem. With the increase in computational resources and improvements in satellite instrumentation, signatures of flux ropes or "plasmoids" are now observed with increasing regularity, yet their formation and dynamics are poorly understood. It has been demonstrated that even at MHD scales, in 2D rapid non-linear tearing of Sweet-Parker-like layers forms multiple magnetic islands ("plasmoids") and allows the reconnection rate to become almost independent of the Lundquist number (the "plasmoid instability"). This work presents some of our recent theoretical work focussing on an analogous instability in a fully 3D geometry. Using results from a series of 3D high resolution MHD simulations, the formation and evolution of fully three dimensional "flux rope" structures following the 3D plasmoid instability will be presented, and their effects on the manner of the reconnection process as a whole discussed.

  12. Interdendritic Strain and Macrosegregation-Coupled Phenomena for Interdendritic Crack Formation in Direct-Chill Cast Sheet Ingots

    NASA Astrophysics Data System (ADS)

    EL-Bealy, Mostafa Omar

    2012-06-01

    In a study of the early stages of dendritic solidification in the direct-chill cast sheet ingots, the coupled effect of interdendritic strain and macrosegregation on the interdendritic cracks formation in dendritic equiaxed structure has been investigated by the metallographic study of ingot samples and by performing a set of mathematical analyses for AA-6061 and AA-1050 aluminum alloys. The metallographic investigation contains microstructure examinations and macrosegregation measurements of collected samples from plant trials. The mathematical analysis consists of a two-dimensional (2-D) fluid flow, heat flow, interdendritic strain, and macrosegregation-coupled model. Also, a simple approach to measure interdendritic crack has been developed based on the accumulative interdendritic strain criterion, local dendritic phases, and the crystal distortion correlation factor resulting from steep positive local segregation. The model predications have clarified the effect of high positive macrosegregation on the surface and subsurface interdendritic crack formation. It has been revealed that interdendritic strain starts to generate just below the liquidus temperature, resulting from shrinkage of liquid→solid phase transformation and contraction of dendritic solid in the incoherent mushy region. In this region, the coupled effect of the shrinkage/contraction mechanism increases the interdendritic distances between equiaxed crystals and the interdendritic crack begins to nucleate. Subsequently, in the coherent mushy region, the different interdendritic strain sources start to affect significantly the distances between equiaxed crystals in a diverse way, and therefore, the final morphology of interdendritic crack begins to form. The mechanism of interdendritic crack formation during dendritic equiaxed structure solidification and the possible solutions to this problem are discussed.

  13. Synthetic peptides corresponding to human follicle-stimulating hormone (hFSH)-beta-(1-15) and hFSH-beta-(51-65) induce uptake of 45Ca++ by liposomes: evidence for calcium-conducting transmembrane channel formation

    SciTech Connect

    Grasso, P.; Santa-Coloma, T.A.; Reichert, L.E. Jr. )

    1991-06-01

    We have previously described FSH receptor-mediated influx of 45Ca++ in cultured Sertoli cells from immature rats and receptor-enriched proteoliposomes via activation of voltage-sensitive and voltage-independent calcium channels. We have further shown that this effect of FSH does not require cholera toxin- or pertussis toxin-sensitive guanine nucleotide binding protein or activation of adenylate cyclase. In the present study, we have identified regions of human FSH-beta-subunit which appear to be involved in mediating calcium influx. We screened 11 overlapping peptide amides representing the entire primary structure of hFSH-beta-subunit for their effects on 45Ca++ flux in FSH receptor-enriched proteoliposomes. hFSH-beta-(1-15) and hFSH-beta-(51-65) induced uptake of 45Ca++ in a concentration-related manner. This effect of hFSH-beta-(1-15) and hFSH-beta-(51-65) was also observed in liposomes lacking incorporated FSH receptor. Reducing membrane fluidity by incubating liposomes (containing no receptor) with hFSH-beta-(1-15) or hFSH-beta-(51-65) at temperatures lower than the transition temperatures of their constituent phospholipids resulted in no significant (P greater than 0.05) difference in 45Ca++ uptake. The effectiveness of the calcium ionophore A23187, however, was abolished. Ruthenium red, a voltage-independent calcium channel antagonist, was able to completely block uptake of 45Ca++ induced by hFSH-beta-(1-15) and hFSH-beta-(51-65) whereas nifedipine, a calcium channel blocker specific for L-type voltage-sensitive calcium channels, was without effect. These results suggest that in addition to its effect on voltage-sensitive calcium channel activity, interaction of FSH with its receptor may induce formation of transmembrane aqueous channels which also facilitate influx of extracellular calcium.

  14. Effects of the Formation of Al x Cu y Gradient Interfaces on Mechanical Property of Steel/Al Laminated Sheets by Introducing Cu Binding-Sheets

    NASA Astrophysics Data System (ADS)

    Wei, Aili; Liu, Xinghai; Shi, Quanxin; Liang, Wei

    2015-07-01

    Steel/Cu/Al laminated sheets were fabricated by two-pass hot rolling to improve the mechanical properties of steel/Al sheets. The bonding properties and deformability of the steel/Cu/Al sheets were studied. Steel/Al and steel/Cu/Al samples were rolled at 350°C for 15 min with the first-pass reduction of 40%, and then heated at 600°C for 5 min with different reductions. It was found that the steel/Cu/Al samples rolled by the second-pass reduction of 85% could endure the maximum 90° bend cycle times of 45, exhibiting excellent fatigue resistance as well as deformability. The steel/Al samples could only reach the maximum 90° bend cycle times of 20. Furthermore, the scanning electron microscope, energy-dispersive spectrometer, and electron backscattered diffraction results showed that the preferred growth orientations of Cu, Al4Cu9, and Al2Cu on the steel/Cu/Al laminated sheets are {-1, 1, 2} <1, -1, 1>, {1, 0, 0} <0, 1, 0> and {-1, 1, 2} <1, -1, 1> {1, 1, 0} <0, 0, 1>. The orientation relationships between Cu and Al2Cu are {1, 1, 0}(fcc)//{1, 1, 0}(bct) and {1, 1, 1}(fcc)//{1, 1, 1}(bct). The improved bonding property and excellent fatigue resistance as well as deformability were mainly ascribed to the tight combination and consistent deformability across steel, Al, and the transition layers (Cu, Al4Cu9, and Al2Cu).

  15. Film formation and paper coating with poly ([beta]-hydroxyalkanoate), a biodegradable latex

    SciTech Connect

    Lauzier, C.A.; Monasterios, C.J.; Saracovan, I.; Marchessault, R.H. ); Ramsay, B.A. )

    1993-05-01

    An aqueous latex of a poly ([beta]-hydroxyalkanoate) (PHA) coated on paper imparted water imperviousness without changing mechanical properties. Hot-pressed films biodegraded faster than solvent cast films. The PHA coating on paper degraded totally in activated sludge within 12 days, leaving the cellulose matrix relatively untouched. Blends of PHA latexes with sodium carboxymethl cellulose, polystyrene latex, carboxylated styrenel butadiene latex, natural rubber latex, carboxylated styrenel butadiene latex; natural rubber latex, and starch powders form satisfactory films at room temperature.

  16. Spontaneous Formation of Oligomers and Fibrils in Large-Scale Molecular Dynamics Simulations of A-beta Peptides

    NASA Astrophysics Data System (ADS)

    Hall, Carol

    2013-03-01

    Protein aggregation is associated with serious and eventually-fatal neurodegenerative diseases including Alzheimer's and Parkinson's. While atomic resolution molecular dynamics simulations have been useful in this regard, they are limited to examination of either oligomer formation by a small number of peptides or analysis of the stability of a moderate number of peptides placed in trial or known experimental structures. We describe large scale intermediate-resolution molecular dynamics simulations of the spontaneous formation of fibrils by systems containing large numbers (48) of peptides including A-beta (16-22), and A-beta (17-42) peptides. We trace out the aggregation process from an initial configuration of random coils to proto-filaments with cross- β structures and demonstrate how kinetics dictates the structural details of the fully formed fibril. Fibrillization kinetics depends strongly on the temperature. Nucleation and templated growth via monomer addition occur at and near a transition temperature above which fibrils are unlikely to form. Oligomeric merging and structural rearrangement are observed at lower temperatures. In collaboration with Mookyung Cheon, Iksoo Chang, Pusan University; and David Latshaw, North Carolina State University.

  17. Driving Cartilage Formation in High-Density Human Adipose-Derived Stem Cell Aggregate and Sheet Constructs Without Exogenous Growth Factor Delivery

    PubMed Central

    Dang, Phuong N.; Solorio, Loran D.

    2014-01-01

    An attractive cell source for cartilage tissue engineering, human adipose-derived stem cells (hASCs) can be easily expanded and signaled to differentiate into chondrocytes. This study explores the influence of growth factor distribution and release kinetics on cartilage formation within 3D hASC constructs incorporated with transforming growth factor-β1 (TGF-β1)-loaded gelatin microspheres. The amounts of microspheres, TGF-β1 concentration, and polymer degradation rate were varied within hASC aggregates. Microsphere and TGF-β1 loading concentrations were identified that resulted in glycosaminoglycan (GAG) production comparable to those of control aggregates cultured in TGF-β1-containing medium. Self-assembling hASC sheets were then engineered for the production of larger, more clinically relevant constructs. Chondrogenesis was observed in hASC-only sheets cultured with exogenous TGF-β1 at 3 weeks. Importantly, sheets with incorporated TGF-β1-loaded microspheres achieved GAG production similar to sheets treated with exogenous TGF-β1. Cartilage formation was confirmed histologically via observation of cartilage-like morphology and GAG staining. This is the first demonstration of the self-assembly of hASCs into high-density cell sheets capable of forming cartilage in the presence of exogenous TGF-β1 or with TGF-β1-releasing microspheres. Microsphere incorporation may bypass the need for extended in vitro culture, potentially enabling hASC sheets to be implanted more rapidly into defects to regenerate cartilage in vivo. PMID:24873753

  18. Formation of alpha and beta tantalum at the variation of magnetron sputtering conditions

    NASA Astrophysics Data System (ADS)

    Nasakina, E. O.; Sevostyanov, M. A.; Mikhaylova, A. B.; Baikin, A. S.; Sergienko, K. V.; Leonov, A. V.; Kolmakov, A. G.

    2016-02-01

    Nano- and microdimensional surface layers of α and β tantalum on flat NiTi, Ti, glass, etc. substrates were created. Structure and composition of samples were defined by SEM, AES and x-ray diffractometry. With increase in deposition time surface layer thickness not linearly increases. The transitional layer provide high adhesion of a surface layer to a substrate. Irrespective of summary sputtering time the β phase is formed in the beginning and at sputtering time more than 20 min on it α tantalum is deposited, while temperature remains below 150°C. Keywords: composite materials, surface layer, tantalum, alpha and beta phase, nitinol, corrosion resistance.

  19. The cognitive effects of trauma: reversal of alpha function and the formation of a beta screen.

    PubMed

    Brown, Lawrence J

    2005-04-01

    Following a brief review of Freud's writings on trauma, the author discusses relevant theories of Bion, and in particular the concepts of the alpha function and the beta screen. A clinical example is presented in which the patient's relatively recent trauma in adulthood had become fused with prior related experiences, leading to a propensity for repeated enactments in analysis and a failure to learn from experience. Drawing on the analyst's alpha function, the patient was gradually able to use mentalization to transform her rigidly structured traumatic organization. The author highlights the roles of dreams/dream associations and of screen memories in the patient's analysis. PMID:15889686

  20. Formation of deglycosylated alpha-L-fucosidase by endo-beta-N-acetylglucosaminidase in Fusarium oxysporum.

    PubMed Central

    Tsuji, Y; Yamamoto, K; Tochikura, T

    1990-01-01

    Two forms of alpha-L-fucosidase, deglycosylated and glycosylated, were found in the fucose-inducing culture broth of Fusarium oxysporum. Endo-beta-N-acetylglucosaminidase was also found in the same culture broth. The deglycosylated alpha-L-fucosidase was purified from the culture broth to homogeneity on polyacrylamide disc gel electrophoresis and analytical ultracentrifugation. Purified deglycosylated alpha-L-fucosidase was compared in chemical composition and immunological homology with glycosylated alpha-L-fucosidase which had been reported previously (K. Yamamoto, Y. Tsuji, H. Kumagai, and T. Tochikura, Agric. Biol. Chem. 50: 1689, 1986). Both enzymes had nearly the same amino acid compositions and were immunologically identical. Glycosylated alpha-L-fucosidase had mannose, galactose, and N-acetylglucosamine residues. In contrast, the deglycosylated enzyme had only N-acetylglucosamine residues. These results suggest that the deglycosylated alpha-L-fucosidase is formed by the release of sugar chains from the glycosylated form by Fusarium endo-beta-N-acetylglucosaminidase. Furthermore, various enzymatic properties were compared: the two alpha-L-fucosidases were found to exhibit similar catalytic activities and thermal stability profiles. The deglycosylated enzyme, however, was slightly unstable in the acidic pH range compared with the glycosylated enzyme. Images PMID:2111117

  1. Astrocyte transforming growth factor beta 1 promotes inhibitory synapse formation via CaM kinase II signaling.

    PubMed

    Diniz, Luan Pereira; Tortelli, Vanessa; Garcia, Matheus Nunes; Araújo, Ana Paula Bérgamo; Melo, Helen M; Silva, Gisele S Seixas da; Felice, Fernanda G De; Alves-Leon, Soniza Vieira; Souza, Jorge Marcondes de; Romão, Luciana Ferreira; Castro, Newton Gonçalves; Gomes, Flávia Carvalho Alcantara

    2014-12-01

    The balance between excitatory and inhibitory synaptic inputs is critical for the control of brain function. Astrocytes play important role in the development and maintenance of neuronal circuitry. Whereas astrocytes-derived molecules involved in excitatory synapses are recognized, molecules and molecular mechanisms underlying astrocyte-induced inhibitory synapses remain unknown. Here, we identified transforming growth factor beta 1 (TGF-β1), derived from human and murine astrocytes, as regulator of inhibitory synapse in vitro and in vivo. Conditioned media derived from human and murine astrocytes induce inhibitory synapse formation in cerebral cortex neurons, an event inhibited by pharmacologic and genetic manipulation of the TGF-β pathway. TGF-β1-induction of inhibitory synapse depends on glutamatergic activity and activation of CaM kinase II, which thus induces localization and cluster formation of the synaptic adhesion protein, Neuroligin 2, in inhibitory postsynaptic terminals. Additionally, intraventricular injection of TGF-β1 enhanced inhibitory synapse number in the cerebral cortex. Our results identify TGF-β1/CaMKII pathway as a novel molecular mechanism underlying astrocyte control of inhibitory synapse formation. We propose here that the balance between excitatory and inhibitory inputs might be provided by astrocyte signals, at least partly achieved via TGF-β1 downstream pathways. Our work contributes to the understanding of the GABAergic synapse formation and may be of relevance to further the current knowledge on the mechanisms underlying the development of various neurological disorders, which commonly involve impairment of inhibitory synapse transmission. PMID:25042347

  2. Inhibition of beta-amyloid aggregation by fluorescent dye labels

    NASA Astrophysics Data System (ADS)

    Amaro, Mariana; Wellbrock, Thorben; Birch, David J. S.; Rolinski, Olaf J.

