Size-dependent density of nanoparticles and nanostructured materials

We discuss the size-dependent density of nanoparticles and nanostructured materials keeping the recent experimental results in mind. The density is predicted to increase with decreasing size for nanoparticles but it can decrease with size for nanostructured materials that corroborates the experimental results reported in the literature. (C) 2012 Elsevier B.V. All rights reserved.

Characterization of DNA topoisomerase I from Mycobacterium tuberculosis: DNA cleavage and religation properties and inhibition of its activity

Type I DNA topoisomerases from bacteria catalyse relaxation of negatively supercoiled DNA in a Mg2+ dependent manner. Although topoisomerases of distinct classes have been subjected for anti-cancer and anti-infective drug development, bacterial type I enzymes are way behind in this regard. Our studies with Mycobacterium smegmatis topoisomerase I (MstopoI) revealed several of its distinct properties compared to the well studied Escherichia coli topoisomerase I (EctopoI) suggesting the possibility of targeting the mycobacterial enzyme for inhibitor development. Here, we describe Mycobacterium tuberculosis topoisomerase I (MttopoI) and compare its properties with MstopoI and EctopoI. The enzyme cleaves DNA at preferred sites in a pattern similar to its ortholog from M. smegmatis. Oligonucleotides containing the specific recognition sequence inhibited the activity of the enzyme in a manner similar to that of MstopoI. Substitution of the acidic residues, D111 and E115 which are involved in Mg2+ co-ordination, to alanines affected the DNA relaxation activity. Unlike the wild type enzyme, D111A was dependent on Mg2+ for DNA cleavage and both the mutants were compromised in religation. The monoclonal antibody (mAb), 2F3G4, developed against MstopoI inhibited the relaxation activity of MttopoI. These studies affirm the characteristics of MttopoI to be similar to MstopoI and set a stage to target it for the development of specific small molecule inhibitors. (C) 2012 Elsevier Inc. All rights reserved.

Phospholipid Mediated Activation of Calcium Dependent Protein Kinase 1 (CaCDPK1) from Chickpea: A New Paradigm of Regulation

Phospholipids, the major structural components of membranes, can also have functions in regulating signaling pathways in plants under biotic and abiotic stress. The effects of adding phospholipids on the activity of stress-induced calcium dependent protein kinase (CaCDPK1) from chickpea are reported here. Both autophosphorylation as well as phosphorylation of the added substrate were enhanced specifically by phosphatidylcholine and to a lesser extent by phosphatidic acid, but not by phosphatidylethanolamine. Diacylgylerol, the neutral lipid known to activate mammalian PKC, stimulated CaCDPK1 but at higher concentrations. Increase in V-max of the enzyme activity by these phospholipids significantly decreased the K-m indicating that phospholipids enhance the affinity towards its substrate. In the absence of calcium, addition of phospholipids had no effect on the negligible activity of the enzyme. Intrinsic fluorescence intensity of the CaCDPK1 protein was quenched on adding PA and PC. Higher binding affinity was found with PC (K-1/2 = 114 nM) compared to PA (K-1/2 = 335 nM). We also found that the concentration of PA increased in chickpea plants under salt stress. The stimulation by PA and PC suggests regulation of CaCDPK1 by these phospholipids during stress response.

Electrical transport characteristics of ZnO-Bi2O3-B2O3 glasses

Optically clear glasses in the ZnO-Bi2O3-B2O3 (ZBBO) system were fabricated via the conventional melt-quenching technique. Dielectric constant and loss measurements carried out on ZBBO glasses unraveled nearly frequency (1 kHz-10 MHz)-independent dielectric characteristics associated with significantly low loss (D = 0.004). However, weak temperature response was found with temperature coefficient of dielectric constant 18 +/- 4 ppm A degrees C-1 in the 35-250 A degrees C temperature range. The conduction and relaxation phenomena were rationalized using universal AC conductivity power law and modulus formalism respectively. The activation energy for relaxation determined using imaginary parts of modulus peaks was 2.54 eV which was close to that of the DC conduction implying the involvement of similar energy barriers in both the processes. Stretched and power exponents were temperature dependent. The relaxation and conduction in these glasses were attributed to the hoping and migration of Bi3+ cations in their own and different local environment.

