ATM- and ATR-mediated phosphorylation of XRCC3 regulates DNA double-strand break-induced checkpoint activation and repair

The RAD51 paralogs XRCC3 and RAD51C have been implicated in homologous recombination (HR) and DNA damage responses. However, the molecular mechanism(s) by which these paralogs regulate HR and DNA damage signaling remains obscure. Here, we show that an SQ motif serine 225 in XRCC3 is phosphorylated by ATR kinase in an ATM signaling pathway. We find that RAD51C but not XRCC2 is essential for XRCC3 phosphorylation, and this modification follows end resection and is specific to S and G(2) phases. XRCC3 phosphorylation is required for chromatin loading of RAD51 and HR-mediated repair of double-strand breaks (DSBs). Notably, in response to DSBs, XRCC3 participates in the intra-S-phase checkpoint following its phosphorylation and in the G(2)/M checkpoint independently of its phosphorylation. Strikingly, we find that XRCC3 distinctly regulates recovery of stalled and collapsed replication forks such that phosphorylation is required for the HR-mediated recovery of collapsed replication forks but is dispensable for the restart of stalled replication forks. Together, these findings suggest that XRCC3 is a new player in the ATM/ATR-induced DNA damage responses to control checkpoint and HR-mediated repair.

Pressure induced structural phase transformation in TiN: a first-principles study

Titanium nitride (TiN), which is widely used for hard coatings, reportedly undergoes a pressure-induced structural phase transformation, from a NaCl to a CsCl structure, at similar to 7 GPa. In this paper, we use first-principles calculations based on density functional theory with a generalized gradient approximation of the exchange correlation energy to determine the structural stability of this transformation. Our results show that the stress required for this structural transformation is substantially lower (by more than an order of magnitude) when it is deviatoric in nature vis-a-vis that under hydrostatic pressure. Local stability of the structure is assessed with phonon dispersion determined at different pressures, and we find that CsCl structure of TiN is expected to distort after the transformation. From the electronic structure calculations, we estimate the electrical conductivity of TiN in the CsCl structure to be about 5 times of that in NaCl structure, which should be observable experimentally. (C) 2013 American Institute of Physics. http://dx.doi.org/10.1063/1.4798591]

Narrowing of resonances in electromagnetically induced transparency and absorption using a Laguerre-Gaussian control beam

We study the phenomenon of electromagnetically induced transparency and absorption (EITA) using a control laser with a Laguerre-Gaussian (LG) profile instead of the usual Gaussian profile, and observe significant narrowing of the resonance widths. Aligning the probe beam to the central hole in the doughnut-shaped LG control beam allows simultaneously a strong control intensity required for high signal-to-noise ratio and a low intensity in the probe region required to get narrow resonances. Experiments with an expanded Gaussian control and a second-order LG control show that transit time and orbital angular momentum do not play a significant role. This explanation is borne out by a density-matrix analysis with a radially varying control Rabi frequency. We observe these resonances using degenerate two-level transitions in the D-2 line of Rb-87 in a room temperature vapor cell, and an EIA resonance with width up to 20 times below the natural linewidth for the F = 2 -> F' = 3 transition. Thus the use of LG beams should prove advantageous in all applications of EITA and other kinds of pump-probe spectroscopy as well.

Microbially-induced pyrite removal from galena using Bacillus subtilis

Cells and metabolic products of Bacillus subtilis were used in microbially-induced flocculation and flotation to separate pyrite from galena. Enhanced selective affinity of bacterial cells towards pyrite was observed when compared to galena through adsorption studies. Both extracellular (EP) and intracellular (IP) bacterial proteins were isolated from B. subtilis before and after interaction with the minerals and their profiles established through SDS-PAGE. Protein fractions exhibited significant surface affinity towards galena when compared to pyrite. Presence of galena during bacterial growth promoted increased generation of extracellular proteins, while that of pyrite resulted in enhanced production of exopolysaccharides. Galena surfaces were rendered hydrophobic after bacterial interaction.

