Molecular and Functional Characterization of RecD, a Novel Member of the SF1 Family of Helicases, from Mycobacterium tuberculosis

Background: The heterotrimeric M. tuberculosis RecBCD complex, or each of its individual subunits, remains uncharacterized. Results: MtRecD exists as a homodimer in solution, catalyzes ssDNA-dependent ATP hydrolysis, unwinding of DNA replication/recombination intermediates, and interacts with RecA. Conclusion: MtRecD possesses strong 5 3- and weak 3 5-helicase activities. Significance: These findings provide insights into the mechanism underlying DSB repair and homologous recombination in mycobacteria. The annotated whole-genome sequence of Mycobacterium tuberculosis revealed the presence of a putative recD gene; however, the biochemical characteristics of its encoded protein product (MtRecD) remain largely unknown. Here, we show that MtRecD exists in solution as a stable homodimer. Protein-DNA binding assays revealed that MtRecD binds efficiently to single-stranded DNA and linear duplexes containing 5 overhangs relative to the 3 overhangs but not to blunt-ended duplex. Furthermore, MtRecD bound more robustly to a variety of Y-shaped DNA structures having 18-nucleotide overhangs but not to a similar substrate containing 5-nucleotide overhangs. MtRecD formed more salt-tolerant complexes with Y-shaped structures compared with linear duplex having 3 overhangs. The intrinsic ATPase activity of MtRecD was stimulated by single-stranded DNA. Site-specific mutagenesis of Lys-179 in motif I abolished the ATPase activity of MtRecD. Interestingly, although MtRecD-catalyzed unwinding showed a markedly higher preference for duplex substrates with 5 overhangs, it could also catalyze significant unwinding of substrates containing 3 overhangs. These results support the notion that MtRecD is a bipolar helicase with strong 5 3 and weak 3 5 unwinding activities. The extent of unwinding of Y-shaped DNA structures was approximate to 3-fold lower compared with duplexes with 5 overhangs. Notably, direct interaction between MtRecD and its cognate RecA led to inhibition of DNA strand exchange promoted by RecA. Altogether, these studies provide the first detailed characterization of MtRecD and present important insights into the type of DNA structure the enzyme is likely to act upon during the processes of DNA repair or homologous recombination.

Specificity of the ModA11, ModA12 and ModD1 epigenetic regulator N-6-adenine DNA methyltransferases of Neisseria meningitidis

Phase variation (random ON/OFF switching) of gene expression is a common feature of host-adapted pathogenic bacteria. Phase variably expressed N-6-adenine DNA methyltransferases (Mod) alter global methylation patterns resulting in changes in gene expression. These systems constitute phase variable regulons called phasevarions. Neisseria meningitidis phasevarions regulate genes including virulence factors and vaccine candidates, and alter phenotypes including antibiotic resistance. The target site recognized by these Type III N-6-adenine DNA methyltransferases is not known. Single molecule, real-time (SMRT) methylome analysis was used to identify the recognition site for three key N. meningitidis methyltransferases: ModA11 (exemplified by M.NmeMC58I) (5'-CGY(m6)AG-3'), ModA12 (exemplified by M.Nme77I, M.Nme18I and M.Nme579II) (5'-AC(m6)ACC-3') and ModD1 (exemplified by M.Nme579I) (5'-CC(m6)AGC-3'). Restriction inhibition assays and mutagenesis confirmed the SMRT methylome analysis. The ModA11 site is complex and atypical and is dependent on the type of pyrimidine at the central position, in combination with the bases flanking the core recognition sequence 5'-CGY(m6)AG-3'. The observed efficiency of methylation in the modA11 strain (MC58) genome ranged from 4.6% at 5'-GCGC(m6)AGG-3' sites, to 100% at 5'-ACGT(m6)AGG-3' sites. Analysis of the distribution of modified sites in the respective genomes shows many cases of association with intergenic regions of genes with altered expression due to phasevarion switching.

