DNA topoisomerase I from mycobacteria - A potential drug target

DNA topoisomerases are ubiquitous group of enzymes altering the topology of DNA by concerted breakage and rejoining of the phosphodiester backbone of DNA. The enzymes are classified based on the pattern of DNA cleavage. Type IA enzymes found in all bacteria nick the DNA and attach themselves covalently to the 5' side of the nick during the first transesterification reaction. Most of the information on this group of enzymes comes from studies with E. coli topoisomerase I and III. Members of type IA group are single subunit Zn++ metalloenzymes recognizing single stranded DNA without high degree of sequence specificity during relaxation reaction of negatively super coiled DNA. So far no inhibitors are known for this group of enzymes inspite of their important role in maintaining homeostasis of DNA topology. Molecular characterization of DNA topoisomerase I from mycobacteria has revealed some of the important features of type IA enzymes hitherto unknown and provide scope for identifying novel inhibitors. The present review describes the recent developments in the area summarizing the distinctive features of mycobacterial topoisomerase I. The enzyme has several properties not shared by either type IA or 113 enzymes with respect to DNA binding, recognition, sequence specificity and interaction pattern. The physiological basis of the unusual features is discussed. The unique properties described would aid in developing the enzyme as a target molecule in pharmaceutical design. In addition, the findings lead to address some fundamental questions on the intracellular role of topoisomerase I in the biology of mycobacteria which are one of the most formidable group of pathogenic organisms.

Embrittlement of a bulk metallic glass due to low-temperature annealing

Embrittlement of a bulk La-based metallic glass due to isothermal and isochronal annealing below the T-g was investigated. Results show that the impact toughness decreases with increasing annealing time or temperature, accompanied by a change in fracture morphology. Reasons for this are discussed in terms of structural relaxation. (C) 2002 Acta Materialia Inc. Published by Elsevier Science Ltd. All rights reserved.

Proton NMR T-1 studies in methylammonium trichloro stannate(II) (CH3NH3SnCl3)

Proton spin lattice relaxation time (T-1) measurements have been carried out in methylammonium trichloro stannate(II) (CH3NH3SnCl3) as a function of temperature in the range 317-5 K at a Larmor frequency of 10 MHz. The temperature dependence of T-1 shows a phase transition around 220 K and four T-1 minima (294 K, 62 K, 32 K and 12 K). The results are discussed in terms of proton dynamics, namely, uncorrelated reorientation of NH3 and CH3 groups at high temperatures and tunnelling of NH3 and CH3 protons at low temperatures.

Synthesis of acicular hydrogoethite (alpha-FeOOH center dot xH(2)O; 0.1 < x < 0.22) particles using morphology controlling cationic additives and magnetic properties of maghemite derived from hydrogoethite

A method for the preparation of acicular hydrogoethite (alpha -FeOOH.xH(2)O, 0.1 < x < 0.22) particles of 0.3-1 mm length has been optimized by air oxidation of Fe( II) hydroxide gel precipitated from aqueous (NH4)(2)Fe(SO4)(2) solutions containing 0.005-0.02 atom% of cationic Pt, Pd or Rh additives as morphology controlling agents. Hydrogoethite particles are evolved from the amorphous ferrous hydroxide gel by heterogeneous nucleation and growth. Preferential adsorption of additives on certain crystallographic planes thereby retarding the growth in the perpendicular direction, allows the particles to acquire acicular shapes with high aspect ratios of 8-15. Synthetic hydrogoethite showed a mass loss of about 14% at similar to 280 degreesC, revealing the presence of strongly coordinated water of hydration in the interior of the goethite crystallites. As evident from IR spectra, excess H2O molecules (0.1- 0.22 per formula unit) are located in the strands of channels formed in between the double ribbons of FeO6 octahedra running parallel to the c- axis. Hydrogoethite particles constituted of multicrystallites are formed with Pt as additive, whereas single crystallite particles are obtained with Pd (or Rh). For both dehydroxylation as well as H-2 reduction, a lower reaction temperature (similar to 220 degreesC) was observed for the former (Pt treated) compared to the latter (Pd or Rh) (similar to 260 degreesC). Acicular magnetite (Fe3O4) was prepared either by reducing hydrogoethite (magnetite route) or dehydroxylating hydrogoethite to hematite and then reducing it to magnetite (hematite- magnetite route). According to TEM studies, preferential dehydroxylation of hydrogoethite along < 010 > leads to microporous hematite. Maghemite (gamma -Fe2O3 (-) (delta), 0 < < 0.25) was obtained by reoxidation of magnetite. The micropores are retained during the topotactic transformation to magnetite and finally to maghemite, whereas cylindrical mesopores are formed due to rearrangement of the oxygen sublattice from hexagonal to cubic close packing during the conversion of hydrogoethite to magnetite and then to maghemite. Accordingly, three different types of maghemite particles are realized: strongly oriented multicrystalline particles, single crystalline acicular particles with micropores or crystallites having mesopores. Higher values of saturation magnetization ((s) = 74 emu g(-1)) and coercivity (H-c = 320 Oe) are obtained for single crystalline mesoporous particles. In the other cases, the smaller size of particles and larger distribution of micropores decreases sigma (s) considerably ( < 60 emu g(-1)) due to relaxation effects of spins on the surface atoms as revealed by Mossbauer spectroscopy.

