Structural effects of a dimer interface mutation on catalytic activity of triosephosphate isomerase.The role of conserved residues and complementary mutations

The active site of triosephosphate isomerase (TIM, EC: 5.3.1.1), a dimeric enzyme, lies very close to the subunit interface. Attempts to engineer monomeric enzymes have yielded well-folded proteins with dramatically reduced activity. The role of dimer interface residues in the stability and activity of the Plasmodium falciparum enzyme, PfTIM, has been probed by analysis of mutational effects at residue 74. The PfTIM triple mutant W11F/W168F/Y74W (Y74W*) has been shown to dissociate at low protein concentrations, and exhibits considerably reduced stability in the presence of denaturants, urea and guanidinium chloride. The Y74W* mutant exhibits concentration-dependent activity, with an approximately 22-fold enhancement of kcat over a concentration range of 2.5–40 μm, suggesting that dimerization is obligatory for enzyme activity. The Y74W* mutant shows an approximately 20-fold reduction in activity compared to the control enzyme (PfTIM WT*, W11F/W168F). Careful inspection of the available crystal structures of the enzyme, together with 412 unique protein sequences, revealed the importance of conserved residues in the vicinity of the active site that serve to position the functional K12 residue. The network of key interactions spans the interacting subunits. The Y74W* mutation can perturb orientations of the active site residues, due to steric clashes with proximal aromatic residues in PfTIM. The available crystal structures of the enzyme from Giardia lamblia, which contains a Trp residue at the structurally equivalent position, establishes the need for complementary mutations and maintenance of weak interactions in order to accommodate the bulky side chain and preserve active site integrity.

Free range chicken farms - odour emissions and nutrient management

Quantification of air emissions, in particular, from free range farms for comparison with conventional farming may demonstrate that free range farming has lower emissions. This finding may support conventional farms that are under pressure due to air quality impacts to more readily convert to free range. Industry will benefit by maintaining/increasing production and the community will benefit from fewer impacts.

Ce1-xRuxO2-delta (x=0.05, 0.10): A New High Oxygen Storage Material and Pt, Pd-Free Three-Way Catalyst

Nanocrystalline Ce1-xRuxO2-delta (x = 0.05 and 0.10) of 8-10 nm sizes have been synthesized by hydrothermal method using melamine as complexing agent. Compounds have been characterized by powder X-ray diffraction (XRD), transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), and energy-dispersive X-ray analysis (EDX) and their structures have been refined by the Rietveld method.The compounds crystallize in fluorite structure and the composition is Ce1-xRuxO2-x/2 where Ru is in +4 state and Ce is in mixed-valence (+3, +4) state. Substitution of Ru4+ ion in CeO2 activated the lattice oxygen. Ce1-xRuxO2-x/2 reversibly releases 0.22[O] and 0.42[O] for x = 0.05 and 0.10, respectively, which is higher than the maximumpossible OSC of 0.22 [O] observed for Ce0.50Zr0.50O2. Utilization of Higher OSC of Ce1-xRuxO2-delta (x = 0.05 and 0.10) is also reflected in terms of low-temperature CO oxidation with these catalysts, both in the presence and absence of feed oxygen. The Ru4+ ion acts as an active center for reducing molecules (CO, hydrocarbon ``HC'') and oxide ion vacancy acts as an active center for O-2 and NO, leading to low-temperature NO conversion to N-2. Thus due to Ru4+ ion, Ce1-xRuxO2-delta is not just a high oxygen storage material but also shows high activity toward CO, hydrocarbon ``HC'' oxidation, and NO reduction by CO at low temperature with high N-2 selectivity for three-way catalysis.

