Functional Bacterial Amyloids: Understanding Fibrillation,Regulating Biofilm Fibril Formation and Organizing Surface Assemblies

Functional amyloid is produced by many organisms but is particularly well understood in bacteria, where proteins such as CsgA (E. coli) and FapC (Pseudomonas) are assembled as functional bacterial amyloid (FuBA) on the cell surface in a carefully optimized process. Besides a host of helper proteins, FuBA formation is aided by multiple imperfect repeats which stabilize amyloid and streamline the aggregation mechanism to a fast-track assembly dominated by primary nucleation. These repeats, which are found in variable numbers in Pseudomonas, are most likely the structural core of the fibrils, though we still lack experimental data to determine whether the repeats give rise to β-helix structures via stacked β-hairpins (highly likely for CsgA) or more complicated arrangements (possibly the case for FapC). The response of FuBA fibrillation to denaturants suggests that nucleation and elongation involve equal amounts of folding, but protein chaperones preferentially target nucleation for effective inhibition. Smart peptides can be designed based on these imperfect repeats and modified with various flanking sequences to divert aggregation to less stable structures, leading to a reduction in biofilm formation. Small molecules such as EGCG can also divert FuBA to less organized structures, such as partially-folded oligomeric species, with the same detrimental effect on biofilm. Finally, the strong tendency of FuBA to self-assemble can lead to the formation of very regular two-dimensional amyloid films on structured surfaces such as graphite, which strongly implies future use in biosensors or other nanobiomaterials. In summary, the properties of functional amyloid are a much-needed corrective to the unfortunate association of amyloid with neurodegenerative disease and a testimony to nature’s ability to get the best out of a protein fold.     

Determination of H2S,COS, CS2 and SO2 by an aluminium nitride nanocluster: DFT studies

ABSTRACT

Density functional theory calculations were used to investigate the potential application of an AlN nanocluster in the detection of H₂S, COS, CS₂ and SO₂ gases. In overall, the order of strength of interaction of these gases with the nanocluster is as follows: SO₂ (E_ad?=??17.6?kcal/mol)?>?H₂S (E_ad?=??14.0?kcal/mol)?>?COS (E_ad?=??8.4?kcal/mol)?>?CS₂ (E_ad?=??4.5?kcal/mol). This indicates that by increasing the electric dipole moment, the adsorption energy becomes more negative. We found that the Al₁₂N₁₂ nanocluster may be a promising work function-type sensor for SO₂ gas among the studied gases. Also, it is an electronic sensor for both SO₂ and CS₂ gases but selectively acts between them because of their different effects on the electrical conductivity. It is neither work function-type nor electronic sensor for H₂S and COS gases. The AlN nanocluster benefits from a short recovery time about 7.7?s and 18.0?ms for desorption of SO₂ and CS₂ gases from its surface at room temperature, respectively. It is also concluded that this cluster can work at a humid environment.     

A combined crossed molecular beam and quasiclassical trajectory study of the Titan-relevant N(2D) + D2O reaction

Following a recent investigation on the N(²D) + H₂O reaction [Homayoon et al., J. Phys. Chem. Lett. 5, 3508 (2014)], we report on an experimental and theoretical study of the isotopologue N(²D) + D₂O reaction. Crossed molecular beam (CMB) experiments were conducted at a collision energy of 10.3 kcal mol^–1. Quasiclassical trajectory calculations were performed on a recent potential energy surface to derive the centre-of-mass functions necessary to simulate the CMB laboratory distributions. Excellent agreement was found. The importance of the channel leading to HON/DON was confirmed. The inclusion of this channel, in addition to that leading to the isomer HNO/DNO, can affect the models considering the coupling between nitrogen and oxygen chemistry in the upper atmosphere of Titan.     