Effect of neodymium (Nd) doping on the dielectric and ferroelectric characteristics of sol-gel derived lead zirconate titanate (53/47) thin films

The results of the studies on the effect of rare earth Nd doping on the phase formation behavior and electrical properties of sol-gel derived Pb-1.05(Zr0.53Ti0.47)O-3 (PZT) thin films are presented. The perovskite phase is obtained up to 5 at. % doping and beyond that pyrochlore phase was found to coexist with the perovskite phase in all the films. The transition temperature of undoped lead zirconate titanate (PZT) film was found to be reduced with Nd doping. The Nd doped films also exhibited typical relaxor-type behavior and a diffuse phase transition, similar to that observed in relaxor materials. The introduction of Nd into the PZT lattice probably introduces disorder in the B site of ABO(3) lattice, which causes the observed dielectric relaxation. Efforts were made to isolate the irreversible component contributions in low field dielectric and high field polarization switching behavior. (C) 2001 American Institute of Physics.

Effect of orientational motion of mobile chromophores on the dynamics of Forster energy transfer in polymers

Brownian dynamics (BD) simulations have been carried out to explore the effects of the orientational motion of the donor-acceptor (D-A) chromophore pair on the Forster energy transfer between the D-A pair embedded in a polymer chain in solution. It is found that the usually employed orientational averaging (that is, replacing the orientational factor, kappa, by kappa (2) = 2/3) may lead to an error in the estimation of the rate of the reaction by about 20%. In the limit of slow orientational relaxation, the preaveraging of the orientational factor leads to an overestimation of the rate, while in the opposite limit of very fast orientational relaxation, the usual scheme underestimates the rate. The latter results from an interesting interplay between reaction and diffusion. On the other hand, when one of the chromophores is fixed, the preaveraged rate is found to be fairly reliable if the rotational relaxation of the chromophore is sufficiently fast. The present study also reveals a power law dependence of the FRET rate on the chain length (rate proportional to N- alpha, with alpha approximate to 2.6).

Synthesis, structural characterization, thermal studies and chain dynamics of poly(methacrylonitrile peroxide) by NMR spectroscopy

Poly(methacrylonitrile peroxide) (PMNP) has been synthesized from methacrylonitrile by free radical initiated oxidative polymerization and characterized by different spectroscopic methods. NMR spectroscopy confirmed the alternating copolymer structure with labile peroxy bonds in the main chain. The extreme instability of PMNP was noted from FTIR spectroscopy. Thermal degradation studies by using differential scanning calorimetry and thermogravimetry have revealed that PMNP degrades highly exothermically and the heat of degradation, 42.5 kcal mol−1, is of the same order as that reported for other vinyl polyperoxides. Mass spectral fragmentation pattern under electron impact (EI) condition has also been investigated. The mechanism of the primary exothermic degradation has been substantiated by thermochemical calculations. The chain dynamics of the polyperoxide chain has been studied by means of 13C spin–lattice relaxation times (T1) of the main chain as well as the side chain carbons. The temperature dependence of the spin–lattice relaxation times shows that the PMNP is more flexible compared to the analogous poly(styrene peroxide).

The extended Enskog operator for simple fluids with continuous potentials: single particle and collective properties

We generalized the Enskog theory originally developed for the hard-sphere fluid to fluids with continuous potentials, such as the Lennard–Jones. We derived the expression for the k and ω dependent transport coefficient matrix which enables us to calculate the transport coefficients for arbitrary length and time scales. Our results reduce to the conventional Chapman–Enskog expression in the low density limit and to the conventional k dependent Enskog theory in the hard-sphere limit. As examples, the self-diffusion of a single atom, the vibrational energy relaxation, and the activated barrier crossing dynamics problem are discussed.

