Coherent phonons in pyrochlore titanates A(2)Ti(2)O(7) (A = Dy, Gd, Tb): A phase transition in Dy2Ti2O7 at 110 K

We study the generation of coherent optical phonons in spin-frustrated pyrochlore single crystals Dy2Ti2O7, Gd2Ti2O7, and Tb2Ti2O7 using femtosecond laser pulses (65 fs, 1.57 eV) in degenerate time-resolved transmission experiments as a function of temperature from 4 to 296 K. At 4 K, two coherent phonons are observed at similar to 5.3 THz (5.0 THz) and similar to 9.3 THz (9.4 THz) for Dy2Ti2O7 (Gd2Ti2O7), whereas three coherent phonons are generated at similar to 5.0, 8.6, and 9.7 THz for Tb2Ti2O7. In the case of spin-ice Dy2Ti2O7, a clear discontinuity is observed in the linewidths of both the coherent phonons as well as in the phase of lower-energy coherent phonon mode, indicating a subtle structural change at 110 K. Another important observation is a phase difference of pi between the modes in all the samples, thus suggesting that the driving forces behind the generation of these modes could be different in nature, unlike a purely impulsive or displacive mechanism.

Molecular and serological studies on the recent seal virus epizootics in Europe and Siberia

The virus epizootics which occurred in seals in both Europe and Siberia during 1987/1988 were caused by two different morbillivirus, referred to as phocid distemper virus (PDV) 1 and 2, respectively. Molecular and serological studies have shown that the European virus is quite distinct from canine distemper virus (CDV), its closest relative in the morbillivirus group. Analysis of tissues obtained from infected seals from a wide geographical distrubution over Northern Europe showed that the infectious agent (PDV 1) was identical in all cases. Nucleotide sequence analysis of one of the virus genes suggested that this virus has evolved away from CDV over a long time period and is most probably an enzootic virus of marine mammals. In contrast, the virus (PDV 2) which caused the deaths of many Siberian seals was indistinguishable, both serologically and at the molecular level, from CDV and must have originated from a land source.

Quasicrystals, crystals and multiple twins in rapidly solidified Al-Cr-Si, Al-Mn-Si and Al-Mn-Cr-Si alloys

The coexistence of quasicrystals and rational approximant structures (RAS) has been observed in melt-spun Al80Cr14Si6, Al80Mn14Si6 and Al75Mn10Cr5Si10 alloys. The presence of a b.c.c. alpha-AlMnSi phase in Al-Mn-Si and alpha-AlMnSi(Cr) phase in Al-Mn-Cr-Si has been seen. A multiple twinning around an irrational axis of the RAS has been reported in an aggregate of fine size cubic crystallites in all three alloys. Selected area diffraction patterns show that the crystalline aggregate symmetry is linked to the icosahedral point group symmetry (m35). Various ways of expressing the twin relationship in the cubic crystalline aggregates have been discussed. The thermal stability of the icosahedral phase at high temperatures reveals that the icosahedral phase in Al-Mn-Si and Al-Mn-Cr-Si alloys transforms to alpha-AlMnSi at temperatures of 690 and 670 K, respectively. In Al-Cr-Si alloy, heating to a high temperature (615 K) leads to the transformation of the icosahedral phase into a new metastable phase having an ordered cubic structure equivalent to alpha-AlMnSi. The occurrence of multiple twinning leading to icosahedral symmetry in the as-spun Al-Cr-Si alloy is presumably due to this metastable phase. Copyright (C) 1996 Acta Metallurgica Inc.

Use of a specific aromatase inhibitor for determining whether there is a role for oestrogen in follicle/oocyte maturation, ovulation and preimplantation embryo development

