Evidence that the 36kb plasmid of Brachyspira hyodysenteriae contributes to virulence

Swine dysentery (SD) results from infection of the porcine large intestine with the anaerobic intestinal spirochaete Brachyspira hyodysenteriae. Recently the genome of virulent Australian B. hyodysenteriae strain WA1 was sequenced, and a 36. kilobase (kb) circular plasmid was identified. The plasmid contained 31 genes including six rfb genes that were predicted to be involved with rhamnose biosynthesis, and others associated with glycosylation. In the current study a set of PCRs was developed to amplify portions of nine of the plasmid genes. When used with DNA extracted from virulent strain B204, PCR products were generated, but no products were generated with DNA from avirulent strain A1. Analysis of the DNA using pulsed field gel electrophoresis (PFGE) identified a plasmid band in strains WA1 and B204, but not in strain A1. These results demonstrate that strain A1 does not contain the plasmid, and suggests that lack of the plasmid may explain why this strain is avirulent. To determine how commonly strains lacking plasmids occur, DNA was extracted from 264 Australian field isolates of B. hyodysenteriae and subjected to PCRs for three of the plasmid genes. Only one isolate (WA400) that lacked the plasmid was identified, and this absence was confirmed by PFGE analysis of DNA from the isolate and further PCR testing. To assess its virulence, 24 pigs were experimentally challenged with cultures of WA400, and 12 control pigs were challenged with virulent strain WA1 under the same conditions. Significantly fewer (P= 0.03) of the pigs challenged with WA400 became colonised and developed SD (13/24; 54%) compared to the pigs infected with WA1 (11/12; 92%). Gross lesions in the pigs colonised with WA400 tended to be less extensive than those in pigs colonised with WA1, although there were no obvious differences at the microscopic level. The results support the likelihood that plasmid-encoded genes of B. hyodysenteriae are involved in colonisation and/or disease expression

Intestinal spirochaetes of the genus Brachyspira share a partially conserved 26 kilobase genomic region with Enterococcus faecalis and Escherichia coli

Anaerobic intestinal spirochaetes of the genus Brachyspira include both pathogenic and commensal species. The two best-studied members are the pathogenic species B. hyodysenteriae (the aetiological agent of swine dysentery) and B. pilosicoli (a cause of intestinal spirochaetosis in humans and other species). Analysis of near-complete genome sequences of these two species identifi ed a highly conserved 26 kilobase (kb) region that was shared, against a background of otherwise very little sequence conservation between the two species. PCR amplification was used to identify sets of contiguous genes from this region in the related Brachyspira species B. intermedia, B. innocens, B. murdochii, B. alvinipulli, and B. aalborgi, and demonstrated the presence of at least part of this region in species from throughout the genus. Comparative genomic analysis with other sequenced bacterial species revealed that none of the completely sequenced spirochaete species from different genera contained this conserved cluster of coding sequences. In contrast, Enterococcus faecalis and Escherichia coli contained high gene cluster conservation across the 26 kb region, against an expected background of little sequence conservation between these phylogenetically distinct species. The conserved region in B. hyodysenteriae contained five genes predicted to be associated with amino acid transport and metabolism, four with energy production and conversion, two with nucleotide transport and metabolism, one with ion transport and metabolism, and four with poorly characterised or uncertain function, including an ankyrin repeat unit at the 5’ end. The most likely explanation for the presence of this 26 kb region in the Brachyspira species and in two unrelated enteric bacterial species is that the region has been involved in horizontal gene transfer

Toy Model for Pion Production II: The role of three-particle singularities

The influence of three-particle breakup singularities on s-wave meson production in nucleon-nucleon collisions is studied within the distorted wave Born approximation. This study is based on a simple scalar model for the two-nucleon interaction and the production mechanism. An algorithm for the exact numerical treatment of the inherent three-body cuts, together with its straightforward implementation is presented. It is also shown that two often-used approximations to avoid the calculation of the three-body breakup are not justified. The possible impact on pion production observables is discussed.Comment: 14 pages, 6 figure

Nucleon Spin-Polarisabilities from Polarisation Observables in Low-Energy Deuteron Compton Scattering

We investigate the dependence of polarisation observables in elastic deuteron Compton scattering below the pion production threshold on the spin-independent and spin-dependent iso-scalar dipole polarisabilities of the nucleon. The calculation uses Chiral Effective Field Theory with dynamical Delta(1232) degrees of freedom in the Small Scale Expansion at next-to-leading order. Resummation of the NN intermediate rescattering states and including the Delta induces sizeable effects. The analysis considers cross-sections and the analysing power of linearly polarised photons on an unpolarised target, and cross-section differences and asymmetries of linearly and circularly polarised beams on a vector-polarised deuteron. An intuitive argument helps one to identify kinematics in which one or several polarisabilities do not contribute. Some double-polarised observables are only sensitive to linear combinations of two of the spin-polarisabilities, simplifying a multipole-analysis of the data. Spin-polarisabilities can be extracted at photon energies \gtrsim 100 MeV, after measurements at lower energies of \lesssim 70 MeV provide high-accuracy determinations of the spin-independent ones. An interactive Mathematica 7.0 notebook of our findings is available from [email protected]: 30 pages LaTeX2e, including 22 figures as 66 .eps file embedded with includegraphicx; three errors in initial submission corrected. This submission includes ot the erratum to be published in EPJA (2012) and the corrections in the tex

