Genome-wide methylation profiling identifies an essential role of reactive oxygen species in pediatric glioblastoma multiforme and validates a methylome specific for H3 histone family 3A with absence of G-CIMP/isocitrate dehydrogenase 1 mutation

Background. Pediatric glioblastoma multiforme (GBM) is rare, and there is a single study, a seminal discovery showing association of histone H3.3 and isocitrate dehydrogenase (IDH) 1 mutation with a DNA methylation signature. The present study aims to validate these findings in an independent cohort of pediatric GBM, compare it with adult GBM, and evaluate the involvement of important functionally altered pathways. Methods. Genome-wide methylation profiling of 21 pediatric GBM cases was done and compared with adult GBM data (GSE22867). We performed gene mutation analysis of IDH1 and H3 histone family 3A (H3F3A), status evaluation of glioma cytosine-phosphate-guanine island methylator phenotype (G-CIMP), and Gene Ontology analysis. Experimental evaluation of reactive oxygen species (ROS) association was also done. Results. Distinct differences were noted between methylomes of pediatric and adult GBM. Pediatric GBM was characterized by 94 hypermethylated and 1206 hypomethylated cytosine-phosphate-guanine (CpG) islands, with 3 distinct clusters, having a trend to prognostic correlation. Interestingly, none of the pediatric GBM cases showed G-CIMP/IDH1 mutation. Gene Ontology analysis identified ROS association in pediatric GBM, which was experimentally validated. H3F3A mutants (36.4%; all K27M) harbored distinct methylomes and showed enrichment of processes related to neuronal development, differentiation, and cell-fate commitment. Conclusions. Our study confirms that pediatric GBM has a distinct methylome compared with that of adults. Presence of distinct clusters and an H3F3A mutation-specific methylome indicate existence of epigenetic subgroups within pediatric GBM. Absence of IDH1/G-CIMP status further indicates that findings in adult GBM cannot be simply extrapolated to pediatric GBM and that there is a strong need for identification of separate prognostic markers. A possible role of ROS in pediatric GBM pathogenesis is demonstrated for the first time and needs further evaluation.

Effect of oxygen vacancies on the elastic properties of zinc oxide: A first-principles investigation

The effect of oxygen vacancies on the elastic properties of zinc oxide (ZnO) is examined using first-principles calculations based on density functional theory. Formation energies of vacancies in different types of oxygen deficient structures were analyzed to ascertain their stability. This analysis reveals that the doubly-charged oxygen vacancy under zinc-rich growth conditions is the most stable. Results show considerable degradation of some of the elastic moduli due to the presence of oxygen vacancies, which is in agreement with recent experiments. The decrease observed in elastic constants is more pronounced with increase in vacancy concentration. Further, the charge state of the defect structure was found to influence the shear elastic constants. Evaluation of elastic anisotropy of stoichiometric and oxygen deficient ZnO indicates the significant anisotropy in elastic properties and stiff c-axis orientation. (C) 2014 Elsevier B.V. All rights reserved.

Dynamics of Plasmon in Graphene Oxide

Dynamic effects of plasmon such as scattering with defect boundaries and oxygen impurities in the graphene oxide are investigated. Study of plasmon dynamics helps in understanding electronic, opto-electronic and biological applications of graphene based nanostructures. Tuning or control over such applications is made possible by graphene nanostructure engineering. We have modeled defects with increased smoothing of defect edge in graphene keeping area of the defect constant. Scattering of plasmons in graphene with defects is modeled using an electromagnetic field coupled inter-atomic potential approach with finite element discretization of the atomic vibrational and electromagnetic field degrees of freedom. Our calculations show pi + sigma plasmon red shifting under sharp defect edges whereas pi plasmon show high extinction efficiency. Strong localization of electric fields near the sharp defect edges is observed. Observations on plasmons and its dynamics draws attention in designing novel optoelectronic devices and binders for bio-molecules.