Feasibility of laser-induced breakdown spectroscopy for the study of the temporal distribution of trace elements trapped in snow collected from greater himalayan range

The potential merit of laser-induced breakdown spectroscopy (LIBS) has been demonstrated for detection and quantification of trace pollutants trapped in snow/ice samples. In this technique, a high-power pulsed laser beam from Nd:YAG Laser (Model no. Surelite III-10, Continuum, Santa Clara, CA, USA) is focused on the surface of the target to generate plasma. The characteristic emissions from laser-generated plasma are collected and recorded by a fiber-coupled LIBS 2000+ (Ocean Optics, Santa Clara, CA, USA) spectrometer. The fingerprint of the constituents present in the sample is obtained by analyzing the spectral lines by using OOI LIBS software. Reliable detection of several elements like Zn, Al, Mg, Fe, Ca, C, N, H, and O in snow/ice samples collected from different locations (elevation) of Manali and several snow samples collected from the Greater Himalayan region (from a cold lab in Manali, India) in different months has been demonstrated. The calibration curve approach has been adopted for the quantitative analysis of these elements like Zn, Al, Fe, and Mg. Our results clearly demonstrate that the level of contamination is higher in those samples that were collected in the month of January in comparison to those collected in February and March.

An unusual temperature induced isostructural phase transition in a scheelite, Li0.5Ce0.5MoO4

High resolution synchrotron X-ray diffraction, dielectric and Raman scattering study of a scheelite compound Li0.5Ce0.5MoO4 (LCM) revealed that it transforms to a self similar structure above 400 degrees C. The thermally induced isostructural phase transition (IPT), a phenomenon which has rarely been reported in the literature, is preceded by partial softening of the zone centre phonons followed by their hardening above the IPT transition temperature. The high temperature isostructural phase, which exhibits expanded lattice parameters and cell volume, nucleates and grows in the low temperature matrix over a very wide temperature range. Both the phases show nearly identical thermal expansion suggesting similarities in symmetry, unaltered coordination environments around the atoms across the transition.

Anisotropy induced crossover from weakly to strongly first order melting of two dimensional solids

Melting and freezing transitions in two dimensional (2D) systems are known to show highly unusual characteristics. Most of the earlier studies considered atomic systems: the melting of 2D molecular solids is still largely unexplored. In order to understand the role of anisotropy as well as multiple energy and length scales present in molecular systems, here we report computer simulation studies of melting of 2D molecular systems. We computed a limited portion of the solid-liquid phase diagram. We find that the interplay between the strength of isotropic and anisotropic interactions can give rise to rich phase diagram consisting of isotropic liquid and two crystalline phases-honeycomb and oblique. The nature of the transition depends on the relative strength of the anisotropic interaction and a strongly first order melting turns into a weakly first order transition on increasing the strength of the isotropic interaction. This crossover can be attributed to an increase in stiffness of the solid phase free energy minimum on increasing the strength of the anisotropic interaction. The defects involved in melting of molecular systems are quite different from those known for the atomic systems.

Microglia play a major role in direct viral-induced demyelination

Microglia are the resident macrophage-like populations in the central nervous system (CNS). Microglia remain quiescent, unable to perform effector and antigen presentation (APC) functions until activated by injury or infection, and have been suggested to represent the first line of defence for the CNS. Previous studies demonstrated that microglia can be persistently infected by neurotropic mouse hepatitis virus (MHV) which causes meningoencephalitis, myelitis with subsequent axonal loss, and demyelination and serve as a virus-induced model of human neurological disease multiple sclerosis (MS). Current studies revealed that MHV infection is associated with the pronounced activation of microglia during acute inflammation, as evidenced by characteristic changes in cellular morphology and increased expression of microglia-specific proteins, Iba1 (ionized calcium-binding adaptor molecule 1), which is a macrophage/microglia-specific novel calcium-binding protein and involved in membrane ruffling and phagocytosis. During chronic inflammation (day 30 postinfection), microglia were still present within areas of demyelination. Experiments performed in ex vivo spinal cord slice culture and in vitro neonatal microglial culture confirmed direct microglial infection. Our results suggest that MHV can directly infect and activate microglia during acute inflammation, which in turn during chronic inflammation stage causes phagocytosis of myelin sheath leading to chronic inflammatory demyelination.

A multifold reduction in the transition Reynolds number, and ultra-fast mixing, in a micro-channel due to a dynamical instability induced by a soft wall

