A GRADIENT-LIKE NONAUTONOMOUS EVOLUTION PROCESS

In this paper we consider a dissipative damped wave equation with nonautonomous damping of the form u(tt) + beta(t)u(t) - Delta u + f(u) (1) in a bounded smooth domain Omega subset of R(n) with Dirichlet boundary conditions, where f is a dissipative smooth nonlinearity and the damping beta : R -> (0, infinity) is a suitable function. We prove, if (1) has finitely many equilibria, that all global bounded solutions of (1) are backwards and forwards asymptotic to equilibria. Thus, we give a class of examples of nonautonomous evolution processes for which the structure of the pullback attractors is well understood. That complements the results of [Carvalho & Langa, 2009] on characterization of attractors, where it was shown that a small nonautonomous perturbation of an autonomous gradient-like evolution process is also gradient-like. Note that the evolution process associated to (1) is not a small nonautonomous perturbation of any autonomous gradient-like evolution processes. Moreover, we are also able to prove that the pullback attractor for (1) is also a forwards attractor and that the rate of attraction is exponential.

X-ray photoelectron spectroscopy analysis of zirconium nitride-like films prepared on Si(100) substrates by ion beam assisted deposition

Thin zirconium nitride films were prepared on Si(l 00) substrates at room temperature by ion beam assisted deposition with a 2 keV nitrogen ion beam. Arrival rate ratios ARR(N/Zr) used were 0.19, 0.39, 0.92, and 1.86. The chemical composition and bonding structure of the films were analyzed with X-ray photoelectron spectroscopy (XPS). Deconvolution results for Zr 3d, Zr 3p(3/2), N 1s, O 1s, and C 1s XPS spectra indicated self-consistently the presence of metal Zr-0, nitride ZrN, oxide ZrO2, oxymnide Zr2N2O, and carbide ZrC phases, and the amounts of these compounds were influenced by ARR(N/Zr). The chemical composition ratio N/Zr in the film increased with increasing ARR(N/Zr) until ARR(N/Zr) reached 0.92, reflecting the high reactivity of nitrogen in the ion beam, and stayed almost constant for ARR(N/Zr) >= 1, the excess nitrogen being rejected from the growing film. A considerable incorporation of contaminant oxygen and carbon into the depositing film was attributed to the getter effect of zirconium. (C) 2007 Elsevier B.V. All rights reserved.

Extended analysis of the Al-like argon spectrum

A new analysis of the aluminium-like five times ionized argon (Ar VI) spectrum in the vacuum ultraviolet region is reported in this paper. Two adjusted and 14 new energy levels and 68 new classified lines between the configurations 3s(2)3p, 3p(3), 3s3p3d, 3s(2)4p and 3s3p(2), 3s(2)(3d + 4d + 5d), 3s(2)5s, 3p(2)3d, 3s3d(2) were obtained. Atomic calculation using the HFR program was also used in the analysis.

Vanadium complexes with 2-pyridineformamide thiosemicarbazones: In vitro studies of insulin-like activity

Reaction of VOCl(2) with 2-pyridineformamide thiosemicarbazone (H2Am4DH) and its N(4)-methyl (H2Am4Me), N(4)-ethyl (H2Am4Et) and N(4)-phenyl (H2Am4Ph) derivatives in ethanol gave as products [VO(H2Am4DH) Cl(2)] (1), [VO(H2Am4Me) Cl(2)] center dot 1/2HCl (2), [VO(H2Am4Et) Cl(2)] center dot HCl (3) and [VO(2Am4Ph) Cl] (4). Upon the dissolution of 1-4 in water, oxidation immediately occurs with the formation of [VO(2)(2Am4DH)] (5), [VO(2)(2Am4Me)] (6), [VO(2)(2Am4Et)] (7) and [VO(2)(2Am4Ph)] (8). The crystal and molecular structures of 5 and 6 were determined. Complexes 5-8 inhibited glycerol release in a similar way to that observed with insulin but showed a low enhancing effect on glucose uptake by rat adipocytes. (C) 2008 Elsevier B.V. All rights reserved.

