A linear plasmid truncation induces unidirectional flagellar phase change in H:z66 positive Salmonella Typhi

The process by which bacteria regulate flagellar expression is known as phase variation and in Salmonella enterica this process permits the expression of one of two flagellin genes, fliC or fljB, at any one time. Salmonella Typhi (S. Typhi) is normally not capable of phase variation of flagellar antigen expression as isolates only harbour the fliC gene (H:d) and lacks an equivalent fljB locus. However, some S. Typhi isolates, exclusively from Indonesia, harbour an fljB equivalent encoded on linear plasmid, pBSSB1 that drives the expression of a novel flagellin named H:z66. H:z66+S. Typhi isolates were stimulated to change flagellar phase and genetically analysed for the mechanism of variation. The phase change was demonstrated to be unidirectional, reverting to expression from the resident chromosomal fliC gene. DNA sequencing demonstrated that pBSSB1 linear DNA was still detectable but that these derivatives had undergone deletion and were lacking fljAz66 (encoding a flagellar repressor) and fljBz66. The deletion end-point was found to involve one of the plasmid termini and a palindromic repeat sequence within fljBz66, distinct to that found at the terminus of pBSSB1. These data demonstrate that, like some Streptomyces linear elements, at least one of the terminal inverted repeats of pBSSB1 is non-essential, but that a palindromic repeat sequence may be necessary for replication

Combined effect of coherent Z exchange and the hyperfine interaction in atomic PNC

The nuclear spin-dependent parity nonconserving (PNC) interaction arising from a combination of the hyperfine interaction and the coherent, spin-independent, PNC interaction from Z exchange is evaluated using many-body perturbation theory. For the 6s-7s transition in 133Cs, we obtain a result that is about 40% smaller than that found previously by Bouchiat and Piketty [Phys. Lett. B 269, 195 (1991)]. Applying this result to 133Cs, leads to an increase in the experimental value of nuclear anapole moment and exacerbates differences between constraints on PNC meson coupling constants obtained from the Cs anapole moment and those obtained from other nuclear parity violating experiments. Nuclear spin-dependent PNC dipole matrix elements, including contributions from the combined weak-hyperfine interaction, are also given for the 7s-8s transition in 211Fr and for transitions between ground-state hyperfine levels in K, Rb, Cs, Ba+, Au, Tl, Fr, and Ra+.Comment: Revtex4 preprint 19 pages 4 table

Bifurcations of a driven granular system under gravity

Molecular dynamics study on the granular bifurcation in a simple model is presented. The model consists of hard disks, which undergo inelastic collisions; the system is under the uniform external gravity and is driven by the heat bath. The competition between the two effects, namely, the gravitational force and the heat bath, is carefully studied. We found that the system shows three phases, namely, the condensed phase, locally fluidized phase, and granular turbulent phase, upon increasing the external control parameter. We conclude that the transition from the condensed phase to the locally fluidized phase is distinguished by the existence of fluidized holes, and the transition from the locally fluidized phase to the granular turbulent phase is understood by the destabilization transition of the fluidized holes due to mutual interference.Comment: 35 pages, 17 figures, to be published in PR

Density functional theories and self-energy approaches

A purpose-designed microarray platform (Stressgenes, Phase 1) was utilised to investigate the changes in gene expression within the liver of rainbow trout during exposure to a prolonged period of confinement. Tissue and blood samples were collected from trout at intervals up to 648 h after transfer to a standardised confinement stressor, together with matched samples from undisturbed control fish. Plasma ACTH, cortisol, glucose and lactate were analysed to confirm that the neuroendocrine response to confinement was consistent with previous findings and to provide a phenotypic context to assist interpretation of gene expression data. Liver samples for suppression subtractive hybridisation (SSH) library construction were selected from within the experimental groups comprising “early” stress (2–48 h) and “late” stress (96–504 h). In order to reduce redundancy within the four SSH libraries and yield a higher number of unique clones an additional subtraction was carried out. After printing of the arrays a series of 55 hybridisations were executed to cover 6 time points. At 2 h, 6 h, 24 h, 168 h and 504 h 5 individual confined fish and 5 individual control fish were used with control fish only at 0 h. A preliminary list of 314 clones considered differentially regulated over the complete time course was generated by a combination of data analysis approaches and the most significant gene expression changes were found to occur during the 24 h to 168 h time period with a general approach to control levels by 504 h. Few changes in expression were apparent over the first 6 h. The list of genes whose expression was significantly altered comprised predominantly genes belonging to the biological process category (response to stimulus) and one cellular component category (extracellular region) and were dominated by so-called acute phase proteins. Analysis of the gene expression profile in liver tissue during confinement revealed a number of significant clusters. The major patterns comprised genes that were up-regulated at 24 h and beyond, the primary examples being haptoglobin, β-fibrinogen and EST10729. Two representative genes from each of the six k-means clusters were validated by qPCR. Correlations between microarray and qPCR expression patterns were significant for most of the genes tested. qPCR analysis revealed that haptoglobin expression was up-regulated approximately 8-fold at 24 h and over 13-fold by 168 h.This project was part funded by the European Commission (Q5RS-2001-02211), Enterprise Ireland and the Natural Environment Research Council of the United Kingdom

