Structure determination of Split-soret Cytochrome from a Desulfovibrio species isolated from a human abdominal abcess

The determined structure of the split-soret cytochrome (SSC) isolated from Desulfovibrio desulfuricans ATCC 27774 (D.d.) revealed a new Heme arrangement, which suggests that this protein constitutes a new cytochrome class.. SSC is a 52.6kDa homodimer containing four hemes at one end of the molecule. In each monomer the two hemes have their edges overlapped within van der Waals contacts. The polypeptide chain of each monomer supplies the sixth ligand to the heme-iron of the other monomer. A similar protein was recently purified from a homologous Desulfovibrio clinical strain isolated from an abdominal wall abscess in human patient2. Crystals of this SSC were grown using vapour diffusion method in the presence of agarose gel. Diffraction data were collected using X-ray synchrotron radiation at the ESRF, beamline, ID 14-1. The structure will be solved by molecular replacement using the structure of the D.d. as a starting model

APOE genotyping: comparison of three methods

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On the Nonlinear Stability of Asymptotically Anti-de Sitter Solutions

Despite the recent evidence that anti-de Sitter spacetime is nonlinearly unstable, we argue that many asymptotically anti-de Sitter solutions are nonlinearly stable. This includes geons, boson stars, and black holes. As part of our argument, we calculate the frequencies of long-lived gravitational quasinormal modes of AdS black holes in various dimensions. We also discuss a new class of asymptotically anti-de Sitter solutions describing noncoalescing black hole binaries.Comment: 26 pages. 5 figure

Behavior of a Model Dynamical System with Applications to Weak Turbulence

We experimentally explore solutions to a model Hamiltonian dynamical system derived in Colliander et al., 2012, to study frequency cascades in the cubic defocusing nonlinear Schr\"odinger equation on the torus. Our results include a statistical analysis of the evolution of data with localized amplitudes and random phases, which supports the conjecture that energy cascades are a generic phenomenon. We also identify stationary solutions, periodic solutions in an associated problem and find experimental evidence of hyperbolic behavior. Many of our results rely upon reframing the dynamical system using a hydrodynamic formulation.Comment: 22 pages, 14 figure

Effective numerical simulation of the Klein–Gordon–Zakharov system in the Zakharov limit

Solving the Klein-Gordon-Zakharov (KGZ) system in the high-plasma frequency regime $c\gg1$ is numerically severely challenging due to the highly oscillatory nature or the problem. To allow reliable approximations classical numerical schemes require severe step size restrictions depending on the small parameter $c^{−2}$ . This leads to large errors and huge computational costs. In the singular limit $c\to\infty$ the Zakharov system appears as the regular limit system for the KGZ system. It is the purpose of this paper to use this approximation in the construction of an effective numerical scheme for the KGZ system posed on the torus in the highly oscillatory regime $c\gg1$. The idea is to filter out the highly oscillatory phases explicitly in the solution. This allows us to play back the numerical task to solving the non-oscillatory Zakharov limit system. The latter can be solved very efficiently without any step size restrictions. The numerical approximation error is then estimated by showing that solutions of the KGZ system in this singular limit can be approximated via the solutions of the Zakharov system and by proving error estimates for the numerical approximation of the Zakharov system. We close the paper with numerical experiments which show that this method is more effective than other methods in the high-plasma frequency regime $c\gg1$

Extracellular Vesicles from Fusarium graminearum Contain Protein Effectors Expressed during Infection of Corn.

Fusarium graminearum (Fgr) is a devastating filamentous fungal pathogen that causes diseases in cereals, while producing mycotoxins that are toxic for humans and animals, and render grains unusable. Low efficiency in managing Fgr poses a constant need for identifying novel control mechanisms. Evidence that fungal extracellular vesicles (EVs) from pathogenic yeast have a role in human disease led us to question whether this is also true for fungal plant pathogens. We separated EVs from Fgr and performed a proteomic analysis to determine if EVs carry proteins with potential roles in pathogenesis. We revealed that protein effectors, which are crucial for fungal virulence, were detected in EV preparations and some of them did not contain predicted secretion signals. Furthermore, a transcriptomic analysis of corn (Zea mays) plants infected by Fgr revealed that the genes of some of the effectors were highly expressed in vivo, suggesting that the Fgr EVs are a mechanism for the unconventional secretion of effectors and virulence factors. Our results expand the knowledge on fungal EVs in plant pathogenesis and cross-kingdom communication, and may contribute to the discovery of new antifungals

Orbital stability: analysis meets geometry

We present an introduction to the orbital stability of relative equilibria of Hamiltonian dynamical systems on (finite and infinite dimensional) Banach spaces. A convenient formulation of the theory of Hamiltonian dynamics with symmetry and the corresponding momentum maps is proposed that allows us to highlight the interplay between (symplectic) geometry and (functional) analysis in the proofs of orbital stability of relative equilibria via the so-called energy-momentum method. The theory is illustrated with examples from finite dimensional systems, as well as from Hamiltonian PDE's, such as solitons, standing and plane waves for the nonlinear Schr{\"o}dinger equation, for the wave equation, and for the Manakov system

Non-ergodicity of Nose-Hoover dynamics

The numerical integration of the Nose-Hoover dynamics gives a deterministic method that is used to sample the canonical Gibbs measure. The Nose-Hoover dynamics extends the physical Hamiltonian dynamics by the addition of a "thermostat" variable, that is coupled nonlinearly with the physical variables. The accuracy of the method depends on the dynamics being ergodic. Numerical experiments have been published earlier that are consistent with non-ergodicity of the dynamics for some model problems. The authors recently proved the non-ergodicity of the Nose-Hoover dynamics for the one-dimensional harmonic oscillator. In this paper, this result is extended to non-harmonic one-dimensional systems. It is also shown for some multidimensional systems that the averaged dynamics for the limit of infinite thermostat "mass" have many invariants, thus giving theoretical support for either non-ergodicity or slow ergodization. Numerical experiments for a two-dimensional central force problem and the one-dimensional pendulum problem give evidence for non-ergodicity

Compilation of Giant Electric Dipole Resonances Built on Excited States

Giant Electric Dipole Resonance (GDR) parameters for gamma decay to excited states with finite spin and temperature are compiled. Over 100 original works have been reviewed and from some 70 of which more than 300 parameter sets of hot GDR parameters for different isotopes, excitation energies, and spin regions have been extracted. All parameter sets have been brought onto a common footing by calculating the equivalent Lorentzian parameters. The current compilation is complementary to an earlier compilation by Samuel S. Dietrich and Barry L. Berman (At. Data Nucl. Data Tables 38(1988)199-338) on ground-state photo-neutron and photo-absorption cross sections and their Lorentzian parameters. A comparison of the two may help shed light on the evolution of GDR parameters with temperature and spin. The present compilation is current as of January 2006.Comment: 31 pages including 1 tabl