Lateral gene transfer in phylogeny of azoreductase enzyme

This paper attempts to reconstruct the phylogeny of azoreductase enzyme from different organisms and compare it with the small subunit rRNA-based phylogeny of the organisms. The two phylogenies were found to be incongruent, indicating several events of lateral transfer of azoreductase gene between phylogenetically diverse organisms. However, the phylogenetic analysis methods have several limitations and a single method may not give the true pattern. Hence, it is necessary to corroborate the results with other complementary analysis tools. We used several tools to test our hypothesis of lateral transfer and found that it was supported not only by the analysis of the whole sequences, but also by the conserved motifs detected in these sequences. There were ample evidences for lateral transfer of azoreductase gene among enteric bacteria. There were also indications that azoreductase probably evolved in prokaryotes and then it was laterally transferred to eukaryotes in multiple events, resulting in some sequence variation among eukaryotic azoreductases. Finally, profile HMMs and conserved motifs extracted from these azoreductase sequences were found to provide sensitive tools for identifying potential azoreductases from the database. The analysis techniques used in this study can be extended to other gene trees to verify their evolutionary histories.     

Two highly similar LAEDDTNAQKT and LTDKIGTEI epitopes in G glycoprotein may be useful for effective epitope based vaccine design against pathogenic Henipavirus

Nipah virus and Hendra virus, two members of the genus Henipavirus, are newly emerging zoonotic pathogens which cause acute respiratory illness and severe encephalitis in human. Lack of the effective antiviral therapy endorses the urgency for the development of vaccine against these deadly viruses. In this study, we employed various computational approaches to identify epitopes which has the potential for vaccine development. By analyzing the immune parameters of the conserved sequences of G glycoprotein using various databases and bioinformatics tools, we identified two potential epitopes which may be used as peptide vaccines. Using different B cell epitope prediction servers, four highly similar B cell epitopes were identified. Immunoinformatics analyses revealed that LAEDDTNAQKT is a highly flexible and accessible B-cell epitope to antibody. Highly similar putative CTL epitopes were analyzed for their binding with the HLA-C 12*03 molecule. Docking simulation assay revealed that LTDKIGTEI has significantly lower binding energy, which bolstered its potential as epitope-based vaccine design. Finally, cytotoxicity analysis has also justified their potential as promising epitope-based vaccine candidate. In sum, our computational analysis indicates that either LAEDDTNAQKT or LTDKIGTEI epitope holds a promise for the development of universal vaccine against all kinds of pathogenic Henipavirus. Further in vivo and in vitro studies are necessary to validate the obtained findings.     

A note on conserved charges of asymptotically flat and anti-de Sitter spaces in arbitrary dimensions

The calculation of conserved charges of black holes is a rich problem, for which many methods are known. Until recently, there was some controversy on the proper definition of conserved charges in asymptotically anti-de Sitter (AdS) spaces in arbitrary dimensions. This paper provides a systematic and explicit Hamiltonian derivation of the energy and the angular momenta of both asymptotically flat and asymptotically AdS spacetimes in any dimension D  ≥  4. This requires as a first step a precise determination of the asymptotic conditions of the metric and of its conjugate momentum. These conditions happen to be achieved in ellipsoidal coordinates adapted to the rotating solutions. The asymptotic symmetry algebra is found to be isomorphic either to the Poincaré algebra or to the so(D − 1,2) algebra, as expected. In the asymptotically flat case, the boundary conditions involve a generalization of the parity conditions, introduced by Regge and Teitelboim, which are necessary to make the angular momenta finite. The charges are explicitly computed for Kerr and Kerr–AdS black holes for arbitrary D and they are shown to be in agreement with thermodynamical arguments. The author is a FRIA-FNRS bursar (National Fund for Scientific Research, Belgium).     