    2014-02-01

    The fluorescence decay of beta-amyloid's (Aβ) intrinsic fluorophore tyrosine has been used for sensing the oligomer formation of dye-labelled Aβ monomers and the results compared with previously studied oligomerization of the non-labelled Aβ peptides. It has been demonstrated that two different sized, covalently bound probes 7-diethylaminocoumarin-3-carbonyl and Hilyte Fluor 488 (HLF), alter the rate and character of oligomerization to different extents. The ability of HLF to inhibit formation of highly ordered structures containing beta-sheets was also shown. The implications of our findings for using fluorescence methods in amyloidosis research are discussed and the advantages of this auto-fluorescence approach highlighted.

  3. Inhibition of beta-amyloid aggregation by fluorescent dye labels

    SciTech Connect

    Amaro, Mariana; Wellbrock, Thorben; Birch, David J. S.; Rolinski, Olaf J.

    2014-02-10

    The fluorescence decay of beta-amyloid's (Aβ) intrinsic fluorophore tyrosine has been used for sensing the oligomer formation of dye-labelled Aβ monomers and the results compared with previously studied oligomerization of the non-labelled Aβ peptides. It has been demonstrated that two different sized, covalently bound probes 7-diethylaminocoumarin-3-carbonyl and Hilyte Fluor 488 (HLF), alter the rate and character of oligomerization to different extents. The ability of HLF to inhibit formation of highly ordered structures containing beta-sheets was also shown. The implications of our findings for using fluorescence methods in amyloidosis research are discussed and the advantages of this auto-fluorescence approach highlighted.

  4. Beta- Lactam Antibiotics Stimulate Biofilm Formation in Non-Typeable Haemophilus influenzae by Up-Regulating Carbohydrate Metabolism

    PubMed Central

    Wu, Siva; Li, Xiaojin; Gunawardana, Manjula; Maguire, Kathleen; Guerrero-Given, Debbie; Schaudinn, Christoph; Wang, Charles; Baum, Marc M.; Webster, Paul

    2014-01-01

    Non-typeable Haemophilus influenzae (NTHi) is a common acute otitis media pathogen, with an incidence that is increased by previous antibiotic treatment. NTHi is also an emerging causative agent of other chronic infections in humans, some linked to morbidity, and all of which impose substantial treatment costs. In this study we explore the possibility that antibiotic exposure may stimulate biofilm formation by NTHi bacteria. We discovered that sub-inhibitory concentrations of beta-lactam antibiotic (i.e., amounts that partially inhibit bacterial growth) stimulated the biofilm-forming ability of NTHi strains, an effect that was strain and antibiotic dependent. When exposed to sub-inhibitory concentrations of beta-lactam antibiotics NTHi strains produced tightly packed biofilms with decreased numbers of culturable bacteria but increased biomass. The ratio of protein per unit weight of biofilm decreased as a result of antibiotic exposure. Antibiotic-stimulated biofilms had altered ultrastructure, and genes involved in glycogen production and transporter function were up regulated in response to antibiotic exposure. Down-regulated genes were linked to multiple metabolic processes but not those involved in stress response. Antibiotic-stimulated biofilm bacteria were more resistant to a lethal dose (10 µg/mL) of cefuroxime. Our results suggest that beta-lactam antibiotic exposure may act as a signaling molecule that promotes transformation into the biofilm phenotype. Loss of viable bacteria, increase in biofilm biomass and decreased protein production coupled with a concomitant up-regulation of genes involved with glycogen production might result in a biofilm of sessile, metabolically inactive bacteria sustained by stored glycogen. These biofilms may protect surviving bacteria from subsequent antibiotic challenges, and act as a reservoir of viable bacteria once antibiotic exposure has ended. PMID:25007395

  5. Formation of discontinuities and expansion waves in the outflow region of magnetic reconnection in an asymmetric current sheet

    NASA Astrophysics Data System (ADS)

    Lee, L. C.; Hsupeng, B. Y.; Lee, K. H.; Chao, J. K.

    2015-12-01

    The current sheets observed in the solar wind, magnetopause, and nightside plasma sheet can be asymmetric, in which the plasma densities and/or magnetic field magnitudes on the two sides of the current sheet are not equal. A hybrid code is used to simulate the 1-D Riemann problem for the generation and evolution of MHD discontinuities and expansion waves in the outflow region of magnetic reconnection in an asymmetric current sheet. In a symmetric current sheet, four types of compound structures are found: (a) RD-SS compound structure: show shock (SS) is attached to the downstream of rotational discontinuity (RD), (b) SS-RD: SS is followed by an adjacent RD, (c) SS-RD-SS: RD is trapped inside SS, and (d) switch-off slow shock (SSS). In the asymmetric current sheet, the rotational angle of magnetic field across an RD on the side with a higher plasma density is usually larger than that with a lower plasma density. In the asymmetric cases, a pure RD, a single SS, or a pure slow expansion wave (SE) may appear. When the asymmetry is further increased, RD may become absent in the low density side. For a highly asymmetric current sheet, a slow expansion wave (SE) is formed behind the SS-RD compound structure on the side with a very high plasma density.

  6. Direct Monitoring of β-Sheet Formation in the Outer Membrane Protein TtoA Assisted by TtOmp85.

    PubMed

    Henke, Katharina; Welte, Wolfram; Hauser, Karin

    2016-08-01

    Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy was applied to investigate the folding of an outer membrane protein, TtoA, assisted by TtOmp85, both from the thermophilic eubacterium Thermus thermophilus. To directly monitor the formation of β-sheet structure in TtoA and to analyze the function of TtOmp85, we immobilized unfolded TtoA on an ATR crystal. Interaction with TtOmp85 initiated TtoA folding as shown by time-dependent spectra recorded during the folding process. Our ATR-FTIR experiments prove that TtOmp85 possesses specific functionality to assist β-sheet formation of TtoA. We demonstrate the potential of this spectroscopic approach to study the interaction of outer membrane proteins in vitro and in a time-resolved manner. PMID:27400268

  7. Chimeric DNA-RNA hammerhead ribozyme targeting transforming growth factor-beta 1 mRNA inhibits neointima formation in rat carotid artery after balloon injury.

    PubMed

    Ando, Hideyuki; Fukuda, Noboru; Kotani, Motoko; Yokoyama, Shin ichiro; Kunimoto, Satoshi; Matsumoto, Koichi; Saito, Satoshi; Kanmatsuse, Katsuo; Mugishima, Hideo

    2004-01-12

    We designed and synthesized a chimeric DNA-RNA hammerhead ribozyme targeting transforming growth factor (TGF)-beta 1 mRNA and found that this ribozyme effectively and specifically inhibited growth of vascular smooth muscle cells. We examined the effects of the chimeric DNA-RNA hammerhead ribozyme targeting TGF-beta 1 mRNA on neointima formation and investigated the underlying mechanism to develop a possible gene therapy for coronary artery restenosis after percutaneous transluminal coronary angioplasty. Expression of mRNAs encoding TGF-beta 1, p27kip1, and connective tissue growth factor (CTGF) in carotid artery increased after balloon injury. Fluorescein-isothiocyanate (FITC)-labeled ribozyme was taken up into the midlayer smooth muscle of the injured carotid artery. Both 2 and 5 mg of ribozyme reduced neointima formation by 65% compared to that of controls. Ribozyme markedly decreased expression of TGF-beta 1 mRNA and protein in injured vessel. Mismatch ribozyme had no effect on expression of TGF-beta 1 mRNA protein in injured vessel. Ribozyme markedly decreased expression of fibronectin, p27kip1, and CTGF mRNAs in injured vessel, whereas a mismatch ribozyme had no effect on these mRNAs. These findings indicate that the chimeric DNA-RNA hammerhead ribozyme targeting TGF-beta 1 mRNA inhibits neointima formation in rat carotid artery after balloon injury with suppression of TGF-beta 1 and inhibition of extracellular matrix and CTGF. In conclusion, the hammerhead ribozyme against TGF-beta 1 may have promise as a therapy for coronary artery restenosis after percutaneous transluminal coronary angioplasty. PMID:14729108

  8. Rubella - Fact Sheet for Parents

    MedlinePlus

    ... this page: About CDC.gov . Redirect for the Rubella fact sheet page. The current fact sheet can ... http://www.cdc.gov/vaccines/parents/diseases/child/rubella.html Print page Share Compartir File Formats Help: ...

  9. Formation of high-{beta} plasma and stable confinement of toroidal electron plasma in Ring Trap 1

    SciTech Connect

    Saitoh, H.; Yoshida, Z.; Morikawa, J.; Furukawa, M.; Yano, Y.; Kawai, Y.; Kobayashi, M.; Vogel, G.; Mikami, H.

    2011-05-15

    Formation of high-{beta} electron cyclotron resonance heating plasma and stable confinement of pure electron plasma have been realized in the Ring Trap 1 device, a magnetospheric configuration generated by a levitated dipole field magnet. The effects of coil levitation resulted in drastic improvements of the confinement properties, and the maximum local {beta} value has exceeded 70%. Hot electrons are major component of electron populations, and its particle confinement time is 0.5 s. Plasma has a peaked density profile in strong field region [H. Saitoh et al., 23rd IAEA Fusion Energy Conference EXC/9-4Rb (2010)]. In pure electron plasma experiment, inward particle diffusion is realized, and electrons are stably trapped for more than 300 s. When the plasma is in turbulent state during beam injection, plasma flow has a shear, which activates the diocotron (Kelvin-Helmholtz) instability. The canonical angular momentum of the particle is not conserved in this phase, realizing the radial diffusion of charged particles across closed magnetic surfaces. [Z. Yoshida et al., Phys Rev. Lett. 104, 235004 (2010); H. Saitoh et al., Phys. Plasmas 17, 112111 (2010).].

  10. The influence of beta subunit structure on the interaction of Na+/K(+)-ATPase complexes with Na+. A chimeric beta subunit reduces the Na+ dependence of phosphoenzyme formation from ATP.

    PubMed

    Eakle, K A; Lyu, R M; Farley, R A

    1995-06-01

    High-affinity ouabain binding to Na+/K(+)-ATPase (sodium- and potassium-transport adenosine triphosphatase (EC 3.6.1.37)) requires phosphorylation of the alpha subunit of the enzyme either by ATP or by inorganic phosphate. For the native enzyme (alpha/beta 1), the ATP-dependent reaction proceeds about 4-fold more slowly in the absence of Na+ than when saturating concentrations of Na+ are present. Hybrid pumps were formed from either the alpha 1 or the alpha 3 subunit isoforms of Na+/K(+)-ATPase and a chimeric beta subunit containing the transmembrane segment of the Na+/K(+)-ATPase beta 1 isoform and the external domain of the gastric H+/K(+)-ATPase beta subunit (alpha/NH beta 1 complexes). In the absence of Na+, these complexes show a rate of ATP-dependent ouabain binding from approximately 75-100% of the rate seen in the presence of Na+ depending on buffer conditions. Nonhydrolyzable nucleotides or treatment of ATP with apyrase abolishes ouabain binding, demonstrating that ouabain binding to alpha/NH beta 1 complexes requires phosphorylation of the protein. Buffer ions inhibit ouabain binding by alpha/NH beta 1 in the absence of Na+ rather than promote ouabain binding, indicating that they are not substituting for sodium ions in the phosphorylation reaction. The pH dependence of ATP-dependent ouabain binding in the presence or absence of Na+ is similar, suggesting that protons are probably not substituting for Na+. Hybrid alpha/NH beta 1 pumps also show slightly higher apparent affinities (2-3-fold) for ATP, Na+, and ouabain; however, these are not sufficient to account for the increase in ouabain binding in the absence of Na+. In contrast to phosphoenzyme formation and ouabain binding by alpha/NH beta 1 complexes in the absence of Na+, ATPase activity, measured as release of phosphate from ATP, requires Na+. These data suggest that the transition from E1P to E2P during the catalytic cycle does not occur when the sodium binding sites are not occupied. Thus, the

  11. Complex formation equilibria of some beta-amino-alcohols with lead(II) and cadmium(II) in aqueous solution.

    PubMed

    Canepari, S; Carunchio, V; Castellano, P; Messina, A

    1998-12-01

    A study of complex formation equilibria of some beta-amino-alcohols with lead(II) and cadmium(II) ions at 25 degrees C and in 0.5 M KNO(3) is reported. The amino-alcohols considered are 2-amino-1-propanol, 2-amino-1-butanol, 2-amino-1-pentanol and 2-amino-1,3-propanediol. sec-Buthylamine and 2-amino-1-methoxy-propane have been also considered for comparison. The results are discussed in terms of ligand structure, paying attention to the number of hydroxyl groups and to the length of the alkyl residual. A weak contribution of the alcoholic oxygen in the coordination of cadmium(II) and the presence of a mixed hydroxyl species in lead(II) containing systems are hypothesized. PMID:18967412

  12. The Role of Plasma Sheet Conditions in Ring Current Formation and Energetic Neutral Atom Emissions: TWINS Results and CRCM Comparison

    NASA Astrophysics Data System (ADS)

    Fok, M.; Buzulukova, N.; McComas, D.; Brandt, P.; Goldstein, J.; Valek, P.; Alquiza, J.

    2009-05-01

    The dynamics of the ring current is sensitive to plasma sheet density and temperature. The situation is further complicated by ionospheric feedback and the existence of electric shielding at low latitudes. Most of the ring current pressure is carried by ions with energies of ~5-50 keV. In this energy range, H-H+ charge exchange cross section falls sharply with increasing energy. As a result, the intensity of energetic neutral atoms (ENA) emitted from the ring current is very sensitive to the ion energy distribution, which, in turn, is controlled by the plasma sheet temperature. Using the Comprehensive Ring Current Model (CRCM) with different plasma sheet models, we calculate ENA emissions during several moderate storms in years 2008 and 2009. We compare the simulated images with those from the TWINS imagers and study the effects of plasma sheet conditions on the ring current and the associated ENA emissions.

