ALBERT

Description: Background: Single-stranded DNA binding proteins (SSB) are essential for DNA replication, repair, and recombination in all organisms. SSB works in concert with a variety of DNA metabolizing enzymes such as DNA polymerase. Results: We have cloned and purified SSB from Bacillus anthracis (SSBBA). In the absence of DNA, at concentrations [less than or equal to]100 mug/ml, SSBBA did not form a stable tetramer and appeared to resemble bacteriophage T4 gene 32 protein. Fluorescence anisotropy studies demonstrated that SSBBA bound ssDNA with high affinity comparable to other prokaryotic SSBs. Thermodynamic analysis indicated both hydrophobic and ionic contributions to ssDNA binding. FRET analysis of oligo(dT)70 binding suggested that SSBBA forms a tetrameric assembly upon ssDNA binding. This report provides evidence of a bacterial SSB that utilizes a novel mechanism for DNA binding through the formation of a transient tetrameric structure. Conclusions: Unlike other prokaryotic SSB proteins, SSBBA from Bacillus anthracis appeared to be monomeric at concentrations [less than or equal to]100 mug/ml as determined by SE-HPLC. SSBBA retained its ability to bind ssDNA with very high affinity, comparable to SSB proteins which are tetrameric. In the presence of a long ssDNA template, SSBBA appears to form a transient tetrameric structure. Its unique structure appears to be due to the cumulative effect of multiple key amino acid changes in its sequence during evolution, leading to perturbation of stable dimer and tetramer formation. The structural features of SSBBA could promote facile assembly and disassembly of the protein-DNA complex required in processes such as DNA replication.

Description: Here, we present x-ray resonant magnetic dichroism and x-ray resonant magnetic scattering measurements of the temperature dependence of magnetism in Pr-doped La-Ca-Mn-O films grown on (110) NdGaO 3 substrates. We observed thermal hysteresis of the ferromagnetism in one film that also showed large thermal hysteresis of ∼18 K in transport measurements. While in a second film of a different nominal chemistry, which showed very small thermal hysteresis ∼3 K in transport measurements, no thermal hysteresis of the ferromagnetism was observed. These macroscopic properties are correlated with evolution of surface magnetization across metal insulator transition for these films as observed by soft x-ray resonant magnetic scattering measurements.

Description: South Purulia Shear Zone (SPSZ) is an important area for the prospect of uranium mineralization and no detailed geophysical investigations have been carried out in this region. To delineate the subsurface structure in the present area, vertical electrical soundings using Schlumberger array and gravity survey were carried out along a profile perpendicular to the SPSZ. Apparent conductance in the subsurface revealed a possible connection from SPSZ to Raghunathpur. The gravity model reveals the presence of a northerly dipping low density zone (most likely the shear zone) extending up to Raghunathpur under a thin cover of granitic schist of Chotanagpur Granite Gneissic Complex (CGGC). The gravity model also depicts the depth of the zone of density low within this shear zone at ~400 m near Raghunathpur village and this zone truncates with a steep slope. Integration of resistivity and gravity study revealed two possible contact zones within this low density zone in the subsurface at depth of 40 m and 200 m. Our study reveals a good correlation with previous studies in Raghunathpur area characterized by medium to high hydro-uranium anomaly. Thus the conducting zone coinciding with the low gravity anomaly is inferred to be a possible uranium mineralized zone.

Description: On-water hydrothiolation reaction between terminal alkyne and thiol has been probed in the presence of various additives. Aromatic alkynes yield corresponding 1-alkenyl sulfides, whereas aliphatic alkynes undergo double-addition yielding vicinal disulfides in good to excellent yields. Formation of 1-alkenyl sulfides proceeds with a high degree of regioselectivity (via anti-Markovnikov addition), and switching the stereoselectivity between E/Z isomers has been noticeably realized in the presence of different additives/promoters.

Description: This study is an attempt to correlate VLF-EM data with the radiometric measurements to decipher the subsurface structure and to locate uranium mineralization in the shear zone. The study area is around Beldih mine which is an open cast apatite mine located on the South Purulia Shear Zone. VLF method has been applied to map the structure and the presence of radioactive minerals has been delineated by the detection of high α and γ counts with respect to the background radiations. High radiation counts and high surface γ activity are found just above the higher apparent current-density zones in all the profiles studied, at various locations, indicating uranium and/or thorium mineralization as well as good correlation between these techniques.