High Catalytic Activity of Amorphous Ir-Pi for Oxygen Evolution Reaction

Large-scale production of hydrogen gas by water electrolysis is hindered by the sluggish kinetics of oxygen evolution reaction (OER) at the anode. The development of a highly active and stable catalyst for OER is a challenging task. Electrochemically prepared amorphous metal-based catalysts have gained wide attention after the recent discovery of a cnbalt-phosphate (Co-Pi) catalyst: Herein, an amorphous iridium-phosphate (Ir-Pi) is investigated as an oxygen evolution catalyst. The catalyst is prepared by the anodic polarization of carbon paper electrodes in neutral phosphate buffer solutions containing IrCl3. The Ir-Pi film deposited on the substrate has significant amounts of phosphate and It centers in an oxidation state higher than +4. Phosphate plays a significant role in the deposition of the catalyst and also in its activity toward OER. The onset potential of OER on the Ir-Pi is about 150 mV lower in comparison with the Co-Pi under identical experimental conditions. Thus, Ir-Pi is a promising catalyst for electrochemical oxidation of water.

A novel interferometric technique to estimate thermal diffusivity of `optically transparent solid' using `Isothermal surface velocimetry'

One-dimensional transient heat flow is interpreted as a procession of `macro-scale translatory motion of indexed isothermal surfaces'. A new analytical model is proposed by introducing velocity of isothermal surface in Fourier heat diffusion equation. The velocity dependent function is extracted by revisiting `the concept of thermal layer of heat conduction in solid' and `exact solution' to estimate thermal diffusivity. The experimental approach involves establishment of 1 D unsteady heat flow inside the sample through Step-temperature excitation. A novel self-reference interferometer is utilized to separate a `unique isothermal surface' in time-varying temperature field. The translatory motion of the said isothermal surface is recorded using digital camera to estimate its velocity. From the knowledge of thermo-optic coefficient, temperature of the said isothermal surface is predicted. The performance of proposed method is evaluated for Quartz sample and compared with literature.

Effect of Size Reduction on Magnetic Ordering in Sm1-x Ca (x) MnO3 (x=0.35, 0.65 and 0.92) Manganites: Magnetic and EMR Studies

We have employed the highly sensitive electron magnetic resonance technique complimented by magnetization measurements to study the impact of size reduction on the magnetic ordering in nanosized Sm1-x Ca (x) MnO3 (x = 0.35, 0.65 and 0.92). In the bulk form, x = 0.35 sample shows a charge ordering transition at 235 K followed by a mixed magnetic phase, the sample with x = 0.65 exhibits charge order below 275 K and shows an antiferromagnetic insulator phase below 135 K while that with x = 0.92 has a ferromagnetic-cluster glass ground state. Thus, a comparative study of magnetic ground states of bulk and nanoparticles (diameter similar to 25 nm) enables us to investigate size-induced effects on different types of magnetic ordering. It is seen that in the bulk samples the temperature dependences of the EPR parameters are quite different from each other. This difference diminishes for the nanosamples where all the three samples show qualitatively similar behavior. The magnetization measurements corroborate this conclusion.

The influence of reduced oxygen availability on gene expression in laboratory (H37Rv) and clinical strains (S7 and S10) of Mycobacterium tuberculosis

Mycobacterium tuberculosis has the ability to persist within the host in a dormant stage. One important condition believed to contribute to dormancy is reduced access to oxygen known as hypoxia. However, the response of M. tuberculosis to such hypoxia condition is not fully characterized. Virtually all dormant models against tuberculosis tested in animals used laboratory strain H37Rv or Erdman strain. But major outbreaks of tuberculosis (TB) occur with the strains that have widely different genotypes and phenotypes compared to H37Rv. In this study, we used a custom oligonucleotide microarray to determine the overall transcriptional response of laboratory strain (H37Rv) and most prevalent clinical strains (S7 and S10) of M. tuberculosis from South India to hypoxia. Analysis of microarray results revealed that a total of 1161 genes were differentially regulated (>= 1.5 fold change) in H37Rv, among them 659 genes upregulated and 502 genes down regulated. Microarray data of clinical isolates showed that a total of 790 genes were differentially regulated in S7 among which 453 genes were upregulated and 337 down regulated. Interestingly, numerous genes were also differentially regulated in S10 (total 2805 genes) of which 1463 genes upregulated and 1342 genes down regulated during reduced oxygen condition (Wayne's model). One hundred and thirty-four genes were found common and upregulated among all three strains (H37Rv, S7, and S10) and can be targeted for drug/vaccine development against TB. (C) 2015 Published by Elsevier B.V.