Carrier density-dependent transport in poly(3-methylthiophene): from injection-limited to space-charge-limited current

Current-voltage (I-V) and impedance measurements were carried out in doped poly(3-methylthiophene) devices by varying the carrier density. As the carrier concentration reduces the I-V characteristics indicate that the conduction mechanism is limited by metal-polymer interface, as also observed in impedance data. The temperature dependence of I-V in moderately doped samples shows a trap-controlled space-charge-limited conduction (SCLC); whereas in lightly doped devices injection-limited conduction is observed at lower bias and SCLC at higher voltages. The carrier density-dependent quasi-Fermi level adjustment and trap-limited transport could explain this variation in conduction mechanism. Capacitance measurements at lower frequencies and higher bias voltages show a sign change in values due to the significant variations in the relaxation behaviour for lightly and moderately doped samples. The electrical hysteresis increases as carrier density is reduced due to the time scales involved in the de-trapping of carriers.

On the Magnetic Ground State of La(0.85)Sr(0.15)CoO(3) Single Crystals

We present an extensive study on magnetic and transport properties of La(0.85)Sr(0.15)CoO(3) single crystals grown by a float zone method to address the issue of phase separation versus spin-glass (SG) behavior. The dc magnetization study reveals a kink in field-cooled magnetization, and the peak in the zero-field-cooling curve shifts to lower temperature at modest dc fields, indicating the SG magnetic phase. The ac susceptibility study exhibits a considerable frequency-dependent peak shift (similar to 4 K) and a time-dependent memory effect below the freezing temperature. In addition, the characteristic time scale tau(0) estimated from the frequency-dependent ac susceptibility measurement is found to be similar to 10(-13) s, which matches well with typical values observed in canonical SG systems. The transport relaxation study evidently demonstrates the time-dependent glassy phenomena. In essence, all our experimental results corroborate the existence of SG behavior in La(0.85)Sr(0.15)CoO(3) single crystals.

Turbulent non-equlibrium wakes

We consider here the detailed application of a model Reynolds stress equation (Narasimha 1969) to plane turbulent wakes subjected to pressure gradients. The model, which is a transport equation for the stress exhibiting relaxation and diffusion, is found to be consistent with the observed response of a wake to a nearly impulsive pressure gradient (Narasimha & Prabhu 1971). It implies in particular that a wake can be in equilibrium only if the longitudinal strain rate is appreciably less than the wake shear. We then describe a further series of experiments, undertaken to investigate the range of validity of the model. It is found that, with an appropriate convergence correction when necessary, the model provides excellent predictions of wake development under favourable, adverse and mixed pressure gradients. Furthermore, the behaviour of constant-pressure distorted wakes, as reported by Keffer (1965, 1967), is also explained very well by the model when account is taken of the effective flow convergence produced by the distortion. In all these calculations, only a simple version of the model is used, involving two non-dimensional constants both of which have been estimated from a single relaxation experiment.

Particle dynamics in a turbulent particle–gas suspension at high Stokes number. Part 2. The fluctuating-force model

A fluctuating-force model is developed for representing the effect of the turbulent fluid velocity fluctuations on the particle phase in a turbulent gas–solid suspension in the limit of high Stokes number, where the particle relaxation time is large compared with the correlation time for the fluid velocity fluctuations. In the model, a fluctuating force is incorporated in the equation of motion for the particles, and the force distribution is assumed to be an anisotropic Gaussian white noise. It is shown that this is equivalent to incorporating a diffusion term in the Boltzmann equation for the particle velocity distribution functions. The variance of the force distribution, or equivalently the diffusion coefficient in the Boltzmann equation, is related to the time correlation functions for the fluid velocity fluctuations. The fluctuating-force model is applied to the specific case of a Couette flow of a turbulent particle–gas suspension, for which both the fluid and particle velocity distributions were evaluated using direct numerical simulations by Goswami & Kumaran (2010). It is found that the fluctuating-force simulation is able to quantitatively predict the concentration, mean velocity profiles and the mean square velocities, both at relatively low volume fractions, where the viscous relaxation time is small compared with the time between collisions, and at higher volume fractions, where the time between collisions is small compared with the viscous relaxation time. The simulations are also able to predict the velocity distributions in the centre of the Couette, even in cases in which the velocity distribution is very different from a Gaussian distribution.

