Isolation and characterization of DNA polymerase epsilon from the silk glands of Bombyx mori

The silk gland of Bombyx mori, an endomitotically replicative tissue shows high levels of DNA polymerases alpha, delta, and epsilon activities. The ratio of polymerase alpha to that of delta plus epsilon is maintained at 1.1 to 1.3 in both the posterior and middle silk glands for the entire duration of late larval development. The three activities copurify in the initial stages of fractionation through phosphocellulose and DE52 but polymerase alpha gets resolved from the others on hydroxylapatite column. Separation between polymerase delta and epsilon is achieved by chromatography on QAE-Sephadex. DNA polymerase epsilon is a heterodimer comprising of 215- and 42-kDa subunits. The activity is maximum at pH 6.5 and the Km values for dNTPs vary between 3-9 microM. The enzyme possesses an intrinsically associated exonuclease activity which functions in the mismatch repair during DNA synthesis. Both polymerase and 3'-->5' exonuclease activities are associated with the 215-kDa subunit. By itself, DNA polymerase epsilon is processive and the catalytic activity is not enhanced by externally added bPCNA (Bombyx-proliferating cell nuclear antigen, an auxiliary protein for DNA polymerase delta). The enzyme resembles polymerase delta in having the exonuclease activity and in its response to aphidicolin or substrate analogs, but could be distinguished from the latter by its lack of response to the bPCNA and sensitivity to dimethyl sulfoxide. The two enzymes show partial immunological cross-reactivity with each other but no immunological relatedness to polymerase alpha. The absence of the repair enzyme DNA polymerase beta and the presence of substantial levels of polymerase epsilon in the silk glands suggest a possible role for the latter in DNA repair in that tissue.

Orientational glassy phases of C60 and neopentane. A Monte Carlo study

Based on an isothermal, isobaric simulation the structure and properties of the plastic crystalline phases of C60 and neopentane have been examined. Instantaneous cooling of the plastic crystalline phases of both C60 and neopentane leads to orientational glassy phases. These are accompanied by significant slowing down of reorientational motion. Constant pressure quench experiments on C60 yield a glass transition temperature of around 80 K.

The superheating of Pb embedded in a Zn matrix the role of interface melting

Evidence of a shape-dependent superheating of entrained nanosized Pb particles in a Zn matrix has been presented. It is shown that size dependence and pressure effects cannot explain the observed differences in melting points. The importance of crystallography and morphology at the microlevel at the interphase interface in controlling interfacial melting has been emphasized in order to explain the melting of entrained particles.

The variants of the protein toxins abrin and ricin A useful guide to understanding the processing events in the toxin transport

Kinetic data on inhibition of protein synthesis in thymocyte by three abrins and ricin have been obtained. The intrinsic efficiencies of A chains of four toxins to inactivate ribosomes, as analyzed by k1-versus-concentration plots were abrin II, III > ricin > abrin I. The lag times were 90, 66, 75 and 105 min at a 0.0744 nM concentration of each of abrin I, II, III and ricin, respectively. To account for the observed differences in the dose-dependent lag time, functional and structural variables of toxins such as binding efficiency of B chains to receptors and low-pH-induced structural alterations have been analyzed. The association constants obtained by stopped flow studies showed that abrin-I (4.13 × 105 M−1 s−1) association with putative receptor (4-methylumbelliferyl-α-D-galactoside) is nearly two times more often than abrin III (2.6 × 105 M−1 s−1) at 20°C. Equillibrium binding constants of abrin I and II to thymocyte at 37°C were 2.26 × 107 M−1 and 2.8 × 107 M−1 respectively. pH-induced structural alterations as studied by a parallel enhancement in 8-anilino-L-naphthalene sulfonate fluorescence revealed a high degree of qualitative similarity. These results taken with a nearly identical concentration-independent lag time (minimum lag of 41–42 min) indicated that the binding efficiencies and internalization efficiencies of these toxins are the same and that the observed difference in the dose-dependent lag time is causally related to the proposed processing event. The rates of reduction of inter-subunit disulfide bond, an obligatory step in the intoxication process, have been measured and compared under a variety of conditions. Intersubunit disulfide reduction of abrin I is fourfold faster than that of abrin II at pH 7.2. The rate of disulfide reduction in abrin I could be decreased 1 I-fold by adding lactose, compared to that without lactose. The observed differences in the efficiencies of A chains, the dose-dependent lag period, the modulating effect of lactose on the rates of disulfide reduction and similarity in binding properties make the variants a valuable tool to probe the processing events in toxin transport in detail.

A simplified kinetic model for oxidative dehydrogenation of ethylbenzene over Pd-NaBr/Al2O3 catalyst

The oxidative dehydrogenation of ethylbenzene is gaining considerable importance in recent years as a promising alternative for styrene production. This vapour phase reaction has been studied over Pd-NaBr/Al2O3 catalyst in the temperature range 623-793 K in a fixed bed reactor. Kinetic analysis of this reaction has been done using a recursion procedure developed in this work from first principles. The advantage of this method is the absence of any restriction on the conversion level as it uses an integrated rate equation. The rate of styrene formation was found to follow a linear relationship with concentration of ethylbenzene and shows a Langmuir type dependence on the concentration of oxygen.

