Potential G-quadruplex formation at breakpoint regions of chromosomal translocations in cancer may explain their fragility

Genetic alterations like point mutations, insertions, deletions, inversions and translocations are frequently found in cancers. Chromosomal translocations are one of the most common genomic aberrations associated with nearly all types of cancers especially leukemia and lymphoma. Recent studies have shown the role of non-B DNA structures in generation of translocations. In the present study, using various bioinformatic tools, we show the propensity of formation of different types of altered DNA structures near translocation breakpoint regions. In particular, we find close association between occurrence of G-quadruplex forming motifs and fragile regions in almost 70% of genes involved in rearrangements in lymphoid cancers. However, such an analysis did not provide any evidence for the occurrence of G-quadruplexes at the close vicinity of translocation breakpoint regions in nonlymphoid cancers. Overall, this study will help in the identification of novel non-B DNA targets that may be responsible for generation of chromosomal translocations in cancer. (C) 2012 Elsevier Inc. All rights reserved.

Nucleation-Growth Mode of Cubic-Tetragonal Transition with Coexistence of Phases over a Wide Temperature Interval in the High Temperature Ferroelectric Systems PbTiO3-BiMeO3:Me = Sc , and Zn1/2Ti1/2

Temperature dependent X-ray powder diffraction and dielectric studies have been carried out on tetragonal compositions of (1-x) PbTiO 3(x) BiMeO 3; Me similar to Sc and Zn 1/2 Ti 1/2. The cubic and the tetragonal phases coexist over more than 100 degrees C for 0.70 PbTiO 30.3 Bi ( Zn 1/2 Ti 1/2) O 3 and 0.66 PbTiO 30.34 BiScO 3. The wide temperature range of phase coexistence is shown to be an intrinsic feature of the system, and is attributed to the increase in the degree of the covalent character of the ( Pb +Bi ) O bond with increasing concentration of Bi at the Pb -site. The d-values of the {111} planes of the coexisting phases are nearly identical, suggesting this plane to be the invariant plane for the martensitic type cubic-tetragonal transformation occurring in these systems.

Cis-trans peptide variations in structurally similar proteins

The presence of energetically less favourable cis peptides in protein structures has been observed to be strongly associated with its structural integrity and function. Inter-conversion between the cis and trans conformations also has an important role in the folding process. In this study, we analyse the extent of conservation of cis peptides among similar folds. We look at both the amino acid preferences and local structural changes associated with such variations. Nearly 34% of the Xaa-Proline cis bonds are not conserved in structural relatives; Proline also has a high tendency to get replaced by another amino acid in the trans conformer. At both positions bounding the peptide bond, Glycine has a higher tendency to lose the cis conformation. The cis conformation of more than 30% of beta turns of type VIb and IV are not found to be conserved in similar structures. A different view using Protein Block-based description of backbone conformation, suggests that many of the local conformational changes are highly different from the general local structural variations observed among structurally similar proteins. Changes between cis and trans conformations are found to be associated with the evolution of new functions facilitated by local structural changes. This is most frequent in enzymes where new catalytic activity emerges with local changes in the active site. Cis-trans changes are also seen to facilitate inter-domain and inter-protein interactions. As in the case of folding, cis-trans conversions have been used as an important driving factor in evolution.

Averting biodiversity collapse in tropical forest protected areas

The rapid disruption of tropical forests probably imperils global biodiversity more than any other contemporary phenomenon(1-3). With deforestation advancing quickly, protected areas are increasingly becoming final refuges for threatened species and natural ecosystem processes. However, many protected areas in the tropics are themselves vulnerable to human encroachment and other environmental stresses(4-9). As pressures mount, it is vital to know whether existing reserves can sustain their biodiversity. A critical constraint in addressing this question has been that data describing a broad array of biodiversity groups have been unavailable for a sufficiently large and representative sample of reserves. Here we present a uniquely comprehensive data set on changes over the past 20 to 30 years in 31 functional groups of species and 21 potential drivers of environmental change, for 60 protected areas stratified across the world's major tropical regions. Our analysis reveals great variation in reserve `health': about half of all reserves have been effective or performed passably, but the rest are experiencing an erosion of biodiversity that is often alarmingly widespread taxonomically and functionally. Habitat disruption, hunting and forest-product exploitation were the strongest predictors of declining reserve health. Crucially, environmental changes immediately outside reserves seemed nearly as important as those inside in determining their ecological fate, with changes inside reserves strongly mirroring those occurring around them. These findings suggest that tropical protected areas are often intimately linked ecologically to their surrounding habitats, and that a failure to stem broad-scale loss and degradation of such habitats could sharply increase the likelihood of serious biodiversity declines.