The specific role of oestrogen in follicular maturation, ovulation and early embryonic development was investigated using Fadrozole (CGS 16949A), a non-steroidal aromatase inhibitor, to block oestrogen synthesis specifically and effectively in experimental animals. Induced and normal cyclical follicular maturation as well as normal and hCG/LH-induced ovulation were relatively unaffected by significantly depleting oestrogen in all animals (hamsters, rabbits, monkeys) studied other than rats. Fadrozole treatment significantly reduced the number of healthy antral follicles produced and the ovulatory response to exogenous hCG of immature rats primed with pregnant mares' serum gonadotrophin. The effect was specific, in that exogenously administered oestrogen reversed the blockade. Depletion of oestrogen, starting early in pro-oestrus in hamsters, had no effect on ovulation, oocyte maturation and fertilization, as normal implantation sites were seen on day 6 after coitus. In rabbits, oestrogen depletion during the periovulatory phase affected oviductal morphology and function. Although fertilization was not impaired, early embryo development did not appear to be normal. In monkeys, oestrogen depletion during the follicular phase did not lead to a block of follicular maturation or ovulation but resulted in a significant reduction in secretion of cervical mucus. Administration of either Fadrozole or Tamoxifen during the early luteal phase in cyclic monkeys that were allowed to mate prevented implantation and this appears to be due to impaired fertilization or faulty embryo development. These results suggest that, although there is a clear requirement for oestrogen to support the reproductive cycle in the female, the need for oestrogen in regulating specific events is species dependent.

Role of Water in the Enzymatic Catalysis: Study of ATP plus AMP -> 2ADP Conversion by Adenylate Kinase

The catalytic conversion ATP + AMP -> 2ADP by the enzyme adenylate kinase (ADK) involves the binding of one ATP. molecule to the LID domain and one AMP molecule to the NMP domain. The latter is followed by a. phosphate transfer and then the release of two ADP molecules. We have computed a novel two-dimensional configurational free energy surface (2DCFES), with one reaction coordinate each for the LID and the NMP domain motions, while considering explicit water interactions. Our computed 2DCFES clearly reveals the existence of a stable half-open half-closed (HOHC) intermediate stale of the enzyme. Cycling of the enzyme through the HOHC state reduces the conformational free energy barrier for. the reaction by about 20 kJ/mol. We find that the stability of the HOHC state (missed in all earlier studies with implicit solvent model) is largely because of the increase of specific interactions of the polar amino acid side chains with water, particularly with the arginine and the histidine residues. Free energy surface of the LID domain is rather rugged, which can conveniently slow down LID's conformational motion, thus facilitating a new substrate capture after the product release in the catalytic cycle.

Facial Coordination in BIS[BIS(Benzimidazol-2-Ylmethyl)Amine]Copper(II) Perchlorate Dihydrate - Synthesis, Structure, Spectra and Redox Behavior

The 1:1 and 1:2 cooper(II) complexes with the tridentate compound bis(benzimidazol-2-ylmethyl)amine (L(1)) and its benzimidazole (L(2)) and amine (L(3)) N-methyl-substituted derivatives have been prepared and their spectroscopic properties studied. While the 1:1 complexes are of the type CuLX(2) nH(2)O (X = C/O-4(-), NO3-, Cl- or Br-), the 1:2 complexes are of the type CuL(2) (ClO4)(2) nH(2)O (L = L(1) or L(3), n = 0-4). In all these complexes L acts as a tridentate ligand with the amine nitrogen and both the benzimidazole nitrogens co-ordinating to Cu-II. The complex [CuL(2)(1)][ClO4](2) 2H(2)O crystallises in the monoclinic space group P2(1)/c with a = 9.828(2), b = 9.546(2) and c = 19.906(2) Angstrom and beta = 95.71(1)degrees, for Z = 2. The R value is 0.0635 for 2180 significant reflections. The copper(II) ion has an elongated octahedral geometry with four equatorial benzimidazole and two long-distance axial amine N donors. The Cu-N-bzim and Cu-N-amine distances are 2.011(4) and 2.597(6) Angstrom respectively. Factors favouring facial co-ordination to tridentate ligands are discussed. The 1:1 complexes involve meridonal co-ordination of the ligands, with square-based geometry as revealed by ligand-field and EPR spectral properties. The NMe substitution as in CuL(3)(ClO4)(2) confers low V ($) over tilde$$(max) and high E(1/2) for the cu(II)-Cu-I couple. Most of the 1:1 complexes are less reversible but exhibit E(1/2) values more positive than those of the corresponding 1:2 complexes.