Conjugate MHD flow past a flat plate

A boundary layer solution for the conjugate forced convection flow of an electrically conducting fluid over a semi-infinite flat plate in the presence of a transverse magnetic field is presented. The governing nonsimilar partial differential equations are solved numerically using the Keller box method. Values of the temperature profiles of the plate are obtained for various values of the parameters entering the problem and are given in a table and shown on graphs.

Magnetism, exchange and crystal field parameters in the orbitally unquenched Ising antiferromagnet FePS3

FePS3 is a layered antiferromagnet (T N=123 K) with a marked Ising anisotropy in magnetic properties. The anisotropy arises from the combined effect of the trigonal distortion from octahedral symmetry and spin-orbit coupling on the orbitally degenerate5 T 2g ground state of the Fe2+ ion. The anisotropic paramagnetic susceptibilities are interpreted in terms of the zero field Hamiltonian, ?=?i [?(L iz 2 ?2)+|?|L i .S i ]?? ij J ij S i .S j . The crystal field trigonal distortion parameter ?, the spin-orbit coupling ? and the isotropic Heisenberg exchange,J ij, were evaluated from an analysis of the high temperature paramagnetic susceptibility data using the Correlated Effective Field (CEF) theory for many-body magnetism developed by Lines. Good agreement with experiment were obtained for ?/k=215.5 K; ?/k=166.5 K;J nn k=27.7 K; andJ nnn k=?2.3 K. Using these values of the crystal field and exchange parameters the CEF predicts aT N=122 K for FePS3, which is remarkably close to the observed value of theT N. The accuracy of the CEF approximation was also ascertained by comparing the calculated susceptibilities in the CEF with the experimental susceptibility for the isotropic Heisenberg layered antiferromagnet MnPS3, for which the high temperature series expansion susceptibility is available.

CM defect and Hilbert functions of monomial curves

In this article we consider a semigroup ring R = KGamma] of a numerical semigroup Gamma and study the Cohen- Macaulayness of the associated graded ring G(Gamma) := gr(m), (R) := circle plus(n is an element of N) m(n)/m(n+1) and the behaviour of the Hilbert function H-R of R. We define a certain (finite) subset B(Gamma) subset of F and prove that G(Gamma) is Cohen-Macaulay if and only if B(Gamma) = empty set. Therefore the subset B(Gamma) is called the Cohen-Macaulay defect of G(Gamma). Further, we prove that if the degree sequence of elements of the standard basis of is non-decreasing, then B(F) = empty set and hence G(Gamma) is Cohen-Macaulay. We consider a class of numerical semigroups Gamma = Sigma(3)(i=0) Nm(i) generated by 4 elements m(0), m(1), m(2), m(3) such that m(1) + m(2) = mo m3-so called ``balanced semigroups''. We study the structure of the Cohen-Macaulay defect B(Gamma) of Gamma and particularly we give an estimate on the cardinality |B(Gamma, r)| for every r is an element of N. We use these estimates to prove that the Hilbert function of R is non-decreasing. Further, we prove that every balanced ``unitary'' semigroup Gamma is ``2-good'' and is not ``1-good'', in particular, in this case, c(r) is not Cohen-Macaulay. We consider a certain special subclass of balanced semigroups Gamma. For this subclass we try to determine the Cohen-Macaulay defect B(Gamma) using the explicit description of the standard basis of Gamma; in particular, we prove that these balanced semigroups are 2-good and determine when exactly G(Gamma) is Cohen-Macaulay. (C) 2011 Published by Elsevier B.V.

Resonant absorption of alfvén waves near a neutral point

It is shown that, although the mathematical analysis of the Alfven-wave equation does not show any variation at non-zero or zero singular points, the role of surface waves in the physical mechanism of resonant absorption of Alfven waves is very different at these points. This difference becomes even greater when resistivity is taken into account. At the neutral point the zero-frequency surface waves that are symmetric surface modes of the structured neutral layer couple to the tearing mode instability of the layer. The importance of this study for the energy balance in tearing modes and the association of surface waves with driven magnetic reconnection is also pointed out.

On generating optimal signal probabilities for random tests: A genetic approach

Genetic Algorithms are robust search and optimization techniques. A Genetic Algorithm based approach for determining the optimal input distributions for generating random test vectors is proposed in the paper. A cost function based on the COP testability measure for determining the efficacy of the input distributions is discussed, A brief overview of Genetic Algorithms (GAs) and the specific details of our implementation are described. Experimental results based on ISCAS-85 benchmark circuits are presented. The performance pf our GA-based approach is compared with previous results. While the GA generates more efficient input distributions than the previous methods which are based on gradient descent search, the overheads of the GA in computing the input distributions are larger. To account for the relatively quick convergence of the gradient descent methods, we analyze the landscape of the COP-based cost function. We prove that the cost function is unimodal in the search space. This feature makes the cost function amenable to optimization by gradient-descent techniques as compared to random search methods such as Genetic Algorithms.

