Enhanced non-homologous end joining contributes toward synthetic lethality of pathological RAD51C mutants with poly (ADP-ribose) polymerase

Here, we show that PARP inhibitor-mediated cell death of RAD51C-deficient cells occur by NHEJ-driven illegitimate repair of one-ended double-strand breaks, and the hypomorphic RAD51C pathological mutant cells can be targeted by `synergistic toxicity' induced by low-dose PARP inhibitor and IR.Poly (ADP-ribose) polymerase 1 (PARP1) inhibitors are actively under clinical trials for the treatment of breast and ovarian cancers that arise due to mutations in BRCA1 and BRCA2. The RAD51 paralog RAD51C has been identified as a breast and ovarian cancer susceptibility gene. The pathological RAD51C mutants that were identified in cancer patients are hypomorphic with partial repair function. However, targeting cancer cells that express hypomorphic mutants of RAD51C is highly challenging. Here, we report that RAD51C-deficient cells can be targeted by a `synthetic lethal' approach using PARP inhibitor and this sensitivity was attributed to accumulation of cells in the G(2)/M and chromosomal aberrations. In addition, spontaneous hyperactivation of PARP1 was evident in RAD51C-deficient cells. Interestingly, RAD51C-negative cells exhibited enhanced recruitment of non-homologous end joining (NHEJ) proteins onto chromatin and this accumulation correlated with increased activity of error-prone NHEJ as well as genome instability leading to cell death. Notably, inhibition of DNA-PKcs or depletion of KU70 or Ligase IV rescued this phenotype. Strikingly, stimulation of NHEJ by low dose of ionizing radiation (IR) in the PARP inhibitor-treated RAD51C-deficient cells and cells expressing pathological RAD51C mutants induced enhanced toxicity `synergistically'. These results demonstrate that cancer cells arising due to hypomorphic mutations in RAD51C can be specifically targeted by a `synergistic approach' and imply that this strategy can be potentially applied to cancers with hypomorphic mutations in other homologous recombination pathway genes.

Driving force of water entry into hydrophobic channels of carbon nanotubes: entropy or energy?

Spontaneous entry of water molecules inside single-wall carbon nanotubes (SWCNTs) has been confirmed by both simulations and experiments. Using molecular dynamics simulations, we have studied the thermodynamics of filling of a (6,6) carbon nanotube in a temperature range from 273 to 353K and with different strengths of the nanotube-water interaction. From explicit energy and entropy calculations using the two-phase thermodynamics method, we have presented a thermodynamic understanding of the filling behaviour of a nanotube. We show that both the energy and the entropy of transfer decrease with increasing temperature. On the other hand, scaling down the attractive part of the carbon-oxygen interaction results in increased energy of transfer while the entropy of transfer increases slowly with decreasing the interaction strength. Our results indicate that both energy and entropy favour water entry into (6,6) SWCNTs. Our results are compared with those of several recent studies of water entry into carbon nanotubes.

Low frequency modulation of jets in quasigeostrophic turbulence

Quasigeostrophic turbulence on a beta-plane with a finite deformation radius is studied numerically, with particular emphasis on frequency and combined wavenumber-frequency domain analyses. Under suitable conditions, simulations with small-scale random forcing and large-scale drag exhibit a spontaneous formation of multiple zonal jets. The first hint of wave-like features is seen in the distribution of kinetic energy as a function of frequency; specifically, for progressively larger deformation scales, there are systematic departures in the form of isolated peaks (at progressively higher frequencies) from a power-law scaling. Concomitantly, there is an inverse flux of kinetic energy in frequency space which extends to lower frequencies for smaller deformation scales. The identification of these peaks as Rossby waves is made possible by examining the energy spectrum in frequency-zonal wavenumber and frequency-meridional wavenumber diagrams. In fact, the modified Rhines scale turns out to be a useful measure of the dominant meridional wavenumber of the modulating Rossby waves; once this is fixed, apart from a spectral peak at the origin (the steady jet), almost all the energy is contained in westward propagating disturbances that follow the theoretical Rossby dispersion relation. Quite consistently, noting that the zonal scale of the modulating waves is restricted to the first few wavenumbers, the energy spectrum is almost entirely contained within the corresponding Rossby dispersion curves on a frequency-meridional wavenumber diagram. Cases when jets do not form are also considered; once again, there is a hint of Rossby wave activity, though the spectral peaks are quite muted. Further, the kinetic energy scaling in frequency domain follows a -5/3 power-law and is distributed much more broadly in frequency-wavenumber diagrams. (C) 2015 AIP Publishing LLC.

