Crystallographic and modelling studies on Mycobacterium tuberculosis RuvA: Additional role of RuvB-binding domain and inter species variability

RuvA, along with RuvB, is involved in branch migration of heteroduplex DNA in homologous recombination. The structures of three new crystal forms of RuvA from Mycobacterium tuberculosis (MtRuvA) have been determined. The RuvB-binding domain is cleaved off in one of them. Detailed models of the complexes of octameric RuvA from different species with the Holliday junction have also been constructed. A thorough examination of the structures presented here and those reported earlier brings to light the hitherto unappreciated role of the RuvB-binding domain in determining inter-domain orientation and oligomerization. These structures also permit an exploration of the interspecies variability of structural features such as oligomerization and the conformation of the loop that carries the acidic pin, in terms of amino acid substitutions. These models emphasize the additional role of the RuvB-binding domain in Holliday junction binding. This role along with its role in oligomerization could have important biological implications.

Understanding Protein Structure from a Percolation Perspective

Underlying the unique structures and diverse functions of proteins area vast range of amino-acid sequences and a highly limited number of folds taken up by the polypeptide backbone. By investigating the role of noncovalent connections at the backbone level and at the detailed side-chain level, we show that these unique structures emerge from interplay between random and selected features. Primarily, the protein structure network formed by these connections shows simple (bond) and higher order (clique) percolation behavior distinctly reminiscent of random network models. However, the clique percolation specific to the side-chain interaction network bears signatures unique to proteins characterized by a larger degree of connectivity than in random networks. These studies reflect some salient features of the manner in which amino acid sequences select the unique structure of proteins from the pool of a limited number of available folds.

Rainfall changes over tropical montane cloud forests of southern Western Ghats, India

The southern Western Ghats tropical montane cloud forest sites (Gavi, Periyar, High wavys and Venniyar), which are characterized by frequent or seasonal cloud cover at the vegetation level, are considered one of the most threatened ecosystems in India and the world. Three out of four montane cloud forest sites studied in the southern Western Ghats had experienced diminishing trends of seasonal average and total rainfall, especially during summer monsoon season. The highest level of reduction for summer monsoon season was observed at Gavi rainforest station (>20 mm/14 years) in Kerala followed by Venniyar (>20 mm/20 years) site in Tamil Nadu. Average annual and total precipitation increased during the study period irrespective of the seasons over Periyar area, and the greatest values were recorded for season 2 (>25 mm/28 years). Positive trends for winter monsoon rainfall has been observed for three stations (Periyar, High wavys and Venniyar) except Gavi, and the trend was positive and significant (90%) for Periyar and High wavys. Increase in summer monsoon rainfall was observed for Periyar site and the trend was found to be significant (95%).

Effect of La modification on antiferroelectricity and dielectric phase transition in sol-gel grown PbZrO3 thin films

Antiferroelectricity of sol-gel grown pure and La modified PbZrO3 thin films, with a maximum extent of 6 mol%, has been characterized by temperature dependent P-E hysteresis loops within the applied electric field of 60 MV/m. It has been seen that on extent of La modification electric field induced phase transformation can be altered and at 40 degrees C its maximum value has been observed at +/- 38 MV/m on 6 mol% modifications whereas the minimum value is +/- 22 MV/m on 1 mol%. On La modification the variation of electric field induced phase transformations at 40 degrees C has been correlated with the temperature of ntiferroelectric phase condensation on cooling. The critical electric fields for saturated P-E hysteresis loops have been defined from field dependent maximum polarizations and their variations on La modification show a similar trend as found in their dielectric phase transition temperatures. (C) 2010 Elsevier Ltd. All rights reserved.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2010-30 September 2010

This article documents the addition of 229 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acacia auriculiformis x Acacia mangium hybrid, Alabama argillacea, Anoplopoma fimbria, Aplochiton zebra, Brevicoryne brassicae, Bruguiera gymnorhiza, Bucorvus leadbeateri, Delphacodes detecta, Tumidagena minuta, Dictyostelium giganteum, Echinogammarus berilloni, Epimedium sagittatum, Fraxinus excelsior, Labeo chrysophekadion, Oncorhynchus clarki lewisi, Paratrechina longicornis, Phaeocystis antarctica, Pinus roxburghii and Potamilus capax. These loci were cross-tested on the following species: Acacia peregrinalis, Acacia crassicarpa, Bruguiera cylindrica, Delphacodes detecta, Tumidagena minuta, Dictyostelium macrocephalum, Dictyostelium discoideum, Dictyostelium purpureum, Dictyostelium mucoroides, Dictyostelium rosarium, Polysphondylium pallidum, Epimedium brevicornum, Epimedium koreanum, Epimedium pubescens, Epimedium wushanese and Fraxinus angustifolia.

