Role of the two-component regulator CpxAR in the virulence of Salmonella entetica serotype typhimurium

The CpxAR (Cpx) two-component regulator controls the expression of genes in response to a variety of environmental cues. The Cpx regulator has been implicated in the virulence of several gram-negative pathogens, although a role for Cpx in vivo has not been demonstrated directly. Here we investigate whether positive or negative control of gene expression by Cpx is important for the pathogenesis of Salmonella enterica serotype Typhimurium. The Cpx signal pathway in serotype Typhimurium was disrupted by insertional inactivation of the cpxA and cpxR genes. We also constitutively activated the Cpx pathway by making an internal in-frame deletion in cpxA (a cpxA* mutation). Activation of the Cpx pathway inhibited induction of the envelope stress response pathway controlled by the alternative sigma factor sigma(E) (encoded by rpoE). Conversely, the Cpx pathway was highly up-regulated (>40-fold) in a serotype Typhimurium rpoE mutant. The cpxA* mutation, but not the cpxA or the cpxR mutation, significantly reduced the capacity of serotype Typhimurium to adhere to and invade eucaryotic cells, although intracellular replication was not affected. The cpxA and cpxA* mutations significantly impaired the ability of serotype Typhimurium to grow in vivo in mice. To our knowledge, this is the first demonstration that the Cpx system is important for a bacterial pathogen in vivo.

Role of intimin-Tir interactions and the Tir-cytoskeleton coupling protein in the colonization of calves and lambs by Escherichia coli O157:H7

Intimin facilitates intestinal colonization by enterohemorrhagic Escherichia coli O157:H7; however, the importance of intimin binding to its translocated receptor (Tir) as opposed to cellular coreceptors is unknown. The intimin-Tir interaction is needed for optimal actin assembly under adherent bacteria in vitro, a process which requires the Tir-cytoskeleton coupling protein (TccP/EspF(U)) in E. coli O157:H7. Here we report that E. coli O157:H7 tir mutants are at least as attenuated as isogenic eae mutants in calves and lambs, implying that the role of intimin in the colonization of reservoir hosts can be explained largely by its binding to Tir. Mutation of tccP uncoupled actin assembly from the intimin-Tir-mediated adherence of E. coli O157:H7 in vitro but did not impair intestinal colonization in calves and lambs, implying that pedestal formation may not be necessary for persistence. However, an E. coli O157:H7 tccP mutant induced typical attaching and effacing lesions in a bovine ligated ileal loop model of infection, suggesting that TccP-independent mechanisms of actin assembly may operate in vivo.

Sources of variation in the ampicillin-resistant Escherichia coli concentration in the feces of organic broiler chickens

Currently, there are limited published data for the population dynamics of antimicrobial-resistant commensal bacteria. This study was designed to evaluate both the proportions of the Escherichia coli populations that are resistant to ampicillin at the level of the individual chicken on commercial broiler farms and the feasibility of obtaining repeated measures of fecal E. coli concentrations. Short-term temporal variation in the concentration of fecal E. coli was investigated, and a preliminary assessment was made of potential factors involved in the shedding of high numbers of ampicillin-resistant E. coli by growing birds in the absence of the use of antimicrobial drugs. Multilevel linear regression modeling revealed that the largest component of random variation in log-transformed fecal E. coli concentrations was seen between sampling occasions for individual birds. The incorporation of fixed effects into the model demonstrated that the older, heavier birds in the study were significantly more likely (P = 0.0003) to shed higher numbers of ampicillin-resistant E. coli. This association between increasing weight and high shedding was not seen for the total fecal E. coli population (P = 0.71). This implies that, in the absence of the administration of antimicrobial drugs, the proportion of fecal E. coli that was resistant to ampicillin increased as the birds grew. This study has shown that it is possible to collect quantitative microbiological data on broiler farms and that such data could make valuable contributions to risk assessments concerning the transfer of resistant bacteria between animal and human populations.

