Electron collisions with the CH(2)O-H(2)O complex

We report cross sections for elastic collisions of low-energy electrons with the CH(2)O-H(2)O complex. We employed the Schwinger multichannel method with pseudopotentials in the static-exchange and in the static-exchange-polarization approximations for energies from 0.1 to 20 eV. We considered four different hydrogen-bonded structures for the complex that were generated by classical Monte Carlo simulations. Our aim is to investigate the effect of the water molecule on the pi* shape resonance of formaldehyde. Previous studies reported a pi* shape resonance for CH(2)O at around 1 eV. The resonance positions of the complexes appear at lower energies in all cases due to the mutual polarization between the two molecules. This indicates that the presence of water may favor dissociation by electron impact and may lead to an important effect on strand breaking in wet DNA by electron impact.

Experimental observation of a complex periodic window

The existence of a special periodic window in the two-dimensional parameter space of an experimental Chua's circuit is reported. One of the main reasons that makes such a window special is that the observation of one implies that other similar periodic windows must exist for other parameter values. However, such a window has never been experimentally observed, since its size in parameter space decreases exponentially with the period of the periodic attractor. This property imposes clear limitations for its experimental detection.

Jensen inequalities for tunneling probabilities in complex systems

The Jensen theorem is used to derive inequalities for semiclassical tunneling probabilities for systems involving several degrees of freedom. These Jensen inequalities are used to discuss several aspects of sub-barrier heavy-ion fusion reactions. The inequality hinges on general convexity properties of the tunneling coefficient calculated with the classical action in the classically forbidden region.

Border detection in complex networks

One important issue implied by the finite nature of real-world networks regards the identification of their more external (border) and internal nodes. The present work proposes a formal and objective definition of these properties, founded on the recently introduced concept of node diversity. It is shown that this feature does not exhibit any relevant correlation with several well-established complex networks measurements. A methodology for the identification of the borders of complex networks is described and illustrated with respect to theoretical (geographical and knitted networks) as well as real-world networks (urban and word association networks), yielding interesting results and insights in both cases.

Iridium(III)-surfactant complex immobilized in mesoporous silica via templated synthesis: a new route to optical materials

In this work we report the preparation of a new blue-emitting material based on the templated synthesis of mesoporous silica (MCM-41) using micellar solutions of the newly synthesized monocationic metallosurfactant complex bis[1-benzyl-4-(2,4-difluorophenyl)-1H-1,2,3-triazole](4,4'-diheptadecyl-2,2'- bipyridine)-iridium(III) chloride in hexadecyl-trimethyl-ammonium bromide (CTAB). Under ambient conditions, significant increases in excited state lifetime and quantum yield values (up to 45%), were obtained for the solid materials in comparison to the corresponding micellar solutions. Solid state (1)H and (19)F NMR spectroscopies were successfully employed for quantifying the luminophore content in terms of Ir-surfactant to CTAB and Ir-surfactant to silica ratios.

Purine nucleoside phosphorylase from Schistosoma mansoni in complex with ribose-1-phosphate

Schistosomes are blood flukes which cause schistosomiasis, a disease affecting approximately 200 million people worldwide. Along with several other important human parasites including trypanosomes and Plasmodium, schistosomes lack the de novo pathway for purine synthesis and depend exclusively on the salvage pathway for their purine requirements, making the latter an attractive target for drug development. Part of the pathway involves the conversion of inosine (or guanosine) into hypoxanthine (or guanine) together with ribose-1-phosphate (R1P) or vice versa. This inter-conversion is undertaken by the enzyme purine nucleoside phosphorylase (PNP) which has been used as the basis for the development of novel anti-malarials, conceptually validating this approach. It has been suggested that, during the reverse reaction, R1P binding to the enzyme would occur only as a consequence of conformational changes induced by hypoxanthine, thus making a binary PNP-R1P complex unlikely. Contradictory to this statement, a crystal structure of just such a binary complex involving the Schistosoma mansoni enzyme has been successfully obtained. The ligand shows an intricate hydrogen-bonding network in the phosphate and ribose binding sites and adds a further chapter to our knowledge which could be of value in the future development of selective inhibitors.