Dynamics of ions in the selectivity filter of the KcsA channel

The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic solution. A new approach to the derivation of a Brownian dynamics (BD) model of ion permeation through the filter is discussed, based on unbiased MD simulations. It is shown that depending on additional assumptions, ion’s dynamics can be described either by under-damped Langevin equation with constant damping and white noise or by Langevin equation with a fractional memory kernel. A comparison of the potential of the mean force derived from unbiased MD simulations with the potential produced by the umbrella sampling method demonstrates significant differences in these potentials. The origin of these differences is an open question that requires further clarifications

Nucleon Polarizabilities from Deuteron Compton Scattering within a Green's-Function Hybrid Approach

We examine elastic Compton scattering from the deuteron for photon energies ranging from zero to 100 MeV, using state-of-the-art deuteron wave functions and NN-potentials. Nucleon-nucleon rescattering between emission and absorption of the two photons is treated by Green's functions in order to ensure gauge invariance and the correct Thomson limit. With this Green's-function hybrid approach, we fulfill the low-energy theorem of deuteron Compton scattering and there is no significant dependence on the deuteron wave function used. Concerning the nucleon structure, we use Chiral Effective Field Theory with explicit \Delta(1232) degrees of freedom within the Small Scale Expansion up to leading-one-loop order. Agreement with available data is good at all energies. Our 2-parameter fit to all elastic $\gamma d$ data leads to values for the static isoscalar dipole polarizabilities which are in excellent agreement with the isoscalar Baldin sum rule. Taking this value as additional input, we find \alpha_E^s= (11.3+-0.7(stat)+-0.6(Baldin)) x 10^{-4} fm^3 and \beta_M^s = (3.2-+0.7(stat)+-0.6(Baldin)) x 10^{-4} fm^3 and conclude by comparison to the proton numbers that neutron and proton polarizabilities are essentially the same.Comment: 47 pages LaTeX2e with 20 figures in 59 .eps files, using graphicx. Minor modifications; extended discussion of theoretical uncertainties of polarisabilities extraction. Version accepted for publication in EPJ

Synchronization of Hamiltonian motion and dissipative effects in optical lattices: Evidence for a stochastic resonance

We theoretically study the influence of the noise strength on the excitation of the Brillouin propagation modes in a dissipative optical lattice. We show that the excitation has a resonant behavior for a specific amount of noise corresponding to the precise synchronization of the Hamiltonian motion on the optical potential surfaces and the dissipative effects associated with optical pumping in the lattice. This corresponds to the phenomenon of stochastic resonance. Our results are obtained by numerical simulations and correspond to the analysis of microscopic quantities (atomic spatial distributions) as well as macroscopic quantities (enhancement of spatial diffusion and pump-probe spectra). We also present a simple analytical model in excellent agreement with the simulations

Isotope Effect for the Penetration Depth in Superconductors

We show that various factors can lead to an isotopic dependence of the penetration depth $\delta$. Non-adiabaticity (Jahn-Teller crossing) leads to the isotope effect of the charge carrier concentration $n$ and, consequently, of $\delta$ in doped superconductors such as the cuprates. A general equation relating the isotope coefficients of $T_c$ and of $\delta$ is presented for London superconductors. We further show that the presence of magnetic impurities or a proximity contact also lead to an isotopic dependence of $\delta$; the isotope coefficient turns out to be temperature dependent, $\beta(T)$, in these cases. The existence of the isotope effect for the penetration depth is predicted for conventional as well as for high-temperature superconductors. Various experiments are proposed and/or discussed.Comment: 11 pages, 8 figures, accepted for publication in Phys. Rev.

Optical Properties of Layered Superconductors near the Josephson Plasma Resonance

We study the optical properties of crystals with spatial dispersion and show that the usual Fresnel approach becomes invalid near frequencies where the group velocity of the wave packets inside the crystal vanishes. Near these special frequencies the reflectivity depends on the atomic structure of the crystal provided that disorder and dissipation are very low. This is demonstrated explicitly by a detailed study of layered superconductors with identical or two different alternating junctions in the frequency range near the Josephson plasma resonance. Accounting for both inductive and charge coupling of the intrinsic junctions, we show that multiple modes are excited inside the crystal by the incident light, determine their relative amplitude by the microscopic calculation of the additional boundary conditions and finally obtain the reflectivity. Spatial dispersion also provides a novel method to stop light pulses, which has possible applications for quantum information processing and the artificial creation of event horizons in a solid.Comment: 25 pages, 20 figures, submitted to Phys. Rev.