  13. A cylinder-shaped double ribbon structure formed by an amyloid hairpin peptide derived from the beta-sheet of murine PrP: an X-ray and molecular dynamics simulation study.

    PubMed

    Croixmarie, Vincent; Briki, Fatma; David, Gabriel; Coïc, Yves-Marie; Ovtracht, Ludmila; Doucet, Jean; Jamin, Nadège; Sanson, A

    2005-06-01

    A structural model of the murine PrP small beta-sheet was obtained by synthesizing the RGYMLGSADPNGNQVYYRG peptide comprising the two beta-strands 127-133 and 159-164 linked by a four-residue sequence of high turn propensity. The DPNG turn sequence is a "short circuit" replacing the original protein sequence between the two strands. This 19-residue peptide spontaneously forms very long single fibrils as observed by electron microscopy. The X-ray diffraction patterns of a partially oriented sample reveals an average arrangement of the hairpin peptides into a structure which can be geometrically approximated by an empty-core cylinder. The hairpins are oriented perpendicular to the cylinder axis and a 130 A helix period is observed. Based on X-ray diffraction constraints and on more indirect general protein structure considerations, a precise and consistent fibril model was built. The structure consists of two beta-sheet ribbons wound around a cylinder and assembled into a single fibril with a hairpin orientation perpendicular to the fibril axis. Subsequent implicit and explicit solvent molecular dynamics simulations provided the final structure at atomic resolution and further insights into the stabilizing interactions. Particularly important are the zipper-like network of polar interactions between the edges of the two ribbons, including the partially buried water molecules. The hydrophobic core is not optimally compact explaining the low density of this region seen by X-ray diffraction. The present findings provide also a simple model for further investigating the sequence-stability relationship using a mutational approach with a quasi-independent consideration of the polar and apolar interactions. PMID:15890277

  14. Pattern formation in icosahedral virus capsids: the papova viruses and Nudaurelia capensis beta virus.

    PubMed Central

    Marzec, C J; Day, L A

    1993-01-01

    The capsids of the spherical viruses all show underlying icosahedral symmetry, yet they differ markedly in capsomere shape and in capsomere position and orientation. The capsid patterns presented by the capsomere shapes, positions, and orientations of three viruses (papilloma, SV40, and N beta V) have been generated dynamically through a bottom-up procedure which provides a basis for understanding the patterns. A capsomere shape is represented in two-dimensional cross-section by a mass or charge density on the surface of a sphere, given by an expansion in spherical harmonics, and referred to herein as a morphological unit (MU). A capsid pattern is represented by an icosahedrally symmetrical superposition of such densities, determined by the positions and orientations of its MUs on the spherical surface. The fitness of an arrangement of MUs is measured by an interaction integral through which all capsid elements interact with each other via an arbitrary function of distance. A capsid pattern is generated by allowing the correct number of approximately shaped MUs to move dynamically on the sphere, positioning themselves until an extremum of the fitness function is attained. The resulting patterns are largely independent of the details of both the capsomere representation and the interaction function; thus the patterns produced are generic. The simplest useful fitness function is sigma 2, the average square of the mass (or charge) density, a minimum of which corresponds to a "uniformly spaced" MU distribution; to good approximation, the electrostatic free energy of charged capsomeres, calculated from the linearized Poisson-Boltzmann equation, is proportional to sigma 2. With disks as MUs, the model generates the coordinated lattices familiar from the quasi-equivalence theory, indexed by triangulation numbers. Using fivefold MUs, the model generates the patterns observed at different radii within the T = 7 capsid of papilloma and at the surface of SV40; threefold MUs

  15. Influence of Interleukin-1 Beta on Platelet-Poor Plasma Clot Formation: A Potential Impact on Early Bone Healing

    PubMed Central

    Masci, Paul P.; Crawford, Ross; Xiao, Yin

    2016-01-01

    Objectives Hematoma quality (especially the fibrin matrix) plays an important role in the bone healing process. Here, we investigated the effect of interleukin-1 beta (IL-1β) on fibrin clot formation from platelet-poor plasma (PPP). Methods Five-milliliter of rat whole-blood samples were collected from the hepatic portal vein. All blood samples were firstly standardized via a thrombelastograph (TEG), blood cell count, and the measurement of fibrinogen concentration. PPP was prepared by collecting the top two-fifths of the plasma after centrifugation under 400 × g for 10 min at 20°C. The effects of IL-1β cytokines on artificial fibrin clot formation from PPP solutions were determined by scanning electronic microscopy (SEM), confocal microscopy (CM), turbidity, and clot lysis assays. Results The lag time for protofibril formation was markedly shortened in the IL-1β treatment groups (243.8 ± 76.85 in the 50 pg/mL of IL-1β and 97.5 ± 19.36 in the 500 pg/mL of IL-1β) compared to the control group without IL-1β (543.8 ± 205.8). Maximal turbidity was observed in the control group. IL-1β (500 pg/mL) treatment significantly decreased fiber diameters resulting in smaller pore sizes and increased density of the fibrin clot structure formed from PPP (P < 0.05). The clot lysis assay revealed that 500 pg/mL IL-1β induced a lower susceptibility to dissolution due to the formation of thinner and denser fibers. Conclusion IL-1β can significantly influence PPP fibrin clot structure, which may affect the early bone healing process. PMID:26909757

  16. Natalizumab plus interferon beta-1a reduces lesion formation in relapsing multiple sclerosis.

    PubMed

    Radue, Ernst-Wilhelm; Stuart, William H; Calabresi, Peter A; Confavreux, Christian; Galetta, Steven L; Rudick, Richard A; Lublin, Fred D; Weinstock-Guttman, Bianca; Wynn, Daniel R; Fisher, Elizabeth; Papadopoulou, Athina; Lynn, Frances; Panzara, Michael A; Sandrock, Alfred W

    2010-05-15

    The SENTINEL study showed that the addition of natalizumab improved outcomes for patients with relapsing multiple sclerosis (MS) who had experienced disease activity while receiving interferon beta-1a (IFNbeta-1a) alone. Previously unreported secondary and tertiary magnetic resonance imaging (MRI) measures are presented here. Patients received natalizumab 300 mg (n=589) or placebo (n=582) intravenously every 4 weeks plus IFNbeta-1a 30 microg intramuscularly once weekly. Annual MRI scans allowed comparison of a range of MRI end points versus baseline. Over 2 years, 67% of patients receiving natalizumab plus IFNbeta-1a remained free of new or enlarging T2-lesions compared with 30% of patients receiving IFNbeta-1a alone. The mean change from baseline in T2 lesion volume over 2 years decreased in patients receiving natalizumab plus IFNbeta-1a and increased in those receiving IFNbeta-1a alone (-277.5mm(3) versus 525.6mm(3); p<0.001). Compared with IFNbeta-1a alone, add-on natalizumab therapy resulted in a smaller increase in mean T1-hypointense lesion volume after 2 years (1821.3mm(3) versus 2210.5mm(3); p<0.001), a smaller mean number of new T1-hypointense lesions over 2 years (2.3 versus 4.1; p<0.001), and a slower rate of brain atrophy during the second year of therapy (-0.31% versus -0.40%; p=0.020). Natalizumab add-on therapy reduced gadolinium-enhancing, T1-hypointense, and T2 MRI lesion activity and slowed brain atrophy progression in patients with relapsing MS who experienced disease activity despite treatment with IFNbeta-1a alone. PMID:20236661

  17. A single disulfide bond differentiates aggregation pathways of beta2-microglobulin.

    PubMed

    Chen, Yiwen; Dokholyan, Nikolay V

    2005-11-25

    Deposition of wild-type beta2-microglobulin (beta2m) into amyloid fibrils is a complication in patients undergoing long-term hemodialysis. The native beta-sandwich fold of beta2m has a highly conserved disulfide bond linking Cys25 and Cys80. Oxidized beta2m forms needle-like amyloid fibrils at pH 2.5 in vitro, whereas reduced beta2m, at acid pH, in which the intra-chain disulfide bond is disrupted, cannot form typical fibrils. Instead, reduced beta2m forms thinner and more flexible filaments. To uncover the difference in molecular mechanisms underlying the aggregation of the oxidized and reduced beta2m, we performed molecular dynamics simulations of beta2m oligomerization under oxidized and reduced conditions. We show that, consistent with experimental observations, the oxidized beta2m forms domain-swapped dimer, in which the two proteins exchange their N-terminal segments complementing each other. In contrast, both dimers and trimers, formed by reduced beta2m, are comprised of parallel beta-sheets between monomers and stabilized by the hydrogen bond network along the backbone. The oligomerized monomers are in extended conformations, capable of further aggregation. We find that both reduced and oxidized dimers are thermodynamically less stable than their corresponding monomers, indicating that beta2m oligomerization is not accompanied by the formation of a thermodynamically stable dimer. Our studies suggest that the different aggregation pathways of oxidized and reduced beta2m are dictated by the formation of distinct precursor oligomeric species that are modulated by Cys25-Cys80 disulfide-bonds. We propose that the propagation of domain swapping is the aggregation mechanism for the oxidized beta2m, while "parallel stacking" of partially unfolded beta2m is the aggregation mechanism for the reduced beta2m. PMID:16242719

  18. Effects of transforming growth factor beta and epidermal growth factor on cell proliferation and the formation of bone nodules in isolated fetal rat calvaria cells.

    PubMed

    Antosz, M E; Bellows, C G; Aubin, J E

    1989-08-01

    When cells enzymatically isolated from fetal rat calvaria (RC cells) are cultured in vitro in the presence of ascorbic acid and Na beta-glycerophosphate, discrete three-dimensional nodules form with the histologic, immunohistochemical, and ultrastructural characteristics of bone (Bellows et al; Calcified Tissue International 38:143-154, 1986; Bhargava et al., Bone, 9:155-163, 1988). Quantitation of the number of bone nodules that forms provides a colony assay for osteoprogenitor cells present in the RC population (Bellows and Aubin, Develop. Biol., 133:8-13, 1989). Continuous culture with either epidermal growth factor (EGF) or transforming growth factor beta (TGF-beta) results in dose-dependent inhibition of bone nodule formation; however, the former causes increased proliferation and saturation density, while the latter reduces both parameters. Addition of EGF (48 h pulse, 2-200 ng/ml) to RC cells at day 1 after plating results in increased proliferation and population saturation density and an increased number of bone nodules formed. Similar pulses at confluence and in postconfluent multilayered cultures when nodules first begin forming (approx. day 11) inhibited bone nodule formation and resulted in a smaller stimulation of cell proliferation. Forty-eight hour pulses of TGF-beta (0.01-1 ng/ml) reduced bone nodule formation and proliferation at all times examined, with pulses on day 1 causing maximum inhibition. The effects of pulses with TGF-beta and EGF on inhibition of nodule formation are independent of the presence of serum in the culture medium during the pulse. The data suggest that whereas EGF can either stimulate or inhibit the formation of bone nodules depending upon the time and duration of exposure, TGF-B inhibits bone nodule formation under all conditions tested. Moreover, these effects on osteoprogenitor cell differentiation do not always correlate with the effects of the growth factors on RC cell proliferation. PMID:2787326

  19. Evidence for adduct formation at the semiconductor-solution interface. Photoluminescent properties of cadmium selenide in the presence of lanthanide. beta. -diketonate complexes

    SciTech Connect

    Murphy, C.J.; Ellis, A.B. )

    1990-04-05

    Photoluminescence (PL) measurements of etched, single-crystal n-CdSe demonstrate that the semiconductor surface engages in adduct formation with a family of lanthanide {beta}-diketonate complexes, Ln(fod){sub 3} (Ln = lanthanide; fod = 6,6,7,7,8,8,8-heptafluoro-2,2-dimethyl-3,5-octanedionato anion), in isooctane ambient.

  20. Sub-100 nm Si nanowire and nano-sheet array formation by MacEtch using a non-lithographic InAs nanowire mask

    NASA Astrophysics Data System (ADS)

    Shin, Jae Cheol; Zhang, Chen; Li, Xiuling

    2012-08-01

    We report a non-lithographical method for the fabrication of ultra-thin silicon (Si) nanowire (NW) and nano-sheet arrays through metal-assisted-chemical-etching (MacEtch) with gold (Au). The mask used for metal patterning is a vertical InAs NW array grown on a Si substrate via catalyst-free, strain-induced, one-dimensional heteroepitaxy. Depending on the Au evaporation angle, the shape and size of the InAs NWs are transferred to Si by Au-MacEtch as is (NWs) or in its projection (nano-sheets). The Si NWs formed have diameters in the range of ˜25-95 nm, and aspect ratios as high as 250 in only 5 min etch time. The formation process is entirely free of organic chemicals, ensuring pristine Au-Si interfaces, which is one of the most critical requirements for high yield and reproducible MacEtch.