Pressure-induced structural phase transitions and phonon anomalies in ReO3: Raman and first-principles study

We report high-pressure Raman-scattering studies on single-crystal ReO3 up to 26.9 GPa at room temperature, complemented by first-principles density functional calculations to assign the modes and to develop understanding of the subtle features of the low-pressure phase transition. The pressure (P) dependence of phonon frequencies (omega) reveals three phase transitions at 0.6, 3, and 12.5 GPa with characteristic splitting and changes in the slope of omega(P). Our first-principles theoretical analysis confirms the role of the rotational modes of ReO6, M-3, to the lowest pressure structural transition, and shows that the transition from the Pm3m to the Im3 structure is a weak first-order transition, originating from the strong anharmonic coupling of the M-3 modes with the acoustic modes (strain).

Optical and dielectric study of strontium modified barium zirconium titanate ceramic prepared by high energy ball milling

Strontium modified barium zirconium titanate with general formula Ba1-xSrxZr0.05Ti0.95O3 ceramics have been prepared by solid state and high energy ball milling technique. The X-ray diffraction and Rietveld refinement studies show that all the compositions have single phase symmetry. The composition BaZr0.05Ti0.95O3 shows orthorhombic symmetric with space group Amm2. The structure changes from orthorhombic to tetragonal with strontium doping up to x = 0.3 and with further addition, changes to cubic. The scanning electron micrographs show that the grain size decreases with increase in strontium content. The temperature dependent dielectric behavior shows three phase transition in the parent material which merges with an increase in Sr content The transition temperature and dielectric constant decreases with an increase in Sr concentration. The phase transition becomes more diffused with increment in doping concentration. The ferroelectric behavior of the ceramics is studied by the hysteresis loop. The optical behavior is studied by the UV-visible spectroscopy and found that the optical band gap increases with Sr concentration. (C) 2015 Elsevier B.V. All rights reserved.

Retrieval and Multi-scale Validation of Soil Moisture from Multi-temporal SAR Data in a Semi-Arid Tropical Region

The current study presents an algorithm to retrieve surface Soil Moisture (SM) from multi-temporal Synthetic Aperture Radar (SAR) data. The developed algorithm is based on the Cumulative Density Function (CDF) transformation of multi-temporal RADARSAT-2 backscatter coefficient (BC) to obtain relative SM values, and then converts relative SM values into absolute SM values using soil information. The algorithm is tested in a semi-arid tropical region in South India using 30 satellite images of RADARSAT-2, SMOS L2 SM products, and 1262 SM field measurements in 50 plots spanning over 4 years. The validation with the field data showed the ability of the developed algorithm to retrieve SM with RMSE ranging from 0.02 to 0.06 m(3)/m(3) for the majority of plots. Comparison with the SMOS SM showed a good temporal behaviour with RMSE of approximately 0.05 m(3)/m(3) and a correlation coefficient of approximately 0.9. The developed model is compared and found to be better than the change detection and delta index model. The approach does not require calibration of any parameter to obtain relative SM and hence can easily be extended to any region having time series of SAR data available.

Thermalization of Green functions and quasinormal modes

We develop a new method to study the thermalization of time dependent retarded Green function in conformal field theories holographically dual to thin shell AdS Vaidya space times. The method relies on using the information of all time derivatives of the Green function at the shell and then evolving it for later times. The time derivatives of the Green function at the shell is given in terms of a recursion formula. Using this method we obtain analytic results for short time thermalization of the Green function. We show that the late time behaviour of the Green function is determined by the first quasinormal mode. We then implement the method numerically. As applications of this method we study the thermalization of the retarded time dependent Green function corresponding to a minimally coupled scalar in the AdS 3 and AdS 5 thin Vaidya shells. We see that as expected the late time behaviour is determined by the first quasinormal mode. We apply the method to study the late time behaviour of the shear vector mode in AdS 5 Vaidya shell. At small momentum the corresponding time dependent Green function is expected to relax to equilibrium by the shear hydrodynamic mode. Using this we obtain the universal ratio of the shear viscosity to entropy density from a time dependent process.