Effect of source strength on dislocation pileups in the presence of stress gradients

The behaviour of a dislocation pileup with a finite-strength source is investigated in the presence of various stress gradients within a continuum model where a free-dislocation region exists around the source. Expressions for dislocation density and stress field within the pileup are derived for the situation where there are first and second spatial gradients in applied stress. For a pileup configuration under an applied stress, yielding occurs when the force acting on the leading dislocations at the pileup tips reaches the obstacle strength, and at the same time, it is required that the source be at the threshold stress for dislocation production. A numerical methodology is presented to solve the underlying equations that represent the yielding conditions. The yield stress calculated for a pileup configuration is found to depend on stress gradients, obstacle spacing and source/obstacle strengths. It increases with increasing the first stress gradient, yet dependent on the second stress gradient. Furthermore, while the dependency of yield stress on the obstacle spacing intensifies with increasing the first stress gradient, it diminishes with an increase of second stress gradient. Therefore, the second stress gradient, as a newly introduced parameter, can provide a new physical insight into the size-dependent plasticity phenomena at small length scales.     

Investigation of a novel serpentine micromixer based on Dean flow and separation vortices

Meccanica - Passive micromixers, due to their relatively high mixing efficiency and simple fabrication, have wide applications in biological, medical, and chemical processes. Serpentine and...     

Bond graph modeling of a typical flapping wing micro-air-vehicle with the elastic articulated wings

In the present research, a new comprehensive model of a flexible articulated flapping wing robot using the bond graph approach is presented. The flapping kinematics of a two-section wing is introduced via the bond graph based approach on a hybrid mechanism providing amplitude and phase characteristics. The aerodynamic quasi-steady approach equipped with stall correlation is utilized according to the reduced flapping frequency and the angle of attack ranges. The local flow velocity and the wing position are calculated in both wing and body coordinates taking into account rotation and translation of the wing different parts. Estimation of the effective angle of attack is performed by calculating the instantaneous torque distribution on both wing sections. Aeroelastic modeling is employed in which the wing structure is assumed as an elastic Euler–Bernoulli beam at the leading edge with three linear torsional modes. In this novel integrated bond graph model, computation of the performance indices including the average lift and thrust, consumed and produced powers by flapping and mechanical efficiency are presented. Due to existence of the numerous geometric and kinematic parameters in articulated flexible flapping wing, such a model is essential for design and optimization. Consequently, an example of a typical parametric study and the results validation are carried out. It is indicated that the sensitivity of the bird performance to relative change in design variables would increase for out of phase flapping, second part stiffness, flapping amplitude, frequency and velocity respectively. It is interesting that by employing the reverse-phase flapping which is possible only via articulated wings, the maximum efficiency could be achieved. In addition, it is shown that adjusting the wing torsional stiffness is a crucial item in design of passive flapping robots. The key advantage of the two-section flapping wing is depicted as the controlling capability of the angle of attack in the outer part of the wing. Finally, the improved version of the bird is being addressed by approximately 15% progress in propulsive efficiency.

     

Thermodynamics and Phase Transition of Topological Dilatonic Lifshitz-Like Black Holes

It is known that scalar-tensor gravity models can be studied in Einstein and Jordan frames. In this paper, a model of scalar-tensor gravity in Einstein's frame is considered to calculate the Lifshitz-like black hole solutions with different horizon topologies. Thermodynamic properties and first order van der Waals-like phase transition are studied, and it is found that the Lifshitz parameter affects the phase structure. In addition, thermal stability is investigated by using the behavior of heat capacity and various methods of geometrical thermodynamics.     

Seed priming with cold plasma improved seedling performance,secondary metabolism,and expression of deacetylvindoline O-acetyltransferase gene in Catharanthus roseus

The plasma-primed seeds of Catharanthus roseus were cultured in a hormone-free culture medium under sterile conditions. Plasma of 30 or 60 s improved root length (mean = 41.4%) and biomass (mean = 47%), whereas plasma of 90 s delayed plant growth. The plasma treatments enhanced concentrations of photosynthetic pigments and soluble phenols. Plasma of 90 s increased the proline level. With a similar trend, plasma priming induced activities of phenylalanine ammonia-lyase, catalase (about twofold) and peroxidase (31%) enzymes. Plasma also upregulated the expressions of deacetylvindoline O-acetyltransferase gene by an average of 7.8 times. Similarly, the plasma-treated seedlings contained higher concentrations of alkaloids (mean = 72%). Here, molecular evidence is provided on the plasma-associated modifications in secondary metabolism.