Active Viscoelastic Matter: From Bacterial Drag Reduction to Turbulent Solids

A paradigm for internally driven matter is the active nematic liquid crystal, whereby the equations of a conventional nematic are supplemented by a minimal active stress that violates time-reversal symmetry. In practice, active fluids may have not only liquid-crystalline but also viscoelastic polymer degrees of freedom. Here we explore the resulting interplay by coupling an active nematic to a minimal model of polymer rheology. We find that adding a polymer can greatly increase the complexity of spontaneous flow, but can also have calming effects, thereby increasing the net throughput of spontaneous flow along a pipe (a ``drag-reduction'' effect). Remarkably, active turbulence can also arise after switching on activity in a sufficiently soft elastomeric solid.

Metastable monoclinic and orthorhombic phases and electric field induced irreversible phase transformation at room temperature in the lead-free classical ferroelectric BaTiO3

For decades it has been a well-known fact that among the few ferroelectric compounds in the perovskite family, namely, BaTiO3, KNbO3, PbTiO3, and Na1/2Bi1/2TiO3, the dielectric and piezoelectric properties of BaTiO3 are considerably higher than the others in polycrystalline form at room temperature. Further, similar to ferroelectric alloys exhibiting morphotropic phase boundary, single crystals of BaTiO3 exhibit anomalously large piezoelectric response when poled away from the direction of spontaneous polarization at room temperature. These anomalous features in BaTiO3 remained unexplained so far from the structural standpoint. In this work, we have used high-resolution synchrotron x-ray powder diffraction, atomic resolution aberration-corrected transmission electron microscopy, in conjunction with a powder poling technique, to reveal that at 300 K (i) the equilibrium state of BaTiO3 is characterized by coexistence of metastable monoclinic Pm and orthorhombic (Amm2) phases along with the tetragonal phase, and (ii) strong electric field switches the polarization direction from the 001] direction towards the 101] direction. These results suggest that BaTiO3 at room temperature is within an instability regime, and that this instability is the fundamental factor responsible for the anomalous dielectric and piezoelectric properties of BaTiO3 as compared to the other homologous ferroelectric perovskite compounds at room temperature. Pure BaTiO3 at room temperature is therefore more akin to lead-based ferroelectric alloys close to the morphotropic phase boundary where polarization rotation and field induced ferroelectric-ferroelectric phase transformations play a fundamental role in influencing the dielectric and piezoelectric behavior.

Pt-Poisoning-Free Efficient CO Oxidation on Pt3Co Supported on MgO(100): An Ab Initio Study

Late-transition-metal-doped Pt clusters are prevalent in CO oxidation catalysis, as they exhibit better catalytic activity than pure Pt, while reducing the effective cost and poisoning However, completely eliminating the critical problem of Pt poisoning still poses a big challenge. Here, we report for the first time that, among the bimetallic clusters ((Pt3M where M = Co, Ni, and Cu)/MgO(100)), the CO adsorption site inverts for Pt3Co/MgO(100) from Pt to Co, due to the complete uptake of Pt d-states by lattice oxygen. While this resolves the problem of Pt poisoning, good reaction kinetics are predicted through low barriers for Langmuir-Hinshelwood and Mars van Krevelen (MvK) mechanisms of CO oxidation for Pt3Co/MgO(100) and Li-doped MgO(100), respectively. Li doping in MgO(100) compensates for the charge imbalance caused by a spontaneous oxygen vacancy formation. Pt-3 Co/Li-doped MgO(100) stands out as an exceptional CO oxidation catalyst, giving an MvK reaction barrier as low as 0.11 eV. We thereby propose a novel design strategy of d-band center inversion for CO oxidation catalysts with no Pt poisoning and excellent reaction kinetics.

