Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding

We show that diffusion can play an important role in protein-folding kinetics. We explicitly calculate the diffusion coefficient of protein folding in a lattice model. We found that diffusion typically is configuration- or reaction coordinate-dependent. The diffusion coefficient is found to be decreasing with respect to the progression of folding toward the native state, which is caused by the collapse to a compact state constraining the configurational space for exploration. The configuration- or position-dependent diffusion coefficient has a significant contribution to the kinetics in addition to the thermodynamic free-energy barrier. It effectively changes (increases in this case) the kinetic barrier height as well as the position of the corresponding transition state and therefore modifies the folding kinetic rates as well as the kinetic routes. The resulting folding time, by considering both kinetic diffusion and the thermodynamic folding free-energy profile, thus is slower than the estimation from the thermodynamic free-energy barrier with constant diffusion but is consistent with the results from kinetic simulations. The configuration- or coordinate-dependent diffusion is especially important with respect to fast folding, when there is a small or no free-energy barrier and kinetics is controlled by diffusion. Including the configurational dependence will challenge the transition state theory of protein folding. The classical transition state theory will have to be modified to be consistent. The more detailed folding mechanistic studies involving phi value analysis based on the classical transition state theory also will have to be modified quantitatively.

The critical barrier to progress in dentine bonding with the etch-and-rinse technique

Objectives: The lack of durability in resin-dentine bonds led to the use of chlorhexidine as MMP-inhibitor to prevent the degradation of hybrid layers. Biomimetic remineralisation is a concept-proven approach in preventing the degradation of resin-dentine bonds. The purpose of this study is to examine the integrity of aged resin-dentine interfaces created with a nanofiller-containing etch-and-rinse adhesive after the application of these two approaches.Methods: The more established MMP-inhibition approach was examined using a parallel in vivo and in vitro ageing design to facilitate comparison with the biomimetic remineralisation approach using an in vitro ageing design. Specimens bonded without chlorhexidine exhibited extensive degradation of the hybrid layer after 12 months of in vivo ageing.Results: Dissolution of nanofillers could be seen within a water-rich zone within the adhesive layer. Although specimens bonded with chlorhexidine exhibited intact hybrid layers, water-rich regions remained in those hybrid layers and degradation of nanofillers occurred within the adhesive layer. Specimens subjected to in vitro biomimetic remineralisation followed by in vitro ageing demonstrated intrafibrillar collagen remineralisation within hybrid layers and deposition of mineral nanocrystals in nanovoids within the adhesive.Conclusions: The impact was realized by understanding the lack of an inherent mechanism to remove water from resin-dentine interfaces as the critical barrier to progress in bonding with the etch-and-rinse technique. The experimental biomimetic remineralisation strategy offers a creative solution for incorporating a progressive hydration mechanism to achieve this goal, which warrants its translation into a clinically applicable technique. (C) 2011 Elsevier Ltd. All rights reserved.

Tunneling time through a barrier using the local value of a time operator

A time for a quantum particle to traverse a barrier is obtained for stationary states by setting the local value of a time operator equal to a constant. This time operator, called the tempus operator because it is distinct from the time of evolution, is defined as the operator canonically conjugate to the energy operator. The local value of the tempus operator gives a complex time for a particle to traverse a barrier. The method is applied to a particle with a semiclassical wave function, which gives, in the classical limit, the correct classical traversal time. It is also applied to a quantum particle tunneling through a rectangular barrier. The resulting complex tunneling time is compared with complex tunneling times from other methods.

Dynamical localization of matter-wave solitons in managed barrier potentials

The bright matter-wave soliton propagation through a barrier with a rapidly oscillating position is investigated. The averaged-over rapid oscillations Gross-Pitaevskii equation is derived, where the effective potential has the form of a finite well. Dynamical trapping and quantum tunneling of the soliton in the effective finite well are investigated. The analytical predictions for the effective soliton dynamics is confirmed by numerical simulations of the full Gross-Pitaevskii equation.

Tunneling time through a rectangular barrier

In this paper, we discuss the tunneling time of a quantum particle through a rectangular barrier. The reflection and transmission times associated with the wave packets representing the particle are discussed. By using an initial Gaussian momentum distribution, we carry out a comparative analysis of the stationary phases of the incident, reflected, and transmitted wave packets leading to the reflection and transmission times at, and Delta t(T), respectively. In the present treatment of this old and very known problem we take into account the deformations of the reflected and transmitted momentum distributions. These deformations produce a dependence of the reflection and transmission times on the location of the initial wave packet. In a parallel calculation, by numerically monitoring the time evolution of the system, we characterize a reflection and a transmission time. Such times agree with the ones obtained via the stationary phase method. [S1050-2947(98)07912-8].