Adenosine binding to low-molecular-weight purine nucleoside phosphorylase: the structural basis for recognition based on its complex with the enzyme from Schistosoma mansoni

Schistosomes are unable to synthesize purines de novo and depend exclusively on the salvage pathway for their purine requirements. It has been suggested that blockage of this pathway could lead to parasite death. The enzyme purine nucleoside phosphorylase (PNP) is one of its key components and molecules designed to inhibit the low-molecular-weight (LMW) PNPs, which include both the human and schistosome enzymes, are typically analogues of the natural substrates inosine and guanosine. Here, it is shown that adenosine both binds to Schistosoma mansoni PNP and behaves as a weak micromolar inhibitor of inosine phosphorolysis. Furthermore, the first crystal structures of complexes of an LMW PNP with adenosine and adenine are reported, together with those with inosine and hypoxanthine. These are used to propose a structural explanation for the selective binding of adenosine to some LMW PNPs but not to others. The results indicate that transition-state analogues based on adenosine or other 6-amino nucleosides should not be discounted as potential starting points for alternative inhibitors.

Gene Expression Complex Networks: Synthesis, Identification, and Analysis

Thanks to recent advances in molecular biology, allied to an ever increasing amount of experimental data, the functional state of thousands of genes can now be extracted simultaneously by using methods such as cDNA microarrays and RNA-Seq. Particularly important related investigations are the modeling and identification of gene regulatory networks from expression data sets. Such a knowledge is fundamental for many applications, such as disease treatment, therapeutic intervention strategies and drugs design, as well as for planning high-throughput new experiments. Methods have been developed for gene networks modeling and identification from expression profiles. However, an important open problem regards how to validate such approaches and its results. This work presents an objective approach for validation of gene network modeling and identification which comprises the following three main aspects: (1) Artificial Gene Networks (AGNs) model generation through theoretical models of complex networks, which is used to simulate temporal expression data; (2) a computational method for gene network identification from the simulated data, which is founded on a feature selection approach where a target gene is fixed and the expression profile is observed for all other genes in order to identify a relevant subset of predictors; and (3) validation of the identified AGN-based network through comparison with the original network. The proposed framework allows several types of AGNs to be generated and used in order to simulate temporal expression data. The results of the network identification method can then be compared to the original network in order to estimate its properties and accuracy. Some of the most important theoretical models of complex networks have been assessed: the uniformly-random Erdos-Renyi (ER), the small-world Watts-Strogatz (WS), the scale-free Barabasi-Albert (BA), and geographical networks (GG). The experimental results indicate that the inference method was sensitive to average degree k variation, decreasing its network recovery rate with the increase of k. The signal size was important for the inference method to get better accuracy in the network identification rate, presenting very good results with small expression profiles. However, the adopted inference method was not sensible to recognize distinct structures of interaction among genes, presenting a similar behavior when applied to different network topologies. In summary, the proposed framework, though simple, was adequate for the validation of the inferred networks by identifying some properties of the evaluated method, which can be extended to other inference methods.

Identification of archaeal proteins that affect the exosome function in vitro

Background: The archaeal exosome is formed by a hexameric RNase PH ring and three RNA binding subunits and has been shown to bind and degrade RNA in vitro. Despite extensive studies on the eukaryotic exosome and on the proteins interacting with this complex, little information is yet available on the identification and function of archaeal exosome regulatory factors. Results: Here, we show that the proteins PaSBDS and PaNip7, which bind preferentially to poly-A and AU-rich RNAs, respectively, affect the Pyrococcus abyssi exosome activity in vitro. PaSBDS inhibits slightly degradation of a poly-rA substrate, while PaNip7 strongly inhibits the degradation of poly-A and poly-AU by the exosome. The exosome inhibition by PaNip7 appears to depend at least partially on its interaction with RNA, since mutants of PaNip7 that no longer bind RNA, inhibit the exosome less strongly. We also show that FITC-labeled PaNip7 associates with the exosome in the absence of substrate RNA. Conclusions: Given the high structural homology between the archaeal and eukaryotic proteins, the effect of archaeal Nip7 and SBDS on the exosome provides a model for an evolutionarily conserved exosome control mechanism.