Avalanche Dynamics in Evolution, Growth, and Depinning Models

The dynamics of complex systems in nature often occurs in terms of punctuations, or avalanches, rather than following a smooth, gradual path. A comprehensive theory of avalanche dynamics in models of growth, interface depinning, and evolution is presented. Specifically, we include the Bak-Sneppen evolution model, the Sneppen interface depinning model, the Zaitsev flux creep model, invasion percolation, and several other depinning models into a unified treatment encompassing a large class of far from equilibrium processes. The formation of fractal structures, the appearance of $1/f$ noise, diffusion with anomalous Hurst exponents, Levy flights, and punctuated equilibria can all be related to the same underlying avalanche dynamics. This dynamics can be represented as a fractal in $d$ spatial plus one temporal dimension. We develop a scaling theory that relates many of the critical exponents in this broad category of extremal models, representing different universality classes, to two basic exponents characterizing the fractal attractor. The exact equations and the derived set of scaling relations are consistent with numerical simulations of the above mentioned models.Comment: 27 pages in revtex, no figures included. Figures or hard copy of the manuscript supplied on reques

Active Brownian Particles. From Individual to Collective Stochastic Dynamics

We review theoretical models of individual motility as well as collective dynamics and pattern formation of active particles. We focus on simple models of active dynamics with a particular emphasis on nonlinear and stochastic dynamics of such self-propelled entities in the framework of statistical mechanics. Examples of such active units in complex physico-chemical and biological systems are chemically powered nano-rods, localized patterns in reaction-diffusion system, motile cells or macroscopic animals. Based on the description of individual motion of point-like active particles by stochastic differential equations, we discuss different velocity-dependent friction functions, the impact of various types of fluctuations and calculate characteristic observables such as stationary velocity distributions or diffusion coefficients. Finally, we consider not only the free and confined individual active dynamics but also different types of interaction between active particles. The resulting collective dynamical behavior of large assemblies and aggregates of active units is discussed and an overview over some recent results on spatiotemporal pattern formation in such systems is given.Comment: 161 pages, Review, Eur Phys J Special-Topics, accepte

Search for charged Higgs bosons in top quark decays

We present a search for charged Higgs bosons in top quark decays. We analyze the \eplus, \muplus, $ee$, $e\mu$, $\mu\mu$, \etau and \mutau final states from top quark pair production events, using data from about 1${\text{fb}}^{-1}$ of integrated luminosity recorded by the \dzero experiment at the Fermilab Tevatron Collider. We consider different scenarios of possible charged Higgs boson decays, one where the charged Higgs boson decays purely hadronically into a charm and a strange quark, another where it decays into a $\tau$ lepton and a $\tau$ neutrino and a third one where both decays appear. We extract limits on the branching ratio $B(t\to H^+ b)$ for all these models. We use two methods, one where the $t\bar{t}$ production cross section is fixed, and one where the cross section is fitted simultaneously with $B(t\to H^+b)$. Based on the extracted limits, we exclude regions in the charged Higgs boson mass and $\tan \beta$ parameter space for different scenarios of the minimal supersymmetric standard model.Comment: 10 pages, 8 figures, submitted to PL

Study of conversion decays phi->etae+e-, eta->e+e-g and eta->pi+pi-e+e- at CMD-2

Using 15.1 pb^{-1} of data collected by CMD-2 in the phi-meson energy range, the branching ratios of the following conversion decays have been measured: B(\phi\to\eta e^+e^-) = (1.14\pm0.10\pm0.06)\cdot10^{-4}, B(\eta\to e^+e^-\gamma) = (7.10\pm0.64\pm0.46)\cdot10^{-3}, B(\eta\to\pi^+\pi^-e^+e^-) = (3.7^{+2.5}_{-1.8}\pm0.3)\cdot10^{-4}. The upper limits for the following rare conversion decays have been obtained at the 90% confidence level: B(\phi\to\eta\mu^+\mu^-) < 9.4\cdot10^{-6}, B(\eta\to e^+e^-e^+e^-) < 6.9\cdot10^{-5}.Comment: 16 pages, 7 PostScript figures. To be published in Phys. Lett.