  1. Sub-100 nm Si nanowire and nano-sheet array formation by MacEtch using a non-lithographic InAs nanowire mask.

    PubMed

    Shin, Jae Cheol; Zhang, Chen; Li, Xiuling

    2012-08-01

    We report a non-lithographical method for the fabrication of ultra-thin silicon (Si) nanowire (NW) and nano-sheet arrays through metal-assisted-chemical-etching (MacEtch) with gold (Au). The mask used for metal patterning is a vertical InAs NW array grown on a Si substrate via catalyst-free, strain-induced, one-dimensional heteroepitaxy. Depending on the Au evaporation angle, the shape and size of the InAs NWs are transferred to Si by Au-MacEtch as is (NWs) or in its projection (nano-sheets). The Si NWs formed have diameters in the range of ∼25-95 nm, and aspect ratios as high as 250 in only 5 min etch time. The formation process is entirely free of organic chemicals, ensuring pristine Au-Si interfaces, which is one of the most critical requirements for high yield and reproducible MacEtch. PMID:22781145

  2. Metal ion-dependent, reversible, protein filament formation by designed beta-roll polypeptides

    PubMed Central

    Scotter, Andrew J; Guo, Meng; Tomczak, Melanie M; Daley, Margaret E; Campbell, Robert L; Oko, Richard J; Bateman, David A; Chakrabartty, Avijit; Sykes, Brian D; Davies, Peter L

    2007-01-01

    Background A right-handed, calcium-dependent β-roll structure found in secreted proteases and repeat-in-toxin proteins was used as a template for the design of minimal, soluble, monomeric polypeptides that would fold in the presence of Ca2+. Two polypeptides were synthesised to contain two and four metal-binding sites, respectively, and exploit stacked tryptophan pairs to stabilise the fold and report on the conformational state of the polypeptide. Results Initial analysis of the two polypeptides in the presence of calcium suggested the polypeptides were disordered. The addition of lanthanum to these peptides caused aggregation. Upon further study by right angle light scattering and electron microscopy, the aggregates were identified as ordered protein filaments that required lanthanum to polymerize. These filaments could be disassembled by the addition of a chelating agent. A simple head-to-tail model is proposed for filament formation that explains the metal ion-dependency. The model is supported by the capping of one of the polypeptides with biotin, which disrupts filament formation and provides the ability to control the average length of the filaments. Conclusion Metal ion-dependent, reversible protein filament formation is demonstrated for two designed polypeptides. The polypeptides form filaments that are approximately 3 nm in diameter and several hundred nm in length. They are not amyloid-like in nature as demonstrated by their behaviour in the presence of congo red and thioflavin T. A capping strategy allows for the control of filament length and for potential applications including the "decoration" of a protein filament with various functional moieties. PMID:17908326

  3. MMS Spacecraft Observation of Near Tail Thin Current Sheets: Their Locations, Conditions for Formation and Relation to Geomagnetic Activity

    NASA Astrophysics Data System (ADS)

    Zhao, C.; Russell, C. T.; Strangeway, R. J.; Anderson, B. J.; Baumjohann, W.; Bromund, K. R.; Chutter, M.; Fischer, D.; Kepko, L.; Le Contel, O.; Leinweber, H. K.; Magnes, W.; Nakamura, R.; Plaschke, F.; Slavin, J. A.; Torbert, R. B.

    2015-12-01

    During the commissioning phase of the MMS mission, when the apogee (~12Re) of MMS orbit swept from the pre-midnight to the dusk section of the magnetosphere, the four spacecraft probed the dynamic region of the near-Earth magnetotail. The MMS fleet encountered many structures with unambiguously small-scale spatial gradient in magnetic field (comparable to the separation of the fleet), indicating the existence of very thin current sheets in this near-tail region. During this commissioning phase, the MMS spacecraft were in a string of pearls configuration, not ideally suitable for "curlometer" determination of the current density. Thus the current density and thickness of the sheets are only roughly determined using reasonable assumptions. In this study we correlate the current sheet's location and thickness with solar wind conditions and the ground magnetic field records.

  4. Specific collapse followed by slow hydrogen-bond formation of β-sheet in the folding of single-chain monellin

    PubMed Central

    Kimura, Tetsunari; Uzawa, Takanori; Ishimori, Koichiro; Morishima, Isao; Takahashi, Satoshi; Konno, Takashi; Akiyama, Shuji; Fujisawa, Tetsuro

    2005-01-01

    Characterization of the conformational landscapes for proteins with different secondary structures is important in elucidating the mechanism of protein folding. The folding trajectory of single-chain monellin composed of a five-stranded β-sheet and a helix was investigated by using a pH-jump from the alkaline unfolded to native state. The kinetic changes in the secondary structures and in the overall size and shape were measured by circular dichroism spectroscopy and small-angle x-ray scattering, respectively. The formation of the tertiary structure was monitored by intrinsic and extrinsic fluorescence. A significant collapse was observed within 300 μs after the pH-jump, leading to the intermediate with a small amount of secondary and tertiary structures but with an overall oblate shape. Subsequently, the stepwise formation of secondary and tertiary structures was detected. The current observation was consistent with the theoretical prediction that a more significant collapse precedes the formation of secondary structures in the folding of β-sheet proteins than that of helical proteins [Shea, J. E., Onuchic, J. N. & Brooks, C. L., III (2002) Proc. Natl. Acad. Sci. USA 99, 16064–16068]. Furthermore, it was implied that the initial collapse was promoted by the formation of some specific structural elements, such as tight turns, to form the oblate shape. PMID:15710881

  5. Co-translational formation and pharmacological characterization of beta1-adrenergic receptor/nanodisc complexes with different lipid environments.

    PubMed

    Rues, Ralf-Bernhardt; Dötsch, Volker; Bernhard, Frank

    2016-06-01

    G protein-coupled receptors are of key significance for biomedical research. Streamlined approaches for their efficient recombinant production are of pivotal interest in order to explore their intrinsic conformational dynamics and complex ligand binding behavior. We have systematically optimized the co-translational association and folding of G protein-coupled receptors with defined membranes of nanodiscs by cell-free expression approaches. Each optimization step was quantified and the ligand binding active fraction of the receptor samples could drastically be improved. The strategy was exemplified with a stabilized and a non-stabilized derivative of the turkey beta1-adrenergic receptor. Systematic lipid screens with preformed nanodiscs revealed that generation of ligand binding active conformations of the analyzed beta1-adrenergic receptors strongly depends on lipid charge, flexibility and chain length. The lipid composition of the nanodisc membranes modulates the affinities to a variety of ligands of both receptor derivatives. In addition, the thermostabilization procedure had a significant impact on specific ligand affinities of the receptor and abolished or reduced the binding of certain antagonists. Both receptors were highly stable after purification with optimized nanodisc membranes. The procedure avoids any detergent contact of the receptors and sample production takes less than two days. Moreover, even non-stabilized receptors can be analyzed and their prior purification is not necessary for the formation of nanodisc complexes. The established process appears therefore to be suitable as a new platform for the functional or even structural characterization of recombinant G protein-coupled receptors associated with defined lipid environments. PMID:26922884

  6. Beta-radiation-induced resistance to MNNG initiation of papilloma but not carcinoma formation in mouse skin

    SciTech Connect

    Mitchel, R.E.; Gragtmans, N.J.; Morrison, D.P. )

    1990-02-01

    We have shown previously that the risk of tumor initiation, promotion, and progression in animals initiated with alkylating agents can be drastically altered by hyperthermia treatments. We show here that ionizing radiation can also alter the risk of tumor initiation by alkylating agents. Using a two-step skin tumorigenesis protocol in female SENCAR mice (initiation by MNNG, promotion with TPA), we exposed the dorsal skin of the mice to various doses of 90Sr/90Y beta radiation near the time of initiation. The radiation produced a dose-dependent reduction in the number of papillomas which appeared after TPA promotion, with about a 20% reduction in animals receiving 0.5 Gy surface dose just before initiation, about 50% reduction after 2.5 Gy, and greater than 80% at doses above 5 Gy. A dose of 2.5 Gy in animals initiated with DMBA produced no significant reduction. One skin hyperthermia treatment along with radiation in MNNG-initiated animals partially blocked the protective effect of radiation and increased the papilloma frequency. Radiation (2.5 Gy) given either 6 days before or after MNNG initiation was less effective but still reduced papilloma frequency about 20%. In sharp contrast to the marked reduction in papilloma formation, these same animals showed no change in carcinoma frequency with any of the doses or schedules of beta radiation. MNNG initiation alone produced three types of initiated cells. One type, produced in low yield, was promotion-independent with a high probability of progression to a carcinoma and appeared unaffected by the radiation. A second type, produced in intermediate yield, was promotion-dependent and also had a high progression probability, but was likewise unaffected by the radiation. The third and most abundant type was promotion-dependent with a very low progression probability.

  7. Roles of magnetic reconnection and buoyancy in the formation of dipolarization fronts: three-dimensional particle simulations of two-dimensional current sheet equilibria

    NASA Astrophysics Data System (ADS)

    Knizhnik, K.; Sitnov, M. I.; Swisdak, M. M.

    2012-12-01

    Unsteady magnetic reconnection in the magnetosphere and in the solar corona involves the formation of localized ejecta, such as the magnetotail dipolarization fronts (DFs) and coronal supra-arcade downflowing loops (SADLs). Both DFs and SADLs move in the direction opposite to the initial magnetic field stretching with a speed comparable to the Alfven speed. However, the DF scales are comparable to the ion gyro radius and therefore their analysis requires kinetic theory and simulations. Recent kinetic theory and PIC simulations of 2D magnetotail equilibria revealed two possible mechanisms of the DF formation, namely mutual attraction of parallel current filaments in thin current sheets causing magnetic reconnection via the tearing instability and magnetic buoyancy resulting in the ballooning-interchange instability. Both mechanisms are most efficient in the geometries with accumulation of magnetic flux at the tailward end of a thin current sheet. To understand the roles of magnetic reconnection and buoyancy in the formation and evolution of DFs we perform 3D PIC simulations of 2D current sheets, where two magnetotails are separated by an equilibrium X-line. To justify modeling the long terrestrial magnetotail in a relatively small simulation box: Lx x Ly x Lz= 40d x 20d x 5d (d is the ion inertial length; GSM coordinate system is used) open boundary conditions are employed in the x-direction. The magnetotail parts of the 2D equilibrium include regions of accumulated magnetic flux, consistent with the Geotail observations of similar signatures prior to substorm onset. We investigate which of the mechanisms is responsible for the formation of DF-like structures in 3D configurations and discuss their subsequent motion and structure. Simulations are compared with recent THEMIS observations of DFs and ballooning-interchange oscillations in the magnetotail, as well as SDO observations of solar flares.

  8. TGF-{beta} signals the formation of a unique NF1/Smad4-dependent transcription repressor-complex in human diploid fibroblasts

    SciTech Connect

    Luciakova, Katarina; Kollarovic, Gabriel; Kretova, Miroslava; Sabova, Ludmila; Nelson, B. Dean

    2011-08-05

    Highlights: {yields} TGF-{beta} induces the formation of unique nuclear NF1/Smad4 complexes that repress expression of the ANT-2 gene. {yields} Repression is mediated through an NF1-dependent repressor element in the promoter. {yields} The formation of NF1/Smad4 complexes and the repression of ANT2 are prevented by inhibitors of p38 kinase and TGF-{beta} RI. {yields} NF1/Smad complexes implicate novel role for NF1 and Smad proteins in the regulation of growth. -- Abstract: We earlier reported the formation of a unique nuclear NF1/Smad complex in serum-restricted fibroblasts that acts as an NF1-dependent repressor of the human adenine nucleotide translocase-2 gene (ANT2) [K. Luciakova, G. Kollarovic, P. Barath, B.D. Nelson, Growth-dependent repression of human adenine nucleotide translocator-2 (ANT2) transcription: evidence for the participation of Smad and Sp family proteins in the NF1-dependent repressor complex, Biochem. J. 412 (2008) 123-130]. In the present study, we show that TGF-{beta}, like serum-restriction: (a) induces the formation of NF1/Smad repressor complexes, (b) increases binding of the complexes to the repressor elements (Go elements) in the ANT2 promoter, and (c) inhibits ANT2 expression. Repression of ANT2 by TGF-{beta} is eliminated by mutating the NF1 binding sites in the Go repressor elements. All of the above responses to TGF-{beta} are prevented by inhibitors of TGF-{beta} RI and MAPK p38. These inhibitors also prevent NF1/Smad4 repressor complex formation and repression of ANT2 expression in serum-restricted cells, suggesting that similar signaling pathways are initiated by TGF-{beta} and serum-restriction. The present finding that NF1/Smad4 repressor complexes are formed through TGF-{beta} signaling pathways suggests a new, but much broader, role for these complexes in the initiation or maintenance of the growth-inhibited state.

  9. DEFECT PROPERTIES IN beta-SiC UNDER IRRADIATION-FORMATION ENERGY OF INTERSTITIAL CLUSTERS

    SciTech Connect

    Watanabe, Y.; Morishita, K.; Kohyama, Akira; Heinisch, Howard L.; Gao, Fei

    2009-07-01

    Molecular dynamics and molecular statics calculations have been performed to evaluate the formation energy of self-interstitial atom (SIA) clusters in -SiC. For SIA-clusters with stoichiometric composition, an attempt has been made to fit the calculated data points to a polynomial function of cluster size n. The resultant equation EF=1.01n1+2.04n1/2 may indicate the applicability to a wide range of cluster sizes. This formalization will be useful for the development of accurate model on nucleation and growth of SIA-clusters, which is required for the modeling on irradiation-induced microstructural evolutions of materials in nuclear fusion reactors.

  10. Molecular description of the formation and structure of plasticized globular protein films.

    PubMed

    Lefèvre, Thierry; Subirade, Muriel; Pézolet, Michel

    2005-01-01

    To optimize the properties of plasticized globular proteins films, a clear comprehension of the structure and molecular events occurring during film formation is required. In this work, the structural organization of beta-lactoglobulin (beta-lg) films plasticized with diethyelene glycol are investigated for the first time during the entire film formation process by attenuated total reflectance and transmission infrared spectroscopy. The films are made by a common two-step procedure consisting of a first heat treatment (80 degrees C/30 min) followed by the casting of the film-forming solution for dehydration. Heating at 80 degrees C leads to the self-aggregation of the proteins with a conversion of regular secondary structures into antiparallel beta-sheets. The kinetics of the conformational conversion shows that approximately 10% of the amino acids are involved in beta-sheets after the first step. Dehydration induces a further aggregation, with approximately 46% of the amino acids involved in beta-sheets in the final film. Water evaporation results in the association of the aggregates formed during the heating step. The presence of the plasticizer during water removal is essential as it allows specific conformational rearrangements into extended beta-sheets and ordering of the polypeptide chains. This work underlines that the assembly of building blocks is common in beta-lg networks and it emphasizes the widespread occurrence of beta-structures in synthetic and natural protein networks. PMID:16283748

  11. Quantitative analysis of co-oligomer formation by amyloid-beta peptide isoforms

    NASA Astrophysics Data System (ADS)

    Iljina, Marija; Garcia, Gonzalo A.; Dear, Alexander J.; Flint, Jennie; Narayan, Priyanka; Michaels, Thomas C. T.; Dobson, Christopher M.; Frenkel, Daan; Knowles, Tuomas P. J.; Klenerman, David

    2016-06-01

    Multiple isoforms of aggregation-prone proteins are present under physiological conditions and have the propensity to assemble into co-oligomers with different properties from self-oligomers, but this process has not been quantitatively studied to date. We have investigated the amyloid-β (Aβ) peptide, associated with Alzheimer’s disease, and the aggregation of its two major isoforms, Aβ40 and Aβ42, using a statistical mechanical modelling approach in combination with in vitro single-molecule fluorescence measurements. We find that at low concentrations of Aβ, corresponding to its physiological abundance, there is little free energy penalty in forming co-oligomers, suggesting that the formation of both self-oligomers and co-oligomers is possible under these conditions. Our model is used to predict the oligomer concentration and size at physiological concentrations of Aβ and suggests the mechanisms by which the ratio of Aβ42 to Aβ40 can affect cell toxicity. An increased ratio of Aβ42 to Aβ40 raises the fraction of oligomers containing Aβ42, which can increase the hydrophobicity of the oligomers and thus promote deleterious binding to the cell membrane and increase neuronal damage. Our results suggest that co-oligomers are a common form of aggregate when Aβ isoforms are present in solution and may potentially play a significant role in Alzheimer’s disease.

