Tests of sunspot number sequences: 1. Using ionosonde data

More than 70 years ago it was recognised that ionospheric F2-layer critical frequencies [foF2] had a strong relationship to sunspot number. Using historic datasets from the Slough and Washington ionosondes, we evaluate the best statistical fits of foF2 to sunspot numbers (at each Universal Time [UT] separately) in order to search for drifts and abrupt changes in the fit residuals over Solar Cycles 17-21. This test is carried out for the original composite of the Wolf/Zürich/International sunspot number [R], the new “backbone” group sunspot number [RBB] and the proposed “corrected sunspot number” [RC]. Polynomial fits are made both with and without allowance for the white-light facular area, which has been reported as being associated with cycle-to-cycle changes in the sunspot number - foF2 relationship. Over the interval studied here, R, RBB, and RC largely differ in their allowance for the “Waldmeier discontinuity” around 1945 (the correction factor for which for R, RBB and RC is, respectively, zero, effectively over 20 %, and explicitly 11.6 %). It is shown that for Solar Cycles 18-21, all three sunspot data sequences perform well, but that the fit residuals are lowest and most uniform for RBB. We here use foF2 for those UTs for which R, RBB, and RC all give correlations exceeding 0.99 for intervals both before and after the Waldmeier discontinuity. The error introduced by the Waldmeier discontinuity causes R to underestimate the fitted values based on the foF2 data for 1932-1945 but RBB overestimates them by almost the same factor, implying that the correction for the Waldmeier discontinuity inherent in RBB is too large by a factor of two. Fit residuals are smallest and most uniform for RC and the ionospheric data support the optimum discontinuity multiplicative correction factor derived from the independent Royal Greenwich Observatory (RGO) sunspot group data for the same interval.

(1)H, (15)N and (13)C assignments of the Rhipicephalus (Boophilus) microplus anti-microbial peptide microplusin

Microplusin, a Rhipicephalus (Boophilus) microplus anti-microbial peptide (AMP) is the first member of a new family of cysteine-rich AMPs with histidine-rich regions at the N- and C-termini, which is being fully characterized by biophysical and biochemical methods. Here we report the NMR resonance assignments for (1)H, (15)N, and (13)C nuclei in the backbone and side chains of the microplusin as basis for further studies of structure, backbone dynamics and interactions mapping.

Selectivity in the mechanism of action of antimicrobial mastoparan peptide Polybia-MP1

Many potent antimicrobial peptides also present hemolytic activity, an undesired collateral effect for the therapeutic application. Unlike other mastoparan peptides, Polybia-MP1 (IDWKKLLDAAKQIL), obtained from the venom of the social wasp Polybia paulista, is highly selective of bacterial cells. The study of its mechanism of action demonstrated that it permeates vesicles at a greater rate of leakage on the anionic over the zwitterionic, impaired by the presence of cholesterol or cardiolipin; its lytic activity is characterized by a threshold peptide to lipid molar ratio that depends on the phospholipid composition of the vesicles. At these particular threshold concentrations, the apparent average pore number is distinctive between anionic and zwitterionic vesicles, suggesting that pores are similarly formed depending on the ionic character of the bilayer. To prospect the molecular reasons for the strengthened selectivity in Polybia-MP1 and its absence in Mastoparan-X, MD simulations were carried out. Both peptides presented amphipathic alpha-helical structures, as previously observed in Circular Dichroism spectra, with important differences in the extension and stability of the helix; their backbone solvation analysis also indicate a different profile, suggesting that the selectivity of Polybia-MP1 is a consequence of the distribution of the charged and polar residues along the peptide helix, and on how the solvent molecules orient themselves according to these electrostatic interactions. We suggest that the lack of hemolytic activity of Polybia-MP1 is due to the presence and position of Asp residues that enable the equilibrium of electrostatic interactions and favor the preference for the more hydrophilic environment.

Excited State Absorption of Doped and Undoped Polyanyline

Polyaniline is a conducting polymer with appealing electrical and optical properties, arising from the -conjugation along the polymer backbone. The understanding of its excited state absorption is of prime importance for designing and fabricating optical devices. Here, we report on the study of the excited state absorption of doped and undoped PANI by using femtosecond pulses in the spectral range from 450nm up to 850nm. For undoped PANI, we observed saturation of absorption as well as reverse saturable absorption, depending on the excitation wavelength. For doped PANI, however, only saturable absorption was observed.