Room temperature ferromagnetism and white light emissive CdS:Cr nanoparticles synthesized by chemical co-precipitation method

Undoped and Cr (3% and 5%) doped CdS nanoparticles were synthesized by chemical co-precipitation method. The synthesized nanocrystalline particles are characterized by energy dispersive X-ray analysis (EDAX), scanning electron microscope (SEM), X-ray Diffraction (XRD), transmission electron microscopy (TEM), diffuse reflectance spectroscopy (DRS), photoluminescence (PL), Electron paramagnetic resonance (EPR), vibrating sample magnetometer (VSM) and Raman spectroscopy. XRD studies indicate that Cr doping in host CdS result a structural change from Cubic phase to mixed (cubic + hexagonal) phase. Due to quantum confinement effect, widening of the band gap is observed for undoped and Cr doped CdS nanoparticles compared to bulk CdS. The average particle size calculated from band gap values is in good agreement with the TEM study calculation and it is around 4-5 nm. A strong violet emission band consisting of two emission peaks is observed for undoped CdS nanoparticles, whereas for CdS:Cr nanoparticles, a broad emission band ranging from 420 nm to 730 nm with a maximum at similar to 587 nm is observed. The broad emission band is due to the overlapped emissions from variety of defects. EPR spectra of CdS:Cr samples reveal resonance signal at g = 2.143 corresponding to interacting Cr3+ ions. VSM studies indicate that the diamagnetic CdS nanoparticles are transform to ferromagnetic for 3% Cr3+ doping and the ferromagnetic nature is diminished with increasing the doping concentration to 5%. (C) 2015 Elsevier B.V. All rights reserved.

Ac2PIM-responsive miR-150 and miR-143 Target Receptor-interacting Protein Kinase 2 and Transforming Growth Factor Beta-activated Kinase 1 to Suppress NOD2-induced Immunomodulators

Specific and coordinated regulation of innate immune receptor-driven signaling networks often determines the net outcome of the immune responses. Here, we investigated the cross-regulation of toll-like receptor (TLR)2 and nucleotide-binding oligomerization domain (NOD)2 pathways mediated by Ac2PIM, a tetra-acylated form of mycobacterial cell wall component and muramyl dipeptide (MDP), a peptidoglycan derivative respectively. While Ac2PIM treatment of macrophages compromised their ability to induce NOD2-dependent immunomodulators like cyclooxygenase (COX)-2, suppressor of cytokine signaling (SOCS)-3, and matrix metalloproteinase (MMP)-9, no change in the NOD2-responsive NO, TNF-alpha, VEGF-A, and IL-12 levels was observed. Further, genome-wide microRNA expression profiling identified Ac2PIM-responsive miR-150 and miR-143 to target NOD2 signaling adaptors, RIP2 and TAK1, respectively. Interestingly, Ac2PIM was found to activate the SRC-FAK-PYK2-CREB cascade via TLR2 to recruit CBP/P300 at the promoters of miR-150 and miR-143 and epigenetically induce their expression. Loss-of-function studies utilizing specific miRNA inhibitors establish that Ac2PIM, via the miRNAs, abrogate NOD2-induced PI3K-PKC delta-MAPK pathway to suppress beta-catenin-mediated expression of COX-2, SOCS-3, and MMP-9. Our investigation has thus underscored the negative regulatory role of Ac2PIM-TLR2 signaling on NOD2 pathway which could broaden our understanding on vaccine potential or adjuvant utilities of Ac2PIM and/or MDP.

Thermal, magnetic and electrical properties of Tb1-xDyxMnO3 multiferroics

A series of multiferroic materials with the compositional formula, Tb1 - xDyxMnO3 (where x=0, 0.1, 0.2, 0.3 and 0.4) were prepared by the sol gel method. After characterizing the samples structurally, a systematic investigation of specific heat, magnetization and dielectric properties over the temperature range, 4-300 K, was undertaken. Based on these studies, it was found that all the samples exhibit a transition at 40 K and the observed behavior may be attributed to the ordering of Mn3+ ions. Further, all the five samples are found to exhibit a ferroelectric transition in the temperature range 20-24 K. Finally, yet another transition was also exhibited by all the samples at temperatures below 10 K and is attributed to the antiferromagnetic (AF) ordering of rare-earth ionic moments. The magnetic entropy of all the samples was also computed with the help of their heat capacity data. (C) 2015 Elsevier B.V. All rights reserved.