A dynamical instability is observed in experimental studies on micro-channels of rectangular cross-section with smallest dimension 100 and 160 mu m in which one of the walls is made of soft gel. There is a spontaneous transition from an ordered, laminar flow to a chaotic and highly mixed flow state when the Reynolds number increases beyond a critical value. The critical Reynolds number, which decreases as the elasticity modulus of the soft wall is reduced, is as low as 200 for the softest wall used here (in contrast to 1200 for a rigid-walled channel) The instability onset is observed by the breakup of a dye-stream introduced in the centre of the micro-channel, as well as the onset of wall oscillations due to laser scattering from fluorescent beads embedded in the wall of the channel. The mixing time across a channel of width 1.5 mm, measured by dye-stream and outlet conductance experiments, is smaller by a factor of 10(5) than that for a laminar flow. The increased mixing rate comes at very little cost, because the pressure drop (energy requirement to drive the flow) increases continuously and modestly at transition. The deformed shape is reconstructed numerically, and computational fluid dynamics (CFD) simulations are carried out to obtain the pressure gradient and the velocity fields for different flow rates. The pressure difference across the channel predicted by simulations is in agreement with the experiments (within experimental errors) for flow rates where the dye stream is laminar, but the experimental pressure difference is higher than the simulation prediction after dye-stream breakup. A linear stability analysis is carried out using the parallel-flow approximation, in which the wall is modelled as a neo-Hookean elastic solid, and the simulation results for the mean velocity and pressure gradient from the CFD simulations are used as inputs. The stability analysis accurately predicts the Reynolds number (based on flow rate) at which an instability is observed in the dye stream, and it also predicts that the instability first takes place at the downstream converging section of the channel, and not at the upstream diverging section. The stability analysis also indicates that the destabilization is due to the modification of the flow and the local pressure gradient due to the wall deformation; if we assume a parabolic velocity profile with the pressure gradient given by the plane Poiseuille law, the flow is always found to be stable.

Ultranarrow and Widely Tunable Mn2+-Induced Photoluminescence from Single Mn-Doped Nanocrystals of ZnS-CdS Alloys

Extensively studied Mn-doped semiconductor nanocrystals have invariably exhibited photoluminescence over a narrow energy window of width <= 150 meV in the orange-red region and a surprisingly large spectral width (>= 180 meV), contrary to its presumed atomic-like origin. Carrying out emission measurements on individual single nanocrystals and supported by ab initio calculations, we show that Mn PL emission, in fact, can (i) vary over a much wider range (similar to 370 meV) covering the deep green-deep red region and (ii) exhibit widths substantially lower (similar to 60-75 meV) than reported so far, opening newer application possibilities and requiring a fundamental shift in our perception of the emission from Mn-doped semiconductor nanocrystals.

Visualization of coherent structures in turbulent subsonic jet using planar laser induced fluorescence of acetone

In this paper, we present the molecular density distribution measurement in turbulent nitrogen jet (Re approximate to 3 x 10(3)), using acetone as molecular tracer. The tracer was seeded in the nitrogen jet by purging through the liquid acetone at ambient temperature. Planar laser sheet of 266 nm wavelength from frequency quadrupled, Q-switched, Nd:YAG laser was used as an excitation source. Emitted fluorescence images of jet flow field were recorded on CMOS camera. The dependence of planar laser induced fluorescence (PLIF) intensity on acetone vapor density was used to convert PLIF image of nitrogen jet into the density image on pixel-by-pixel basis. Instantaneous quantitative density image of nitrogen jet, seeded with acetone, was obtained. The arrowhead-shaped coherent turbulent structures were observed in the present work. It was found that coherent structures were non-overlapping with separate boundaries. Breaking of coherent structures into turbulence was clearly observed above four times jet width.

Segmental relaxations and crystallization-induced phase separation in PVDF/PMMA blends in the presence of surface-functionalized multiwall carbon nanotubes

Crystallization-induced phase separation and segmental relaxations in poly(vinylidene fluoride)/poly(methyl methacrylate) (PVDF/PMMA) blends was systematically investigated by melt-rheology and broadband dielectric spectroscopy in the presence of multiwall carbon nanotubes (MWNTs). Different functionalized MWNTs (amine, -NH2; acid, -COOH) were incorporated in the blends by melt-mixing above the melting temperature of PVDF, where the blends are miscible, and the crystallization induced phase separation was probed in situ by shear rheology. Interestingly, only -NH2 functionalized MWNTs (a-MWNTs) aided in the formation of beta-phase (trans-trans) crystals in PVDF, whereas both the neat blends and the blends with -COOH functionalized MWNTs (c-MWNTs) showed only alpha-phase (trans-gauche-trans-gauche') crystals as inferred from wide-angle X-ray diffraction (WXRD) and Fourier transform infrared (FTIR). Furthermore, blends with only a-MWNTs facilitated in heterogeneous nucleation in the blends manifesting in an increase in the calorimetric crystallization temperature and hence, augmented the theologically determined crystallintion induced phase separation temperature. The dielectric relaxations associated with the crystalline phase of PVDF (alpha(c)) was completely absent in the blends with a-MWNTs in contrast to neat blends and the blends with c-MWNTs in the dielectric loss spectra. The relaxations in the blends investigated here appeared to follow Havriliak-Negami (HN) empirical equations, and, more interestingly, the dynamic heterogeneity in the system could be mapped by an extra relaxation at higher frequency at the crystallization-induced phase separation temperature. The mean relaxation time (tau(HN)) was evaluated and observed to be delayed in the presence of MWNTs in the blends, more prominently in the case of blends with a-MWNTs. The latter also showed a significant increase in the dielectric relaxation strength (Delta epsilon). Electron microscopy and selective etching was used to confirm the localization of MWNTs in the amorphous phases of the interspherulitic regions as observed from scanning electron microscopy (SEM). The evolved crystalline morphology, during crystallization-induced phase separation, was observed to have a strong influence on the charge transport processes in the blends. These observations were further supported by the specific interactions (like dipole induced dipole interaction) between a-MWNTs and PVDF, as inferred from FTIR, and the differences in the crystalline morphology as observed from WXRD and polarized optical microscopy (POM).