Optical birefringence induced by two-photon absorption in polythiophene bearing an azochromophore

We carried out experiments of induced birefringence via two-photon absorption in spin-coated films of the conjugated polymer poly[2-[ethyl-[4-(4-nitro-phenylazo)-phenyl] -amino]-ethane (3-thienyl)ethanoate], PAzT, at 680 and 775 nm. This process allows recording in the bulk because of the spatial confinement of the bireffingence provided by the two-photon absorption. The induced birefringence is associated with molecular reorientation caused by the two-photon induced isomerization of the azochromophores attached to the polymer backbone. In addition, the two-photon absorption spectrum of PAzT was measured to help selecting the excitation wavelength for two-photon absorption induced birefringence. (c) 2008 Elsevier Ltd. All rights reserved.

From Rational Design of Drug Crystals to Understanding of Nucleic Acid Structures: Lamivudine Duplex

A DNA-like duplex of nucleosides is probable to exist even without the 5`-phosphate groups needed to assemble the chain backbone. However, double-stranded helical structures of nucleosides are unknown. Here, we report a duplex of nucleoside analogs that is spontaneously assembled due to stacking of the neutral and protonated molecules of lamivudine, a nucleoside reverse transcriptase inhibitor (NTRI) widely used in anti-HIV drug combinatory medication. The left-handed lamivudine duplex has features similar to those of i-motif DNA, as the face-to-face base stacking and the helix rise per base pair. Furthermore, the protonation pattern on alternate bases expected for it DNA-like duplex stabilized by pairing of neutral and protonated cytosine fragments was observed for the first time in the lamivudine double-stranded helix. This structure demonstrates that hydrogen bonds can substitute for covalent phosphodiester linkage in the stabilization of the duplex backbone. This interesting example of spontaneous molecular self-organization indicates that the 5`-phosphate group could not be a requirement for duplex assembly.

A Multitechnique Study of Structure and Dynamics of Polyfluorene Cast Films and the Influence on Their Photoluminescence

This article describes the microstructure and dynamics in the solid state of polyfluorene-based polymers, poly(9,)-dioctylfluorenyl-2,7-diyl) (PFO), a semicrystalline polymer, and poly [(9,9-dioctyl- 2,7-divinylene-fluorenylene)-alt-co-{2-methoxy-5-(2-ethyl-hexyloxy)- 1,4-phenylene vinylene}, a copolymer with mesomorphic phase properties. These Structures were determined by wide-angle X-ray scattering (WAXS) measurements, Assuming a packing model for the copolymer structure, where the planes of the phenyl rings are stacked and separated by an average distance of similar to 4.5 angstrom and laterally spaced by about similar to 16 angstrom, we followed the evolution of these distances as a function of temperature using WAXS and associated the changes observed to the polymer relaxation processes identified by dynamical mechanical thermal analysis. Specific molecular motions were studied by solid-state nuclear magnetic resonance. The onset of the side-chain motion at about 213 K (beta-relaxation) produced a small increase in the lateral spacing and in the stacking distance of the phenyl rings in them aggregated Structures, Besides, at about 383 K (alpha-relaxation) there occurs a significant increase in the amplitude of the torsion motion in the backbone, producing a greater increase in the stacking distance of the phenyl rings. Similar results were observed in the semicrystalline phase of PFO, but in this case the presence of the crystalline structure affects considerably the overall dynamics, which tends to be more hindered. Put together, Our data explain many features of the temperature dependence of the photoluminescence of these two polymers.