Colossal nonsaturating linear magnetoresistance in two-dimensional electron systems at a GaAs/(Al,Ga)As heterointerface

Engineering devices with a large electrical response to magnetic field is of fundamental importance for a range of applications such as magnetic field sensing and magnetic read heads. We show that a colossal nonsaturating linear magnetoresistance (NLMR) arises in two-dimensional electron systems hosted in a GaAs/AlGaAs heterostructure in the strongly insulating regime. When operated at high source-drain bias, the magnetoresistance of our devices increases almost linearly with magnetic field, reaching nearly 10 000% at 8 T, thus surpassing many known nonmagnetic materials that exhibit giant NLMR. The temperature dependence and mobility analysis indicate that the NLMR has a purely classical origin, driven by nanoscale inhomogeneities. A large NLMR combined with small device dimensions makes these systems an attractive candidate for on-chip magnetic field sensing.

Diffusion mechanism in the mu phase in Nb-X (X = Ni, Co, Fe) systems

Nb is one of the common refractory elements added in Ni, Co and Fe based superalloys. This lead to the formation of brittle topological close packed (tcp) mu phase, which is deleterious to the structure. It mainly grows by interdiffusion and in the present article, the interdiffusion process in different Nb-X (X=Ni, Co, Fe) systems is discussed. The activation energy for interdiffusion is lower in the Co-Nb system (173 kJ/mol) than Fe-Nb system (233 kJ/mol), which is again lower than the value found in the Ni-Nb system (319.7 kJ/mol). The mole fraction of Nb in this phase is less than Fe or Co at stoichiometric compositions in the Nb-Fe (that is Fe7Nb6) and Nb-Co (that is Co7Nb6) systems. On the other hand, the mole fraction of Nb is higher than Ni in the same phase (Ni6Nb2) in Ni-Nb system. However, in all the phases, Nb has lower diffusion rate. Possible diffusion mechanism in this phase is discussed with respect to the crystal structure.

A versatile resolving agent for diffusion edited separation of enantiomers, complex mixtures and constitutional isomers

The study is the first report of the utilization of a crown ether as a new and versatile resolving agent for the diffusion edited separation of enantiomers, complex mixtures and constitutional isomers. As a consequence of different binding affinities of enantiomers of a chiral molecule and individual components of the complex mixtures with the crown ether, the molecules diffuse at different rates. The enhanced separation achieved due to matrix assisted diffusion permitted their separation in the diffusion dimension. The generality and wide utility of the new resolving agent and the methodology are demonstrated on diverse examples, such as an organic chiral molecule, constitutional isomers and complex mixture of molecules possessing different functional groups that possess nearly identical molecular weights.

Charge transport in functionalized multi-wall carbon nanotube-Nafion composite

The charge transport in sulfonated multi-wall carbon nanotube (sMWNT)-Nafion composite is reported. The scanning electron microscope images of the composite, at 1 and 10 wt % of sMWNT, show that the nanotubes are well dispersed in polymer matrix, with conductivity values of 0.005 and 3.2 S/cm, respectively; and the percolation threshold is nearly 0.42 wt. %. The exponent (∼0.25) of the temperature dependence of conductivity in both samples indicates Mott's variable range hopping (VRH) transport. The conductance in 1 wt. % sample increases by three orders of magnitude at high electric-fields, consistent with VRH model. The negative magnetoresistance in 10 wt. % sample is attributed to the forward interference scattering mechanism in VRH transport. The ac conductance in 1 wt. % sample is expressed by σ(ω)∝ωs, and the temperature dependence of s follows the correlated barrier hopping model.

Nonstoichiometry, defects and thermodynamic properties of YFeO3, YFe2O4 and Y3Fe5O12