Stiffness- and wettability-dependent myoblast cell compatibility of transparent poly(vinyl alcohol) hydrogels

This study reports the in vitro compatibility of muscle cells (C2C12 mouse myoblast cell line) with the transparent poly(vinyl alcohol) (PVA) hydrogels and the results are explained on the basis of surface wettability, crystallinity, and nanoscale elastic stiffness property. Nanoindentation was carried out with a maximum load of 100 mu N for all the hydrogel compositions and the properties such as elastic stiffness, hardness and total work done during indentation were computed. The difference in cell viability as well as adhesion of cultured myoblast cells on the investigated hydrogel substrates were discussed in reference to the difference in the nanoscale elastic properties, crystallinity, and surface wettability. An important result has been that both elastic stiffness and surface wettability synergistically influence myoblast viability/adhesion on PVA hydrogels. (c) 2012 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2013.

A physics-based flexural phonon-dependent thermal conductivity model for single layer graphene

In this paper, we address a physics-based closed-form analytical model of flexural phonon-dependent diffusive thermal conductivity (kappa) of suspended rectangular single layer graphene sheet. A quadratic dependence of the out-of-plane phonon frequency, generally called flexural phonons, on the phonon wave vector has been taken into account to analyze the behavior of kappa at lower temperatures. Such a dependence has further been used for the determination of second-order three-phonon Umklapp and isotopic scatterings. We find that these behaviors in our model are best explained through the upper limit of Debye cut-off frequency in the second-order three-phonon Umklapp scattering of the long phonon waves that actually remove the thermal conductivity singularity by contributing a constant scattering rate at low frequencies and note that the out-of-plane Gruneisen parameter for these modes need not be too high. Using this, we clearly demonstrate that. follows a T-1.5 and T-2 law at lower and higher temperatures in the absence of isotopes, respectively. However in their presence, the behavior of kappa sharply deviates from the T-2 law at higher temperatures. The present geometry-dependent model of kappa is found to possess an excellent match with various experimental data over a wide range of temperatures which can be put forward for efficient electro-thermal analyses of encased/supported graphene.

SPARSE SIGNAL RECONSTRUCTION BASED ON SIGNAL DEPENDENT NON-UNIFORM SAMPLES

The classical approach to A/D conversion has been uniform sampling and we get perfect reconstruction for bandlimited signals by satisfying the Nyquist Sampling Theorem. We propose a non-uniform sampling scheme based on level crossing (LC) time information. We show stable reconstruction of bandpass signals with correct scale factor and hence a unique reconstruction from only the non-uniform time information. For reconstruction from the level crossings we make use of the sparse reconstruction based optimization by constraining the bandpass signal to be sparse in its frequency content. While overdetermined system of equations is resorted to in the literature we use an undetermined approach along with sparse reconstruction formulation. We could get a reconstruction SNR > 20dB and perfect support recovery with probability close to 1, in noise-less case and with lower probability in the noisy case. Random picking of LC from different levels over the same limited signal duration and for the same length of information, is seen to be advantageous for reconstruction.

Temperature dependent structural and dielectric investigations of PbZr0.5Ti0.5O3 solid solution at the morphotropic phase boundary

PbZr1-xTixO3 ceramics synthesised by low temperature calcination followed by sintering at 1280 degrees C show a Morphotropic Phase Boundary (MPB) for compositions of x=0.44-0.51. The morphotropic phase boundary is wider for samples with smaller grain sizes due to the synthesis route. A Rietveld analysis is performed on a composition of x=0.5 composition to quantify the phase fractions of the tetragonal and monoclinic phases present in the PZT system. Temperature dependent X-ray diffraction and dielectric studies of PbZr0.5Ti0.5O3 composition demonstrated a phase transformation from monoclinic to tetragonal at 270 degrees C followed by a ferroelectric tetragonal to a paraelectric cubic transition at 370 degrees C. Thus, the poling of these ceramics should be performed below 270 degrees C to benefit from the presence of a monoclinic phase. (C) 2012 Elsevier Ltd and Techna Group S.r.l. All rights reserved.