  12. Quantitative analysis of co-oligomer formation by amyloid-beta peptide isoforms

    PubMed Central

    Iljina, Marija; Garcia, Gonzalo A.; Dear, Alexander J.; Flint, Jennie; Narayan, Priyanka; Michaels, Thomas C. T.; Dobson, Christopher M.; Frenkel, Daan; Knowles, Tuomas P. J.; Klenerman, David

    2016-01-01

    Multiple isoforms of aggregation-prone proteins are present under physiological conditions and have the propensity to assemble into co-oligomers with different properties from self-oligomers, but this process has not been quantitatively studied to date. We have investigated the amyloid-β (Aβ) peptide, associated with Alzheimer’s disease, and the aggregation of its two major isoforms, Aβ40 and Aβ42, using a statistical mechanical modelling approach in combination with in vitro single-molecule fluorescence measurements. We find that at low concentrations of Aβ, corresponding to its physiological abundance, there is little free energy penalty in forming co-oligomers, suggesting that the formation of both self-oligomers and co-oligomers is possible under these conditions. Our model is used to predict the oligomer concentration and size at physiological concentrations of Aβ and suggests the mechanisms by which the ratio of Aβ42 to Aβ40 can affect cell toxicity. An increased ratio of Aβ42 to Aβ40 raises the fraction of oligomers containing Aβ42, which can increase the hydrophobicity of the oligomers and thus promote deleterious binding to the cell membrane and increase neuronal damage. Our results suggest that co-oligomers are a common form of aggregate when Aβ isoforms are present in solution and may potentially play a significant role in Alzheimer’s disease. PMID:27346247

  13. Quantitative analysis of co-oligomer formation by amyloid-beta peptide isoforms.

    PubMed

    Iljina, Marija; Garcia, Gonzalo A; Dear, Alexander J; Flint, Jennie; Narayan, Priyanka; Michaels, Thomas C T; Dobson, Christopher M; Frenkel, Daan; Knowles, Tuomas P J; Klenerman, David

    2016-01-01

    Multiple isoforms of aggregation-prone proteins are present under physiological conditions and have the propensity to assemble into co-oligomers with different properties from self-oligomers, but this process has not been quantitatively studied to date. We have investigated the amyloid-β (Aβ) peptide, associated with Alzheimer's disease, and the aggregation of its two major isoforms, Aβ40 and Aβ42, using a statistical mechanical modelling approach in combination with in vitro single-molecule fluorescence measurements. We find that at low concentrations of Aβ, corresponding to its physiological abundance, there is little free energy penalty in forming co-oligomers, suggesting that the formation of both self-oligomers and co-oligomers is possible under these conditions. Our model is used to predict the oligomer concentration and size at physiological concentrations of Aβ and suggests the mechanisms by which the ratio of Aβ42 to Aβ40 can affect cell toxicity. An increased ratio of Aβ42 to Aβ40 raises the fraction of oligomers containing Aβ42, which can increase the hydrophobicity of the oligomers and thus promote deleterious binding to the cell membrane and increase neuronal damage. Our results suggest that co-oligomers are a common form of aggregate when Aβ isoforms are present in solution and may potentially play a significant role in Alzheimer's disease. PMID:27346247

  14. Formation and evolution of high-plasma-pressure region in the near-Earth plasma sheet: Precursor and postcursor of substorm expansion onset

    NASA Astrophysics Data System (ADS)

    Yao, Y.; Ebihara, Y.; Tanaka, T.

    2015-08-01

    Cause of substorm expansion onset is one of the major problems in the magnetospheric study. On the basis of a global magnetohydrodynamic (MHD) simulation, Tanaka et al. (2010) suggested that formation and evolution of a high-pressure region (HPR) in the near-Earth plasma sheet could result in sudden intensification of the Region 1 field-aligned current and the westward auroral electrojet. In this sense, the formation and evolution of the HPR are a key in understanding the cause of the onset. On 5 April 2009, three probes of the Time History of Events and Macroscale Interactions during Substorms (THEMIS) were located at XGSM~-11 Re around the equator, which provide unique opportunity to investigate the spatial-temporal evolution of the HPR near the substorm expansion onset. Just before the onset, a positive excursion of the plasma pressure appeared at the outermost probe first, followed by the inner ones. Just after the onset, the opposite sequence took place. A positive excursion of the Y component of the current density was observed near the onset by the THEMIS probes and followed by a decrease trend. A similar variation was also found in the MHD simulation. All these features are consistent with the simulation result that a squeeze of the plasma from the plasma sheet results in the formation of the HPR before the onset and that the accumulated plasma spreads outward after the onset. The HPR is shown to be important for the dynamics of the magnetosphere during a substorm.

  15. Formation of. beta. ,. gamma. -methylene-7,8-dihydroneopterin 3'-triphosphate from. beta. ,. gamma. -methyleneguanosine 5'-triphosphate by GTP cyclohydrolase I of Escherichia coli

    SciTech Connect

    Ferre, J.; Jacobson, K.B.

    1984-01-01

    GTP cyclohydrolase I of Escherichia coli converts (..beta..,..gamma..-methylene)GTP to a fluorescent product that is characterized as (..beta..,..gamma..-methylene)dihydroneopterin triphosphate. Interaction between the GTP analog and the enzyme gave a K/sub i/ of 3.0 ..mu..M, which may be compared to the K/sub m/ of 0.1 ..mu..M for GTP. This new analog of dihydroneopterin triphosphate may, in turn, be converted to the same greenish-yellow pteridines (compounds X, X1, and X2) that are obtained from dihydroneopterin triphosphate. Because of its stability to phosphatase action, this analog may be useful for studies in pteridine metabolism. 14 references, 5 figures.

  16. Anatomy and controlling factors of a Late Cretaceous Aeolian sand sheet: The Marília and the Adamantina formations, NW Bauru Basin, Brazil

    NASA Astrophysics Data System (ADS)

    Basilici, Giorgio; Führ Dal'Bó, Patrick Francisco

    2010-04-01

    Few previous studies have given significant consideration to the palaeosols in aeolian sand sheet sedimentary successions and, mainly, to their palaeoenvironmental and stratigraphic meaning in interaction with the deposits. These themes are considered in this study that deals with the depositional architecture and the factors controlling the construction, accumulation and preservation of an ancient aeolian sand sheet, that forms part of the Adamantina and Marília formations, in the Bauru Basin (Late Cretaceous, Brazil). In the NW portion of the Bauru Basin, these two units, ca 220 m thick, consist of sandstone, and secondarily of sandy conglomerate and mudstone, and are characterised by vertically alternated palaeosols and deposits. Facies analyses of the deposits and macroscopic characterisation of the palaeosols in 45 outcrops were integrated with laboratory analyses that consisted in descriptions of slabs of rock samples, petrographic analyses, clay mineralogy determination, geochemical analyses of the major oxides, and micromorphological characterisation of the palaeosols. Three architectural elements were recognised: palaeosols, wind-ripple-dominated aeolian sand sheet deposits, and ephemeral river deposits. The palaeosols constitute 66% of the entire sedimentary succession, and consist principally of Aridisols and, subordinately, of Alfisols, Vertisols, and Entisols. The wind-ripple-dominated aeolian sand sheet deposits (25%) are composed of sandstone, organised in translatent climbing wind-ripple strata, and secondarily of sandstone and mudstone deposited by infrequent floods. The ephemeral river deposits (9%) consist of sandy conglomerates 4 m thick and ca 2 km wide. Wind-ripple-dominated aeolian sand sheet deposits formed during relatively dry climate period on an unstable topographic surface of an aeolian sand sheet, where aeolian deposition or erosion prevailed. Palaeosols and ephemeral river deposits formed in a more humid climate period on a stable

  17. Formation of bcc non-equilibrium La, Gd, and Dy alloys and the magnetic structure of Mg-stabilized. beta. Gd and. beta. Dy

    SciTech Connect

    Herchenroeder, J.W.

    1988-01-01

    The high temperature bcc allotrope of a rare earth metal has the potential for substantially different magnetic properties than the room temperature hexagonal (hcp or dcp) counterpart because of its more symmetrical crystal field. The stabilization by alloying and quenching of this bcc phase was studied for La-M alloys where M is a non-rare earth metal from Group II or III. The factors influencing the stabilization, such as size of M and quench rate, are discussed. {gamma}La (bcc) could be retained over a composition range around the eutectoid composition by Mg or Cd alloying. A comparison of T{sub o} curves of the various alloy systems suggest that the eutectoid temperature of the La-M system must be approximately equal to or less than a critical T{sub o} temperature of 515{degree}C if the bcc phase is to be retained by quenching. The thermal stability of {beta}Gd (bcc) was investigated by DTA and isothermal annealing. It was found to transform to an intermediate phase before reverting to the equilibrium phases in contrast to {gamma}La alloys which decompose directly on heating to the equilibrium phases. Bcc {beta}Gd and {beta}Dy stabilized by Mg additions exhibit spin glass-like behavior. Both systems show field cooling effects in the magnetic susceptibility which is indicative of spin freezing reactions.

  18. Soluble penicillin-binding protein 2a: beta-lactam binding and inhibition by non-beta-lactams using a 96-well format.

    PubMed

    Toney, J H; Hammond, G G; Leiting, B; Pryor, K D; Wu, J K; Cuca, G C; Pompliano, D L

    1998-01-01

    High level methicillin resistance in Staphylococcus aureus is dependent upon the acquisition of the mecA gene encoding penicillin-binding protein 2a (PBP2a). PBP2a is a member of a family of peptidoglycan biosynthetic enzymes involved in assembly of the cell wall in bacteria and is poorly inactivated by beta-lactam antibiotics. We describe a 96-well-filter binding assay using recombinant, soluble PBP2a which allows for kinetic measurement of penicillin binding. The deacylation rate constant for the PBP2a-penicillin G covalent complex was found to be 5.7 +/- 1.0 x 10(-5) s-1 at 30 degrees C (half-life of approximately 200 min). For the PBP2a acylation reaction, the value of K(m) (penicillin G) = 0.5 +/- 0.1 mM and kcat = 1 x 10(-3) s-1, which yields a second-order rate constant (kcat/K(m)) for inactivation of 2.0 M-1 s-1. Using this assay, several non-beta-lactam inhibitors including Cibacron blue have been found which exhibit IC50 values between 10 and 30 microM. The binding affinities of several carbapenems and beta-lactams correlated well between the filter binding assay described in this report and an electrophoretic assay for PBP2a using membranes prepared form methicillin-resistant S. aureus. PMID:9448849

  19. Using ice-penetrating radars to date ice-rise formation and Late Holocene ice-sheet retreat in the Ronne Ice Shelf region, West Antarctica

    NASA Astrophysics Data System (ADS)

    Kingslake, Jonathan; Hindmarsh, Richard; King, Edward; Corr, Hugh

    2015-04-01

    The history of the West Antarctic Ice Sheet in the region currently occupied by the Ronne Ice Shelf is poorly known. This reflects a lack of accessible recently deglaciated surfaces, which prohibits conventional paleo glaciological techniques that can provide evidence of past ice-sheet extent and retreat, for example ocean coring or exposure-dating of geological material. We use a glaciological technique, Raymond Effect Dating, to constrain the retreat of the ice sheet through the Ronne Ice Shelf region. During two Antarctic field seasons, we used a pulse-echo ice-penetrating radar to image the base and internal stratigraphy of four ice rises - areas of grounded ice containing ice divides. Towing the radar with skidoos, we conducted over 2000 km of surveys on the Skytrain, Korff, Henry and Fowler Ice Rises and the ice shelf between them. We also used a step-frequency radar called pRES to measure the vertical ice flow in the vicinity of each ice divide. Isochronal ice layers imaged during the surveys deforming in a predictable way with ice flow, meaning that their shape contains information about past ice flow. Directly beneath ice divides the downward motion of the ice is impeded by an ice-dynamical phenomenon called the Raymond Effect. This causes layers beneath the divides to form 'Raymond Arches' that grow over time. We will present the data and simulate the growth of the Raymond Arches using our pRES-measured vertical ice velocities and date the onset of ice-divide flow at each ice rise by comparing the size of simulated arches to the arches imaged during our radar surveys. We consider the main sources of uncertainty associated with these ice-rise formation dates and discuss what they can tell us about the retreat of the West Antarctic Ice Sheet through this region during the last few thousand years.

  20. Multiprotein complex formation at the beta myosin heavy chain distal muscle CAT element correlates with slow muscle expression but not mechanical overload responsiveness.