Modeling and design of a solar thermal system for hybrid cooking application

This paper proposes a hybrid solar cooking system where the solar energy is brought to the kitchen. The energy source is a combination of the solar thermal energy and the Liquefied Petroleum Gas (LPG) that is in common use in kitchens. The solar thermal energy is transferred to the kitchen by means of a circulating fluid. The transfer of solar heat is a twofold process wherein the energy from the collector is transferred first to an intermediate energy storage buffer and the energy is subsequently transferred from the buffer to the cooking load. There are three parameters that are controlled in order to maximize the energy transfer from the collector to the load viz, the fluid flow rate from collector to buffer, fluid flow rate from buffer to load and the diameter of the pipes. This is a complex multi energy domain system comprising energy flow across several domains such as thermal, electrical and hydraulic. The entire system is modeled using the bond graph approach with seamless integration of the power flow in these domains. A method to estimate different parameters of the practical cooking system is also explained. Design and life cycle costing of the system is also discussed. The modeled system is simulated and the results are validated experimentally. (C) 2010 Elsevier Ltd. All rights reserved.

Nanoscale Ag–Pd and Cu–Pd alloys

Nanoparticles of Ag-Pd and Gu-Pd alloys with diameters in the 5-40 nm range have been prepared over the entire range of compositions, by employing the heterogeneous reaction of dry methanol or ethanol with intimate mixtures of AgNO3+PdOx and CuOx+PdOx, respectively. The nanoscale alloys have been characterized by energy-dispersive Xray (EDX) analysis, transmission electron microscopy (TEM) and X-ray diffraction (XRD). All the alloy particles possess the fee structure and can be obtained in bulk quantities.

Amorphous, Monoclinic, and Tetragonal Porous Zirconia Through a Controlled Self-Sustained Combustion Route

Porous, large surface area, metastable zirconias, are of importance to catalytic, electrochemical, biological, and thermal insulation applications. Combustion synthesis is a very commonly used method for producing such zirconias. However, its rapid nature makes control difficult. A simple modification has been made to traditional solution combustion synthesis to address this problem. It involves the addition of starch to yield a starting mixture with a ``dough-like'' consistency. Just 5 wt% starch is seen to significantly alter the combustion characteristics of the ``dough.'' In particular, it helps to achieve better control over reaction zone temperature that is significantly lower than the one calculated by the adiabatic approximation typically used in self-propagating high-temperature synthesis. The effect of such control is demonstrated by the ability to tune dough composition to yield zirconias with different phase compositions from the relatively elusive ``amorphous'' to monoclinic (> 30 nm grain size) and tetragonal pure zirconia (< 30 nm grain size). The nature of this amorphous phase has been investigated using infrared spectroscopy. Starch content also helps tailor porosity in the final product. Zirconias with an average pore size of about 50 mu m and specific surface area as large as 110 m2/g have been obtained.

Solubilities of Pb+2, Bi+3, Sb+3 and Cu+1 sulphides in (NaCl KCl Na2S) melts

Solubilities of common metal sulfides have been determined in the (NaCl+KCl) eutectic melt with and without Na2S. A novel gas-phase equilibrium technique has been used for PbS, Bi2S3, and So2S3, and an improved liquid phase equilibrium technique for Cu2S, which eliminates the errors due to physical entrapment of the sulfide phase and segregation on quenching, enabling precise measurements to be made. Solubilities in the (NaCl+KCl) eutectic melt were determined as a function of temperature in the rante 700° to 950°C, and were found to be small. The partial molar heats of mixing of the sulfides in the eutectic melt have been calculated from the solubility measurements, to be 13.3, 31.4, 37.1, and 49.0 kcal for PbSs), Sb2S2(l), and Cu2S(s), respectively. Sodium sulfide addition was observed to enhance these solubilities, the effect being largest for Cu2S followed by Sb2S3, Bi2S3, and PbS. This effect is explained qualitatively. It was observed that PbS and Sb2S3 obey Henry's law up to saturation in (NaCl+KCl+Na2S) melts.

Analysis of Natural Half-Wave-Length Power Transmission Lines

This paper provides additional theoretical information on half-wave-length power transmission. The analysis is rendered more general by consideration of a natural half-wave line instead of a short line tuned to half-wave. The effects of line loading and its power factor on the voltage and current profiles of the line and ganerator excitation have been included. Some of the operating problems such as charging of the line and synchronization of the half-wave system are also discussed. The inevitability of power-frequency overvoltages during faults is established. Stability studies have indicated that the use of switching stations is not beneficial. Typical swing curves are also presented.