Describing seasonal variability in the distribution of daily effective temperatures for 1985-2009 compared to 1904-1984 for De Bilt, Holland

This paper proposes a method for describing the distribution of observed temperatures on any day of the year such that the distribution and summary statistics of interest derived from the distribution vary smoothly through the year. The method removes the noise inherent in calculating summary statistics directly from the data thus easing comparisons of distributions and summary statistics between different periods. The method is demonstrated using daily effective temperatures (DET) derived from observations of temperature and wind speed at De Bilt, Holland. Distributions and summary statistics are obtained from 1985 to 2009 and compared to the period 1904–1984. A two-stage process first obtains parameters of a theoretical probability distribution, in this case the generalized extreme value (GEV) distribution, which describes the distribution of DET on any day of the year. Second, linear models describe seasonal variation in the parameters. Model predictions provide parameters of the GEV distribution, and therefore summary statistics, that vary smoothly through the year. There is evidence of an increasing mean temperature, a decrease in the variability in temperatures mainly in the winter and more positive skew, more warm days, in the summer. In the winter, the 2% point, the value below which 2% of observations are expected to fall, has risen by 1.2 °C, in the summer the 98% point has risen by 0.8 °C. Medians have risen by 1.1 and 0.9 °C in winter and summer, respectively. The method can be used to describe distributions of future climate projections and other climate variables. Further extensions to the methodology are suggested.

The surprising role of orography in the initiation of an isolated thunderstorm in southern England

Many factors, both mesoscale and larger scale, often come together in order for a particular convective initiation to take place. The authors describe a modeling study of a case from the Convective Storms Initiation Project (CSIP) in which a single thunderstorm formed behind a front in the southern United Kingdom. The key features of the case were a tongue of low-level high θw air associated with a forward-sloping split front (overrunning lower θw air above), a convergence line, and a “lid” of high static stability air, which the shower was initially constrained below but later broke through. In this paper, the authors analyze the initiation of the storm, which can be traced back to a region of high ground (Dartmoor) at around 0700 UTC, in more detail using model sensitivity studies with the Met Office Unified Model (MetUM). It is established that the convergence line was initially caused by roughness effects but had a significant thermal component later. Dartmoor had a key role in the development of the thunderstorm. A period of asymmetric flow over the high ground, with stronger low-level descent in the lee, led to a hole in a layer of low-level clouds downstream. The surface solar heating through this hole, in combination with the tongue of low-level high θw air associated with the front, caused the shower to initiate with sufficient lifting to enable it later to break through the lid.

Assessing the spatial and temporal variation in the skill of precipitation forecasts from an NWP model

It is becoming increasingly important to be able to verify the spatial accuracy of precipitation forecasts, especially with the advent of high-resolution numerical weather prediction (NWP) models. In this article, the fractions skill score (FSS) approach has been used to perform a scale-selective evaluation of precipitation forecasts during 2003 from the Met Office mesoscale model (12 km grid length). The investigation shows how skill varies with spatial scale, the scales over which the data assimilation (DA) adds most skill, and how the loss of that skill is dependent on both the spatial scale and the rainfall coverage being examined. Although these results come from a specific model, they demonstrate how this verification approach can provide a quantitative assessment of the spatial behaviour of new finer-resolution models and DA techniques.

Understanding advances in the simulation of intraseasonal variability in the ECMWF model. Part I: the representation of the MJO

As a major mode of intraseasonal variability, which interacts with weather and climate systems on a near-global scale, the Madden – Julian Oscillation (MJO) is a crucial source of predictability for numerical weather prediction (NWP) models. Despite its global significance and comprehensive investigation, improvements in the representation of the MJO in an NWP context remain elusive. However, recent modifications to the model physics in the ECMWF model led to advances in the representation of atmospheric variability and the unprecedented propagation of the MJO signal through the entire integration period. In light of these recent advances, a set of hindcast experiments have been designed to assess the sensitivity of MJO simulation to the formulation of convection. Through the application of established MJO diagnostics, it is shown that the improvements in the representation of the MJO can be directly attributed to the modified convective parametrization. Furthermore, the improvements are attributed to the move from a moisture-convergent- to a relative-humidity-dependent formulation for organized deep entrainment. It is concluded that, in order to understand the physical mechanisms through which a relative-humidity-dependent formulation for entrainment led to an improved simulation of the MJO, a more process-based approach should be taken. T he application of process-based diagnostics t o t he hindcast experiments presented here will be the focus of Part II of this study.