Swing amplification of nonaxisymmetric perturbations in stars and gas in a sheared galactic disk

We present a study of the growth of local, nonaxisymmetric perturbations in gravitationally coupled stars and gas in a differentially rotating galactic disk. The stars and gas are treated as two isothermal fluids of different velocity dispersions, with the stellar velocity dispersion being greater than that for the gas. We examine the physical effects of inclusion of a low-velocity dispersion component (gas) on the growth of non-axisymmetric perturbations in both stars and gas, as done for the axisymmetric case by Jog & Solomon. The amplified perturbations in stars and gas constitute trailing, material, spiral features which may be identified with the local spiral features seen in all spiral galaxies. The formulation of the two-fluid equations closely follows the one-fluid treatment by Goldreich & Lynden-Bell. The local, linearized perturbation equations in the sheared frame are solved to obtain the results for a temporary growth via swing amplification. The problem is formulated in terms of five dimensionless parameters-namely, the Q-factors for stars and gas, respectively; the gas mass fraction; the shearing rate in the galactic disk; and the length scale of perturbation. By using the observed values of these parameters, we obtain the amplifications and the pitch angles for features in stars and gas for dynamically distinct cases, as applicable for different regions of spiral galaxies. A real galaxy consisting of stars and gas may display growth of nonaxisymmetric perturbations even when it is stable against axisymmetric perturbations and/or when either fluid by itself is stable against non-axisymmetric perturbations. Due to its lower velocity dispersion, the gas exhibits a higher amplification than do the stars, and the amplified gas features are slightly more tightly wound than the stellar features. When the gas contribution is high, the stellar amplification and the range of pitch angles over which it can occur are both increased, due to the gravitational coupling between the two fluids. Thus, the two-fluid scheme can explain the origin of the broad spiral arms in the underlying old stellar populations of galaxies, as observed by Schweizer and Elmegreen & Elmegreen. The arms are predicted to be broader in gas-rich galaxies, as is indeed seen for example in M33. In the linear regime studied here, the arm contrast is shown to increase with radius in the inner Galaxy, in agreement with observations of external galaxies by Schweizer. These results follow directly due to the inclusion of gas in the problem.

Orientational relaxation in dipolar systems: How much do we understand the role of correlations

Dipolar systems, both liquids and solids, constitute a class of naturally abundant systems that are important in all branches of natural science. The study of orientational relaxation provides a powerful method to understand the microscopic properties of these systems and, fortunately, there are many experimental tools to study orientational relaxation in the condensed phases. However, even after many years of intense research, our understanding of orientational relaxation in dipolar systems has remained largely imperfect. A major hurdle towards achieving a comprehensive understanding is the long range and complex nature of dipolar interactions which also made reliable theoretical study extremely difficult. These difficulties have led to the development of continuum model based theories, which although they provide simple, elegant expressions for quantities of interest, are mostly unsatisfactory as they totally neglect the molecularity of inter-molecular interactions. The situation has improved in recent years because of renewed studies, led by computer simulations. In this review, we shall address some of the recent advances, with emphasis on the work done in our laboratory at Bangalore. The reasons for the failure of the continuum model, as revealed by the recent Brownian dynamics simulations of the dipolar lattice, are discussed. The main reason is that the continuum model predicts too fast a decay of the torque-torque correlation function. On the other hand, a perturbative calculation, based on Zwanzig's projection operator technique, provides a fairly satisfactory description of the single particle orientational dynamics for not too strongly polar dipolar systems. A recently developed molecular hydrodynamic theory that properly includes the effects of intermolecular orientational pair correlations provides an even better description of the single-particle orientational dynamics. We also discuss the rank dependence of the dielectric friction. The other topics reviewed here includes dielectric relaxation and solvation dynamics, as they are intimately connected with orientational relaxation. Recent molecular dynamics simulations of the dipolar lattice are also discussed. The main theme of the present review is to understand the effects of intermolecular interactions on orientational relaxation. The presence of strong orientational pair correlation leads to a strong coupling between the single particle and the collective dynamics. This coupling can lead to rich dynamical properties, some of which are detailed here, while a major part remains yet unexplored.