Layer-dependent resonant Raman scattering of a few layer MoS2

We report resonant Raman scattering of MoS2 layers comprising of single, bi, four and seven layers, showing a strong dependence on the layer thickness. Indirect band gap MoS2 in bulk becomes a direct band gap semiconductor in the monolayer form. New Raman modes are seen in the spectra of single- and few-layer MoS2 samples which are absent in the bulk. The Raman mode at similar to 230 cm(-1) appears for two, four and seven layers. This mode has been attributed to the longitudinal acoustic phonon branch at the M point (LA(M)) of the Brillouin zone. The mode at similar to 179 cm(-1) shows asymmetric character for a few-layer sample. The asymmetry is explained by the dispersion of the LA(M) branch along the G-M direction. The most intense spectral region near 455 cm(-1) shows a layer-dependent variation of peak positions and relative intensities. The high energy region between 510 and 645 cm(-1) is marked by the appearance of prominent new Raman bands, varying in intensity with layer numbers. Resonant Raman spectroscopy thus serves as a promising non invasive technique to accurately estimate the thickness of MoS2 layers down to a few atoms thick. Copyright (C) 2012 John Wiley & Sons, Ltd.

Force and ATP hydrolysis dependent regulation of RecA nucleoprotein filament by single-stranded DNA binding protein

In Escherichia coli, the filament of RecA formed on single-stranded DNA (ssDNA) is essential for recombinational DNA repair. Although ssDNA-binding protein (SSB) plays a complicated role in RecA reactions in vivo, much of our understanding of the mechanism is based on RecA binding directly to ssDNA. Here we investigate the role of SSB in the regulation of RecA polymerization on ssDNA, based on the differential force responses of a single 576-nucleotide-long ssDNA associated with RecA and SSB. We find that SSB outcompetes higher concentrations of RecA, resulting in inhibition of RecA nucleation. In addition, we find that pre-formed RecA filaments de-polymerize at low force in an ATP hydrolysis- and SSB-dependent manner. At higher forces, re-polymerization takes place, which displaces SSB from ssDNA. These findings provide a physical picture of the competition between RecA and SSB under tension on the scale of the entire nucleoprotein SSB array, which have broad biological implications particularly with regard to competitive molecular binding.

Two-Dimensional Correlation Analysis of Temperature-Dependent FT-IR Spectra of Oleic Acid

In the present study, variable temperature FT-IR spectroscopic investigations were used to characterize the spectral changes in oleic acid during heating oleic acid in the temperature range from -30 degrees;C to 22 degrees C. In order to extract more information about the spectral variations taking place during the phase transition process, 2D correlation spectroscopy (2DCOS) was employed for the stretching (C?O) and rocking (CH2) band of oleic acid. However, the interpretation of these spectral variations in the FT-IR spectra is not straightforward, because the absorption bands are heavily overlapped and change due to two processes: recrystallization of the ?-phase and melting of the oleic acid. Furthermore, the solid phase transition from the ?- to the a-phase was also observed between -4 degrees C and -2 degrees C. Thus, for a more detailed 2DCOS analysis, we have split up the spectral data set in the subsets recorded between -30 degrees C to -16 degrees C, -16 degrees C to 10 degrees C, and 10 degrees C to 22 degrees C. In the corresponding synchronous and asynchronous 2D correlation plots, absorption bands that are characteristic of the crystalline and amorphous regions of oleic acid were separated.

A Calcium-Dependent Plasticity Rule for HCN Channels Maintains Activity Homeostasis and Stable Synaptic Learning

Theoretical and computational frameworks for synaptic plasticity and learning have a long and cherished history, with few parallels within the well-established literature for plasticity of voltage-gated ion channels. In this study, we derive rules for plasticity in the hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, and assess the synergy between synaptic and HCN channel plasticity in establishing stability during synaptic learning. To do this, we employ a conductance-based model for the hippocampal pyramidal neuron, and incorporate synaptic plasticity through the well-established Bienenstock-Cooper-Munro (BCM)-like rule for synaptic plasticity, wherein the direction and strength of the plasticity is dependent on the concentration of calcium influx. Under this framework, we derive a rule for HCN channel plasticity to establish homeostasis in synaptically-driven firing rate, and incorporate such plasticity into our model. In demonstrating that this rule for HCN channel plasticity helps maintain firing rate homeostasis after bidirectional synaptic plasticity, we observe a linear relationship between synaptic plasticity and HCN channel plasticity for maintaining firing rate homeostasis. Motivated by this linear relationship, we derive a calcium-dependent rule for HCN-channel plasticity, and demonstrate that firing rate homeostasis is maintained in the face of synaptic plasticity when moderate and high levels of cytosolic calcium influx induced depression and potentiation of the HCN-channel conductance, respectively. Additionally, we show that such synergy between synaptic and HCN-channel plasticity enhances the stability of synaptic learning through metaplasticity in the BCM-like synaptic plasticity profile. Finally, we demonstrate that the synergistic interaction between synaptic and HCN-channel plasticity preserves robustness of information transfer across the neuron under a rate-coding schema. Our results establish specific physiological roles for experimentally observed plasticity in HCN channels accompanying synaptic plasticity in hippocampal neurons, and uncover potential links between HCN-channel plasticity and calcium influx, dynamic gain control and stable synaptic learning.