Oxygen nonstoichiometry of three ternary oxides. YFeO3-delta, YFe2O4-alpha and Y3Fe5O12-theta. in the system Y-Fe-O was investigated as a function of oxygen partial pressure by thermogravimetry at high temperature. The defects responsible for nonstoichiometry were identified as oxygen vacancies for YFeO3-delta and YFe2O4-alpha although the manner of variation of nonstoichiometric parameter with oxygen partial pressure for these two oxides is quite different. Cation interstitials are the predominant defects in Y3Fe5O12-theta. Gibbs energies of formation of the three nonstoichiometric oxides were determined using solid-state electrochemical cells in the temperature range from 975 to 1475 K. YFe2O4-alpha was found to be stable only above 1391 K. Gibbs energies of formation of the three stoichiometric compounds from their component binary oxides were obtained by combining information from solid state cells with results of thermogravimetric analysis using the Gibbs-Duhem relation. The results can be summarized as: (1/2)Y2O3 + (1/2)Fe2O3 -> YFeO3;Delta G(f(ox))(O)(+/- 250)(J/mol) = 17, 126-8.263T (1/2)Y2O3 + FeO + (1/2)Fe2O3 -> YFe2O4;Delta G(f(ox))(O)(+/- 260)(J/mol) = -10,352-13.24T (3/2)Y2O3 + (5/2)Fe2O3 -> Y3Fe5O12;Delta G(f(ox))(O)(+/- 780)(J/mol) = -56, 647-31.091T. (C) 2012 Elsevier B.V. All rights reserved.

Microstructural Evolution of A356 Al Alloy During Flow Along a Cooling Slope

Cooling slope (CS) has been used in this study to prepare semi-solid slurry of A356 Al alloy, keeping in view of slurry generation on demand for Rheo-pressure die casting process. Understanding the physics of microstructure evolution during cooling slope slurry formation is important to satisfy the need of semi-sold slurry with desired shape, size and morphology of primary Al phase. Mixture of spherical and rosette shaped primary Al phase has been observed in the samples collected during melt flow through the slope as well as in the cast (mould) samples compared to that of dendritic shape, observed in case of conventionally cast A356 alloy. The liquid melt has been poured into the slope at 650 A degrees C temperature and during flow it falls below the liquidus temperature of the said alloy, which facilitates crystallization of alpha-Al crystals on the cooling slope wall. Crystal separation due to melt flow is found responsible for nearly spherical morphology of the primary Al phase.

Strength of hot pressed ZrB2-SiC composite after exposure to high temperatures (1000-1700 degrees C)

Residual strength (room temperature strength after exposure in air at high temperatures) of hot pressed ZrB2-SiC composites was evaluated as function of SiC contents (10-30 vol%) as well as exposure temperatures for 5 h (1000-1700 degrees C). Multilayer oxide scale structures were found after exposures. The composition and thickness of these multilayered oxide scale structure was dependent on exposure temperature and SiC contents in composites. After exposure to 1000 degrees C for 5 h, the residual strength of ZrB2-SiC composites improved by nearly 60% compared to the as-hot pressed composites with 20 and 30 vol% SiC. On the other hand, the residual strength of these composites remained unchanged after 1500 degrees C for 5 h. A drastic degradation in residual strength was observed in composites with 20 and 30 vol% SiC after exposure to 1700 degrees C for 5 h in ZrB2-SiC. An attempt was made to correlate the microstructural changes and oxide scales with residual strength with respect to variation in SiC content and temperature of expsoure. (C) 2012 Elsevier Ltd. All rights reserved.

In situ structural studies on orthorhombic SnS micro-crystals

In situ powder X-ray diffraction (XRD) studies on 3D micro-crystalline tin (II) sulfide (SnS) were carried out at different temperatures. While increasing temperature, the crystal structure of SnS remains stable as orthorhombic, whereas its lattice parameters and unit-cell volume are considerably varied. Further, these 3D micro-crystalline structures have showed a negative thermal expansion along the a-axis and positive expansion along the b- and c-axes. However, the overall drop along the a-axis of SnS crystals is nearly equal to their expansion along the c-axis. The observed changes in the structural properties of SnS micro-crystallites with temperature are discussed and reported.