Tailoring local density of optical states to control emission intensity and anisotropy of quantum dots in hybrid photonic-plasmonic templates

We report results of controlled tuning of the local density of states (LDOS) in versatile, flexible, and hierarchical self assembled plasmonic templates. Using 5 nm diameter gold (Au) spherical nanoantenna within a polymer template randomly dispersed with quantum dots, we show how the photoluminescence intensity and lifetime anisotropy of these dots can be significantly enhanced through LDOS tuning. Finite difference time domain simulations corroborate the experimental observations and extend the regime of enhancement to a wider range of geometric and spectral parameters bringing out the versatility of these functional plasmonic templates. It is also demonstrated how the templates act as plasmonic resonators for effectively engineer giant enhancement of the scattering efficiency of these nano antenna embedded in the templates. Our work provides an alternative method to achieve spontaneous emission intensity and anisotropy enhancement with true nanoscale plasmon resonators. (C) 2015 AIP Publishing LLC.

Effect of ultra-fast mixing in a microchannel due to a soft wall on the room temperature synthesis of gold nanoparticles

The room-temperature synthesis of mono-dispersed gold nanoparticles, by the reduction of chlorauric acid (HAuCl4) with tannic acid as the reducing and stabilizing agent, is carried out in a microchannel. The microchannel is fabricated with one soft wall, so that there is a spontaneous transition to turbulence, and thereby enhanced mixing, when the flow Reynolds number increases beyond a critical value. The objective of the study is to examine whether the nanoparticle size and polydispersity can be modified by enhancing the mixing in the microchannel device. The flow rates are varied in order to study nanoparticle formation both in laminar flow and in the chaotic flow after transition, and the molar ratio of the chlorauric acid to tannic acid is also varied to study the effect of molar ratio on nanoparticle size. The formation of gold nanoparticles is examined by UV-visual spectroscopy and the size distribution is determined using scanning electron microscopy. The synthesized nanoparticles size decreases from a parts per thousand yen6 nm to a parts per thousand currency sign4 nm when the molar ratio of chlorauric acid to tannic acid is increased from 1 to 20. It is found that there is no systematic variation of nanoparticle size with flow velocity, and the nanoparticle size is not altered when the flow changes from laminar to turbulent. However, the standard deviation of the size distribution decreases by about 30% after transition, indicating that the enhanced mixing results in uniformity of particle size.

Imidazolium based ionic liquid type surfactant improves activity and thermal stability of lipase of Rhizopus oryzae

Lipase and surfactant together form a potent pair in various biotransformation, industrial application and biotechnological studies. The present investigation deals with changes in the activity, stability and structure of lipase from Rhizopus oryzae NRRL 3562 in presence of long chain ionic liquid-type imidazolium surfactant. Both the activity and stability were found to be enhanced in presence of the surfactant at low concentration (1-125 mu M) followed by inhibition at high concentration. The activity increased by 80% and thermal deactivation temperature raised by 2.5 degrees C. Investigations by ultraviolet-visible spectroscopy and circular dichroism revealed structural changes leading to rise in beta-sheet content and lowering of a-helix at low surfactant concentrations. Deactivation at high concentration correlated with greater structural changes depicted by spectroscopic studies. Isothermal titration calorimetric studies showed the binding to be spontaneous in nature involving non-covalent interactions. High negative value of entropy signifies exposure of hydrophobic domains and increase in structural rigidity, which correlates with active site being more accessible and rigid in presence of the surfactant. Application of these surfactants hold greater potential in the field of lipase based biotransformations, enzyme structural modifications and studies. (C) 2015 Elsevier B.V. All rights reserved.

Synthesis, photoluminescence and Judd-Ofelt parameters of LiNa3P2O7:Eu3+ orthorhombic microstructures

We report, for the first time, the photoluminescence properties of Eu3+-doped LiNa3P2O7 phosphor, synthesized by a facile solid-state reaction method in air atmosphere. The crystal structure and phase purity of the phosphors were analyzed by X-ray diffraction analysis. Orthorhombic structural morphology was identified by scanning electron microscopy. The phosphate groups in the phosphor were confirmed by Fourier transform infrared analysis. Bandgap of the phosphor was calculated from the diffuse reflectance spectra data using Kubelka-Munk function. Under 395-nm UV excitation, the phosphors show signs of emitting red color due to the D-5(0) -> F-7(2) transition. In accordance with Judd-Ofelt theory, spectroscopic parameters such as oscillator intensity parameter Omega(t) (t = 2), spontaneous emission probabilities, fluorescence branching ratios and radiative lifetimes were calculated and analyzed for the first time in this system.