    PubMed

    Vyas, D R; McCarthy, J J; Tsika, G L; Tsika, R W

    2001-01-12

    To examine the role of the beta-myosin heavy chain (betaMyHC) distal muscle CAT (MCAT) element in muscle fiber type-specific expression and mechanical overload (MOV) responsiveness, we conducted transgenic and in vitro experiments. In adult transgenic mice, mutation of the distal MCAT element led to significant reductions in chloramphenicol acetyltransferase (CAT) specific activity measured in control soleus and plantaris muscles when compared with wild type transgene beta293WT but did not abolish MOV-induced CAT specific activity. Electrophoretic mobility shift assay revealed the formation of a specific low migrating nuclear protein complex (LMC) at the betaMyHC MCAT element that was highly enriched only when using either MOV plantaris or control soleus nuclear extract. Scanning mutagenesis of the betaMyHC distal MCAT element revealed that only the nucleotides comprising the core MCAT element were essential for LMC formation. The proteins within the LMC when using either MOV plantaris or control soleus nuclear extracts were antigenically related to nominal transcription enhancer factor 1 (NTEF-1), poly(ADP-ribose) polymerase (PARP), and Max. Only in vitro translated TEF-1 protein bound to the distal MCAT element, suggesting that this multiprotein complex is tethered to the DNA via TEF-1. Protein-protein interaction assays revealed interactions between nominal TEF-1, PARP, and Max. Our studies show that for transgene beta293 the distal MCAT element is not required for MOV responsiveness but suggest that a multiprotein complex likely comprised of nominal TEF-1, PARP, and Max forms at this element to contribute to basal slow fiber expression. PMID:11010974

  1. An RGD spacing of 440 nm is sufficient for integrin alpha V beta 3- mediated fibroblast spreading and 140 nm for focal contact and stress fiber formation

    PubMed Central

    1991-01-01

    The synthetic peptide Gly-Arg-Gly-Asp-Tyr (GRGDY), which contains the RGD sequence of several adhesion molecules, was covalently grafted to the surface of otherwise poorly adhesive glass substrates and was used to determine the minimal number of ligand-receptor interactions required for complete spreading of human foreskin fibroblasts. Well- defined adhesion substrates were prepared with GRGDY between 10(-3) fmol/cm2 and 10(4) fmol/cm2. As the adhesion ligand surface concentration was varied, several distinct morphologies of adherent cells were observed and categorized. The population of fully spread cells at 4 h reached a maximum at 1 fmol/cm2, with no further increases up to 10(4) fmol/cm2. Although maximal cell spreading was obtained at 1 fmol/cm2, focal contacts and stress fibers failed to form at RGD surface concentrations below 10 fmol/cm2. The minimal peptide spacings obtained in this work correspond to 440 nm for spreading and 140 nm for focal contact formation, and are much larger than those reported in previous studies with adsorbed adhesion proteins, adsorbed RGD-albumin conjugates, or peptide-grafted polyacrylamide gels. Vitronectin receptor antiserum specific for integrin alpha V beta 3 blocked cell adhesion and spreading on substrates containing 100 fmol/cm2 of surface- bound GRGDY, while fibronectin receptor antiserum specific for alpha 5 beta 1 did not. Furthermore, alpha V beta 3 was observed to cluster into focal contacts in spread cells, but alpha 5 beta 1 did not. It was thus concluded that a peptide-to-peptide spacing of 440 nm was required for alpha V beta 3-mediated cellular spreading, while 140 nm was required for alpha V beta 3-mediated focal contact formation and normal stress fiber organization in human foreskin fibroblasts; these spacings represent much fewer ligands than were previously thought to be required. PMID:1714913

  2. Intrastriatal injection of interleukin-1 beta triggers the formation of neuromyelitis optica-like lesions in NMO-IgG seropositive rats

    PubMed Central

    2013-01-01

    Background Neuromyelitis optica (NMO) is a severe, disabling disease of the central nervous system (CNS) characterized by the formation of astrocyte-destructive, neutrophil-dominated inflammatory lesions in the spinal cord and optic nerves. These lesions are initiated by the binding of pathogenic aquaporin 4 (AQP4)-specific autoantibodies to astrocytes and subsequent complement-mediated lysis of these cells. Typically, these lesions form in a setting of CNS inflammation, where the blood–brain barrier is open for the entry of antibodies and complement. However, it remained unclear to which extent pro-inflammatory cytokines and chemokines contribute to the formation of NMO lesions. To specifically address this question, we injected the cytokines interleukin-1 beta, tumor necrosis factor alpha, interleukin-6, interferon gamma and the chemokine CXCL2 into the striatum of NMO-IgG seropositive rats and analyzed the tissue 24 hours later by immunohistochemistry. Results All injected cytokines and chemokines led to profound leakage of immunoglobulins into the injected hemisphere, but only interleukin-1 beta induced the formation of perivascular, neutrophil-infiltrated lesions with AQP4 loss and complement-mediated astrocyte destruction distant from the needle tract. Treatment of rat brain endothelial cells with interleukin-1 beta, but not with any other cytokine or chemokine applied at the same concentration and over the same period of time, caused profound upregulation of granulocyte-recruiting and supporting molecules. Injection of interleukin-1 beta caused higher numbers of blood vessels with perivascular, cellular C1q reactivity than any other cytokine tested. Finally, the screening of a large sample of CNS lesions from NMO and multiple sclerosis patients revealed large numbers of interleukin-1 beta-reactive macrophages/activated microglial cells in active NMO lesions but not in MS lesions with comparable lesion activity and location. Conclusions Our data strongly

  3. AmrZ Beta-Sheet Residues Are Essential for DNA Binding and Transcriptional Control of Pseudomonas aeruginosa Virulence Genes ▿ †

    PubMed Central

    Waligora, Elizabeth A.; Ramsey, Deborah M.; Pryor, Edward E.; Lu, Haiping; Hollis, Thomas; Sloan, Gina P.; Deora, Rajendar; Wozniak, Daniel J.

    2010-01-01

    AmrZ is a putative ribbon-helix-helix (RHH) transcriptional regulator. RHH proteins utilize residues within the β-sheet for DNA binding, while the α-helices promote oligomerization. AmrZ is of interest due to its dual roles as a transcriptional activator and as a repressor, regulating genes encoding virulence factors associated with both chronic and acute Pseudomonas aeruginosa infection. In this study, cross-linking revealed that AmrZ forms oligomers in solution but that the amino terminus, containing an unordered region and a β-sheet, were not required for oligomerization. The first 12 unordered residues (extended amino terminus) contributed minimally to DNA binding. Mutagenesis of the AmrZ β-sheet demonstrated that residues 18, 20, and 22 were essential for DNA binding at both activation and repressor sites, suggesting that AmrZ utilizes a similar mechanism for binding to these sites. Mice infected with amrZ mutants exhibited reduced bacterial burden, morbidity, and mortality. Direct in vivo competition assays showed a 5-fold competitive advantage for the wild type over an isogenic amrZ mutant. Finally, the reduced infection phenotype of the amrZ-null strain was similar to that of a strain expressing a DNA-binding-deficient AmrZ variant, indicating that DNA binding and transcriptional regulation by AmrZ is responsible for the in vivo virulence defect. These recent infection data, along with previously identified AmrZ-regulated virulence factors, suggest the necessity of AmrZ transcriptional regulation for optimal virulence during acute infection. PMID:20709902

  4. [Beta]-Adrenergic Receptors in the Insular Cortex are Differentially Involved in Aversive vs. Incidental Context Memory Formation

    ERIC Educational Resources Information Center

    Miranda, Maria Isabel; Sabath, Elizabeth; Nunez-Jaramillo, Luis; Puron-Sierra, Liliana

    2011-01-01

    The goal of this research was to determine the effects of [beta]-adrenergic antagonism in the IC before or after inhibitory avoidance (IA) training or context pre-exposure in a latent inhibition protocol. Pretraining intra-IC infusion of the [beta]-adrenergic antagonist propranolol disrupted subsequent IA retention and impaired latent inhibition…

  5. Double Mantle Plume Upwelling—A Possible Formation Mechanism of Beta Plateau and Devana Chasma,Venus

    NASA Astrophysics Data System (ADS)

    Ding, N.

    2009-12-01

    Ning Ding,Zuoxun Zeng,China University of Geosciences,Wuhan,430074,China NingDing.eagle@gmail.com Introduction:Venus represents a‘one plate planet’[1],and the uplift,fractures and volcanism in Beta Regio on Venus are considered to be formed by lithosphere uplift driven by a hot plume[2]. Based on the double peaking saddle landform,we suggest the tectonic pattern of double mantle plume upwelling to interpret the formation mechanism of Beta Plateau and Devana Chasma.We take a physical modeling to validate this possibility. Model:There is no ductile shear in Venus[3],so we use quartz sands to simulate the crust of Venus.We use two wood stickes 1.5cm in diameter rising from the rubber canvas slowly and straight till about half of the model,then falling down slowly and straight.The base is a hard rubber plate,in the center of which,there are two holes 3cm in diameter,and the distance between them is 5cm.The holes are covered by rubber canvas.We use the quartz sands in colours of white, red and black with particle size of 70 mess as the model materials. Result:Fig.1:At the beginning of the wood stickes upwelling,only fine radial cracks are formed above the upwelling from central to outside.With the upwelling continue,surface energy of the fine radial cracks increase and make the cracks unstable,finally,the fine radial cracks connect each other and form a fracture zone.And then the two mantle plume downwelling,the fracture zone is developed to form a chasma at the end. Fig.2:The four profiles all form reverse faults outside and normal faults inside.But the difference is the faults in the middle of the chasma goes deeper than others.It is the pattern of Beta Plateau where the tectonic rising is cut by Devana Chasma zone in the topographic features. Fig.3:From the tow fig., we can see two points similar:a.the elevation is high and distribution area is large around the area of two upwelling and it is high around the area of chasma,but the distribution area is small

  6. Efficient triple helix formation by oligodeoxyribonucleotides containing alpha- or beta-2-amino-5-(2-deoxy-D-ribofuranosyl) pyridine residues.

    PubMed Central

    Bates, P J; Laughton, C A; Jenkins, T C; Capaldi, D C; Roselt, P D; Reese, C B; Neidle, S

    1996-01-01

    Triple helices containing C+xGxC triplets are destabilised at physiological pH due to the requirement for base protonation of 2'-deoxycytidine (dC), which has a pKa of 4.3. The C nucleoside 2-amino-5-(2'-deoxy-beta-D-ribofuranosyl)pyridine (beta-AP) is structurally analogous to dC but is considerably more basic, with a pKa of 5.93. We have synthesised 5'-psoralen linked oligodeoxyribonucleotides (ODNs) containing thymidine (dT) and either beta-AP or its alpha-anomer (alpha-AP) and have assessed their ability to form triplexes with a double-stranded target derived from standard deoxynucleotides (i.e. beta-anomers). Third strand ODNs derived from dT and beta-AP were found to have considerably higher binding affinities for the target than the corresponding ODNs derived from dT and either dC or 5-methyl-2'-deoxycytidine (5-Me-dC). ODNs containing dT and alpha-AP also showed enhanced triplex formation with the duplex target and, in addition are more stable in serum-containing medium than standard oligopyrimidine-derived ODNs or ODNs derived from dT and beta-AP. Molecular modelling studies showed that an alpha-anomeric AP nucleotide can be accommodated within an otherwise beta-anomeric triplex with only minor perturbation of the triplex structure. Molecular dynamics (MD) simulations on triplexes containing either the alpha- or beta-anomer of (N1-protonated) AP showed that in both cases the base retained two standard hydrogen bonds to its associated guanine when the 'A-type' model of the triplex was used as the start-point for the simulation, but that bifurcated hydrogen bonds resulted when the alternative 'B-type' triplex model was used. The lack of a differential stability between alpha-AP- and beta-AP-containing triplexes at pH >7, predicted from the behaviour of the B-type models, suggests that the A-type models are more appropriate. PMID:8932369

  7. Formation of {beta}-nickel hydroxide plate-like structures under mild conditions and their optical properties

    SciTech Connect

    Moura, A.P. de; Lima, R.C.; Paris, E.C.; Li, M.S.; Varela, J.A.; Longo, E.

    2011-10-15

    Nanostructural {beta}-nickel hydroxide ({beta}-Ni(OH){sub 2}) plates were prepared using the microwave-hydrothermal (MH) method at a low temperature and short reaction times. An ammonia solution was employed as the coordinating agent, which reacts with [Ni(H{sub 2}O){sub 6}]{sup 2+} to control the growth of {beta}-Ni(OH){sub 2} nuclei. A trigonal {beta}-Ni(OH){sub 2} single phase was observed by X-ray diffraction (XRD) analyses, and the crystal cell was constructed with structural parameters and atomic coordinates obtained from Rietveld refinement. Field emission scanning electron microscopy (FE-SEM) images revealed that the samples consisted of hexagonal-shaped nanoplates with a different particle size distribution. Broad absorption bands assigned as transitions of Ni{sup 2+} in oxygen octahedral sites were revealed by UV-vis spectra. Photoluminescence (PL) properties observed with a maximum peak centered in the blue-green region were attributed to different defects, which were produced during the nucleation process. We present a growth process scheme of the {beta}-Ni(OH){sub 2} nanoplates. - Graphical abstract: Nanostructural {beta}-Ni(OH){sub 2} crystalline powders were prepared by rapid microwave-hydrothermal method for 1, 8 and 32 min. The hexagonal-shaped nanoplates obtained presented PL emission in the blue-green region and each decomposed component represents a different type of electronic transition, which can be linked to the structural arrangement or surface defects. Highlights: > Ammonia solution to control the growth of {beta}-Ni(OH){sub 2} nuclei. > Regular plates-shape related to crystallization-dissolution-recrystallization. > The surface states and lattice defects generated in growth mechanism of crystals. > Different defects produced in the growth process responsible by photoluminescence. > Each component of photoluminescence curve linked to structural arrangement or surface defects.

  8. Stability of single sheet GNNQQNY aggregates analyzed by replica exchange molecular dynamics: Antiparallel versus parallel association

    SciTech Connect

    Vitagliano, Luigi; Esposito, Luciana; Pedone, Carlo; De Simone, Alfonso

    2008-12-26

    Protein and peptide aggregation into amyloid plaques is associated with a large variety of neurodegenerative diseases. The definition of the molecular bases of these pathologies is hampered by the transient nature of pre-fibrillar small-oligomers that are considered the toxic species. The ability of the peptide GNNQQNY to form amyloid-like structures makes it a good model to investigate the complex processes involved into amyloid fiber formation. By employing full atomistic replica exchange molecular dynamics simulations, we constructed the free energy surface of small assemblies of GNNQQNY to gain novel insights into the fiber formation process. The calculations suggest that the peptide exhibits a remarkable tendency to form both parallel and antiparallel {beta}-sheets. The data show that GNNQQNY preference for parallel or antiparallel {beta}-sheets is governed by a subtle balance of factors including assemblies' size, sidechain-sidechain interactions and pH. The samplings analysis provides a rationale to the observed trends.

  9. Formation of bcc non-equilibrium La, Gd and Dy alloys and the magnetic structure of Mg-stabilized. beta. Gd and. beta. Dy

    SciTech Connect

    Herchenroeder, J.W.

    1989-02-01

    The high temperature bcc allotrope of a rare earth metal has the potential for substantially different magnetic properties than the room temperature hexagonal (hcp or dhcp) counterpart because of its more symmetrical crystal field. The stabilization by alloying and quenching of this bcc phase was studied for La-M alloys where M is an non-rare earth metal from Group II or III. The factors influencing the stabilization, such as size of M and quench rate, are discussed. ..gamma..La (bcc) could be retained over a composition range around the eutectoid composition by Mg or Cd alloying. A comparison of T/sub o/ curves of the various alloy systems suggest that the eutectoid temperature of the La-M system must be approximately equal to or less than a critical T/sub o/ temperature of 515/degree/C if the bcc phase is to be retained by quenching. The thermal stability of ..beta..Gd (bcc) was investigated by DTA and isothermal annealing. It was found to transform to an intermediate phase before reverting to the equilibrium phases in contrast to ..gamma..La alloys which decompose directly on heating to the equilibrium phases. 71 refs., 52 figs., 7 tabs.

