Regulation of xylanase in Aspergillus phoenicis: a physiological and molecular approach

Microbial xylanolytic enzymes have a promising biotechnological potential, and are extensively applied in industries. In this study, induction of xylanolytic activity was examined in Aspergillus phoenicis. Xylanase activity induced by xylan, xylose or beta-methylxyloside was predominantly extracellular (93-97%). Addition of 1% glucose to media supplemented with xylan or xylose repressed xylanase production. Glucose repression was alleviated by addition of cAMP or dibutyryl-cAMP. These physiological observations were supported by a Northern analysis using part of the xylanase gene ApXLN as a probe. Gene transcription was shown to be induced by xylan, xylose, and beta-methylxyloside, and was repressed by the addition of 1% glucose. Glucose repression was partially relieved by addition of cAMP or dibutyryl cAMP.

Endophytic bacteria in long-term in vitro cultivated axenic pineapple microplants revealed by PCR-DGGE

In vitro propagated plants are believed to be free of microbes. However, after 5 years of in vitro culture of pineapple plants, without evidence of microbial contamination, the use of culture-independent molecular approach [classifying heterogeneous nucleic acids amplified via universal and specific 16S rRNA gene by polymerase chain reaction (PCR)], and further analysis by denaturing gradient gel electrophoresis (DGGE) revealed endophytic bacteria in roots, young and mature leaves of such plants. The amplification of 16S rRNA gene (Bacteria domain) with the exclusion of the plant chloroplast DNA interference, confirmed the presence of bacterial DNA, from endophytic microorganisms within microplant tissues. PCR-DGGE analysis revealed clear differences on bacterial communities depending on plant organ. Group-specific DGGE analyses also indicated differences in the structures of Actinobacteria, Alphaproteobacteria and Betaproteobacteria communities in each part of plants. The results suggest the occurrence of a succession of bacterial communities colonizing actively the microplants organs. This study is the first report that brings together evidences that pineapple microplants, previously considered axenic, harbor an endophytic bacterial community encompassing members of Actinobacteria, Alphaproteobacteria and Betaproteobacteria group which is responsive to differences in organs due to plant development.

Dynamic polarizability, Cauchy moments, and the optical absorption spectrum of liquid water: A sequential molecular dynamics/quantum mechanical approach

The dynamic polarizability and optical absorption spectrum of liquid water in the 6-15 eV energy range are investigated by a sequential molecular dynamics (MD)/quantum mechanical approach. The MD simulations are based on a polarizable model for liquid water. Calculation of electronic properties relies on time-dependent density functional and equation-of-motion coupled-cluster theories. Results for the dynamic polarizability, Cauchy moments, S(-2), S(-4), S(-6), and dielectric properties of liquid water are reported. The theoretical predictions for the optical absorption spectrum of liquid water are in good agreement with experimental information.

Electronic properties of liquid ammonia: A sequential molecular dynamics/quantum mechanics approach

The electronic properties of liquid ammonia are investigated by a sequential molecular dynamics/quantum mechanics approach. Quantum mechanics calculations for the liquid phase are based on a reparametrized hybrid exchange-correlation functional that reproduces the electronic properties of ammonia clusters [(NH(3))(n); n=1-5]. For these small clusters, electron binding energies based on Green's function or electron propagator theory, coupled cluster with single, double, and perturbative triple excitations, and density functional theory (DFT) are compared. Reparametrized DFT results for the dipole moment, electron binding energies, and electronic density of states of liquid ammonia are reported. The calculated average dipole moment of liquid ammonia (2.05 +/- 0.09 D) corresponds to an increase of 27% compared to the gas phase value and it is 0.23 D above a prediction based on a polarizable model of liquid ammonia [Deng , J. Chem. Phys. 100, 7590 (1994)]. Our estimate for the ionization potential of liquid ammonia is 9.74 +/- 0.73 eV, which is approximately 1.0 eV below the gas phase value for the isolated molecule. The theoretical vertical electron affinity of liquid ammonia is predicted as 0.16 +/- 0.22 eV, in good agreement with the experimental result for the location of the bottom of the conduction band (-V(0)=0.2 eV). Vertical ionization potentials and electron affinities correlate with the total dipole moment of ammonia aggregates. (c) 2008 American Institute of Physics.

Electronic properties of liquid hydrogen fluoride: A sequential quantum mechanical/Born-Oppenheimer molecular dynamics approach

The electronic properties of liquid hydrogen fluoride (HF) were investigated by carrying out sequential quantum mechanics/Born-Oppenheimer molecular dynamics. The structure of the liquid is in good agreement with recent experimental information. Emphasis was placed on the analysis of polarisation effects, dynamic polarisability and electronic excitations in liquid HF. Our results indicate an increase in liquid phase of the dipole moment (similar to 0.5 D) and isotropic polarisability (5%) relative to their gas-phase values. Our best estimate for the first vertical excitation energy in liquid HF indicates a blue-shift of 0.4 +/- 0.2 eV relative to that of the gas-phase monomer (10.4 eV). (C) 2010 Elsevier B.V. All rights reserved.

