Purification and characterization of the flagellar basal body of Rhodobacter sphaeroides

Flagellar hook-basal body (HBB) complexes were purified from Rhodobacter sphaeroides. The HBB was more acid labile but more heat stable than that of Salmonella species, and protein identification revealed that HBB components were expressed only from one of the two sets of flagellar gene clusters on the R. sphaeroides genome, under the heterotrophic growth conditions tested here.

Mode I fracture of sheet metal

The perceived wisdom about thin sheet fracture is that (i) the crack propagates under mixed mode I & III giving rise to a slant through-thickness fracture profile and (ii) the fracture toughness remains constant at low thickness and eventually decreases with increasing thickness. In the present study, fracture tests performed on thin DENT plates of various thicknesses made of stainless steel, mild steel, 6082-O and NS4 aluminium alloys, brass, bronze, lead, and zinc systematically exhibit (i) mode I “bath-tub”, i.e. “cup & cup”, fracture profiles with limited shear lips and significant localized necking (more than 50% thickness reduction), (ii) a fracture toughness that linearly increases with increasing thickness (in the range of 0.5–5 mm). The different contributions to the work expended during fracture of these materials are separated based on dimensional considerations. The paper emphasises the two parts of the work spent in the fracture process zone: the necking work and the “fracture” work. Experiments show that, as expected, the work of necking per unit area linearly increases with thickness. For a typical thickness of 1 mm, both fracture and necking contributions have the same order of magnitude in most of the metals investigated. A model is developed in order to independently evaluate the work of necking, which successfully predicts the experimental values. Furthermore, it enables the fracture energy to be derived from tests performed with only one specimen thickness. In a second modelling step, the work of fracture is computed using an enhanced void growth model valid in the quasi plane stress regime. The fracture energy varies linearly with the yield stress and void spacing and is a strong function of the hardening exponent and initial void volume fraction. The coupling of the two models allows the relative contributions of necking versus fracture to be quantified with respect to (i) the two length scales involved in this problem, i.e. the void spacing and the plate thickness, and (ii) the flow properties of the material. Each term can dominate depending on the properties of the material which explains the different behaviours reported in the literature about thin plate fracture toughness and its dependence with thickness.

Wigner Transport models of the electron-phonon kinetics in quantum wires

Two quantum-kinetic models of ultrafast electron transport in quantum wires are derived from the generalized electron-phonon Wigner equation. The various assumptions and approximations allowing one to find closed equations for the reduced electron Wigner function are discussed with an emphasis on their physical relevance. The models correspond to the Levinson and Barker-Ferry equations, now generalized to account for a space-dependent evolution. They are applied to study the quantum effects in the dynamics of an initial packet of highly nonequilibrium carriers, locally generated in the wire. The properties of the two model equations are compared and analyzed.

Conformational polymorphism of the molecular complex of 3-fluorobenzoic acid with 4-acetylpyridine

Two polymorphs of the molecular complex formed between 3-fluorobenzoic acid with 4-acetylpyridine are described and found to be based upon the same dimeric supramolecular construct. The conformational freedom around the hydrogen bond results in a 180 degrees rotation about this intermolecular link, distinguishing the polymorphs and affecting the packing of the dimeric units. The two polymorphs are fully characterised by single crystal X-ray and neutron diffraction and quantum mechanical calculations. There is evidence of structured crystal growth defects in both polymorphic crystals via observation of diffuse scattering and a disorder model for the average structure of Form I, which can be interpreted as a mixing of the two dimer conformations. The similarity of energy of the distinct dimeric units, supporting their likely co-existence, has been verified by periodic quantum chemical calculations.

Characterisation of the intracellular-glutamate decarboxylase system (GAD): analysis of its function, transcription and role in the acid resistance of various strains of Listeria monocytogenes