A LOWER INITIAL ABUNDANCE OF SHORT-LIVED Ca-41 IN THE EARLY SOLAR SYSTEM AND ITS IMPLICATIONS FOR SOLAR SYSTEM FORMATION

The short-lived radionuclide Ca-41 plays an important role in constraining the immediate astrophysical environment and the formation timescale of the nascent solar system due to its extremely short half-life (0.1 Myr). Nearly 20 years ago, the initial ratio of Ca-41/Ca-40 in the solar system was determined to be (1.41 +/- 0.14) x 10(-8), primarily based on two Ca-Al-rich Inclusions (CAIs) from the CV chondrite Efremovka. With an advanced analytical technique for isotopic measurements, we reanalyzed the potassium isotopic compositions of the two Efremovka CAIs and inferred the initial ratios of Ca-41/Ca-40 to be (2.6 +/- 0.9) x 10(-9) and (1.4 +/- 0.6) x 10(-9) (2 sigma), a factor of 7-10 lower than the previously inferred value. Considering possible thermal processing that led to lower Al-26/Al-27 ratios in the two CAIs, we propose that the true solar system initial value of Ca-41/Ca-40 should have been similar to 4.2 x 10(-9). Synchronicity could have existed between Al-26 and Ca-41, indicating a uniform distribution of the two radionuclides at the time of CAI formation. The new initial Ca-41 abundance is 4-16 times lower than the calculated value for steady-state galactic nucleosynthesis. Therefore, Ca-41 could have originated as part of molecular cloud materials with a free decay time of 0.2-0.4 Myr. Alternative possibilities, such as a last-minute input from a stellar source and early solar system irradiation, could not be definitively ruled out. This underscores the need for more data from diverse CAIs to determine the true astrophysical origin of Ca-41.

Activation of Lattice Oxygen of TiO2 by Pd2+ Ion: Correlation of Low-Temperature CO and Hydrocarbon Oxidation with Structure of Ti1-xPdxO2-x (x=0.01-0.03)

Lattice oxygen of TiO2 is activated by the substitution of Pd ion in its lattice. Ti1-xPdxO2-x (x = 0.01-0.03) have been synthesized by solution combustion method crystallizing in anatase TiO2 structure. Pd is in +2 oxidation state and Ti is in +4 oxidation state in the catalyst. Pd is more ionic in TiO2 lattice compared to Pd in PdO. Oxygen storage capacity defined by ``amount of oxygen that is used reversibly to oxidize CO'' is as high as 5100 mu mol/g of Ti0.97Pd0.03O1.97. Oxygen is extracted by CO to CO2 in absence of feed oxygen even at room temperature which is more than 20 times compared to pure TiO2. Rate of CO oxidation is 2.75 mu mol g(-1) s(-1) at 60 degrees C over Ti0.97Pd0.03O1.97 and C2H2 gets oxidized to CO2 and H2O at room temperature. Catalyst is not poisoned on long time operation of the reactor. Such high catalytic activity is due to activated lattice oxygen created by the substitution of Pd ion as seen from first-principles density functional theory (DFT) calculations with 96 atom supercells of Ti32O64, Ti31Pd1O63, Ti30Pd2O62, and Ti29Pd3O61. The compounds crystallize in anatase TiO2 structure with Pd2+ ion in nearly square planar geometry and TiO6 octahedra are distorted by the creation of weakly bound oxygens. Structural analysis of Ti31Pd1O63 which is close to 3% Pd ion substituted TiO2 shows that oxygens associated with both Ti and Pd ions in the lattice show bond valence sum of 1.87, a low value characteristic of weak oxygen in the lattice compared to oxygens with valence 2 and above in the same lattice. Exact positions of activated oxygens have been identified in the lattice from DFT calculations.

Algal biofuel production and mitigation potential in India

Energy and energy services are the backbone of growth and development in India and is increasingly dependent upon the use of fossil based fuels that lead to greenhouse gases (GHG) emissions and related concerns. Algal biofuels are being evolved as carbon (C)-neutral alternative biofuels. Algae are photosynthetic microorganisms that convert sunlight, water and carbon dioxide (CO2) to various sugars and lipids Tri-Acyl-Glycols (TAG) and show promise as an alternative, renewable and green fuel source for India. Compared to land based oilseed crops algae have potentially higher yields (5-12 g/m(2)/d) and can use locations and water resources not suited for agriculture. Within India, there is little additional land area for algal cultivation and therefore needs to be carried out in places that are already used for agriculture, e.g. flooded paddy lands (20 Mha) with village level technologies and on saline wastelands (3 Mha). Cultivating algae under such conditions requires novel multi-tier, multi-cyclic approaches of sharing land area without causing threats to food and water security as well as demand for additional fertilizer resources by adopting multi-tier cropping (algae-paddy) in decentralized open pond systems. A large part of the algal biofuel production is possible in flooded paddy crop land before the crop reaches dense canopies, in wastewaters (40 billion litres per day), in salt affected lands and in nutrient/diversity impoverished shallow coastline fishery. Mitigation will be achieved through avoidance of GHG, C-capture options and substitution of fossil fuels. Estimates made in this paper suggest that nearly half of the current transportation petro-fuels could be produced at such locations without disruption of food security, water security or overall sustainability. This shift can also provide significant mitigation avenues. The major adaptation needs are related to socio-technical acceptance for reuse of various wastelands, wastewaters and waste-derived energy and by-products through policy and attitude change efforts.