Uracil excision repair in Mycobacterium tuberculosis cell-free extracts

Uracil excision repair is ubiquitous in all domains of life and initiated by uracil DNA glycosylases (UDGs) which excise the promutagenic base, uracil, from DNA to leave behind an abasic site (AP-site). Repair of the resulting AP-sites requires an AP-endonuclease, a DNA polymerase, and a DNA ligase whose combined activities result in either short-patch or long-patch repair. Mycobacterium tuberculosis, the causative agent of tuberculosis, has an increased risk of accumulating uracils because of its G + C-rich genome, and its niche inside host macrophages where it is exposed to reactive nitrogen and oxygen species, two major causes of cytosine deamination (to uracil) in DNA. In vitro assays to study DNA repair in this important human pathogen are limited. To study uracil excision repair in mycobacteria, we have established assay conditions using cell-free extracts of M. tuberculosis and M. smegmatis (a fast-growing mycobacterium) and oligomer or plasmid DNA substrates. We show that in mycobacteria, uracil excision repair is completed primarily via long-patch repair. In addition, we show that M. tuberculosis UdgB, a newly characterized family 5 UDG, substitutes for the highly conserved family 1 UDG, Ung, thereby suggesting that UdgB might function as backup enzyme for uracil excision repair in mycobacteria. (C) 2011 Elsevier Ltd. All rights reserved.

Mutagenic significance of proton acidities in methylated guanine and thymine bases and deoxynucleosides: A theoretical study

Proton changes have been advanced as being the key molecular basis for the mutagenecity of alkylated DNA bases and nucleosides, leading to questions as to which protons are involved and whether the protic changes are tautomeric shifts or abstractions. This semiempirical molecular orbital study seeks to clarify the issue by examining the various possibilities open for these protic changes in a number of methylated guanines and thymines and their deoxynucleosides. Proton shifts leading to tautomer formation are not predicted as being thermodynamically favourable in most cases. The most feasible proton abstractions are predicted to involve the Watson-Crick protons in all cases, which corroborates Watson-Crick proton loss as providing the key molecular basis for the induction of point mutations. The calculated proton acidities correlate well with experimental data. The gas-phase deprotonation enthalpies for a number of alkylated nucleosides are found to correlate linearly with the solvent-phase pK(a) values. The theoretically calculated enthalpies in a simulated aqueous solvent phase of the deprotonation reactions of various nucleic acid bases are also found to have good linear correlations with experimental pK(a) values. The consensus of these calculations is that O-6-alkyldeoxyguanosines, and O-2- and O-4-alkyldeoxythymidines would be mutagenic while N-7-alkyldeoxyguanosines would not be mutagenic (as experiment indicates). The untested N-3-methyldeoxyguanosine is predicted to be mutagenic. (C) 1997 Elsevier Science B.V.

A Change in the 3(10)- to alpha-Helical Transition Point in the Heptapeptides Containing Sulfur and Selenium

Crystal structures of three heptapeptides Boc-Ala-Leu-Aib-XXX-Ala-Leu-Aib-OMe (where XXX = methionine in peptide A, selenomethionine in peptide B, and S-benzyl cysteine in peptide C) reveal mixed 3(10)-/alpha-helical conformations with R factors of 6.94, 5.79, and 5.98, respectively. All the structures were solved in the P2(1)2(1)2(1) space group. 3(10)- to a-helical transitions are observed in all of these peptides. The helices begin as a 3(10)-helical segment at the N-terminus and then transit for peptides A and C at residue Aib(3) carbonyl (O(3)), while for peptide B the transition occurs at residue Leu(2) carbonyl oxygen (O(2)). There are water molecules associated in the crystal of each of these peptides and they form different types of hydrogen bonding patterns in each crystal. The observations suggest that 3(10)- to alpha-helical transition is sequence dependent in these short heptapeptide sequences.

Prediction of reaeration rates in square, stirred tanks

Experiments were conducted on the oxygen transfer coefficient, k(L)a(20), through surface aeration in geometrically similar square tanks, with a rotor of diameter D fitted with six flat blades. An optimal geometric similarity of various linear dimensions, which produced maximum k(L)a(20) for any rotational speed of rotor N by an earlier study, was maintained. A simulation equation uniquely correlating k = k(L)a(20)(nu/g(2))(1/3) (nu and g are kinematic viscosity of water and gravitational constant, respectively), and a parameter governing the theoretical power per unit volume, X = (ND2)-D-3/(g(4/3)nu(1/3)), is developed. Such a simulation equation can be used to predict maximum k for any N in any size of such geometrically similar square tanks. An example illustrating the application of results is presented. Also, it has been established that neither the Reynolds criterion nor the Froude criterion is singularly valid to simulate either k or K = k(L)a(20)/N, simultaneously in all the sizes of tanks, even through they are geometrically similar. Occurrence of "scale effects" due to the Reynolds and the Froude laws of similitude on both k and K are also evaluated.