Biochemical and structural characterization of residue 96 mutants of Plasmodium falciparum triosephosphate isomerase: active-site loop conformation, hydration and identification of a dimer-interface ligand-binding site

Plasmodium falciparum TIM (PfTIM) is unique in possessing a Phe residue at position 96 in place of the conserved Ser that is found in TIMs from the majority of other organisms. In order to probe the role of residue 96, three PfTIM mutants, F96S, F96H and F96W, have been biochemically and structurally characterized. The three mutants exhibited reduced catalytic efficiency and a decrease in substrate-binding affinity, with the most pronounced effects being observed for F96S and F96H. The k(cat) values and K-m values are (2.54 +/- 0.19) x 10(5) min(-1) and 0.39 +/- 0.049 mM, respectively, for the wild type; (3.72 +/- 0.28) x 10(3) min(-1) and 2.18 +/- 0.028 mM, respectively, for the F96S mutant;(1.11 +/- 0.03) x 10(4) min(-1) and 2.62 +/- 0.042 mM, respectively, for the F96H mutant; and (1.48 +/- 0.05) x 10(5) min(-1) and 1.20 +/- 0.056 mM, respectively, for the F96W mutant. Unliganded and 3-phosphoglycerate (3PG) complexed structures are reported for the wild-type enzyme and the mutants. The ligand binds to the active sites of the wild-type enzyme (wtPfTIM) and the F96W mutant, with a loop-open state in the former and both open and closed states in the latter. In contrast, no density for the ligand could be detected at the active sites of the F96S and F96H mutants under identical conditions. The decrease in ligand affinity could be a consequence of differences in the water network connecting residue 96 to Ser73 in the vicinity of the active site. Soaking of crystals of wtPfTIM and the F96S and F96H mutants resulted in the binding of 3PG at a dimer-interface site. In addition, loop closure at the liganded active site was observed for wtPfTIM. The dimer-interface site in PfTIM shows strong electrostatic anchoring of the phosphate group involving the Arg98 and Lys112 residues of PfTIM.

Singularity-free cosmology: A simple model

The nonminimal coupling of a self-interacting complex scalar field with gravity is studied. For a Robertson-Walker open universe the stable solutions of the scalar-field equations are time dependent. As a result of this, a novel spontaneous symmetry breaking occurs which leads to a varying effective gravitational coupling coefficient. It is found that the coupling coefficient changes sign below a critical ‘‘radius’’ of the Universe implying the appearance of repulsive gravity. The occurrence of the repulsive interaction at an early epoch facilitates singularity avoidance. The model also provides a solution to the horizon problem.

Transgenic rootstocks for production of GM-free fruit

Development of regeneration and transformation methods for genetic improvement of rootstocks for mango, avocado and citrus.

ACIAR Producing virus-free sweetpotato planting material in Papua New Guinea

The aim of this small research activity (SRA) is to provide a foundation for establishing a national 'clean seed system' for sweetpotato in Papua New Guinea.

Surface-enhanced Raman scattering of molecules adsorbed on nanocrystalline Au and Ag films formed at the organic-aqueous interface

Surface-enhanced Raman scattering (SERS) of pyridine adsorbed on ultrathin nanocrystalline Au and Ag films generated at the liquid-liquid interface has been investigated. The shifts and intensification of bands formed with these films comprising metal nanoparticles are comparable to those found with other types of Au and Ag substrates. SERS of rhodamine 6G adsorbed on Ag films has also been studied. The results demonstrate that nanocrystalline metal films prepared by the simple method involving the organic-aqueous interface can be used effectively for SERS investigations.

Phase field study of precipitate growth: Effect of misfit strain and interface curvature

We have used phase field simulations to study the effect of misfit and interfacial curvature on diffusion-controlled growth of an isolated precipitate in a supersaturated matrix. Treating our simulations as computer experiments, we compare our simulation results with those based on the Zener–Frank and Laraia–Johnson–Voorhees theories for the growth of non-misfitting and misfitting precipitates, respectively. The agreement between simulations and the Zener–Frank theory is very good in one-dimensional systems. In two-dimensional systems with interfacial curvature (with and without misfit), we find good agreement between theory and simulations, but only at large supersaturations, where we find that the Gibbs–Thomson effect is less completely realized. At small supersaturations, the convergence of instantaneous growth coefficient in simulations towards its theoretical value could not be tracked to completion, because the diffusional field reached the system boundary. Also at small supersaturations, the elevation in precipitate composition matches well with the theoretically predicted Gibbs–Thomson effect in both misfitting and non-misfitting systems.