Description: In this study, we have investigated the ion concentration dependent collective dynamics in two series of deep eutectic solvent (DES) systems by femtosecond Raman-induced Kerr effect spectroscopy, as well as some physical properties, e.g., shear viscosity ( η ), density ( ρ ), and surface tension ( γ ). The DES systems studied here are [0.75CH 3 CONH 2 + 0.25{ f  KSCN + (1 – f  )NaSCN}] and [0.78CH 3 CONH 2 + 0.22{ f  LiBr + (1 – f  )LiNO 3 }] with f = 0, 0.2, 0.4, 0.6, 0.8, and 1.0. γ of these DES systems shows near insensitivity to f , while ρ shows a moderate dependence on f . Interestingly, η exhibits a strong dependence on f . In the low-frequency Kerr spectra, obtained via the Fourier transform of the collected Kerr transients, a characteristic band at ∼70 cm −1 is clear in [0.78CH 3 CONH 2 + 0.22{ f  LiBr + (1 – f  )LiNO 3 }] DES especially at the larger f . The band is attributed to the intermolecular hydrogen bond of acetamide. Because of less depolarized Raman activities of intermolecular/interionic vibrational motions, which are mostly translational (collision-induced or interaction-induced) motions, of spherical ions, the intermolecular hydrogen-bonding band is clearly observed. In contrast, the intermolecular hydrogen-bonding band is buried in the other intermolecular/interionic vibrational motions, which includes translational and reorientational (librational) motions and their cross-terms, in [0.75CH 3 CONH 2 + 0.25{ f  KSCN + (1 – f  )NaSCN}] system. The first moment ( M 1 ) of the intermolecular/interionic vibrational band in these DES systems is much higher than that in typical neutral molecular liquids and shows a weak but contrasting dependence on the bulk parameter γ / ρ . The time constants for picosecond overdamped Kerr transients in both the DES systems, which are obtained on the basis of the analysis fitted by a triexponential function, are rather insensitive to f for both the DES systems, but all the three time constants (fast: ∼1–3 ps; intermediate: ∼7–20 ps; and slow: ∼100 ps) are different between the [0.78CH 3 CONH 2 + 0.22{ f  LiBr + (1 – f  )LiNO 3 }] and [0.75CH 3 CONH 2 + 0.25{ f  KSCN + (1 – f  )NaSCN}] systems. These results indicate that the intermolecular/interionic interactions in DES systems is strongly influenced by the ionic species present in these DES systems.

Description: Rugged energy landscapes find wide applications in diverse fields ranging from astrophysics to protein folding. We study the dependence of diffusion coefficient ( D ) of a Brownian particle on the distribution width (ɛ) of randomness in a Gaussian random landscape by simulations and theoretical analysis. We first show that the elegant expression of Zwanzig [Proc. Natl. Acad. Sci. U.S.A.85, 2029 (1988)] for D (ɛ) can be reproduced exactly by using the Rosenfeld diffusion-entropy scaling relation. Our simulations show that Zwanzig's expression overestimates D in an uncorrelated Gaussian random lattice – differing by almost an order of magnitude at moderately high ruggedness. The disparity originates from the presence of “three-site traps” (TST) on the landscape – which are formed by the presence of deep minima flanked by high barriers on either side. Using mean first passage time formalism, we derive a general expression for the effective diffusion coefficient in the presence of TST, that quantitatively reproduces the simulation results and which reduces to Zwanzig's form only in the limit of infinite spatial correlation. We construct a continuous Gaussian field with inherent correlation to establish the effect of spatial correlation on random walk. The presence of TSTs at large ruggedness (ɛ ≫ k B T ) gives rise to an apparent breakdown of ergodicity of the type often encountered in glassy liquids.

Description: A time dependent thermal model for a superconducting constriction based weak-link (WL) is discussed for investigating the deterministic dynamics of its temperature and phase. A new dynamic regime is found where a non-zero voltage exists across the WL, and its temperature stabilizes between the bath temperature and superconductor's critical temperature. This regime exists over a limited bias current range and gives rise to a new hysteretic regime in current-voltage characteristics. We also discuss the effect of fluctuations on the current-voltage characteristics and experimental implications of this dynamic regime.

Description: A semi-molecular theory for studying composition dependent Stokes shift dynamics of a dipolar solute in binary mixtures of (non-dipolar ionic liquid + common dipolar solvent) is developed here. The theory provides microscopic expressions for solvation response functions in terms of static and dynamic structure factors of the mixture components and solute-solvent static correlations. In addition, the theory provides a framework for examining the interrelationship between the time dependent solvation response in and frequency dependent dielectric relaxation of a binary mixture containing electrolyte. Subsequently, the theory has been applied to predict ionic liquid (IL) mole fraction dependent dynamic Stokes shift magnitude and solvation energy relaxation for a dipolar solute, C153, in binary mixtures of an ionic liquid, trihexyltetradecylphosphonium chloride ([P 14,666 ][Cl]) with a common dipolar solvent, methanol (MeOH). In the absence of suitable experimental data, necessary input parameters have been obtained from approximate methods. Dynamic shifts calculated for these mixtures exhibit a linear increase with IL mole fraction for the most part of the mixture composition, stressing the importance of solute-IL dipole-ion interaction. Average solvation rates, on the other hand, show a nonlinear IL mole fraction dependence which is qualitatively similar to what has been observed for such binary mixtures with imidazolium (dipolar) ILs. These predictions should be re-examined in suitable experiments.