Structural plasticity in RNA and its role in the regulation of protein translation in coliphage Q beta

We have analyzed both conformational and functional changes caused by two large cis-acting deletions (delta 159 and delta 549) located within the read-through domain, a 850 nucleotide hairpin, in coliphage Q beta genomic RNA. Studies in vivo show that co-translational regulation of the viral coat and replicase genes has been uncoupled in viral genomes carrying deletion delta 159. Translational regulation is restored in deletion delta 549, a naturally evolved pseudorevertant. Structural analysis by computer modeling shows that structural features within the read-through domain of delta 159 RNA are less well determined than they are in the read-through domain of wild-type RNA, whereas predicted structure in the read-through domain of evolved pseudorevertant delta 549 is unusually well determined. Structural analysis by electron microscopy of the genomic RNAs shows that several long range helices at the base of the read-through domain, that suppress translational initiation of the viral replicase gene in the wild-type genome, have been destabilized in delta 159 RNA. In addition, the structure of local hairpins within the read-through region is more variable in delta 159 RNA than in wild-type RNA. Stable RNA secondary structure is restored in the read-through domain of delta 549 RNA. Our analyses suggest that structure throughout the read-through domain affects the regulation of viral replicase expression by altering the likelihood that long-range interactions at the base of the domain will form. We discuss possible kinetic and equilibrium models that can explain this effect, and argue that observed changes in structural plasticity within the read-through domain of the mutant genomes are key in understanding the process. During the course of these studies, we became aware of the importance of the information contained in the energy dot plot produced by the RNA secondary structure prediction program mfold. As a result, we have improved the graphical representation of this information through the use of color annotation in the predicted optimal folding. The method is presented here for the first time.     

Thermally stimulated discharge current studies in pure and fe-doped polystyrene films

Studies were made on the thermally stimulated discharge currents (TSDCs) in pure (undoped) and Fe-doped polystyrene films as a function of polarizing field, polarizing temperature and dopant concentration. While undoped films exhibited a single peak, doped films showed two peaks one at low temperatures and another at high temperatures. The low temperature peak, which exhibits a shift towards lower temperatures with increasing dopant concentration, is attributed to the relaxation of the main chain, while the high temperature peak, which shows a tendency to shift towards higher temperatures with dopant concentration, is due to space charge polarization. The TSDCs were higher for low dopant concentrations than their undoped counterparts, while for high concentrations of the dopant, the TSDCs decreased. Formation of charge transfer complexes at low dopant concentrations and molecular aggregates at higher dopant concentrations are suggested as the possible reasons for this behaviour.     

Instrumental characterization of clay by XRF,XRD and FTIR

Instrumental characterizations of the clay were performed by different techniques such as XRF, XRD and FTIR. XRF shows the chemical compositions of the clay where Al-oxide and silica oxide are present in major quantity whereas XRD confirms the presence of these minerals in clay. FTIR studies show the presence of quartz, alumina, haematite and different mineral matters.     

Hybrid predictive dynamics: a new approach to simulate human motion

A new methodology, called hybrid predictive dynamics (HPD), is introduced in this work to simulate human motion. HPD is defined as an optimization-based motion prediction approach in which the joint angle control points are unknowns in the equations of motion. Some of these control points are bounded by the experimental data. The joint torque and ground reaction forces are calculated by an inverse algorithm in the optimization procedure. Therefore, the proposed method is able to incorporate motion capture data into the formulation to predict natural and subject-specific human motions. Hybrid predictive dynamics includes three procedures, and each is a sub-optimization problem. First, the motion capture data are transferred from Cartesian space into joint space by using optimization-based inverse kinematics (IK) methodology. Secondly, joint profiles obtained from IK are interpolated by B-spline control points by using an error-minimization algorithm. Third, boundaries are built on the control points to represent specific joint profiles from experiments, and these boundaries are used to guide the predicted human motion. To predict more accurate motion, the boundaries can also be built on the kinetic variables if the experimental data are available. The efficiency of the method is demonstrated by simulating a box-lifting motion. The proposed method takes advantage of both prediction and tracking capabilities simultaneously, so that HPD has more applications in human motion prediction, especially towards clinical applications.     

Predictive simulation of human walking transitions using an optimization formulation

A general optimization formulation for transition walking prediction using 3D skeletal model is presented. The formulation is based on a previously presented one-step walking formulation (Xiang et al., Int J Numer Methods Eng 79:667–695, 2009b). Two basic transitions are studied: walk-to-stand and slow-to-fast walk. The slow-to-fast transition is used to connect slow walk to fast walk by using a step-to-step transition formulation. In addition, the speed effects on the walk-to-stand motion are investigated. The joint torques and ground reaction forces (GRF) are recovered and analyzed from the simulation. For slow-to-fast walk transition, the predicted ground reaction forces in step transition is even larger than that of the fast walk. The model shows good correlation with the experimental data for the lower extremities except for the standing ankle profile. The optimal solution of transition simulation is obtained in a few minutes by using predictive dynamics method.     