Understanding advances in the simulation of intraseasonal variability in the ECMWF model. Part II: the application of process-based diagnostics

In Part I of this study it was shown that moving from a moisture-convergent- to a relative-humidity-dependent organized entrainment rate in the formulation for deep convection was responsible for significant advances in the simulation of the Madden – Julian Oscillation (MJO) in the ECMWF model. However, the application of traditional MJO diagnostics were not adequate to understand why changing the control on convection had such a pronounced impact on the representation of the MJO. In this study a set of process-based diagnostics are applied to the hindcast experiments described in Part I to identify the physical mechanisms responsible for the advances in MJO simulation. Increasing the sensitivity of the deep convection scheme to environmental moisture is shown to modify the relationship between precipitation and moisture in the model. Through dry-air entrainment, convective plumes ascending in low-humidity environments terminate lower in the atmosphere. As a result, there is an increase in the occurrence of cumulus congestus, which acts to moisten the mid troposphere. Due to the modified precipitation – moisture relationship more moisture is able to build up, which effectively preconditions the tropical atmosphere for the t ransition t o d eep convection. R esults from this study suggest that a tropospheric moisture control on convection is key to simulating the interaction between the convective heating and the large-scale wave forcing associated with the MJO.

In the shadow of Grexit: the Greek election of 17 June 2012

This article provides an overview and analysis of the Greek June 2012 elections. Placing the elections within the broader framework of the Greek socio-political and economic context, it discusses the electoral campaign and results, juxtaposing them to the 6 May electoral round. The election results confirmed many of the trends of the previous round, including electoral volatility, the fragmentation of the party system and the rise of anti-establishment forces. The main difference was the entrenchment of the pro- versus anti- bailout division and the prominence of the question of Greece’s continued Eurozone membership.

A dramatic isotope effect in the reaction of ClSiH with trimethylsilane-1-d: experimental evidence for intermediate complexes in silylene Si-H(D) insertion reactions

A kinetic isotope effect (kD/kH) of 7.4 has been found for the reaction of chlorosilylene with trimethysilane (Me3SiD vs Me3SiH). Such a value can be accounted for by theoretical modelling, but only if an internal rearrangement of the initially form complex is included in the mechanism. This provides the first concrete evidence for such complexes.

The role of double-stranded break repair in the creation of phenotypic diversity at cereal VRN1 loci

Nonhomologous repair of double-stranded breaks, although fundamental to the maintenance of genomic integrity in all eukaryotes, has received little attention as to its evolutionary consequences in the generation and selection of phenotypic diversity. Here we document the role of illegitimate recombination in the creation of novel alleles in VRN1 orthologs selected to confer adaptation to annual cropping systems in barley and wheat.

The role of baroclinic waves in the initiation of tropical cyclones across the southern Indian Ocean

Cases where tropical storms are initiated simultaneously along one latitude are investigated. It is argued that such structure arises as part of a baroclinic wave. A case from February 2008 is examined using European Centre for Medium-Range Forecasts (ECMWF) analyses; the birth of three tropical cyclones in the low-level cyclonic regions to the east of upper-level troughs suggests that the wave was instrumental for initiation. Archived satellite imagery and storm warnings reveal that baroclinic waves over the southern Indian Ocean accompany tropical cyclogenesis twice a season on average, mainly in late summer, when breaking Rossby waves on the subtropical westerly jet are closest to the Intertropical Convergence Zone (ITCZ). Copyright © 2012 Royal Meteorological Society

The importance of surface pressure changes in the response of the atmosphere to zonally-symmetric thermal and mechanical forcing

he classical problem of the response of a balanced, axisymmetric vortex to thermal and mechanical forcing is re-examined, paying special attention to the lower boundary condition. The correct condition is DΦ/Dt = 0, where Φ is the geopotential and D/Dt the material derivative, which explicitly accounts for a mass redistribution as part of the mean-flow response. This redistribution is neglected when using the boundary condition Dp/Dt = 0, which has conventionally been applied in this problem. It is shown that applying the incorrect boundary condition, and thereby ignoring the surface pressure change, leads to a zonal wind acceleration δū/δt that is too strong, especially near the surface. The effect is significant for planetary-scale forcing even when applied at tropopause level. A comparison is made between the mean-flow evolution in a baroclinic life-cycle, as simulated in a fully nonlinear, primitive-equation model, and that predicted by using the simulated eddy fluxes in the zonally-symmetric response problem. Use of the correct lower boundary condition is shown to lead to improved agreement.