A Component of the Xanthomonadaceae Type IV Secretion System Combines a VirB7 Motif with a N0 Domain Found in Outer Membrane Transport Proteins

Type IV secretion systems (T4SS) are used by Gram-negative bacteria to translocate protein and DNA substrates across the cell envelope and into target cells. Translocation across the outer membrane is achieved via a ringed tetradecameric outer membrane complex made up of a small VirB7 lipoprotein (normally 30 to 45 residues in the mature form) and the C-terminal domains of the VirB9 and VirB10 subunits. Several species from the genera of Xanthomonas phytopathogens possess an uncharacterized type IV secretion system with some distinguishing features, one of which is an unusually large VirB7 subunit (118 residues in the mature form). Here, we report the NMR and 1.0 angstrom X-ray structures of the VirB7 subunit from Xanthomonas citri subsp. citri (VirB7(XAC2622)) and its interaction with VirB9. NMR solution studies show that residues 27-41 of the disordered flexible N-terminal region of VirB7(XAC2622) interact specifically with the VirB9 C-terminal domain, resulting in a significant reduction in the conformational freedom of both regions. VirB7(XAC2622) has a unique C-terminal domain whose topology is strikingly similar to that of N0 domains found in proteins from different systems involved in transport across the bacterial outer membrane. We show that VirB7(XAC2622) oligomerizes through interactions involving conserved residues in the N0 domain and residues 42-49 within the flexible N-terminal region and that these homotropic interactions can persist in the presence of heterotropic interactions with VirB9. Finally, we propose that VirB(7XAC2622) oligomerization is compatible with the core complex structure in a manner such that the N0 domains form an extra layer on the perimeter of the tetradecameric ring.

Polymer matrix sensitizing effect on photoluminescence properties of Eu(3+)-beta-diketonate complex doped into poly-beta-hydroxybutyrate (PHB) in film form

In this work is reported the sensitization effect by polymer matrices on the photoluminescence properties of diaquatris(thenoyltrifluoroacetonate)europium(III), [Eu(tta)(3)(H(2)O)(2)], doped into poly-beta-hydroxybutyrate (PHB) with doping percentage at 1, 3, 5, 7 and 10% (mass) in film form. TGA results indicated that the Eu(3+) complex precursor was immobilized in the polymer matrix by the interaction between the Eu(3+) complex and the oxygen atoms of the PHB polymer when the rare earth complex was incorporated in the polymeric host. The thermal behaviour of these luminescent systems is similar to that of the undoped polymer, however, the T(onset) temperature of decomposition decreases with increase of the complex doping concentration. The emission spectra of the Eu(3+) complex doped PHB films recorded at 298 K exhibited the five characteristic bands arising from the (5)D(0) -> (7)F(J) intraconfigurational transitions (J = 0-4). The fact that the quantum efficiencies eta of the doped film increased significantly revealed that the polymer matrix acts as an efficient co-sensitizer for Eu(3+) luminescent centres and therefore enhances the quantum efficiency of the emitter (5)D(0) level. The luminescence intensity decreases, however, with increasing precursor concentration in the doped polymer to greater than 5% where a saturation effect is observed at this specific doping percentage, indicating that changes in the polymeric matrix improve the absorption property of the film, consequently quenching the luminescent effect.

Complex kinetics, high frequency oscillations and temperature compensation in the electro-oxidation of ethylene glycol on platinum

Despite the fact that the majority of the catalytic electro-oxidation of small organic molecules presents oscillatory kinetics under certain conditions, there are few systematic studies concerning the influence of experimental parameters on the oscillatory dynamics. Of the studies available, most are devoted to C1 molecules and just some scattered data are available for C2 molecules. We present in this work a comprehensive study of the electro-oxidation of ethylene glycol on polycrystalline platinum surfaces and in alkaline media. The system was studied by means of electrochemical impedance spectroscopy, cyclic voltammetry, and chronoamperometry, and the impact of parameters such as applied current, ethylene glycol concentration, and temperature were investigated. As in the case of other parent systems, the instabilities in this system were associated with a hidden negative differential resistance, as identified by impedance data. Very rich and robust dynamics were observed, including the presence of harmonic and mixed mode oscillations and chaotic states, in some parameter region. Oscillation frequencies of about 16 Hz characterized the fastest oscillations ever reported for the electro-oxidation of small organic molecules. Those high frequencies were strongly influenced by the electrolyte pH and far less affected by the EG concentration. The system was regularly dependent on temperature under voltammetric conditions but rather independent within the oscillatory regime.