Approximation algorithm for maximum independent set in planar traingle-free graphs

The maximum independent set problem is NP-complete even when restricted to planar graphs, cubic planar graphs or triangle free graphs. The problem of finding an absolute approximation still remains NP-complete. Various polynomial time approximation algorithms, that guarantee a fixed worst case ratio between the independent set size obtained to the maximum independent set size, in planar graphs have been proposed. We present in this paper a simple and efficient, O(|V|) algorithm that guarantees a ratio 1/2, for planar triangle free graphs. The algorithm differs completely from other approaches, in that, it collects groups of independent vertices at a time. Certain bounds we obtain in this paper relate to some interesting questions in the theory of extremal graphs.

Dynamic structure factor across the liquid-solid interface: appearance of a delta-function elastic peak

We present a theoretical calculation of the dynamic structure factor, S(k, ω), at the liquid-solid interface for large values of the wavevector k. An analytic expression is derived which shows the evolution of the elastic peak as the solid surface is approached from the liquid side.

Discussion of enthalpy, entropy and free energy of formation of GaN

Presented in this letter is a critical discussion of a recent paper on experimental investigation of the enthalpy, entropy and free energy of formation of gallium nitride (GaN) published in this journal [T.J. Peshek, J.C. Angus, K. Kash, J. Cryst. Growth 311 (2008) 185-189]. It is shown that the experimental technique employed detects neither the equilibrium partial pressure of N-2 corresponding to the equilibrium between Ga and GaN at fixed temperatures nor the equilibrium temperature at constant pressure of N-2. The results of Peshek et al. are discussed in the light of other information on the Gibbs energy of formation available in the literature. Entropy of GaN is derived from heat-capacity measurements. Based on a critical analysis of all thermodynamic information now available, a set of optimized parameters is identified and a table of thermodynamic data for GaN developed from 298.15 to 1400 K.

Free convection heat transfer to mercury in vertical annuli

Data on free convection heat transfer to water and mercury are collected using a test rig in vertical annuli of three radii ratios, the walls of which are maintained at uniform temperatures. A theoretical analysis of the boundary layer equations has been attempted using local similarity transformation and double boundary layer approach. Correlations derived from the present theoretical analysis are compared with the analysis and the experimental data available in literature for non-metallic fluids and also with the present experimental data on water and mercury. Generalised correlations are set up for expressing the ratio of heat transferred by convection to the heat transferred by pure conduction and Nusselt's number, in terms of Grashof, Rayleigh and Prandtl numbers, based on the theoretical analysis and the present data on mercury and water. The present generalised correlations agree with the reported and present data for non-metallic fluids and liquid metals with an average deviation of 9% and maximum deviation of ± 13.7%.

Some studies on free vibration of composite laminates

Free vibration analysis is carried out to study the vibration characteristics of composite laminates using the modified shear deformation, layered, composite plate theory and employing the Rayleigh-Ritz energy approach. The analysis is presented in a unified form so as to incorporate all different combinations of laminate boundary conditions and with full coverage with regard to the various design parameters of a laminated plate. A parametric study is made using a beam characteristic function as the admissible function for the numerical calculations. The numerical results presented here are for an example case of fully clamped boundary conditions and are compared with previously published results. The effect of parameters, such as the aspect ratio of plates, ply-angle, number of layers and also the thickness ratios of plies in laminates on the frequencies of the laminate, is systematically studied. It is found that for anti-symmetric angle-ply or cross-ply laminates unique numerical values of the thickness ratios exist which improve the vibration characteristics of such laminates. Numerical values of the non-dimensional frequencies and nodal patterns, using the thickness ratio distribution of the plies, are then obtained for clamped laminates, fabricated out of various commonly used composite materials, and are presented in the form of the design curves.