The three-dimensional structure of bothropasin, the main hemorrhagic factor from Bothrops jararaca venom: Insights for a new classification of snake venom metalloprotease subgroups

Bothropasin is a 48 kDa hemorrhagic PIII snake venom metalloprotease (SVMP) isolated from Bothrops jararaca, containing disintegrin/cysteine-rich adhesive domains. Here we present the crystal structure of bothropasin complexed with the inhibitor POL647. The catalytic domain consists of a scaffold of two subdomains organized similarly to those described for other SVMPs, including the zinc and calcium-binding sites. The free cysteine residue Cys(189) is located within a hydrophobic core and it is not available for disulfide bonding or other interactions. There is no identifiable secondary structure for the disintegrin domain, but instead it is composed mostly of loops stabilized by seven disulfide bonds and by two calcium ions. The ECD region is in a loop and is structurally related to the RGD region of RGD disintegrins, which are derived from I`ll SVMPs. The ECD motif is stabilized by the Cys(117)_Cys(310) disulfide bond (between the disintegrin and cysteine-rich domains) and by one calcium ion. The side chain of Glu(276) of the ECD motif is exposed to solvent and free to make interactions. In bothropasin, the HVR (hyper-variable region) described for other Pill SVMPs in the cysteine-rich domain, presents a well-conserved sequence with respect to several other Pill members from different species. We propose that this subset be referred to as PIII-HCR (highly conserved region) SVMPs. The differences in the disintegrin-like, cysteine-rich or disintegrin-like cysteine-rich domains may be involved in selecting target binding, which in turn could generate substrate diversity or specificity for the catalytic domain. (C) 2008 Elsevier Ltd. All rights reserved.

Crystallographic Structure of Phosphofructokinase-2 from Escherichia coli in Complex with Two ATP Molecules. Implications for Substrate Inhibition

Phosphofructokinase-1 and -2 (Pfk-1 and Pfk-2, respectively) from Escherichia coli belong to different homologous superfamilies. However, in spite of the lack of a common ancestor, they share the ability to catalyze the same reaction and are inhibited by the substrate MgATP. Pfk-2, an ATP-dependent 6-phosphofructokinase member of the ribokinase-like superfamily, is a homodimer of 66 kDa subunits whose oligomerization state is necessary for catalysis and stability. The presence of MgATP favors the tetrameric form of the enzyme. In this work, we describe the structure of Pfk-2 in its inhibited tetrameric form, with each subunit bound to two ATP molecules and two Mg ions. The present structure indicates that substrate inhibition occurs due to the sequential binding of two MgATP molecules per subunit, the first at the usual site occupied by the nucleotide in homologous enzymes and the second at the allosteric site, making a number of direct and Mg-mediated interactions with the first. Two configurations are observed for the second MgATP, one of which involves interactions with Tyr23 from the adjacent subunit in the dimer and the other making an unusual non-Watson-Crick base pairing with the adenine in the substrate ATP. The oligomeric state observed in the crystal is tetrameric, and some of the structural elements involved in the binding of the Substrate and allosteric ATPs are also participating in the dimer-dimer interface. This structure also provides the grounds to compare analogous features of the nonhomologous phosphofructokinases from E. coli. (C) 2008 Elsevier Ltd. All rights reserved.

Osmotin from Calotropis procera latex: New insights into structure and antifungal properties

This study aimed at investigating the structural properties and mechanisms of the antifungal action of CpOsm, a purified osmotin from Calotropis procera latex. Fluorescence and CD assays revealed that the CpOsm structure is highly stable, regardless of pH levels. Accordingly, CpOsm inhibited the spore germination of Fusarium solani in all pH ranges tested. The content of the secondary structure of CpOsm was estimated as follows: alpha-helix (20%), beta-sheet (33%), turned (19%) and unordered (28%). RMSD 1%. CpOsm was stable at up to 75 degrees C, and thermal denaturation (T(m)) was calculated to be 77.8 degrees C. This osmotin interacted with the negatively charged large unilamellar vesicles (LUVs) of 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-rac-1-glycerol (POPG), inducing vesicle permeabilization by the leakage of calcein. CpOsm induced the membrane permeabilization of spores and hyphae from Fusarium solani, allowing for propidium iodide uptake. These results show that CpOsm is a stable protein, and its antifungal activity involves membrane permeabilization, as property reported earlier for other osmotins and thaumatin-like proteins. (C) 2011 Elsevier B.V. All rights reserved.