Stress induced phase transition in a monomolecular perfluroalkylsilane film self assembled on aluminium surface

We control the stiffnesses of two dual double cantelevers placed in series to control penetration into a perflurooctyltrichlorosilane monolayer self assembled on aluminium and silicon substrates. The top cantilever which carries the probe is displaced with respect to the bottom cantilever which carries the substrate, the difference in displacement recorded using capacitors gives penetration. We further modulate the input displacement sinusoidally to deconvolute the viscoelastic properties of the monolayer. When the intervention is limited to the terminal end of the molecule there is a strong viscous response in consonance with the ability of the molecule to dissipate energy by the generation of gauche defects freely. When the intervention reaches the backbone, at a contact mean pressure of 0.2GPa the damping disappears abruptly and the molecule registers a steep rise in elastic modulus and relaxation time constant, with increasing contact pressure. We offer a physical explanation of the process and describe this change as due to a phase transition from a liquid like to a solid like state.

Particle dynamics in a turbulent particle–gas suspension at high Stokes number. Part 1. Velocity and acceleration distributions

The effect of fluid velocity fluctuations on the dynamics of the particles in a turbulent gas–solid suspension is analysed in the low-Reynolds-number and high Stokes number limits, where the particle relaxation time is long compared with the correlation time for the fluid velocity fluctuations, and the drag force on the particles due to the fluid can be expressed by the modified Stokes law. The direct numerical simulation procedure is used for solving the Navier–Stokes equations for the fluid, the particles are modelled as hard spheres which undergo elastic collisions and a one-way coupling algorithm is used where the force exerted by the fluid on the particles is incorporated, but not the reverse force exerted by the particles on the fluid. The particle mean and root-mean-square (RMS) fluctuating velocities, as well as the probability distribution function for the particle velocity fluctuations and the distribution of acceleration of the particles in the central region of the Couette (where the velocity profile is linear and the RMS velocities are nearly constant), are examined. It is found that the distribution of particle velocities is very different from a Gaussian, especially in the spanwise and wall-normal directions. However, the distribution of the acceleration fluctuation on the particles is found to be close to a Gaussian, though the distribution is highly anisotropic and there is a correlation between the fluctuations in the flow and gradient directions. The non-Gaussian nature of the particle velocity fluctuations is found to be due to inter-particle collisions induced by the large particle velocity fluctuations in the flow direction. It is also found that the acceleration distribution on the particles is in very good agreement with the distribution that is calculated from the velocity fluctuations in the fluid, using the Stokes drag law, indicating that there is very little correlation between the fluid velocity fluctuations and the particle velocity fluctuations in the presence of one-way coupling. All of these results indicate that the effect of the turbulent fluid velocity fluctuations can be accurately represented by an anisotropic Gaussian white noise.

Electron Cyclotron Resonance in Strained Si and Si0.94Ge0.06 Channels on Relaxed Si0.62Ge0.38 Buffers Grown by Rapid Thermal Chemical Vapor Deposition

We report the far-infrared measurements of the electron cyclotron resonance absorption in n-type Si/Si0. 62Ge0.38 and Si0.94Ge0.06 /Si0. 62Ge0.38 modulation- doped heterostructures grown by rapid thermal chemical vapor deposition. The strained Si and Si0.94Ge0.06 channels were grown on relaxed Si0.62Ge0.38 buffer layers, which consist of 0.6 μm uniform Si0.62Ge0.38 layers and 0.5 μm compositionally graded relaxed SiGe layers from 0% Ge to 38 % Ge. The buffer layers were annealed at 800 °C for 1 hr to obtain complete relaxation. The samples had 100 Å spacers and 300 Å 2×1019 cm-3 n-type supply layers on the tops of the 75 Å channels. The far-infrared measurements of electron cyclotron resonance were performed at 4K with the magnetic field of 4 – 8 Tesla. The effective masses determined from the slope of center frequency of absorption peak vs applied magnetic field plot are 0.20 mo and 0.19 mo for the two dimensional electron gases in the Si and Si0.94Ge0.06 channels, respectively. The Si effective mass is very close to that of two dimensional electron gas in Si MOSFET (0.198mo). The electron effective mass of Si0.94Ge0.06 is reported for the first time and about 5 % lower than that of pure Si.