Solid-state photobehaviour and crystal packing of o-chlorobenzylidene-DL-piperitone: influence of molecular topology on photobehaviour

C17H19ClO, M(r) = 274.7, triclinic, P1BAR, a = 11.154 (3), b = 12.685 (2), c = 12.713 (2) angstrom, alpha = 100.68 (1), beta = 113.58 (1), gamma = 104.50 (2)-degrees, V = 1511.1 (6) angstrom3, Z = 4, D(m) = 1.22, D(x) = 1.215 Mg m-3, Cu K-alpha, lambda = 1.5418 angstrom, mu = 2.16 mm-1, F(000) = 584, T = 293 K, R = 0.057 for 3481 observed reflections. The title compound is photostable in the crystalline state and lattice-energy calculations have been employed to rationalize the photobehaviour. The well-known beta-steering ability of the chloro group is not operative in this system as there are no Cl...Cl interactions in the crystal lattice. All five benzylidene-DL-piperitone structures so far studied are alpha-packed and the molecular topology appears to be a deciding factor even in the presence of steering groups.

Crystal structure of Boc-LAla-Delta Phe-Delta Phe-Delta Phe-Delta Phe-NHMe: a left-handed helical peptide

alpha,beta-Dehydrophenylalanine residues constrain the peptide backbone to beta-bend conformation. A pentapeptide containing four consecutive (Delta Phe) residues has been synthesised and crystallised. The peptide Boc-LAla-Delta Phe-Delta Phe-Delta Phe-Delta Phe-NHMe (C45H46N6O7, MW = 782.86) was crystallised from an acetonitrile/methanol mixture. The crystal belongs to the orthorhombic space group P2(1)2(1)2(1) With a = 19.455(6), b = 20.912(9), c = 11.455(4) Angstrom and Z = 4. The X-ray (MoKalpha, lambda = 0.7107 Angstrom) intensity data were collected using the Rigaku-AFC7 diffractrometer. The crystal structure was determined by direct methods and refined using the least-squares technique, R = 8.41% for 1827 reflections with \F-o\ > 4 sigma\F-o\. The molecule contains the largest stretch of consecutive dehydrophenylalanine residues whose crystal structure has been determined so far. The peptide adopts left-handed 3(10)-helical conformation despite the presence of LAla at the N-terminus. The mean phi, psi values, averaged across the last four residues are 56.8 degrees and 17.5 degrees, respectively. There are four 4-->1 intramolecular hydrogen bonds, characteristic of the 3(10)-helix. In the crystal each molecule interacts with four crystallographically symmetric molecules with one hydrogen bond each.

Mechanistic approach to the shear strength behaviour of allophanic soils

The presence of allophane minerals imparts special engineering features to the volcanic ash soils. This study examines the reasons for the allophanic soils exhibiting unusual shear strength properties in comparison to sedimentary clays. The theories of residual shear strength developed for natural soils and artificial soil mixtures and the unusual surface charge properties of the allophane particle are invoked to explain the high shear strength values of these residual soils. The lack of any reasonable correlation between phi' (effective stress-strength parameter) and plasticity index values for allophanic soils is explained on the basis of the unusual structure of the allophane particle. The reasons as to why natural soil slopes in allophanic soil areas (example, Dominica, West Indies) are stable at much steeper angles than natural slopes in sedimentary clay deposits (London clay areas) are explained in light of the hypothesis developed in this study.

Probing the structural changes in the phase transitions of a Bi2MoO6 catalyst: the nature of the intermediate-temperature phase

The nature of the phase transitions of Bi2MoO6 has been investigated by the combined use of X-ray diffraction and Xray absorption spectroscopy. The distorted MoO6 octahedra in the low-temperature form are shown to undergo further distortion in the intermediate-temperature form before transforming to MoO4 tetrahedra in the high-temperature phase. (C) 1995 Academic Press, Inc.

In vitro and in vivo regulation of assimilatory nitrite reductase from Candida utilis

The nitrate assimilation pathway in Candida utilis, as in other assimilatory organisms, is mediated by two enzymes: nitrate reductase and nitrite reductase. Purified nitrite reductase has been shown to be a heterodimer consisting of 58- and 66-kDa subunits. In the present study, nitrite reductase was found to be capable of utilising both NADH and NADPH as electron donors. FAD, which is an essential coenzyme, stabilised the enzyme during the purification process. The enzyme was modified by cysteine modifiers, and the inactivation could be reversed by thiol reagents. One cysteine was demonstrated to be essential for the enzymatic activity. In vitro, the enzyme was inactivated by ammonium salts, the end product of the path way, proving that the enzyme is assimilatory in function. In vivo, the enzyme was induced by nitrate and repressed by ammonium ions. During induction and repression, the levels of nitrite reductase mRNA, protein, and enzyme activity were modulated together, which indicated that the primary level of regulation of this enzyme was at the transcriptional level. When the enzyme was incubated with ammonium salts in vitro or when the enzyme was assayed in cells grown with the same salts as the source of nitrogen, the residual enzymatic activities were similar. Thus, a study of the in vitro inactivation can give a clue to understanding the mechanism of in vivo regulation of nitrite reductase in Candida utilis.