Complex Oscillatory Response of a PEM Fuel Cell Fed with H(2)/CO and Oxygen

Oscillatory kinetics is commonly observed in the electrocatalytic oxidation of most species that can be used in fuel cell devices. Examples include formic acid, methanol, ethanol, ethylene glycol, and hydrogen/carbon monoxide mixtures, and most papers refer to half-cell experiments. We report in this paper the experimental investigation of the oscillatory dynamics in a proton exchange membrane (PEM) fuel cell at 30 degrees C. The system consists of a Pt/C cathode fed with oxygen and a PtRu (1:1)/C anode fed with H(2) mixed with 100 ppm of CO, and was studied at different cell currents and anode flow rates. Many different states including periodic and nonperiodic series were observed as a function of the cell current and the H(2)/CO flow rate. In general, aperiodic/chaotic states were favored at high currents and low flow rates. The dynamics was further characterized in terms of the relationship between the oscillation amplitude and the subsequent time required for the anode to get poisoned by carbon monoxide. Results are discussed in terms of the mechanistic aspects of the carbon monoxide adsorption and oxidation. (C) 2010 The Electrochemical Society. [DOI: 10.1149/1.3463725] All rights reserved.

Dynamic light scattering and optical absorption spectroscopy study of pH and temperature stabilities of the extracellular hemoglobin of Glossoscolex paulistus

The extracellular hemoglobin of Glossoscolex paulistus (HbGp) is constituted of subunits containing heme groups, monomers and trimers, and nonheme structures, called linkers, and the whole protein has a minimum molecular mass near 3.1 x 10(6) Da. This and other proteins of the same family are useful model systems for developing blood substitutes due to their extracellular nature, large size, and resistance to oxidation. HbGp samples were studied by dynamic light scattering (DLS). In the pH range 6.0-8.0, HbGp is stable and has a monodisperse size distribution with a z-average hydrodynamic diameter (D-h) of 27 +/- 1 nm. A more alkaline pH induced an irreversible dissociation process, resulting in a smaller D-h of 10 +/- 1 nm. The decrease in D-h suggests a complete hemoglobin dissociation. Gel filtration chromatography was used to show unequivocally the oligomeric dissociation observed at alkaline pH. At pH 9.0, the dissociation kinetics is slow, taking a minimum of 24 h to be completed. Dissociation rate constants progressively increase at higher pH, becoming, at pH 10.5, not detectable by DILS. Protein temperature stability was also pH-dependent. Melting curves for HbGp showed oligomeric dissociation and protein denaturation as a function of pH. Dissociation temperatures were lower at higher pH. Kinetic studies were also performed using ultraviolet-visible absorption at the Soret band. Optical absorption monitors the hemoglobin autoxidation while DLS gives information regarding particle size changes in the process of protein dissociation. Absorption was analyzed at different pH values in the range 9.0-9.8 and at two temperatures, 25 degrees C and 38 degrees C. At 25 degrees C, for pH 9.0 and 9.3, the kinetics monitored by ultraviolet-visible absorption presents a monoexponential behavior, whereas for pH 9.6 and 9.8, a biexponential behavior was observed, consistent with heme heterogeneity at more alkaline pH. The kinetics at 38 degrees C is faster than that at 25 degrees C and is biexponential in the whole pH range. DLS dissociation rates are faster than the autoxidation dissociation rates at 25 degrees C. Autoxiclation and dissociation processes are intimately related, so that oligomeric protein dissociation promotes the increase of autoxidation rate and vice versa. The effect of dissociation is to change the kinetic character of the autoxidation of hemes from monoexponential to biexponential, whereas the reverse change is not as effective. This work shows that DLS can be used to follow, quantitatively and in real time, the kinetics of changes in the oligomerization of biologic complex supramolecular systems. Such information is relevant for the development of mimetic systems to be used as blood substitutes.

LEARNING A COMPLEX MOTOR SKILL FROM VIDEO AND POINT-LIGHT DEMONSTRATIONS

The aim of this Study was to compare the learning process of a highly complex ballet skill following demonstrations of point light and video models 16 participants divided into point light and video groups (ns = 8) performed 160 trials of a pirouette equally distributed in blocks of 20 trials alternating periods of demonstration and practice with a retention test a day later Measures of head and trunk oscillation coordination d1 parity from the model and movement time difference showed similarities between video and point light groups ballet experts evaluations indicated superiority of performance in the video over the point light group Results are discussed in terms of the task requirements of dissociation between head and trunk rotations focusing on the hypothesis of sufficiency and higher relevance of information contained in biological motion models applied to learning of complex motor skills