Ir nanoparticles-anchored reduced graphene oxide as a catalyst for oxygen electrode in Li-O-2 cells

Iridium nanoparticles-anchored reduced graphene oxide (Ir-RGO) was prepared by simultaneous reduction of graphene oxide and Ir3+ ions and its catalytic activity for oxygen electrode in Li-O-2 cells was demonstrated. Ir particles with an average size of 3.9 nm were uniformly distributed on RGO sheets. The oxygen reduction reaction (ORR) was studied on an Ir-RGO catalyst in non-aqueous electrolytes using cyclic voltammetry and rotating disk electrode techniques. Li-O-2 cells with Ir-RGO as a bifunctional oxygen electrode catalyst were subjected to charge-discharge cycling at several current densities. A discharge capacity of 9529 mA h g(-1) (11.36 mA h cm(-2)) was obtained initially at a current density of 0.5 mA cm(-2) (393 mA g(-1)). A decrease in capacity was observed on increasing the current density. Although there was a decrease in capacity on repeated discharge-charge cycling initially, a stable capacity was observed for about 30 cycles. The results suggest that Ir-RGO is a useful catalyst for rechargeable Li-O-2 cells.

Electronic structure origin of conductivity and oxygen reduction activity changes in low-level Cr-substituted (La, Sr)MnO3

The electronic structure of the (La0.8Sr0.2)(0.98)Mn1-xCrxO3 model series (x = 0, 0.05, or 0.1) was measured using soft X-ray synchrotron radiation at room and elevated temperature. O K-edge near-edge X-ray absorption fine structure (NEXAFS) spectra showed that low-level chromium substitution of (La, Sr)MnO3 resulted in lowered hybridisation between O 2p orbitals and M 3d and M 4sp valance orbitals. Mn L-3-edge resonant photoemission spectroscopy measurements indicated lowered Mn 3d-O 2p hybridisation with chromium substitution. Deconvolution of O K-edge NEXAFS spectra took into account the effects of exchange and crystal field splitting and included a novel approach whereby the pre-peak region was described using the nominally filled t(2g) up arrow state. 10% chromium substitution resulted in a 0.17 eV lowering in the energy of the t(2g) up arrow state, which appears to provide an explanation for the 0.15 eV rise in activation energy for the oxygen reduction reaction, while decreased overlap between hybrid O 2p-Mn 3d states was in qualitative agreement with lowered electronic conductivity. An orbital-level understanding of the thermodynamically predicted solid oxide fuel cell cathode poisoning mechanism involving low-level chromium substitution on the B-site of (La, Sr)MnO3 is presented. (C) 2015 AIP Publishing LLC.

An approximation to the QoS aware throughput region of a tree network under IEEE 802.15.4 CSMA/CA with application to wireless sensor network design

In the context of wireless sensor networks, we are motivated by the design of a tree network spanning a set of source nodes that generate packets, a set of additional relay nodes that only forward packets from the sources, and a data sink. We assume that the paths from the sources to the sink have bounded hop count, that the nodes use the IEEE 802.15.4 CSMA/CA for medium access control, and that there are no hidden terminals. In this setting, starting with a set of simple fixed point equations, we derive explicit conditions on the packet generation rates at the sources, so that the tree network approximately provides certain quality of service (QoS) such as end-to-end delivery probability and mean delay. The structures of our conditions provide insight on the dependence of the network performance on the arrival rate vector, and the topological properties of the tree network. Our numerical experiments suggest that our approximations are able to capture a significant part of the QoS aware throughput region (of a tree network), that is adequate for many sensor network applications. Furthermore, for the special case of equal arrival rates, default backoff parameters, and for a range of values of target QoS, we show that among all path-length-bounded trees (spanning a given set of sources and the data sink) that meet the conditions derived in the paper, a shortest path tree achieves the maximum throughput. (C) 2015 Elsevier B.V. All rights reserved.

A rapid method to assess reactive oxygen species in yeast using H2DCF-DA

A protocol to efficiently assess Reactive Oxygen Species (ROS) levels in yeast cells using H2DCF-DA is described here. This method employs lithium acetate to permeate the cell wall, and thus, augments the release of the fluorescent product, dichlorofluorescein from the cells. This protocol obviates the need for both physical and enzymatic lysis methods that are arduous and time consuming. This method is simple, less time consuming and reproducible, especially while dealing with a large sample size. The lithium acetate method gave significantly reproducible and linear results (P < 0.0001), as compared with direct measurement (P = 0.0005), sonication (P = 0.1466) and bead beating (P = 0.0028).