Impact of pit-toilet leachate on groundwater chemistry and role of vadose zone in removal of nitrate and E-coli pollutants in Kolar District, Karnataka, India

Assessment of chemistry of groundwater infiltrated by pit-toilet leachate and contaminant removal by vadose zone form the focus of this study. The study area is Mulbagal Town in Karnataka State, India. Groundwater level measurements and estimation of unsaturated permeability indicated that the leachate recharged the groundwater inside the town at the rate of 1 m/day. The average nitrate concentration of groundwater inside the town (148 mg/L) was three times larger than the permissible limit (45 mg/L), while the average nitrate concentration of groundwater outside the town (30 mg/L) was below the permissible limit. The groundwater inside the town exhibited E. coli contamination, while groundwater outside the town was free of pathogen contamination. Infiltration of alkalis (Na+, K+) and strong acids (Cl-, SO4 (2-)) caused the mixed Ca-Mg-Cl type (60 %) and Na-Cl type (28 %) facies to predominate groundwater inside the town, while, Ca-HCO3 (35 %), mixed Ca-Mg-Cl type (35 %) and mixed Ca-Na-HCO3 type (28 %) facies predominated groundwater outside/periphery of town. Reductions in E. coli and nitrate concentrations with vadose zone thickness indicated its participation in contaminant removal. A 4-m thickness of unsaturated sand + soft, disintegrated weathered rock deposit facilitates the removal of 1 log of E. coli pathogen. The anoxic conditions prevailing in the deeper layers of the vadose zone (> 19 m thickness) favor denitrification resulting in lower nitrate concentrations (28-96 mg/L) in deeper water tables (located at depths of -29 to -39 m).

Effect of Metal Ions (Ag, Co, Ni, and Pd) on the Visible Light Degradation of Rhodamine B by Carbon-Covered Alumina-Supported TiO2 in Aqueous Solutions

Metal-ion (Ag, Co, Ni, and Pd) doped TiO2 nanocatalysts were successfully embedded on carbon-covered alumina supports. The CCA-embedded catalysts were crystalline and had a high surface area compared to the free metal-ion doped titania nanocatalysts while they still retained the anatase phase of the core TiO2. These catalysts were photocatalytically active under solar light irradiation. Rhodamine B was used as a model pollutant and the reactivity followed a pseudo-first-order reaction kinetics. The reaction rate of the CCA-supported catalysts was Pd > Ag > Co > Ni. Among the ratios of the CCA:catalyst used, it was found that the 1:1 ratio had the fastest reaction rate, followed by the 1:2 ratio, while the 2:1 ratio exhibited the lowest reaction rate. The CCA/metal-ion doped titania were found to have photocatalytic activities comparable with those of CCA-supported titania.

Macro-Level Assessment of Seismically Induced Landslide Hazard for the State of Sikkim, India Based On GIS Technique

This paper presents a macro-level seismic landslide hazard assessment for the entire state of Sikkim, India, based on the Newmark's methodology. The slope map of Sikkim was derived from ASTER Global Digital Elevation Model (GDEM). Seismic shaking in terms of peak horizontal acceleration (PHA) at bedrock level was estimated from deterministic seismic hazard analysis (DSHA), considering point source model. Peak horizontal acceleration at the surface level for the study area was estimated based on nonlinear site amplification technique, considering B-type NEHRP site class. The PHA at surface was considered to induce driving forces on slopes, thus causing landslides. Knowing the surface level PHA and slope angle, the seismic landslide hazard assessment for each grid point was carried out using Newmark's analysis. The critical static factor of safety required to resist landslide for the PHA (obtained from deterministic analysis) was evaluated and its spatial variation throughout the study area is presented. For any slope in the study area, if the in-situ (available) static factor of safety is greater than the static factor of safety required to resist landslide as predicted in the present study, that slope is considered to be safe.

System reliability analysis of granular filter for protection against piping in dams

Granular filters are provided for the safety of water retaining structure for protection against piping failure. The phenomenon of piping triggers when the base soil to be protected starts migrating in the direction of seepage flow under the influence of seepage force. To protect base soil from migration, the voids in the filter media should be small enough but it should not also be too small to block smooth passage of seeping water. Fulfilling these two contradictory design requirements at the same time is a major concern for the successful performance of granular filter media. Since Terzaghi era, conventionally, particle size distribution (PSD) of granular filters is designed based on particle size distribution characteristics of the base soil to be protected. The design approach provides a range of D15f value in which the PSD of granular filter media should fall and there exist infinite possibilities. Further, safety against the two critical design requirements cannot be ensured. Although used successfully for many decades, the existing filter design guidelines are purely empirical in nature accompanied with experience and good engineering judgment. In the present study, analytical solutions for obtaining the factor of safety with respect to base soil particle migration and soil permeability consideration as proposed by the authors are first discussed. The solution takes into consideration the basic geotechnical properties of base soil and filter media as well as existing hydraulic conditions and provides a comprehensive solution to the granular filter design with ability to assess the stability in terms of factor of safety. Considering the fact that geotechnical properties are variable in nature, probabilistic analysis is further suggested to evaluate the system reliability of the filter media that may help in risk assessment and risk management for decision making.