Statistical thermodynamics of lattice models in zeolites: Implications of local versus global mean field interactions

The statistical thermodynamics of adsorption in caged zeolites is developed by treating the zeolite as an ensemble of M identical cages or subsystems. Within each cage adsorption is assumed to occur onto a lattice of n identical sites. Expressions for the average occupancy per cage are obtained by minimizing the Helmholtz free energy in the canonical ensemble subject to the constraints of constant M and constant number of adsorbates N. Adsorbate-adsorbate interactions in the Brag-Williams or mean field approximation are treated in two ways. The local mean field approximation (LMFA) is based on the local cage occupancy and the global mean field approximation (GMFA) is based on the average coverage of the ensemble. The GMFA is shown to be equivalent in formulation to treating the zeolite as a collection of interacting single site subsystems. In contrast, the treatment in the LMFA retains the description of the zeolite as an ensemble of identical cages, whose thermodynamic properties are conveniently derived in the grand canonical ensemble. For a z coordinated lattice within the zeolite cage, with epsilon(aa) as the adsorbate-adsorbate interaction parameter, the comparisons for different values of epsilon(aa)(*)=epsilon(aa)z/2kT, and number of sites per cage, n, illustrate that for -1 In general, the deviation between the LMFA and GMFA is greater for smaller n and less sensitive to n for epsilon(aa)(*)> 0. We compare the isotherms predicted with the LMFA with previous GMFA predictions [K. G. Ayappa, C. R. Kamala, and T. A. Abinandanan, J. Chem. Phys. 110, 8714 (1999)] (which incorporates both the site volume reduction and a coverage-dependent epsilon(aa)) for xenon and methane in zeolite NaA. In all cases the predicted isotherms are very similar, with the exception of a small steplike feature present in the LMFA for xenon at higher coverages. (C) 1999 American Institute of Physics. [S0021-9606(99)70333-8].

Stress-strain Curves and Corresponding Structural Parameters in Mulberry and Non-mulberry Silk Fibers

Mulberry fiber (Bivoltine) and non-mulberry fiber (Tassar) were subjected to stress-strain studies and the corresponding samples were examined using wide angle X-ray scattering studies. Here we have two different characteristic stress-strain curves and this has been correlated with changes in crystallite shape ellipsoids in all the fibers. Exclusive crystal structure studies of Tassar fibers show interesting feature of transformation from antiparallel chains to parallel chains.

Total peroxidase activity and peroxidase isoforms as modified by salt stress in two cultivars of fox-tail millet with differential salt tolerance

The effect of NaCl on total peroxidase activity, induction of isoperoxidases and lipid peroxidation in 5-day-old seedlings of two contrasting genotypes of Setaria italica L. (Prasad, a salt tolerant cultivar and Lepakshi, a salt susceptible cultivar), was studied. Total peroxidase activity increased under NaCl salinity and the degree of elevation in the activity was salt concentration dependent. Nevertheless, a greater activity was recorded in the tolerant cultivar (cv Prasad) compared to the susceptible (cv Lepakshi) one in all days of sampling. Further, the pattern of isoperoxidases was modified during stress conditions as evident from the electrophoregrams. Although, five acidic isoforms were detected in both cultivars, differences were found between the cultivars. Furthermore, it was observed that acidic isoperoxidases were strongly expressed and an acidic isoperoxidase, A(3p) (27 kDa) is specifically found in the tolerant cultivar (cv Prasad) under NaCl stress. This isoform was partially purified and found to be thermostable with pr 5.5 and the optimum pH 7.4. A close correlation exists between the rate of lipid peroxidation in terms of malonaldehyde (MDA) content and total peroxidase activity per gram fresh weight with salt tolerance of the two cultivars. The tolerant cultivar (cv Prasad) had low MDA content and high total peroxidase activity than the susceptible variety (cv Lepakshi) during salinity stress. (C) 1999 Published by Elsevier Science Ireland Ltd. All rights reserved.