Only subtle protein conformational adaptations are required for ligand binding to thyroid hormone receptors: Simulations using a novel multipoint steered molecular dynamics approach

Thyroid hormone receptors (TR) are hormone-dependent transcription regulators that play a major role in human health, development, and metabolic functions. The thyroid hormone resistance syndrome, diabetes, obesity, and some types of cancer are just a few examples of important diseases that are related to TR malfunctioning, particularly impaired hormone binding. Ligand binding to and dissociation from the receptor ultimately control gene transcription and, thus, detailed knowledge of binding and release mechanisms are fundamental for the comprehension of the receptor`s biological function and development of pharmaceuticals. In this work, we present the first computational study of ligand entry into the ligand binding domain (LBD) of a nuclear receptor. We report molecular dynamics simulations of ligand binding to TRs using a generalization of the steered molecular dynamics technique designed to perform single-molecule pulling simulations along arbitrarily nonlinear driving pathways. We show that only gentle protein movements and conformational adaptations are required for ligand entry into the LBDs and that the magnitude of the forces applied to assist ligand binding are of the order of the forces involved in ligand dissociation. Our simulations suggest an alternative view for the mechanisms ligand binding and dissociation of ligands from nuclear receptors in which ligands can simply diffuse through the protein surface to reach proper positioning within the binding pocket. The proposed picture indicates that the large-amplitude protein motions suggested by the apo- and holo-RXR alpha crystallographic structures are not required, reconciling conformational changes of LBDs required for ligand entry with other nuclear receptors apo-structures that resemble the ligand-bound LBDs.

Predicting and characterizing new molecular species at a high-level theoretical approach: HSeCl, HClSe, and SeCl

New molecular species HSeCl, HClSe, and SeCl were investigated at a high level of theory, CCSD(T), with a series of correlation consistent basis sets with extrapolation to the CBS limit. Account has been taken for valence-only and core-valence correlation effects, and of anharmonic effects on the vibrational frequencies. HSeCl is 43.25 kcal mol (1) more stable than HClSe. A barrier (Delta G(#)) of 47.20 kcal mol (1) separates these species. Internuclear distances are generally overestimated by 0.008 angstrom in the valence-only correlation calculations. Inclusion of anharmonicity leads to much improved vibrational frequencies. For SeCl, we estimate Delta H(f) (0 K) = 23.96 and Delta H(f) (298.15 K) = 24.64 kcal mol (1); for HSeCl, we had 4.20 and 4.97 kcal mol (1), respectively. (C) 2010 Elsevier B.V. All rights reserved.

Biologia molecular como ferramenta no esporte de alto rendimento: possibilidades e perspectivas

Várias estratégias têm sido pensadas com o propósito de se utilizar a biologia molecular como ferramenta na pré-seleção e na seleção de talentos esportivos, na manipulação genética visando ao aumento ou à diminuição da produção de determinadas substâncias pelo organismo, na prescrição do treinamento e na recuperação de lesões. Portanto, o objetivo desta revisão é apresentar o DNA como regulador do funcionamento do organismo e de que forma alterações no perfil genético, tanto espontâneas como induzidas artificialmente, podem modular respostas fisiológicas e morfológicas por alterar a expressão de determinadas proteínas. Será dada especial atenção à descrição dos procedimentos utilizados para a manipulação genética, nos baixos riscos associados e nas estratégias que têm sido desenvolvidas com o objetivo de detectá-la. Com base em conhecimentos científicos, coerência e bom senso, diversas visões devem ser expostas e amplamente discutidas para ser definido o que é permitido e o que é proibido nas competições esportivas.

Structural and chemical basis for anticancer activity of a series of 'beta'-tubulin ligands: molecular modeling and 3D QSAR studies

An important approach to cancer therapy is the design of small molecule modulators that interfere with microtubule dynamics through their specific binding to the ²-subunit of tubulin. In the present work, comparative molecular field analysis (CoMFA) studies were conducted on a series of discodermolide analogs with antimitotic properties. Significant correlation coefficients were obtained (CoMFA(i), q² =0.68, r²=0.94; CoMFA(ii), q² = 0.63, r²= 0.91), indicating the good internal and external consistency of the models generated using two independent structural alignment strategies. The models were externally validated employing a test set, and the predicted values were in good agreement with the experimental results. The final QSAR models and the 3D contour maps provided important insights into the chemical and structural basis involved in the molecular recognition process of this family of discodermolide analogs, and should be useful for the design of new specific ²-tubulin modulators with potent anticancer activity.

Estimating losses in teleportation schemes using the phenomenological operator approach to dissipation in cavity quantum electrodynamics

In this paper, we estimate the losses during teleportation processes requiring either two high-Q cavities or a single bimodal cavity. The estimates were carried out using the phenomenological operator approach introduced by de Almeida et al. [Phys. Rev. A 62, 033815 (2000)].