Patch-size and isolation effects in the Fisher-Kolmogorov equation

We examine the classical problem of the existence of a threshold size for a patch to allow for survival of a given population in the case where the patch is not completely isolated. The surrounding habitat matrix is characterized by a non-zero carrying capacity. We show that a critical patch size cannot be strictly defined in this case. We also obtain the saturation density in such a patch as a function of the size of the patch and the relative carrying capacity of the outer region. We argue that this relative carrying capacity is a measure of the isolation of the patch. Our results are then compared with conclusions drawn from observations of the population dynamics of understorey birds in fragments of the Amazonian forest and shown to qualitatively agree with them, offering an explanation for the importance of dispersal and isolation in these observations. Finally, we show that a generalized critical patch size can be introduced resorting to threshold densities for the observation of a given species.

CRITICAL EXPONENTS and SCALING PROPERTIES FOR THE CHAOTIC DYNAMICS of A PARTICLE IN A TIME-DEPENDENT POTENTIAL BARRIER

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The natural radioactivity in water by gross alpha and beta measurements

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A multi-screening approach for marine-derived fungal metabolites and the isolation of cyclodepsipeptides from Beauveria felina

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Influence of cerium (IV) ions on the mechanism of organosilane polymerization and on the improvement of its barrier properties

In this work, the effect of cerium (IV) ammonium nitrate (CAN) addition on the polymerization of bis-[triethoxysilyl]ethane (BTSE) film applied on carbon steel was studied. The electrochemical characterization of the films was carried out in 0.1 mol L(-1) NaCl solution by open-circuit potential measurements, anodic and cathodic polarization curves and electrochemical impedance spectroscopy (EIS). Morphological and chemical characterization were performed by atomic force microscopy (AFM), contact angle measurements, infrared-spectroscopy, nuclear magnetic resonance and thermogravimetric analysis. The results have clearly shown the improvement on the protective properties of the Ce(4+) modified film as a consequence of the formation of a more uniform and densely reticulated silane film. A mechanism is proposed to explain the accelerating role of Ce(4+) ions on the cross-linking of the silane layer. (C) 2008 Elsevier Ltd. All rights reserved.

Bioactive Metabolites Produced by Penicillium sp.1 and sp.2, Two Endophytes Associated with Alibertia macrophylla (Rubiaceae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Preparative separation of flavonoids from the medicinal plant Davilla elliptica St. Hill. by high-speed counter-current chromatography

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Detection of Mycoplasma hyopneumoniae by polymerase chain reaction in swine presenting respiratory problems

A Nested-PCR (N-PCR) tem como objetivo melhorar a sensibilidade do diagnóstico direto da Pneumonia Enzoótica Suína, pois o isolamento do Mycoplasma hyopneumoniae é trabalhoso tornando-se inviável na rotina. Neste trabalho, foi realizado um projeto piloto para a otimização da técnica de N-PCR, utilizando três variáveis: tipo de amostra biológica, meio de transporte da amostra e método de extração do DNA, utilizando oito animais. Os resultados obtidos foram empregados no segundo experimento para a validação do teste utilizando 40 animais. Os resultados obtidos, pela otimização da N-PCR, neste trabalho, permite sugerir esta prova como método de diagnóstico de rotina no monitoramento das infecções por Mycoplasma hyopneumoniae em granjas de suínos.

Isolation and identification of mycobacteria from livestock specimens and milk obtained in Brazil

The prevalence of Mycobacterium bovis and other mycobacterial species in livestock specimens and milk was evaluated. An emphasis was placed upon the distribution of these organisms in milk that is readily available to the public that was either untreated, pasteurized, or treated using ultra high temperature. Twenty-two pathologic specimens from livestock (bovine, swine and bubaline) in five Brazilian states and 128 bovine milk samples from retail markets in the State of São Paulo were examined for mycobacteria. Identification was made by classical biochemical tests, thin layer chromatography of mycolic acids and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. Mycobacteria were isolated from 15 (68.2%) caseous lesions and from 23 (18%) milk samples. Eleven isolates were identified as M. bovis, and the remaining 27 nontuberculous mycobacterial isolates were represented by five species and six unidentified rapidly growing mycobacterial strains. The data demonstrate that animal products in Brazil are frequent reservoirs of mycobacteria and may pose a risk to the public.

Bacterial diversity of soil under eucalyptus assessed by 16S rDNA sequencing analysis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)