Optimal control problem for the time-dependent Kirchhoff-Love plate in a domain with rough boundary

In this paper, we study the asymptotic behavior of an optimal control problem for the time-dependent Kirchhoff-Love plate whose middle surface has a very rough boundary. We identify the limit problem which is an optimal control problem for the limit equation with a different cost functional.

Time dependent superhydrophobicity of drag reducing surfaces

Air can be trapped on the crevices of specially textured hydrophobic surfaces immersed in water. This heterogenous state of wetting in which the water is in contact with both the solid surface and the entrapped air is not stable. Diffusion of air into the surrounding water leads to gradual reduction in the size and numbers of the air bubbles. The sustainability of the entrapped air on such surfaces is important for many underwater applications in which the surfaces have to remain submersed for longer time periods. In this paper we explore the suitability of different classes of surface textures towards the drag reduction application by evaluating the time required for the disappearance of the air bubbles under hydrostatic conditions. Different repetitive textures consisting of holes, pillars and ridges of different sizes have been generated in silicon, aluminium and brass by isotropic etching, wire EDM and chemical etching respectively. These surfaces were rendered hydrophobic with self-assembled layer of fluorooctyl trichlorosilane for silicon and aluminium surfaces and 1-dodecanethiol for brass surfaces. Using total internal reflection the air bubbles are visualized with the help of a microscope and time lapse photography. Irrespective of the texture, both the size and the number of air pockets were found to decrease with time gradually and eventually disappear. In an attempt to reverse the diffusion we explore the possibility of using electrolysis to generate gases at the textured surfaces. The gas bubbles are nucleated everywhere on the surface and as they grow they coalesce with each other and get pinned at the texture edges.

Sonic hedgehog-Dependent Induction of MicroRNA 31 and MicroRNA 150 Regulates Mycobacterium bovis BCG-Driven Toll-Like Receptor 2 Signaling

Hedgehog (HH) signaling is a significant regulator of cell fate decisions during embryogenesis, development, and perpetuation of various disease conditions. Testing whether pathogen-specific HH signaling promotes unique innate recognition of intracellular bacteria, we demonstrate that among diverse Gram-positive or Gram-negative microbes, Mycobacterium bovis BCG, a vaccine strain, elicits a robust activation of Sonic HH (SHH) signaling in macrophages. Interestingly, sustained tumor necrosis factor alpha (TNF-alpha) secretion by macrophages was essential for robust SHH activation, as TNF-alpha(-/-) macrophages exhibited compromised ability to activate SHH signaling. Neutralization of TNF-alpha or blockade of TNF-alpha receptor signaling significantly reduced the infection-induced SHH signaling activation both in vitro and in vivo. Intriguingly, activated SHH signaling downregulated M. bovis BCG-mediated Toll-like receptor 2 (TLR2) signaling events to regulate a battery of genes associated with divergent functions of M1/M2 macrophages. Genome-wide expression profiling as well as conventional gain-of-function or loss-of-function analysis showed that SHH signaling-responsive microRNA 31 (miR-31) and miR-150 target MyD88, an adaptor protein of TLR2 signaling, thus leading to suppression of TLR2 responses. SHH signaling signatures could be detected in vivo in tuberculosis patients and M. bovis BCG-challenged mice. Collectively, these investigations identify SHH signaling to be what we believe is one of the significant regulators of host-pathogen interactions.