Accurate band gaps of AlGaN, InGaN, and AlInN alloys calculations based on LDA-1/2 approach

We present parameter-free calculations of electronic properties of InGaN, InAlN, and AlGaN alloys. The calculations are based on a generalized quasichemical approach, to account for disorder and composition effects, and first-principles calculations within the density functional theory with the LDA-1/2 approach, to accurately determine the band gaps. We provide precise results for AlGaN, InGaN, and AlInN band gaps for the entire range of compositions, and their respective bowing parameters. (C) 2011 American Institute of Physics. [doi:10.1063/1.3576570]

Response surface methodology as an approach to determine optimal activities of lipase entrapped in sol-gel matrix using different vegetable oils

The conditions for maximization of the enzymatic activity of lipase entrapped in sol-gel matrix were determined for different vegetable oils using an experimental design. The effects of pH, temperature, and biocatalyst loading on lipase activity were verified using a central composite experimental design leading to a set of 13 assays and the surface response analysis. For canola oil and entrapped lipase, statistical analyses showed significant effects for pH and temperature and also the interactions between pH and temperature and temperature and biocatalyst loading. For the olive oil and entrapped lipase, it was verified that the pH was the only variable statistically significant. This study demonstrated that response surface analysis is a methodology appropriate for the maximization of the percentage of hydrolysis, as a function of pH, temperature, and lipase loading.

An integrated approach to produce biodiesel and monoglycerides by enzymatic interestification of babassu oil (Orbinya sp)

Two screenings of commercial lipases were performed to find a lipase with superior performance for the integrated production of biodiesel and monoglycerides. The first screening was carried out under alcoholysis conditions using ethanol as acyl acceptor to convert triglycerides to their corresponding ethyl esters (biodiesel). The second screening was performed under glycerolysis conditions to yield monoglycerides (MG). All lipases were immobilized on silica-PVA composite by covalent immobilization. The assays were performed using babassu oil and alcohols (ethanol or glycerol) in solvent free systems. For both substrates, lipase from Burkholderia cepacia (lipase PS) was found to be the most suitable enzyme to attain satisfactory yields. To further improve the process, the Response Surface Methodology (RSM) was used to determine the optima operating conditions for each biotransformation. For biodiesel production, the highest transesterification yield (>98%) was achieved within 48 h reaction at 39 degrees C using an oil-to-ethanol molar ratio of 1:7. For MG production, optima conditions corresponded to oil-to-glycerol molar ratio of 1: 15 at 55 degrees C, yielding 25 wt.% MG in 6 h reaction. These results show the potential of B. cepacia lipase to catalyze both reactions and the feasibility to consider an integrated approach for biodiesel and MG production. (C) 2009 Elsevier Ltd. All rights reserved.

An integrated molecular map of yellow passion fruit based on simultaneous maximum-likelihood estimation of linkage and linkage phases

The development of genetic maps for auto-incompatible species, such as the yellow passion fruit (Passiflora edulis Sims f.flavicarpa Deg.) is restricted due to the unfeasibility of obtaining traditional mapping populations based on inbred lines. For this reason, yellow passion fruit linkage maps were generally constructed using a strategy known as two-way pseudo-testeross, based on monoparental dominant markers segregating in a 1:1 fashion. Due to the lack of information from these markers in one of the parents, two individual (parental) maps were obtained. However, integration of these maps is essential, and biparental markers can be used for such an operation. The objective of our study was to construct an integrated molecular map for a full-sib population of yellow passion fruit combining different loci configuration generated from amplified fragment length polymorphisms (AFLPs) and microsatellite markers and using a novel approach based on simultaneous maximum-likelihood estimation of linkage and linkage phases, specially designed for outcrossing species. Of the total number of loci, approximate to 76%, 21%, 0.7%, and 2.3% did segregate in 1:1, 3:1, 1:2:1, and 1:1:1:1 ratios, respectively. Ten linkage groups (LGs) were established with a logarithm of the odds (LOD) score >= 5.0 assuming a recombination fraction : <= 0.35. On average, 24 markers were assigned per LG, representing a total map length of 1687 cM, with a marker density of 6.9 cM. No markers were placed as accessories on the map as was done with previously constructed individual maps.

Expanding cyclitol structural diversity by biocatalysis and metalocatalysis. A click chemistry approach

The palladium catalyzed cross-coupling reaction of phenyltrifluoroborate with a chemoenzymatically derived bromoazidoconduritol, combined with 1,3-dipolar cycloaddition, with a variety of alkynes is described. Fourteen new compounds were synthesized in moderate to good yields. The click chemistry reaction can be effected by using sodium ascorbate and CuSO(4) center dot 5H(2)O as catalyst in toluene-H(2)O at room temperature.