  10. Till formation under a soft-bedded palaeo-ice stream of the Scandinavian Ice Sheet, constrained using qualitative and quantitative microstructural analyses

    NASA Astrophysics Data System (ADS)

    Narloch, Włodzimierz; Piotrowski, Jan A.; Wysota, Wojciech; Tylmann, Karol

    2015-08-01

    This study combines micro- and macroscale studies, laboratory experiments and quantitative analyses to decipher processes of till formation under a palaeo-ice stream and the nature of subglacial sediment deformation. Till micromorphology (grain lineations, grain stacks, turbate structures, crushed grains, intraclasts and domains), grain-size and till fabric data are used to investigate a basal till generated by the Vistula Ice Stream of the Scandinavian Ice Sheet during the last glaciation in north-central Poland. A comparison of microstructures from the in situ basal till and laboratory-sheared till experiments show statistical relationships between the number of grain lineations and grain stacks; and between the number of grain lineations and turbate structures. Microstructures in the in situ till document both brittle and ductile styles of deformation, possibly due to fluctuating basal water pressures beneath the ice stream. No systematic vertical and lateral trends are detected in the parameters investigated in the in situ till, which suggests a subglacial mosaic of relatively stable and unstable areas. This situation can be explained by an unscaled space-transgressive model of subglacial till formation whereby at any given point in time different processes operated in different places under the ice sheet, possibly related to the distance from the ice margin and water pressure at the ice-bed interface. A new quantitative measure reflecting the relationship between the number of grain lineations and grain stacks may be helpful in discriminating between pervasive and non-pervasive deformation and constraining the degree of stress heterogeneity within a deformed bed. Independent strain magnitude estimations revealed by a quantitative analysis of micro- and macro-particle data show low cumulative strain in the ice-stream till in the order of 10-102.

  11. Calcium ion-induced formation of β-sheet/-turn structure leading to alteration of osteogenic activity of bone morphogenetic protein-2

    PubMed Central

    Zhang, Wenjing; He, Hongyan; Tian, Yu; Gan, Qi; Zhang, Jing; Yuan, Yuan; Liu, Changsheng

    2015-01-01

    Preserving bioactivity of bone morphogenetic protein 2 (BMP-2) still remains a challenge in protein-based therapy. It is not known how Ca2+ released from extracellular matrix or existing in physiological environment influences bioactivity in situ till now. Here, effects of extracellular Ca2+ on conformation and osteogenic bioactivity of recombinant human BMP-2 (rhBMP-2) were investigated systematically. In vitro results indicated that Ca2+ could bind rhBMP-2 rapidly and had no obvious effect on cell behaviors. Low concentration of Ca2+ (0.18 mM) enhanced rhBMP-2-induced osteogenic differentiation, while high Ca2+ concentration (>1.80 mM) exerted negative effect. In vivo ectopic bone formation exhibited similar trend. Further studies by circular dichroism spectroscopy, fluorescence spectroscopy, together with cell culture experiments revealed at low concentration, weak interaction of Ca2+ and rhBMP-2 slightly increased β-sheet/-turn content and facilitated recognition of BMP-2 and BMPRIA. But, high Ca2+ concentration (>1.8 mM) induced formation of Ca-rhBMP-2 complex and markedly increased content of β-sheet/-turn, which led to inhibition binding of rhBMP-2 and BMPRIA and thus suppression of downstream Smad1/5/8, ERK1/2 and p38 mitogen-associated protein kinase signaling pathways. Our work suggests osteogenic bioactivity of BMP-2 can be adjusted via extracellular Ca2+, which should provide guide and assist for development of BMP-2-based materials for bone regeneration. PMID:26212061

  12. Heterotopic endochondrial ossification with mixed tumor formation in C3(1)/Tag transgenic mice is associated with elevated TGF-beta1 and BMP-2 expression.

    PubMed

    Maroulakou, I G; Shibata, M A; Anver, M; Jorcyk, C L; Liu, M l; Roche, N; Roberts, A B; Tsarfaty, I; Reseau, J; Ward, J; Green, J E

    1999-09-23

    Transgenic mice which express the simian virus 40 large T-antigen (Tag) under the regulatory control of the hormone responsive rat C3(1) gene develop unusual lesions of heterotopic bone growth associated with mixed tumor formation arising from eccrine sweat glands found only in the foot pads of mice, ischiocavernosus muscle adjacent to bulbourethral glands and occasionally the salivary and mammary glands. These lesions are very similar to mixed tumors arising in several types of human cancers. Based upon electron microscopic examination and immunocytochemical analyses of cellular differentiation markers, the mixed proliferative lesions in this transgenic mouse model begin with the Tag-induced proliferation of epithelial and myoepithelial cells. The proliferation of these two types of cells results in hyperplasia and adenomatous transformation of the epithelial component, whereas the proliferating myoepithelial cells undergo metaplasia to form chondrocytes which deposit extracellular matrix, including collagen fibers. Cartilage develops focally between areas of epithelial proliferation and subsequently ossifies through a process of endochondrial bone formation. The metaplasia of myoepithelial cells to chondrocytes appears to require the inductive interaction of factors produced by the closely associated proliferating epithelial cells, including members of the TGF-beta superfamily. We demonstrate that TGF-beta1 protein accumulates in the extracellular matrix of the lesions, whereas RNA in situ hybridization reveals that BMP-2, another strong inducer of heterotopic bone formation, is overexpressed by the proliferating epithelial cells during the development of ectopic bone. The formation of sarcomatous tumors within the mixed tumors appears to be androgen-dependent and more frequent in mice lacking a normal allele of p53. This process of cartilage and bone induction may mimic epithelial-mesenchymal interactions which occur during embryonic bone formation. These

  13. Fibril stability in solutions of twisted Format="TEX"/>-sheet peptides: a new kind of micellization in chiral systems

    NASA Astrophysics Data System (ADS)

    Nyrkova, I. A.; Semenov, A. N.; Aggeli, A.; Boden, N.

    2000-10-01

    The problem of fibril (fibre) formation in chiral systems is explored theoretically being supported by experiments on synthetic de novo 11-mer peptide forming self-assembled -sheet tapes. Experimental data unambiguously indicate that the tapes form fibrils of nearly monodisperse thickness ca. 8-10 nm. Fibril formation and stabilisation are attributed to inter-tape face-to-face attraction and their intrinsic twist, correspondingly. The proposed theory is capable of predicting the fibril aggregation number and its equilibrium twist in terms of molecular parameters of the primary tapes. The suggested novel mechanism of twist stabilisation of finite aggregates (fibrils) is different to the well-known stabilisation of micelles in amphiphilic systems, and it is likely to explain the formation and stability of fibrils in a wide variety of systems including proteinaceous amyloid fibres, sickle-cell hemoglobin fibres responsible for HbS anemia, corkscrew threads found in chromonics in the presence of chiral additives and native cellulose microfibrillar crystallites. The theory also makes it possible to extract the basic molecular parameters of primary tapes (inter-tape attraction energy, helical twist step, elastic moduli) from the experimental data.

  14. Whooping Cough (Pertussis) - Fact Sheet for Parents

    MedlinePlus

    ... this page: About CDC.gov . Redirect for the Pertussis fact sheet page. The current fact sheet can ... http://www.cdc.gov/vaccines/parents/diseases/child/pertussis.html Print page Share Compartir File Formats Help: ...

  15. Beta-blocker drug therapy reduces secondary cancer formation in breast cancer and improves cancer specific survival.

    PubMed

    Powe, Desmond G; Voss, Melanie J; Zänker, Kurt S; Habashy, Hany O; Green, Andrew R; Ellis, Ian O; Entschladen, Frank

    2010-11-01

    Laboratory models show that the beta-blocker, propranolol, can inhibit norepinephrine-induced breast cancer cell migration. We hypothesised that breast cancer patients receiving beta-blockers for hypertension would show reduced metastasis and improved clinical outcome. Three patient subgroups were identified from the medical records of 466 consecutive female patients (median age 57, range 28-71) with operable breast cancer and follow-up (>10 years). Two subgroups comprised 43 and 49 hypertensive patients treated with beta-blockers or other antihypertensives respectively, prior to cancer diagnosis. 374 patients formed a non-hypertensive control group. Metastasis development, disease free interval, tumour recurrence and hazards risk were statistically compared between groups. Kaplan-Meier plots were used to model survival and DM. Beta-blocker treated patients showed a significant reduction in metastasis development (p=0.026), tumour recurrence (p=0.001), and longer disease free interval (p=0.01). In addition, there was a 57% reduced risk of metastasis (Hazards ratio=0.430; 95% CI=0.200-0.926, p=0.031), and a 71% reduction in breast cancer mortality after 10 years (Hazards ratio=0.291; 95% CI=0.119-0.715, p=0.007). This proof-of-principle study showed beta-blocker therapy significantly reduces distant metastases, cancer recurrence, and cancer-specific mortality in breast cancer patients suggesting a novel role for beta-blocker therapy. A larger epidemiological study leading to randomised clinical trials is needed for breast and other cancer types including colon, prostate and ovary. PMID:21317458

  16. The region of formation of the ultraviolet high temperature resonance lines in the eclipsing binary Beta Persei (Algol)

    NASA Technical Reports Server (NTRS)

    Brandi, E.; Garcia, L. G.; Kondo, Y.; Sahade, J.

    1989-01-01

    A new series of IUE observations of Beta Persei has shown that the high temperature resonance lines of Si IV and C IV arise in a region that surrounds the brighter, early-type component of the system. The continuum spectrum corresponds to that of a B8V object, and the value of E(B-V) that yielded the best match between the two IUE regions was 0.06, the value quoted for Beta Per in Jamar et al.'s (1976) Catalog.

  17. The Influence of Welding Parameters on the Nugget Formation of Resistance Spot Welding of Inconel 625 Sheets

    NASA Astrophysics Data System (ADS)

    Rezaei Ashtiani, Hamid Reza; Zarandooz, Roozbeh

    2015-09-01

    A 2D axisymmetric electro-thermo-mechanical finite element (FE) model is developed to investigate the effect of current intensity, welding time, and electrode tip diameter on temperature distributions and nugget size in resistance spot welding (RSW) process of Inconel 625 superalloy sheets using ABAQUS commercial software package. The coupled electro-thermal analysis and uncoupled thermal-mechanical analysis are used for modeling process. In order to improve accuracy of simulation, material properties including physical, thermal, and mechanical properties have been considered to be temperature dependent. The thickness and diameter of computed weld nuggets are compared with experimental results and good agreement is observed. So, FE model developed in this paper provides prediction of quality and shape of the weld nuggets and temperature distributions with variation of each process parameter, suitably. Utilizing this FE model assists in adjusting RSW parameters, so that expensive experimental process can be avoided. The results show that increasing welding time and current intensity lead to an increase in the nugget size and electrode indentation, whereas increasing electrode tip diameter decreases nugget size and electrode indentation.

  18. Late Noachian and early Hesperian ridge systems in the south circumpolar Dorsa Argentea Formation, Mars: Evidence for two stages of melting of an extensive late Noachian ice sheet

    NASA Astrophysics Data System (ADS)

    Kress, Ailish M.; Head, James W.

    2015-05-01

    The Dorsa Argentea Formation (DAF), extending from 270°-100° E and 70°-90° S, is a huge circumpolar deposit surrounding and underlying the Late Amazonian South Polar Layered Deposits (SPLD) of Mars. Currently mapped as Early-Late Hesperian in age, the Dorsa Argentea Formation has been interpreted as volatile-rich, possibly representing the remnants of an ancient polar ice cap. Uncertain are its age (due to the possibility of poor crater retention in ice-related deposits), its mode of origin, the origin of the distinctive sinuous ridges and cavi that characterize the unit, and its significance in the climate history of Mars. In order to assess the age of activity associated with the DAF, we examined the ridge populations within the Dorsa Argentea Formation, mapping and characterizing seven different ridge systems (composed of nearly 4,000 ridges covering a total area of ~300,000 km2, with a cumulative length of ridges of ~51,000 km) and performing crater counts on them using the method of buffered crater counting to determine crater retention ages of the ridge populations. We examined the major characteristics of the ridge systems and found that the majority of them were consistent with an origin as eskers, sediment-filled subglacial drainage channels. Ridge morphologies reflect both distributed and channelized esker systems, and evidence is also seen that some ridges form looping moraine-like termini distal to some distributed systems. The ridge populations fall into two age groups: ridge systems between 270° and 0° E date to the Early Hesperian, but to the east, the Promethei Planum and the Chasmata ridge systems date to the Late Noachian. Thus, these ages, and esker and moraine-like morphologies, support the interpretation that the DAF is a remnant ice sheet deposit, and that the esker systems represent evidence of significant melting and drainage of meltwater from portions of this ice sheet, thus indicating at least some regions and/or periods of wet

  19. Sensitivity enhanced (14)N/(14)N correlations to probe inter-beta-sheet interactions using fast magic angle spinning solid-state NMR in biological solids.

    PubMed

    Pandey, Manoj Kumar; Amoureux, Jean-Paul; Asakura, Tetsuo; Nishiyama, Yusuke

    2016-08-10

    observation of inter-β-sheet correlations. PMID:27477057

  20. FORMATION OF BETA-HYDROXYCARBONYLS FROM THE OH RADICAL-INITIATED REACTIONS OF SELECTED ALKENES (R825252)

    EPA Science Inventory

    beta2.gif" BORDER=0 ALIGN="middle">-Hydroxycarbonyls can be formed from the gas-phase
    reactions of alkenes with the OH radical, both in the presence
    and in the absence of NO. To date, because of analytical
    difficulties, few data have been r...

  1. Influence of Water Content on the β-Sheet Formation, Thermal Stability, Water Removal, and Mechanical Properties of Silk Materials.