Endoplasmic reticulum targeting tumour selective photocytotoxic oxovanadium(IV) complexes having vitamin-B6 and acridinyl moieties

Oxovanadium(IV) complexes of vitamin-B6 Schiff base, viz., VO(HL1/L-2/L-3)(B)] Cl (1-4), where B is 2,2'-bipyridine (bpy in 1 and 2), 11-(9-acridinyl)dipyrido3,2-a:2',3'-c]phenazine (acdppz in 3 and 4), H2L1 center dot HCl is 3-hydroxy-5-(hydroxymethyl)-4-(((2-hydroxyphenyl)imino)methyl)-2-methylp yridin-1-ium chloride (in 1 and 4), HL2 is 2-(((2-(1H-imidazol-4-yl)ethyl) imino)methyl) phenol (in 2) and HL3 is 4-(((2-(1H-imidazol-4- yl)ethyl)imino)methyl)-5-(hydroxymethyl)-2-methylpyridin-3-ol (in 3) were synthesized, characterized and their cellular uptake, photo-activated cytotoxicity and intracellular localization were studied. Complexes 1a, as the perchlorate salt of 1, and 2a, as the hexafluorophosphate salt of 2, were structurally characterized. Vitamin-B6 transporting membrane carrier (VTC) mediated entry into tumour cells in preference to the normal ones seems to be responsible for the higher cellular uptake of the complexes into HeLa and MCF-7 cells over MCF-10A cells. Complexes 3 and 4 having acdppz as the photosensitizer exhibit remarkable photocytotoxicity in these cancer cells giving IC50 of < 0.9 mu M. The complexes remain non-toxic in the dark. The complexes show photo-induced apoptotic cell death via singlet oxygen (O-1(2)) generation. Fluorescence microscopy reveals specific localization of complex 4 to endoplasmic reticulum (ER) and generation of O-1(2) possibly leads to apoptotic cell death by triggering ER stress response (ERSR).

Endoplasmic reticulum targeting tumour selective photocytotoxic oxovanadium(IV) complexes having vitamin-B6 and acridinyl moieties

Oxovanadium(IV) complexes of vitamin-B6 Schiff base, viz., VO(HL1/L-2/L-3)(B)] Cl (1-4), where B is 2,2'-bipyridine (bpy in 1 and 2), 11-(9-acridinyl)dipyrido3,2-a:2',3'-c]phenazine (acdppz in 3 and 4), H2L1 center dot HCl is 3-hydroxy-5-(hydroxymethyl)-4-(((2-hydroxyphenyl)imino)methyl)-2-methylp yridin-1-ium chloride (in 1 and 4), HL2 is 2-(((2-(1H-imidazol-4-yl)ethyl) imino)methyl) phenol (in 2) and HL3 is 4-(((2-(1H-imidazol-4- yl)ethyl)imino)methyl)-5-(hydroxymethyl)-2-methylpyridin-3-ol (in 3) were synthesized, characterized and their cellular uptake, photo-activated cytotoxicity and intracellular localization were studied. Complexes 1a, as the perchlorate salt of 1, and 2a, as the hexafluorophosphate salt of 2, were structurally characterized. Vitamin-B6 transporting membrane carrier (VTC) mediated entry into tumour cells in preference to the normal ones seems to be responsible for the higher cellular uptake of the complexes into HeLa and MCF-7 cells over MCF-10A cells. Complexes 3 and 4 having acdppz as the photosensitizer exhibit remarkable photocytotoxicity in these cancer cells giving IC50 of < 0.9 mu M. The complexes remain non-toxic in the dark. The complexes show photo-induced apoptotic cell death via singlet oxygen (O-1(2)) generation. Fluorescence microscopy reveals specific localization of complex 4 to endoplasmic reticulum (ER) and generation of O-1(2) possibly leads to apoptotic cell death by triggering ER stress response (ERSR).

Red-emitting LaOF:Eu3+ phosphors: Synthesis, structure and their Judd-Ofelt analysis for LED applications

In the present study, we have synthesized a series of La1-xEuxOF (0.01 <= x <= 0.09) phosphors by the conventional solid-state reaction route at relatively low temperature (500 degrees C) and shorter duration of 2 h. The compounds were crystallized in the rhombohedral structure with the space group R-3m (No. 166). Upon UV excitation (254 nm), the photoluminescence spectra exhibit characteristic luminescence D-5(0) -> F-7(J) (J= 1, 2, 3, and 4) intra-4f shell Eu3+ ion transitions. An intense red emission peak at 610 nm was observed due to electric dipole (D-5(0) -> F-7(2)) transition. Judd-Ofelt theory was employed to evaluate various radiative parameters such as radiative emission rates, lifetime, branching and asymmetry ratios. CIE color coordinates confirmed the red emission of the phosphors. The luminescent results reveal that LaOF:Eu3+ phosphor can be used as potential candidate for developing red component in white LED applications. (C) 2015 Elsevier Ltd. All rights reserved.