Temperature dependence of molecular dynamics and supramolecular aggregation in MEH-PPV films: A solid-state NMR, X-ray and fluorescence spectroscopy study

This article presents an investigation of the temperature induced modification in the microstructure and dynamics of poly[2-methoxy-5-(2`-ethylhexyloxy)-1,4-phenylenevinylene] (MEH-PPV) cast films using Wide-Angle X-ray Scattering (WAXS), solid-state Nuclear Magnetic Resonance (NMR), and Fluorescence Spectroscopy (PL). MEH-PPV chain motions were characterized as a function of temperature by NMR. The results indicated that the solvent used to cast the films influences the activation energy of the side-chain motions. This was concluded from the comparison of the activation energy of the toluene cast film, E(a) = (54 +/- 8) kJ/mol, and chloroform cast film, E(a) = (69 +/- 5) kJ/mol, and could be attributed to the higher side-chain packing provided by chloroform, that preferentially solvates the side chain in contrast to toluene that solvates mainly the backbone. Concerning the backbone mobility, it was observed that the torsional motions in the MEH-PPV have average amplitude of similar to 10 degrees at 300 K, which was found to be independent of the solvent used to cast the films. In order to correlate the molecular dynamics processes with the changes in the microstructure of the polymer, in situ WAXS experiments as a function of temperature were performed and revealed that the interchain spacing in the MEH-PPV molecular aggregates increases as a function of temperature, particularly at temperatures where molecular relaxations occur. It was also observed that the WAXS peak associated with the bilayer spacing becomes narrower and its intensity increases whereas the peak associated with the inter-backbone planes reduces its intensity for higher temperatures. This last result Could be interpreted as a decrease in the number of aggregates and the reduction of the interchain species during the MEH-PPV relaxation processes. These WAXS results were correlated with PL spectra modifications observed upon temperature treatments. (C) 2008 Elsevier Ltd. All rights reserved.

The effects of anticalcification treatments and hydration on the molecular dynamics of bovine pericardium collagen as revealed by (13)C solid-state NMR

This article describes a solid-state NMR (SSNMR) investigation of the influence of hydration and chemical cross-linking on the molecular dynamics of the constituents of the bovine pericardium (BP) tissues and its relation to the mechanical properties of the tissue. Samples of natural phenetylamine-diepoxide (DE)- and glutaraldehyde (GL)-fixed BP were investigated by (13)C cross-polarization SSNMR to probe the dynamics of the collagen, and the results were correlated to the mechanical properties of the tissues, probed by dynamical mechanical analysis. For samples of natural BP, the NMR results show that the higher the hydration level the more pronounced the molecular dynamics of the collagen backbone and sidechains, decreasing the tissue`s elastic modulus. In contrast, in DE- and GL-treated samples, the collagen molecules are more rigid, and the hydration seems to be less effective in increasing the collagen molecular dynamics and reducing the mechanical strength of the samples. This is mostly attributed to the presence of cross-links between the collagen plates, which renders the collagen mobility less dependent on the water absorption in chemically treated samples. Copyright (C) 2010 John Wiley & Sons, Ltd.

Triple Structural Transition below Room Temperature in the Antifilarial Drug Diethylcarbamazine Citrate

A very unusual triple structural transition pattern below room temperature was observed for the antifilarial drug diethylcarbamazine citrate. Besides the first thermal, crystallographic, and vibrational investigations of this first-line drug used in clinical treatment for lymphatic filariasis, a noteworthy behavior with three structural transformations as a function of temperature was demonstrated by differential scanning calorimetry, Raman spectroscopy, and single-crystal X-ray diffractometry. Our X-ray data on single crystals allow for a complete featuring and understanding of all transitions, since the four structures associated with the three solid-solid phase transformations were accurately determined. Two of three structural transitions show an order-disorder mechanism and temperature hysteresis with exothermic peaks at 224 K (T(1)`) and 213 K (T(2)`) upon cooling and endothermic ones at 248 K (T(1)) and 226 K (T(2)) upon heating. The other transition occurs at 108 K (T(3)) and it is temperature-rate sensitive. Molecular displacements onto the (010) plane and conformational changes of the diethylcarbamazine backbone as a consequence of the C-H center dot center dot center dot N hydrogen bonding formation/cleavage between drug molecules explain the mechanism of the transitions at T(1)`/T(2). However, such changes are observed only on alternate columns of the drug intercalated by citrate chains, which leads to a doubling of the lattice period along the a axis of the 235 K structure with respect to the 150 and 293 K structures. At T(2)`/T(1), these structural alterations occur in all columns of the drug. At T(3), there is a rotation on the axis of the N-C bond between the carbamoyl moiety and an ethyl group of one crystallographically independent diethylcarbamazine molecule besides molecular shifts and other conformational alterations. The impact of this study is based on the fascinating finding in which the versatile capability of structural adaptation dependent on the thermal history was observed for a relatively simple organic salt, diethylcarbamazine citrate.