    PubMed

    Yazawa, Kenjiro; Ishida, Kana; Masunaga, Hiroyasu; Hikima, Takaaki; Numata, Keiji

    2016-03-14

    Silk, which has excellent mechanical toughness and is lightweight, is used as a structural material in nature, for example, in silkworm cocoons and spider draglines. However, the industrial use of silk as a structural material has garnered little attention. For silk to be used as a structural material, its thermal processability and associated properties must be well understood. Although water molecules influence the glass transition of silk, the effects of water content on the other thermal properties of silks are not well understood. In this study, we prepared Bombyx mori cocoon raw fibers, degummed fibers, and films with different water contents and then investigated the effects of water content on crystallization, degradation, and water removal during thermal processing. Thermal gravimetric analyses of the silk materials showed that water content did not affect the thermal degradation temperature but did influence the water removal behavior. By increasing the water content of silk, the water molecules were removed at lower temperatures, indicating that the amount of free water in silk materials increased; additionally, the glass transition temperature decreased with increasing water plasticization. Differential scanning calorimetry and wide-angle X-ray scattering of the silk films also suggested that the water molecules in the amorphous regions of the silk films acted as a plasticizer and induced β-sheet crystallization. The plasticizing effect of water was not detected in silk fibers, owing to their lower amorphous content and mobility. The structural and mechanical characterizations of the silk films demonstrated the silk film prepared at RH 97% realized both crystallinity and ductility simultaneously. Thus, the thermal stability, mechanical, and other properties of silk materials are regulated by their water content and crystallinity. PMID:26835719

  2. A Simple Lattice Model That Captures Protein Folding, Aggregation and Amyloid Formation

    PubMed Central

    Abeln, Sanne; Vendruscolo, Michele; Dobson, Christopher M.; Frenkel, Daan

    2014-01-01

    The ability of many proteins to convert from their functional soluble state to amyloid fibrils can be attributed to inter-molecular beta strand formation. Such amyloid formation is associated with neurodegenerative disorders like Alzheimer's and Parkinson's. Molecular modelling can play a key role in providing insight into the factors that make proteins prone to fibril formation. However, fully atomistic models are computationally too expensive to capture the length and time scales associated with fibril formation. As the ability to form fibrils is the rule rather than the exception, much insight can be gained from the study of coarse-grained models that capture the key generic features associated with amyloid formation. Here we present a simple lattice model that can capture both protein folding and beta strand formation. Unlike standard lattice models, this model explicitly incorporates the formation of hydrogen bonds and the directionality of side chains. The simplicity of our model makes it computationally feasible to investigate the interplay between folding, amorphous aggregation and fibril formation, and maintains the capability of classic lattice models to simulate protein folding with high specificity. In our model, the folded proteins contain structures that resemble naturally occurring beta-sheets, with alternating polar and hydrophobic amino acids. Moreover, fibrils with intermolecular cross-beta strand conformations can be formed spontaneously out of multiple short hydrophobic peptide sequences. Both the formation of hydrogen bonds in folded structures and in fibrils is strongly dependent on the amino acid sequence, indicating that hydrogen-bonding interactions alone are not strong enough to initiate the formation of beta sheets. This result agrees with experimental observations that beta sheet and amyloid formation is strongly sequence dependent, with hydrophobic sequences being more prone to form such structures. Our model should open the way to a

  3. Shear flow promotes amyloid-{beta} fibrilization.

    PubMed

    Dunstan, Dave E; Hamilton-Brown, Paul; Asimakis, Peter; Ducker, William; Bertolini, Joseph

    2009-12-01

    The rate of formation of amyloid fibrils in an aqueous solution of amyloid-beta (Abeta) is greatly increased when the solution is sheared. When Abeta solution is stirred with a magnetic stirrer bar at 37 degrees C, a rapid increase in thioflavin T fluorescence is observed. Atomic Force Microscopy (AFM) images show the formation of aggregates, the growth of fibrils and the intertwining of the fibrils with time. Circular dichroism (CD) spectroscopy of samples taken after stirring shows a transition from random coil to alpha-helix to beta-sheet secondary structure over 20 h at 37 degrees C. The fluorescence, AFM and CD measurements are all consistent with the formation of amyloid fibrils. Quiescent, non-stirred solutions incubated at 37 degrees C showed no evidence of amyloid formation over a period of 3 days. Couette flow was found to accelerate the formation of amyloid fibrils demonstrating that the primary effect of stirring is not mixing but shearing. Only very small shear forces are applied to individual molecules in our experiments. Simple calculation suggests that the force is too small to support a hypothesis that shearing promotes partial unfolding of the protein as is observed. PMID:19850675

  4. Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. I. Importance of hydrophobic interactions in stabilization of beta-hairpin structure.

    PubMed

    Skwierawska, Agnieszka; Makowska, Joanna; Ołdziej, Stanisław; Liwo, Adam; Scheraga, Harold A

    2009-06-01

    We previously studied a 16-amino acid-residue fragment of the C-terminal beta-hairpin of the B3 domain (residues 46-61), [IG(46-61)] of the immunoglobulin binding protein G from Streptoccocus, and found that hydrophobic interactions and the turn region play an important role in stabilizing the structure. Based on these results, we carried out systematic structural studies of peptides derived from the sequence of IG (46-61) by systematically shortening the peptide by one residue at a time from both the C- and the N-terminus. To determine the structure and stability of two resulting 12- and 14-amino acid-residue peptides, IG(48-59) and IG(47-60), respectively, we carried out circular dichroism, NMR, and calorimetric studies of these peptides in pure water. Our results show that IG(48-59) possesses organized three-dimensional structure stabilized by hydrophobic interactions (Tyr50-Phe57 and Trp48-Val59) at T = 283 and 305 K. At T = 313 K, the structure breaks down because of increased chain entropy, but the turn region is preserved in the same position observed for the structure of the whole protein. The breakdown of structure occurs near the melting temperature of this peptide (T(m) = 310 K) measured by differential scanning calorimetry (DSC). The melting temperature of IG(47-60) determined by DSC is T(m) = 330 K and its structure is similar to that of the native beta-hairpin at all (lower) temperatures examined (283-313 K). Both of these truncated sequences are conserved in all known amino acid sequences of the B domains of the immunoglobulin binding protein G from bacteria. Thus, this study contributes to an understanding of the mechanism of folding of this whole family of proteins, and provides information about the mechanism of formation and stabilization of a beta-hairpin structural element. PMID:19089955

  5. (1-(4-(Naphthalen-2-yl)pyrimidin-2-yl)piperidin-4-yl)methanamine: a wingless beta-catenin agonist that increases bone formation rate.

    PubMed

    Pelletier, Jeffrey C; Lundquist, Joseph T; Gilbert, Adam M; Alon, Nipa; Bex, Frederick J; Bhat, Bheem M; Bursavich, Mattew G; Coleburn, Valerie E; Felix, Luciana A; Green, Daniel M; Green, Paula; Hauze, Diane B; Kharode, Yogendra P; Lam, Ho-Sun; Lockhead, Susan R; Magolda, Ronald L; Matteo, Jeanne J; Mehlmann, John F; Milligan, Colleen; Murrills, Richard J; Pirrello, Jennifer; Selim, Sally; Sharp, Michael C; Unwalla, Ray J; Vera, Matthew D; Wrobel, Jay E; Yaworsky, Paul; Bodine, Peter V N

    2009-11-26

    A high-throughput screening campaign to discover small molecule leads for the treatment of bone disorders concluded with the discovery of a compound with a 2-aminopyrimidine template that targeted the Wnt beta-catenin cellular messaging system. Hit-to-lead in vitro optimization for target activity and molecular properties led to the discovery of (1-(4-(naphthalen-2-yl)pyrimidin-2-yl)piperidin-4-yl)methanamine (5, WAY-262611). Compound 5 has excellent pharmacokinetic properties and showed a dose dependent increase in the trabecular bone formation rate in ovariectomized rats following oral administration. PMID:19856966

  6. TGF{beta}-mediated formation of pRb-E2F complexes in human myeloid leukemia cells

    SciTech Connect

    Hu Xiaotang

    2008-05-02

    TGF{beta} is well known for its inhibitory effect on cell cycle G1 checkpoint kinases. However, its role in the control of pRb-E2F complexes is not well established. TGF{beta} inhibits phosphorylation of pRb at several serine and threonine residues and regulates the association of E2F transcription factors with pRb family proteins. Recent studies found that predominantly E2F-4, p130, and histone deacetylase (HDAC) are found to bind to corresponding E2F-responsive promoters in G0/G1 phase. As cells progress through mid-G1, p130-E2F4 complex are replaced by p107-E2F4 followed by activators E2F1, 2, and 3. pRb was not detectable in the promoters containing the E2F-responsive site in cycling cells but was associated with E2F4-p130 complexes or E2F4-p107 complexes during G0/G1 phase. In human myeloid leukemia cell line, MV4-11, TGF{beta} upregulated pRb-E2F-4 and p130-E2F-4, and downregulated p107-E2F-4 complexes. However, pRB-E2F1 and pRb-E2F3 complexes were found in proliferating cells but not in TGF{beta} arrested G1 cells. In addition, electrophoretic gel mobility shift assay (EMSA) could not detect pRb-E2F DNA-binding activities either in S or G1 phase but exhibited the existence of p107-E2F4 in proliferating cells and p130-E2F4 complexes in TGF{beta}-arrested G1 cells, respectively. Our data suggest that p107 and p130, but not pRb, and the repressor E2F, but not activator E2Fs, play a critical role in regulating E2F-responsive gene expression in TGF{beta}-mediated cell cycle control in human myeloid leukemia cells.

  7. The effect of glutamic acid side chain on acidity constant of lysine in beta-sheet: A density functional theory study

    NASA Astrophysics Data System (ADS)

    Sargolzaei, M.; Afshar, M.; Sadeghi, M. S.; Kavee, M.

    2014-07-01

    In this work, the possibility of proton transfer between side chain of lysine and glutamic acid in peptide of Glu--Ala-Lys+ was demonstrated using density functional theory (DFT). We have shown that the proton transfer takes place between side chain of glutamic and lysine residues through the hydrogen bond formation. The structures of transition state for proton transfer reaction were detected in gas and solution phases. Our kinetic studies show that the proton transfer reaction rate in gas phase is higher than solution phase. The ionization constant (p K a) value of lysine residue in peptide was estimated 1.039 which is lower than intrinsic p K a of lysine amino acid.

  8. Overexpression of granulocyte-macrophage colony-stimulating factor induces pulmonary granulation tissue formation and fibrosis by induction of transforming growth factor-beta 1 and myofibroblast accumulation.

    PubMed Central

    Xing, Z.; Tremblay, G. M.; Sime, P. J.; Gauldie, J.

    1997-01-01

    We have previously reported that transfer to rat lung of the granulocyte-macrophage colony-stimulating factor (GM-CSF) gene leads to high expression of GM-CSF between days 1 and 4 and granulation tissue formation followed by an irreversible fibrotic response starting from day 12 onward. In the current study, we investigated the underlying mechanisms. We found that GM-CSF overexpression did not enhance production of tumor necrosis factor-alpha in a significant manner at any time after GM-CSF gene transfer. However, the content of transforming growth factor-beta 1 in bronchoalveolar lavage fluid was markedly induced at day 4 and appeared to be maximal around day 7 and remained high at day 12. Macrophages purified from bronchoalveolar lavage fluid 7 days after GM-CSF gene transfer spontaneously released significant quantities of transforming growth factor-beta 1 protein in vitro. After peak transforming growth factor-beta 1 production was the emergence of alpha-smooth muscle actin-rich myofibroblasts. Accumulation of these cells was most prominent at day 12 within the granulation tissues and they were still present in fibrotic areas between days 12 and 24 and diminished markedly afterward. Thus, we provide the first in vivo evidence that tumor necrosis factor-alpha may be dissociated from participation in a fibrotic process in the lung and GM-CSF may play a more direct role in pulmonary fibrogenesis at least in part through its capability to induce transforming growth factor-beta 1 in macrophages and the subsequent emergence of myofibroblast phenotypes. This GM-CSF transgene lung model is useful for a stepwise dissection of both cellular and molecular events involved in pulmonary fibrosis. Images Figure 2 Figure 5 Figure 6 PMID:9006322

  9. A calorimetric determination of the enthalpy of formation and a description of the defect structure of the ordered beta-phase /Ni, Cu/ /1-x/ Al/x/

    NASA Technical Reports Server (NTRS)

    Henig, E. T.; Lukas, H. L.

    1988-01-01

    In order to describe thermodynamically the defect structure of an ordered B-Hume-Rothery phase, the heat of formation of (Ni,Cu)(1-x)Al(x) was measured at 1100 K as a function of concentration in the range x (sub Al) = 0.4 and 0.55 for three substitution rations x (sub Ni)/x (sub Cu) = infinity; 11; 5. The heat of formation of the NiAl beta-phase is strongly negative. For the stoichiometric composition it is -72.2 kJ/g-atom. On both the nickel-rich side and the aluminum-rich side the magnitude of the enthalpy of formation decreases linearly with concentration. Substitution of nickel for copper decreases the magnitude of the enthalpy of formation over the entire homogeneity range for the phase (Ni,Cu)(1-x)Al(x). The curve for the enthalpy of formation as well as the literature values for the chemical potential of aluminum are described with great accuracy by the disorder model of Wagner-Schottky.

  10. Polyalanine and Abeta Aggregation Kinetics: Probing Intermediate Oligomer Formation and Structure Using Computer Simulations

    NASA Astrophysics Data System (ADS)

    Phelps, Erin Melissa

    2011-12-01

    The aggregation of proteins into stable, well-ordered structures known as amyloid fibrils has been associated with many neurodegenerative diseases. Amyloid fibrils are long straight, and un-branched structures containing several proto-filaments, each of which exhibits "cross beta structure," -- ribbon-like layers of large beta sheets whose strands run perpendicular to the fibril axis. It has been suggested in the literature that the pathway to fibril formation has the following steps: unfolded monomers associate into transient unstable oligomers, the oligomers undergo a rearrangement into the cross-beta structure and form into proto-filaments, these proto-filaments then associate and grow into fully formed fibrils. Recent experimental studies have determined that the unstable intermediate structures are toxic to cells and that their presence may play a key role in the pathogenesis of the amyloid diseases. Many efforts have been made to determine the structure of intermediate oligomer aggregates that form during the fibrillization process. The goal of this work is to provide details about the structure and formation kinetics of the unstable oligomers that appear in the fibril formation pathway. The specific aims of this work are to determine the steps in the fibril formation pathway and how the kinetics of fibrillization changes with variations in temperature and concentration. The method used is the application of discontinuous molecular dynamics to large systems of peptides represented with an intermediate resolution model, PRIME, that was previously developed in our group. Three different peptide sequences are simulated: polyalanine (KA14K), Abeta17-40, and Abeta17-42; the latter two are truncated sequences of the Alzheimer's peptide. We simulate the spontaneous assembly of these peptide chains from a random initial configuration of random coils. We investigate aggregation kinetics and oligomer formation of a system of 192 polyalanine (KA14K) chains over a