Synthesis, molecular structure and physicochemical properties of bis(3 `-azido-3 `-deoxythymidin-5 `-yl) carbonate

3`-Azido-3`-deoxythymidine (zidovudine, AZT), a synthetic analog of natural nucleoside thymidine, has been used extensively in AIDS treatments. We report here the synthesis. X-ray crystal and molecular structure, NMR, IR and Raman spectra and the thermal behavior of a novel carbonate of AZT [(AZT-O)(2)C=O], prepared by the reaction of zidovudine with carbonyldiimidazole. The carbonate compound, C(21)H(24)N(10)O(9), crystallizes in the tetragonal space group P4(1)2(1)2 with a = b = 15.284(1), c = 21.695(1) angstrom, and Z = 8 molecules per unit cell. It consists of two AZT moieties of closely related conformations which are bridged by a carbonyl group to adopt a folded Z-like shape. (C) 2010 Elsevier B.V. All rights reserved.

Structure and Calcium-Binding Activity of LipL32, the Major Surface Antigen of Pathogenic Leptospira sp.

Leptospixosis, a spirochaetal zoonotic disease caused by Leptospira, has been recognized as an important emerging infectious disease. LipL32 is the major exposed outer membrane protein found exclusively in pathogenic leptospires, where it accounts for up to 75% of the total outer membrane proteins. It is highly immunogenic, and recent studies have implicated LipL32 as an extracellular matrix binding protein, interacting with collagens, fibronectin, and laminin. In order to better understand the biological role and the structural requirements for the function of this important lipoprotein, we have determined the 2.25-angstrom-resolution structure of recombinant LipL32 protein corresponding to residues 21-272 of the wild-type protein (LipL32(21-272)). The LipL32(21-272) monomer is made of a jelly-roll fold core from which several peripheral secondary structures protrude. LipL32(21-272) is structurally similar to several other jelly-roll proteins, some of which bind calcium ions and extracellular matrix proteins. Indeed, spectroscopic data (circular dichroism, intrinsic tryptophan fluorescence, and extrinsic 1-amino-2-naphthol-4-sulfonic acid fluorescence) confirmed the calcium-binding properties of LipL32(21-272). Ca(2+) binding resulted in a significant increase in the thermal stability of the protein, and binding was specific for Ca(2+) as no structural or stability perturbations were observed for Mg(2+), Zn(2+), or Cu(2+). Careful examination of the crystal lographic structure suggests the locations of putative regions that could mediate Ca(2+) binding as well as binding to other interacting host proteins, such as collagens, fibronectin, and lamixidn. (C) 2009 Elsevier Ltd. All rights reserved.

The Aedes aegypti larval transcriptome: a comparative perspective with emphasis on trypsins and the domain structure of peritrophins