Late Paleozoic-Early Triassic magmatism on the western margin of Gondwana: Collahuasi area, Northern Chile

The basement in the `Altiplano` high plateau of the Andes of northern Chile mostly consists of late Paleozoic to Early Triassic felsic igneous rocks (Collahuasi Group) that were emplaced and extruded along the western margin of the Gondwana supercontinent. This igneous Suite crops out in the Collalluasi area and forms the backbone of most of the high Andes from latitude 20 degrees to 22 degrees S. Rocks of the Collahuasi Group and correlative formations form art extensive belt of volcanic and subvolcanic rocks throughout the main Andes of Chile, the Frontal Cordillera of Argentina (Choiyoi Group or Choiyoi Granite-Rhyolite Province), and the Eastern Cordillera of Peru. Thirteen new SHRIMP U-Pb zircon ages from the Collahuasi area document a bimodal timing for magnatism, with a dominant peak at about 300 Ma and a less significant one at 244 Ma. Copper-Mo porphyry mineralization is related to the younger igneous event. Initial Hf isotopic ratios for the similar to 300 Ma zircons range from about -2 to +6 indicating that the magmas incorporated components with a significant crustal residence time. The 244 Ma magmas were derived from a less enriched source, with the initial HT values ranging from +2 to +6, suggestive of a mixture with a more depleted component. Limited whole rock (144)Nd/(143)Nd and (87)Sr/(86)Sr isotopic ratios further support the likelihood that the Collahuasi Group magmatism incorporated significant older crustal components, or at least a mixture of crustal sources with more and less evolved isotopic signatures. (C) 2007 International Association for Gondwana Research. Published by Elsevier B.V. All rights reserved.

Flexibility and inhibitor binding in Cdc25 phosphatases

Cdc25 phosphatases involved in cell cycle checkpoints are now active targets for the development of anti-cancer therapies. Rational drug design would certainly benefit from detailed structural information for Cdc25s. However, only apo- or sulfate-bound crystal structures of the Cdc25 catalytic domain have been described so far. Together with previously available crystalographic data, results from molecular dynamics simulations, bioinformatic analysis, and computer-generated conformational ensembles shown here indicate that the last 30-40 residues in the C-terminus of Cdc25B are partially unfolded or disordered in solution. The effect of C-terminal flexibility upon binding of two potent small molecule inhibitors to Cdc25B is then analyzed by using three structural models with variable levels of flexibility, including an equilibrium distributed ensemble of Cdc25B backbone conformations. The three Cdc25B structural models are used in combination with flexible docking, clustering, and calculation of binding free energies by the linear interaction energy approximation to construct and validate Cdc25B-inhibitor complexes. Two binding sites are identified on top and beside the Cdc25B active site. The diversity of interaction modes found increases with receptor flexibility. Backbone flexibility allows the formation of transient cavities or compact hydrophobic units on the surface of the stable, folded protein core that are unexposed or unavailable for ligand binding in rigid and densely packed crystal structures. The present results may help to speculate on the mechanisms of small molecule complexation to partially unfolded or locally disordered proteins.