Ag+-induced reverse vesicle to helical fiber transformation in a self-assembly by adjusting the keto-enol equilibrium of a chiral salicylideneaniline

A new chiral amphiphilic salicylideneaniline bearing a terminal pyridine was synthesized. It formed reverse vesicles in toluene. The addition of Ag+, however, reversibly transforms these reverse vesicles into left-handed nanohelices accompanied by spontaneous gel formation at room temperature.

Cell-Membrane-Mimicking Lipid-Coated Nanoparticles Confer Raman Enhancement to Membrane Proteins and Reveal Membrane-Attached Amyloid-beta Conformation

Identifying the structures of membrane bound proteins is critical to understanding their function in healthy and diseased states. We introduce a surface enhanced Raman spectroscopy technique which can determine the conformation of membrane-bound proteins, at low micromolar concentrations, and also in the presence of a substantial membrane-free fraction. Unlike conventional surface enhanced Raman spectroscopy, our approach does not require immobilization of molecules, as it uses spontaneous binding of proteins to lipid bilayer-encapsulated Ag nanoparticles. We apply this technique to probe membrane-attached oligomers of Amyloid-beta(40) (A beta(40)), whose conformation is keenly sought in the context of Alzheimer's disease. Isotope-shifts in the Raman spectra help us obtain secondary structure information at the level of individual residues. Our results show the presence of a beta-turn, flanked by two beta-sheet regions. We use solid-state NMR data to confirm the presence of the beta-sheets in these regions. In the membrane-attached oligomer, we find a strongly contrasting and near-orthogonal orientation of the backbone H-bonds compared to what is found in the mature, less-toxic A beta fibrils. Significantly, this allows a ``porin'' like beta-barrel structure, providing a structural basis for proposed mechanisms of A beta oligomer toxicity.

Observation of correlated spin-orbit order in a strongly anisotropic quantum wire system

Quantum wires with spin-orbit coupling provide a unique opportunity to simultaneously control the coupling strength and the screened Coulomb interactions where new exotic phases of matter can be explored. Here we report on the observation of an exotic spin-orbit density wave in Pb-atomic wires on Si(557) surfaces by mapping out the evolution of the modulated spin-texture at various conditions with spin-and angle-resolved photoelectron spectroscopy. The results are independently quantified by surface transport measurements. The spin polarization, coherence length, spin dephasing rate and the associated quasiparticle gap decrease simultaneously as the screened Coulomb interaction decreases with increasing excess coverage, providing a new mechanism for generating and manipulating a spin-orbit entanglement effect via electronic interaction. Despite clear evidence of spontaneous spin-rotation symmetry breaking and modulation of spin-momentum structure as a function of excess coverage, the average spin polarization over the Brillouin zone vanishes, indicating that time-reversal symmetry is intact as theoretically predicted.

A Generalization of Gravity

I consider theories of gravity built not just from the metric and affine connection, but also other (possibly higher rank) symmetric tensor(s). The Lagrangian densities are scalars built from them, and the volume forms are related to Cayley's hyperdeterminants. The resulting diff-invariant actions give rise to geometric theories that go beyond the metric paradigm (even metric-less theories are possible), and contain Einstein gravity as a special case. Examples contain theories with generalizeations of Riemannian geometry. The 0-tensor case is related to dilaton gravity. These theories can give rise to new types of spontaneous Lorentz breaking and might be relevant for ``dark'' sector cosmology.

Impact of lifetime control on the threshold of quantum dot lasers

Despite significant improvements in their properties as emitters, colloidal quantum dots have not had much success in emerging as suitable materials for laser applications. Gain in most colloidal systems is short lived, and needs to compete with biexcitonic decay. This has necessitated the use of short pulsed lasers to pump quantum dots to thresholds needed for amplified spontaneous emission or lasing. Continuous wave pumping of gain that is possible in some inorganic phosphors has therefore remained a very distant possibility for quantum dots. Here, we demonstrate that trilayer heterostructures could provide optimal conditions for demonstration of continuous wave lasing in colloidal materials. The design considerations for these materials are discussed in terms of a kinetic model. The electronic structure of the proposed dot architectures is modeled within effective mass theory.