Simultaneous analysis and design optimization of nonlinear response

The optimal structural design requiring nonlinear analysis and design sensitivity analysis can be an enormous computational task. It is extremely important to explore ways to reduce the computational effort so that more realistic and larger-scale structures can be optimized. The optimal design process is iterative requiring response analysis of the structure for each design improvement. A recent study has shown that up to 90 percent of the total computational effort is spent in computing the nonlinear response of the structure during the optimal design process. Thus, efficiency of the optimization process for nonlinear structures can be substantially improved if numerical effort for analyzing the structure can be reduced. This paper explores the idea of using design sensitivity coefficients (computed at each iteration to improve design) to predict displacement response of the structure at a changed design. The iterative procedure for nonlinear analysis of the structure is then started from the predicted response. This optimization procedure is called mixed and the original procedure where sensitivity information is not used is called the conventional approach. The numerical procedures for the two approaches are developed and implemented. They are compared on some truss type structures by including both geometric and material nonlinearities. Stress, strain, displacement, and buckling load constraints are imposed. The study shows the mixed method to be numerically stable and efficient.     

Phosphate sorption isotherms in relation to P nutrition of wheat (Triticum aestivum)

The phosphate sorption isotherms are needed to explain differential plant responses to P fertilization in soils. Laboratory and greenhouse experiments investigated the use of phosphorus sorption isotherms in relation to P fertilizer requirement of wheat in ten benchmark soils of Punjab, India. The modified Mitscherlich Equation (3) was used to describe plant response observed in different soils. Maximum obtainable yield (MOY) ranged from 11.6 g pot^–1 in Gurdaspur (I) sandy clay loam to 7.0 g pot^–1 in Nabha sandy clay loam. Response to P applied @ 25 mg P kg^–1 soil was maximum (77%) in Bathinda sand and minimum in Chuharpur clay loam (33%). The response curvature varied from 3.74 × 10^–2 in Nabha sandy clay loam to 4.43 × 10^–2 in Kanjli sandy loam. The soil solution P required to produce optimum yield (90% MOY) varied from 1.61 µg ml^–1 in Bathinda sand to 0.10 µg ml^–1 in Sadhugarh clay. Dry matter yield obtained at 0.2 µg ml^–1 solution P concentration ranged from 55% in Bathinda sand to 85% of MOY in Gurdaspur (II) clay loam. At the same solution P concentration (0.1 µg P ml^–1), dry matter yield was 91% in Sadhugarh clay, 80% in Gurdaspur (II) clay loam and, 43% of MOY in Bathinda sand and eventually coincided with the decreasing maximum buffer capacity (MBC) in these soils. At the same level of sorbed P (100 mg P kg^–1 soil) the yield was observed to be inversely proportional to MBC. The study, therefore, concludes that, soils should be grouped according to their P sorption characteristics and MBC before using critical soil solution P as a criterion for obtaining optimum yields.     

Micro-computed tomography scanning approaches to quantify,parameterize and visualize bioturbation activity in clogged streambeds: A proof of concept

Fine particle clogging and faunal bioturbation are two key processes co-occurring in the hyporheic zone that potentially affect hyporheic exchange through modifications in the sediment structure of streambeds. Clogging results from excessive fine sediment infiltration and deposition in rivers, and it is known to decrease matrix porosity and potentially reduce permeability. Faunal bioturbation activity may compensate for the negative effect of clogging by reworking the sediment, increasing porosity, and preventing further infiltration of fines. Although both processes of clogging and bioturbation have received significant attention in the literature separately, their combined effects on streambed sediment structure are not well understood, mostly due to the lack of a standard methodology for their assessment. Here, we illustrate a novel methodology using X-ray computed tomography (CT), as proof of concept, to investigate how, together, clogging and bioturbation affect streambed porosity in a controlled flow-through flume. By visualising gallery formations of an upward conveyor macroinvertebrate; Lumbriculus variegatus as a model species, we quantified bioturbation activity in a clogged streambed, focusing on orientation, depth, and volume at downwelling and upwelling areas of the flume. Gallery creation increased the porosity of the streambed sediment, suggesting a potential improvement in permeability and a possible offset of clogging effects. We illustrate the promising use of X-ray CT as a tool to assess bioturbation in clogged streambeds, and the potential role of bioturbation activity supporting hyporheic exchange processes in streambeds, warranting further studies to understand the extent of bioturbation impacts in natural systems.     

(BaTiO3)1-x + (Co0.5Ni0.5Nb0.06Fe1.94O4)x nanocomposites: Structure,morphology, magnetic and dielectric properties

Two phase-based nanocomposites consisting of dielectric barium titanate (BaTiO₃ or BTO) and magnetic spinel ferrite Co_0.5Ni_0.5Nb_0.06Fe_1.94O₄ (CNNFO) have been synthesized through solid state route. Series of (BaTiO₃)_1-x + (Co_0.5Ni_0.5Nb_0.06Fe_1.94O₄)_x nanocomposites with x content of 0.00, 0.25, 0.50, 0.75, and 1.00 were considered. The structure has been examined via X-rays diffraction (XRD) and indicated the occurrence of both perovskite BTO and spinel CNNFO phases in various nanocomposites. A phase transition from tetragonal BTO structure to cubic structure occurs with inclusion of CNNFO phase. The average crystallites size of BTO phase decreases, whereas that for the CNNFO phase increases with increasing x in various nanocomposites. The morphological observations revealed that the porosity is highly reduced, and the connectivity between grains is enhanced with increasing x content. The optical properties have been investigated by UV−vis diffuse reflectance spectroscopy. The deduced band gap energy (E_g) value is found to reduce with increasing the content of spinel ferrite phase. The magnetic as well as the dielectric properties were also investigated. The analysis showed that CNNFO ferrite phase greatly affects the magnetic properties and dielectric response of BTO material. The obtained findings can be useful to enhance the performances of magneto-dielectric composite-based systems.