The genome sequence of Aedes aegypti was recently reported. A significant amount of Expressed Sequence Tags (ESTs) were sequenced to aid in the gene prediction process. In the present work we describe an integrated analysis of the genomic and EST data, focusing on genes with preferential expression in larvae (LG), adults (AG) and in both stages (SG). A total of 913 genes (5.4% of the transcript complement) are LG, including ion transporters and cuticle proteins that are important for ion homeostasis and defense. From a starting set of 245 genes encoding the trypsin domain, we identified 66 putative LG, AG, and SG trypsins by manual curation. Phylogenetic analyses showed that AG trypsins are divergent from their larval counterparts (LG), grouping with blood-induced trypsins from Anopheles gambiae and Simulium vittatum. These results support the hypothesis that blood-feeding arose only once, in the ancestral Culicomorpha. Peritrophins are proteins that interlock chitin fibrils to form the peritrophic membrane (PM) that compartmentalizes the food in the midgut. These proteins are recognized by having chitin-binding domains with 6 conserved Cys and may also present mucin-like domains (regions expected to be highly O-glycosylated). PM may be formed by a ring of cells (type 2, seen in Ae. aegypti larvae and Drosophila melanogaster) or by most midgut cells (type 1, found in Ae. aegypti adult and Tribolium castaneum). LG and D. melanogaster peritrophins have more complex domain structures than AG and T. castaneum peritrophins. Furthermore, mucin-like domains of peritrophins from T. castaneum (feeding on rough food) are lengthier than those of adult Ae. aegypti (blood-feeding). This suggests, for the first time, that type 1 and type 2 PM may have variable molecular architectures determined by different peritrophins and/or ancillary proteins, which may be partly modulated by diet.

The iron stimulon of Xylella fastidiosa includes genes for type IV pilus and colicin V-like bacteriocins

Xylella fastidiosa is the etiologic agent of a wide range of plant diseases, including citrus variegated chlorosis (CVC), a major threat to citrus industry. The genomes of several strains of this phytopathogen were completely sequenced, enabling large-scale functional studies. DNA microarrays representing 2,608 (91.6%) coding sequences (CDS) of X. fastidiosa CVC strain 9a5c were used to investigate transcript levels during growth with different iron availabilities. When treated with the iron chelator 2,2`-dipyridyl, 193 CDS were considered up-regulated and 216 were considered down-regulated. Upon incubation with 100 mu M ferric pyrophosphate, 218 and 256 CDS were considered up- and down-regulated, respectively. Differential expression for a subset of 44 CDS was further evaluated by reverse transcription-quantitative PCR. Several CDS involved with regulatory functions, pathogenicity, and cell structure were modulated under both conditions assayed, suggesting that major changes in cell architecture and metabolism occur when X. fastidiosa cells are exposed to extreme variations in iron concentration. Interestingly, the modulated CDS include those related to colicin V-like bacteriocin synthesis and secretion and to functions of pili/fimbriae. We also investigated the contribution of the ferric uptake regulator Fur to the iron stimulon of X. fastidiosa. The promoter regions of the strain 9a5c genome were screened for putative Fur boxes, and candidates were analyzed by electrophoretic mobility shift assays. Taken together, our data support the hypothesis that Fur is not solely responsible for the modulation of the iron stimulon of X fastidiosa, and they present novel evidence for iron regulation of pathogenicity determinants.

Structure, processing and midgut secretion of putative peritrophic membrane ancillary protein (PMAP) from Tenebrio molitor larvae

A cDNA coding for a Tenebrio molitor midgut protein named peritrophic membrane ancillary protein (PMAP) was cloned and sequenced. The complete cDNA codes for a protein of 595 amino acids with six insect-allergen-related-repeats that may be grouped in A (predicted globular)- and B (predicted nonglobular)-types forming an ABABAB structure. The PMAP-cDNA was expressed in Pichia pastoris and the recombinant protein (64 kDa) was purified to homogeneity and used to raise antibodies in rabbits. The specific antibody detected PMAP peptides (22 kDa) in the anterior and middle midgut tissue, luminal contents, peritrophic membrane and feces. These peptides derive from PMAP, as supported by mass spectrometry, and resemble those formed by the in vitro action of trypsin on recombinant PMAP. Both in vitro and in vivo PMAP processing seem to occur by attack of trypsin to susceptible bonds in the coils predicted to link AB pairs, thus releasing the putative functional AB structures. The AB-domain structure of PMAP is found in homologous proteins from several insect orders, except lepidopterans that have the apparently derived protein known as nitrile-specifier protein. Immunocytolocalization shows that PMAP is secreted by exocytosis and becomes entrapped in the glycocalyx, before being released into midgut contents. Circumstantial evidence suggests that PMAP-like proteins have a role in peritrophic membrane type 2 formation. (C) 2007 Elsevier Ltd. All rights reserved.