Structural modification and enhanced magnetic properties with two phonon modes in Ca-Co codoped BiFeO3 nanoparticles

Bi1-xCaxFe1-xCoxO3 nanoparticles with x=0.0, 0.05, 0.10 and 0.15 were successfully synthesized by cost effective tartaric acid based sol gel route. The alkali earth metal Ca2+ ions and transition metal Co3+ ions codoping at A and B-sites of BiFeO3 results in structural distortion and phase transformation. Rietveld refinement of XRD patterns suggested the coexistence of rhombohedral and orthorhombic phases in codoped BiFeO3 samples. Both XRD and Raman scattering studies showed the compressive lattice distortion in the samples induced by codoping of Ca2+ and Co3+ ions. Two-phonon Raman spectra exhibited the improvement of magnetization in these samples. X-ray photoelectron spectroscopy (XPS) showed the dominancy of Fe3+ and Co3+ oxidation states along with the shifting of the binding energy of Bi 4f orbital which confirms the substitution Ca2+ at Bi-site. The magnetic study showed the enhancement in room temperature ferromagnetic behavior with co-substitution consistent with Rama analysis. The gradual change in line shape of electron spin resonance spectra indicated the local distortion induced by codoping. (C) 2015 Published by Elsevier Ltd and Techna Group S.r.l.

Surface modification of titania aerogel films by oxygen plasma treatment for enhanced dye adsorption

Titania aerogels were synthesized by sol-gel route followed by ambient pressure subcritical drying technique. The aerogels synthesized in the present work possess a maximum surface area of 252 m(2)/g. The pore size distribution is between 2 and 30 nm which confirms their mesoporosity. The oxygen plasma treatment on titania aerogel thin films improved the surface area up to 273 m(2)/g and produced additional hydrophilic groups on the surface. It is confirmed by BET surface area, XPS and thermal analysis in conjunction with dye adsorption studies. After plasma treatment the dye adsorption capacity was increased 2.5 times higher than that of untreated aerogel film. The increased surface area and the hydrophilic groups generated on the titania aerogel surface during plasma treatment are responsible for enhanced dye adsorption. The overall nanoporous morphology of titania aerogel is preserved after plasma treatment. (C) 2015 Elsevier B.V. All rights reserved.

Hetero-atom Doped Carbon Nanotubes for Dye Degradation and Oxygen Reduction Reaction

We report the synthesis of nitrogen doped vertically aligned multi-walled (MWNCNTs) carbon nanotubes by pyrolysis and its catalytic performance for degradation of methylene blue (MB) dye & oxygen reduction reaction (ORR). The degradation of MB was monitored spectrophotometrically with time. Kinetic studies show the degradation of MB follows a first order kinetic with rate constant k=0.0178 min(-1). The present rate constant is better than that reported for various supported/non-supported semiconducting nanomaterials. Further ORR performance in alkaline media makes MWNCNTs a promising cost-effective, fuel crossover tolerance, metal-free, eco-friendly cathode catalyst for direct alcohol fuel cell.

Relaxor ferroelectricity and electric-field-driven structural transformation in the giant lead-free piezoelectric (Ba,Ca)(Ti, Zr)O-3

There is great interest in lead-free (Ba0.85Ca0.15)(Ti0.90Zr0.10)O-3 (15/10BCTZ) because of its exceptionally large piezoelectric response Liu and Ren, Phys. Rev. Lett. 103, 257602 (2009)]. In this paper, we have analyzed the nature of: (i) crystallographic phase coexistence at room temperature, (ii) temperature-and field-induced phase transformation to throw light on the atomistic mechanisms associated with the large piezoelectric response of this system. A detailed temperature-dependent dielectric and lattice thermal expansion study proved that the system exhibits a weak dielectric relaxation, characteristic of a relaxor ferroelectric material on the verge of exhibiting a normal ferroelectric-paraelectric transformation. Careful structural analysis revealed that a ferroelectric state at room temperature is composed of three phase coexistences, tetragonal (P4mm)+ orthorhombic (Amm2) + rhombohedral (R3m). We also demonstrate that the giant piezoresponse is associated with a significant fraction of the tetragonal phase transforming to rhombohedral. It is argued that the polar nanoregions associated with relaxor ferroelectricity amplify the piezoresponse by providing an additional degree of intrinsic structural inhomogeneity to the system.