Structure, Dynamics, and RNA Interaction Analysis of the Human SBDS Protein

Shwachman-Bodian-Diamond syndrome is an autosomal recessive genetic syndrome with pleiotropic phenotypes, including pancreatic deficiencies, bone marrow dysfunctions with increased risk of myelodysplasia or leukemia, and skeletal abnormalities. This syndrome has been associated with mutations in the SBDS gene, which encodes a conserved protein showing orthologs in Archaea and eukaryotes. The Shwachman-Bodian-Diamond syndrome pleiotropic phenotypes may be an indication of different cell type requirements for a fully functional SBDS protein. RNA-binding activity has been predicted for archaeal and yeast SBDS orthologs, with the latter also being implicated in ribosome biogenesis. However, full-length SBDS orthologs function in a species-specific manner, indicating that the knowledge obtained from model systems may be of limited use in understanding major unresolved issues regarding SBDS function, namely, the effect of mutations in human SBDS on its biochemical function and the specificity of RNA interaction. We determined the solution structure and backbone dynamics of the human SBDS protein and describe its RNA binding site using NMR spectroscopy. Similarly to the crystal structures of Archaea, the overall structure of human SBDS comprises three well-folded domains. However, significant conformational exchange was observed in NMR dynamics experiments for the flexible linker between the N-terminal domain and the central domain, and these experiments also reflect the relative motions of the domains. RNA titrations monitored by heteronuclear correlation experiments and chemical shift mapping analysis identified a classic RNA binding site at the N-terminal FYSH (fungal, Yhr087wp, Shwachman) domain that concentrates most of the mutations described for the human SBDS. (C) 2010 Elsevier Ltd. All rights reserved.

DMSO-Induced Denaturation of Hen Egg White Lysozyme

We report on the size, shape, structure, and interactions of lysozyme in the ternary system lysozyme/DMSO/water at low protein concentrations. Three structural regimes have been identified, which we term the ""folded"" (0 < phi(DMSO) < 0.7), ""unfolded"" (0.7 <= phi(DMSO) < 0.9), and ""partially collapsed"" (0.9 <= phi(DMSO) < 1.0) regime. Lysozyme resides in a folded conformation with an average radius of gyration of 1.3 +/- 0.1 nm for phi(DMSO) < 0.7 and unfolds (average R(g) of 2.4 +/- 0.1 nm) above phi(DMSO) > 0.7. This drastic change in the protein`s size coincides with a loss of the characteristic tertiary structure. It is preceded by a compaction of the local environment of the tryptophan residues and accompanied by a large increase in the protein`s overall flexibility. In terms of secondary structure, there is a gradual loss of alpha-helix and concomitant increase of beta-sheet structural elements toward phi(DMSO) = 0.7, while an increase in phi(DMSO) at even higher DMSO volume fractions reduces the presence of both a-helix and beta-sheet secondary structural elements. Protein-protein interactions remain overall repulsive for all values of phi(DMSO) An attempt is made to relate these structural changes to the three most important physical mechanisms that underlie them: the DMSO/water microstructure is strongly dependent on the DMSO volume fraction, DMSO acts as a strong H-bond acceptor, and DMSO is a bad solvent for the protein backbone and a number of relatively polar side groups, but a good solvent for relatively apolar side groups, such as tryptophan.

Electrostatic and Hydrophobic Interactions Involved in CNT Biofunctionalization with Short ss-DNA

This work is aimed at studying the adsorption mechanism of short chain 20-mer pyrimidinic homoss-DNA (oligodeoxyribonucleotide, ODN: polyC(20) and polyT(20)) onto CNT by reflectometry. To analyze the experimental data, the effective-medium theory using the Bruggemann approximation represents a Suitable optical model to account for the surface properties (roughness, thickness, and optical constants) and the size of the adsorbate. Systematic information about the involved interactions is obtained by changing the physicochemical properties of the system. Hydrophobic and electrostatic interactions are evaluated by comparing the adsorption oil hydrophobic CNT and oil hydrophilic silica and by Modulating the ionic Strength With and without Mg(2+). The ODN adsorption process oil CNT is driven by hydrophobic interactions only when the electrostatic repulsion is Suppressed. The adsorption mode results in ODN molecules in a side-on orientation with the bases (nonpolar region) toward the surface. This unfavorable orientation is partially reverse by adding Mg(2+). On the other hand, the adsorption oil silica is dominated by the strong repulsive electrostatic interaction that is screened at high ionic strength or mediated by Mg(2+). The cation-mediated process induces the interaction of the phosphate backbone (polar region) with the surface, leaving the bases free for hybridization. Although the general adsorption behavior of the pyrimidine bases is the same, polyC(20) presents higher affinity for the CNT Surface due to its acid-base properties.