Structure of polyaniline formed in different inorganic porous materials: A spectroscopic study

In this work, the electronic and structural characterization of polyaniline (PANI) formed in cavities of zeolites Y (ZY) and Mordenite (MOR) and montmorillonite (MMT) clay having Cu(II) as oxidant agent are presented. The formation of PANI and its structure is analyzed by Resonance Raman, UV-Vis-NIR, FT-IR and N K XANES techniques. In all cases the structure of PANT formed is different from the ""free"" polymer. The presence of azo bonds linked to phenazine-like rings are observed only for PANI-MMT composites, independent of the kind of oxidant agent employed in the synthesis. The presence of Cu(II) ions leads to the formation of Phenosafranine-like rings. The presence of these phenazine-like rings in the structure of confined PANT chains can also contribute to the enhancement of the thermal stability observed for all composites. (C) 2008 Elsevier Ltd. All rights reserved.

Polyaniline/layered zirconium phosphate nanocomposites: Secondary-like doped polyaniline obtained by the layer-by-layer technique

In the present work, nanocomposites of polyaniline (PANI) and layered alpha-Zr(HPO4)(2).H2O (alpha-ZrP) were prepared using two different approaches: (i) the in situ aniline polymerization in the presence of the layered inorganic material and (ii) the layer-by-layer (LBL) assembly using an aqueous solution of the polycation emeraldine salt (ES-PANI) and a dispersion of exfoliated negative slabs of alpha-ZrP. These materials were characterized spectroscopically using mainly resonance Raman scattering at four exciting radiations and electronic absorption in the UV-VIS-NIR region. Structural and textural characterizations were carried out using powder X-ray diffraction (XRD) and scanning electron microscopy (SEM). The polymer obtained by the in situ aniline polymerization is located primarily in the external surface of the inorganic material although aniline monomers were intercalated between alpha-ZrP interlayer regions before oxidative polymerization. Through resonance Raman spectroscopy, it was observed that the formed polymer has semiquinone units (ES-PANI) and also azo bonds (-N = N-), showing that this method results in a polymer with a different structure from the usual ""head-to-tail"" ES-PANI. The LBL assembly of pre-formed ES-PANI and exfoliated alpha-ZrP particles produces homogeneous films with reproducible deposition from layer to layer, up to 20 bilayers. Resonance Raman (lambda(0) = 632.8 nm) spectrum of PANI/ZrP LBL film shows an enhancement in the intensity of the polaronic band at 1333 cm(-1) (nu C-N center dot+) and the decrease of the band intensity at 1485 cm(-1) compared to bulk ES-PANI. Its UV-VIS-NIR spectrum presents an absorption tail in the NIR region assigned to delocalized free charge carrier. These spectroscopic features are characteristic of highly conductive secondary doped PANI suggesting that polymeric chains in PANI/ZrP LBL film have a more extended conformation than in bulk ES-PANI.

Oxovanadium(IV) and (V) complexes of acetylpyridine-derived semicarbazones exhibit insulin-like activity

Reaction of 2-acetylpyridine semicarbazone (H2APS), 3-acetylpyridine semicarbazone (H3APS) and 4-acetylpyridine semicarbazone (H4APS) with [VO(acac)(2)] (acac = acetylacetonate) gave [VO(H2APS)(acac)(2)] (1), (VO(H3APS)(acac)(2)] (2) and [VO(4APS)(acac) (H2O)] center dot 1/2H(2)O (3). Oxidation of complex 1 in acetonitrile gave [VO2(2APS)] (4). The crystal structures of complexes 1 and 4 have been determined. Complexes 1-3 were able to enhance glucose uptake and to inhibit glycerol release from adipocytes, which indicate their potential to act as insulin-mimics. (C) 2008 Elsevier Ltd. All rights reserved.