No More HF: Teflon-Assisted Ultrafast Removal of Silica to Generate High-Surface-Area Mesostructured Carbon for Enhanced CO2 Capture and Supercapacitor Performance

An innovative technique to obtain high-surface-area mesostructured carbon (2545m(2)g(-1)) with significant microporosity uses Teflon as the silica template removal agent. This method not only shortens synthesis time by combining silica removal and carbonization in a single step, but also assists in ultrafast removal of the template (in 10min) with complete elimination of toxic HF usage. The obtained carbon material (JNC-1) displays excellent CO2 capture ability (ca. 26.2wt% at 0 degrees C under 0.88bar CO2 pressure), which is twice that of CMK-3 obtained by the HF etching method (13.0wt%). JNC-1 demonstrated higher H-2 adsorption capacity (2.8wt%) compared to CMK-3 (1.2wt%) at -196 degrees C under 1.0bar H-2 pressure. The bimodal pore architecture of JNC-1 led to superior supercapacitor performance, with a specific capacitance of 292Fg(-1) and 182Fg(-1) at a drain rate of 1Ag(-1) and 50Ag(-1), respectively, in 1m H2SO4 compared to CMK-3 and activated carbon.

No More HF: Teflon-Assisted Ultrafast Removal of Silica to Generate High-Surface-Area Mesostructured Carbon for Enhanced CO2 Capture and Supercapacitor Performance

An innovative technique to obtain high-surface-area mesostructured carbon (2545m(2)g(-1)) with significant microporosity uses Teflon as the silica template removal agent. This method not only shortens synthesis time by combining silica removal and carbonization in a single step, but also assists in ultrafast removal of the template (in 10min) with complete elimination of toxic HF usage. The obtained carbon material (JNC-1) displays excellent CO2 capture ability (ca. 26.2wt% at 0 degrees C under 0.88bar CO2 pressure), which is twice that of CMK-3 obtained by the HF etching method (13.0wt%). JNC-1 demonstrated higher H-2 adsorption capacity (2.8wt%) compared to CMK-3 (1.2wt%) at -196 degrees C under 1.0bar H-2 pressure. The bimodal pore architecture of JNC-1 led to superior supercapacitor performance, with a specific capacitance of 292Fg(-1) and 182Fg(-1) at a drain rate of 1Ag(-1) and 50Ag(-1), respectively, in 1m H2SO4 compared to CMK-3 and activated carbon.

Orientation Selection and Microstructural Evolution in Directionally Solidified Tb0.3Dy0.7Fe1.95

Tb0.3Dy0.7Fe1.95 alloy was directionally solidified by using a modified Bridgman technique at a wide range of growth rates of 5 to 100 cm/h. The directionally grown samples exhibited plane front solidification morphology up to a growth rate of 90 cm/h. Typical island banding feature was observed closer to the chilled end, which eventually gave rise to irregular peritectic coupled growth (PCG). The PCG gained prominence with an increase in the growth rate. The texture study revealed formation of strong aOE (c) 311 > texture in a lower growth rate regime, aOE (c) 110 > and ``rotated aOE (c) 110 > aEuroe in an intermediate growth regime, and aOE (c) 112 > in a higher growth rate regime. In-depth analysis of the atomic configuration of a solid-liquid interface revealed that the growth texture is influenced by the kinetics of atomic attachment to the solid-liquid interface, which is intimately related to a planar packing fraction and an atomic stacking sequence of the interfacial plane. The mechanism proposed in this article is novel and will be useful in addressing the orientation selection mechanism of topologically closed packed intermetallic systems. The samples grown at a higher growth rate exhibit larger magnetostriction (lambda) and d lambda/dH owing to the absence of pro-peritectic (Tb,Dy)Fe-3 and formation of aOE (c) 112 > texture, which lies closer to the easy magnetization direction (EMD).