新的Liouville完全可积的广义Burgers方程族及其Hamilton结构

基于屠格式,从一个新的等谱问题,本文获得了一族广义Ｂｕｒｇｅｒｓ 方程及其Ｈａｍ ｉｌｔｏｎ 结构．最后证明了该族方程是Ｌｉｏｕｖｉｌｌｅ 完全可积的,并且有无穷多个彼此对合的公共守恒密度     

Symmetry analysis,conserved quantities and applications to a dissipative DGH equation

In this paper, we study a weakly dissipative Dullin–Gottwald–Holm equation from the viewpoint of Lie symmetry analysis. We first perform symmetry analysis and the nonlinear self-adjointness of this equation. Due to a mixed derivatives term in the equation, we need to rewrite the corresponding form Lagrangian in symmetric form to construct conservation laws. From the viewpoint, we present a general procedure of how these conserved quantities come about. Based on these conserved quantities, blow-up analysis and global existence of strong solutions are presented. Finally, we show that this equation admits a weak peakon-type solution.     

Conserved momenta of a ferromagnetic soliton

Linear and angular momenta of a soliton in a ferromagnet are commonly derived through the application of Noether’s theorem. We show that these quantities exhibit unphysical behavior: they depend on the choice of a gauge potential in the spin Lagrangian and can be made arbitrary. To resolve this problem, we exploit a similarity between the dynamics of a ferromagnetic soliton and that of a charged particle in a magnetic field. For the latter, canonical momentum is also gauge-dependent and thus unphysical; the physical momentum is the generator of magnetic translations, a symmetry combining physical translations with gauge transformations. We use this analogy to unambiguously define conserved momenta for ferromagnetic solitons. General considerations are illustrated on simple models of a domain wall in a ferromagnetic chain and of a vortex in a thin film.     

Conservation laws and symmetries of semilinear radial wave equations

Classifications of symmetries and conservation laws are presented for a variety of physically and analytically interesting wave equations with power nonlinearities in n spatial dimensions: a radial hyperbolic equation, a radial Schrödinger equation and its derivative variant, and two proposed radial generalizations of modified Korteweg-de Vries equations, as well as Hamiltonian variants. The mains results classify all admitted local point symmetries and all admitted local conserved densities depending on up to first order spatial derivatives, including any that exist only for special powers or dimensions. All such cases for which these wave equations admit, in particular, dilational energies or conformal energies and inversion symmetries are determined. In addition, potential systems arising from the classified conservation laws are used to determine nonlocal symmetries and nonlocal conserved quantities admitted by these equations. As illustrative applications, a discussion is given of energy norms, conserved Hs norms, critical powers for blow-up solutions, and one-dimensional optimal symmetry groups for invariant solutions.     

Conservation laws via the partial Lagrangian and group invariant solutions for radial and two-dimensional free jets

The conservation laws for Prandtl’s boundary layer equations for an incompressible fluid governing the flow in radial and two-dimensional jets are investigated. For both radial and two-dimensional jets the partial Lagrangian method is used to derive conservation laws for the system of two differential equations for the velocity components. The Lie point symmetries are calculated for both cases and a symmetry is associated with the conserved vector that is used to establish the conserved quantity for the jet. This associated symmetry is then used to derive the group invariant solution for the system governing the flow in the free jet.     

Attractor for a conserved phase‐field system with hyperbolic heat conduction

We consider a conserved phase‐field system of Caginalp type, characterized by the assumption that both the internal energy and the heat flux depend on the past history of the temperature and its gradient, respectively. The latter dependence is a law of Gurtin–Pipkin type, so that the equation ruling the temperature evolution is hyperbolic. Thus, the system consists of a hyperbolic integrodifferential equation coupled with a fourth‐order evolution equation for the phase‐field. This model, endowed with suitable boundary conditions, has already been analysed within the theory of dissipative dynamical systems, and the existence of an absorbing set has been obtained. Here we prove the existence of the universal attractor. Copyright © 2004 John Wiley & Sons, Ltd.     

Corrigendum to “Noether symmetries and conserved quantities for spaces with a section of zero curvature” [J. Geom. Phys. 61 (2011) 658–662]

In Feroze and Hussain (2011) it was proved that the number of new conserved quantities for spaces or spacetimes with an $m$-dimensional section of zero curvature is $m$. This result needs modification as it holds for the spaces having no proper homothetic vector (i.e. other than isometries).