Multiwalled-carbon-nanotube-induced miscibility in near-critical PS/PVME blends: assessment through concentration fluctuations and segmental relaxation

The effects of multiwalled carbon nanotubes (MWNTs) on the concentration fluctuations, interfacial driven elasticity, phase morphology, and local segmental dynamics of chains for near-critical compositions of polystyrene/poly(vinyl to methyl ether) (PS/PVME) blends were systematically investigated using dynamic shear rheology and dielectric spectroscopy. The contribution of the correlation length (xi) of the concentration fluctuations to the evolving stresses was monitored in situ to probe the different stages of demixing in the blends. The classical upturn in the dynamic moduli was taken as the rheological demixing temperature (T-rheo), which was also observed to be in close agreement with those obtained using concentration fluctuation variance, <(delta phi)(2)>, versus temperature curves. Further, Fredrickson and Larson's approach involving the mean-field approximation and the double-reptation self-concentration (DRSC) model was employed to evaluate the spinodal decomposition temperature (T-s). Interestingly, the values of both T-rheo and T-s shifted upward in the blends in the presence of MWNTs, manifesting in molecular-level miscibility. These phenomenal changes were further observed to be a function of the concentration of MWNTs. The evolution of morphology as a function of temperature was studied using polarized optical microscopy (POM). It was observed that PVME, which evolved as an interconnected network during the early stages of demixing, coarsened into a matrix-droplet morphology in the late stages. The preferential wetting of PVME onto MWNTs as a result of physicochemical interactions retained the interconnected network of PVME for longer time scales, as supported by POM and atomic force microscopy (AFM) images. Microscopic heterogeneity in macroscopically miscible systems was studied by dielectric relaxation spectroscopy. The slowing of segmental relaxations in PVME was observed in the presence of both ``frozen'' PS and MWNTs interestingly at temperatures much below the calorimetric glass transition temperature (T-g). This phenomenon was observed to be local rather than global and was addressed by monitoring the evolution of the relaxation spectra near and above the demixing temperature.

pH Induced switching in hydrogel coated fiber bragg grating sensor

In this paper we report a novel hydrogel functionalized optical Fiber Bragg Grating (FBG) sensor based on chemo-mechanical-optical sensing, and demonstrate its specific application in pH activated process monitoring. The sensing mechanism is based on the stress due to ion diffusion and polymer phase transition which produce strain in the FBG. This results in shift in the Bragg wavelength which is detected by an interrogator system. A simple dip coating method to coat a thin layer of hydrogel on the FBG has been established. The gel consists of sodium alginate and calcium chloride. Gel formation is observed in real-time by continuously monitoring the Bragg wavelength shift. We have demonstrated pH sensing in the range of pH of 2 to 10. Another interesting phenomenon is observed by swelling and deswelling of FBG functionalized with hydrogel by a sequence of alternate dipping between acidic and base solutions. It is observed that the Bragg wavelength undergoes reversible and repeatable pH dependent switching.

Molecular flexibility tuned emission in ``V'' shaped naphthalimides: Hg(II) detection and aggregation-induced emission enhancement (AIEE)

Four ``V'' shaped 1,8-naphthalimides (1-4) have been synthesized and their fluorescence quantum-yields correlated to their molecular flexibility. The correlation was used for detection of Hg(II) via a chemodosimetric approach. 4 was found to be an AIE active molecule with the formation of fluorescent nanoaggregates.