The glutamate decarboxylase (GAD) system is important for the acid resistance of Listeria monocytogenes. We previously showed that under acidic conditions, glutamate (Glt)/γ-aminobutyrate (GABA) antiport is impaired in minimal media but not in rich ones, like brain heart infusion. Here we demonstrate that this behavior is more complex and it is subject to strain and medium variation. Despite the impaired Glt/GABA antiport, cells accumulate intracellular GABA (GABA(i)) as a standard response against acid in any medium, and this occurs in all strains tested. Since these systems can occur independently of one another, we refer to them as the extracellular (GAD(e)) and intracellular (GAD(i)) systems. We show here that GAD(i) contributes to acid resistance since in a ΔgadD1D2 mutant, reduced GABA(i) accumulation coincided with a 3.2-log-unit reduction in survival at pH 3.0 compared to that of wild-type strain LO28. Among 20 different strains, the GAD(i) system was found to remove 23.11% ± 18.87% of the protons removed by the overall GAD system. Furthermore, the GAD(i) system is activated at milder pH values (4.5 to 5.0) than the GAD(e) system (pH 4.0 to 4.5), suggesting that GAD(i) is the more responsive of the two and the first line of defense against acid. Through functional genomics, we found a major role for GadD2 in the function of GAD(i), while that of GadD1 was minor. Furthermore, the transcription of the gad genes in three common reference strains (10403S, LO28, and EGD-e) during an acid challenge correlated well with their relative acid sensitivity. No transcriptional upregulation of the gadT2D2 operon, which is the most important component of the GAD system, was observed, while gadD3 transcription was the highest among all gad genes in all strains. In this study, we present a revised model for the function of the GAD system and highlight the important role of GAD(i) in the acid resistance of L. monocytogenes.

Nonlinear wave-activity conservation laws and Hamiltonian structure for the two-dimensional anelastic equations

Exact, finite-amplitude, local wave-activity conservation laws are derived for disturbances to steady flows in the context of the two-dimensional anelastic equations. The conservation laws are expressed entirely in terms of Eulerian quantities, and have the property that, in the limit of a small-amplitude, slowly varying, monochromatic wave train, the wave-activity density A and flux F, when averaged over phase, satisfy F = cgA where cg is the group velocity of the waves. For nonparallel steady flows, the only conserved wave activity is a form of disturbance pseudoenergy; when the steady flow is parallel, there is in addition a conservation law for the disturbance pseudomomentum. The above results are obtained not only for isentropic background states (which give the so-called “deep form” of the anelastic equations), but also for arbitrary background potential-temperature profiles θ0(z) so long as the variation in θ0(z) over the depth of the fluid is small compared with θ0 itself. The Hamiltonian structure of the equations is established in both cases, and its symmetry properties discussed. An expression for available potential energy is also derived that, for the case of a stably stratified background state (i.e., dθ0/dz > 0), is locally positive definite; the expression is valid for fully three-dimensional flow. The counterparts to results for the two-dimensional Boussinesq equations are also noted.

The energy-cycle analysis of the interactions between shallow and deep atmospheric convection

Interactions between different convection modes can be investigated using an energy–cycle description under a framework of mass–flux parameterization. The present paper systematically investigates this system by taking a limit of two modes: shallow and deep convection. Shallow convection destabilizes itself as well as the other convective modes by moistening and cooling the environment, whereas deep convection stabilizes itself as well as the other modes by drying and warming the environment. As a result, shallow convection leads to a runaway growth process in its stand–alone mode, whereas deep convection simply damps out. Interaction between these two convective modes becomes a rich problem, even when it is limited to the case with no large–scale forcing, because of these opposing tendencies. Only if the two modes are coupled at a proper level can a self–sustaining system arise, exhibiting a periodic cycle. The present study establishes the conditions for self–sustaining periodic solutions. It carefully documents the behaviour of the two mode system in order to facilitate the interpretation of global model behaviours when this energy–cycle is implemented as a closure into a convection parameterization in future.

In-situ comparison of the NOy instruments flown in MOZAIC and SPURT

Two aircraft instruments for the measurement of total odd nitrogen (NOy) were compared side by side aboard a Learjet A35 in April 2003 during a campaign of the AFO2000 project SPURT (Spurengastransport in der Tropopausenregion). The instruments albeit employing the same measurement principle (gold converter and chemiluminescence) had different inlet configurations. The ECO-Physics instrument operated by ETH-Zürich in SPURT had the gold converter mounted outside the aircraft, whereas the instrument operated by FZ-Jülich in the European project MOZAIC III (Measurements of ozone, water vapour, carbon monoxide and nitrogen oxides aboard Airbus A340 in-service aircraft) employed a Rosemount probe with 80 cm of FEP-tubing connecting the inlet to the gold converter. The NOy concentrations during the flight ranged between 0.3 and 3 ppb. The two data sets were compared in a blind fashion and each team followed its normal operating procedures. On average, the measurements agreed within 7%, i.e. within the combined uncertainty of the two instruments. This puts an upper limit on potential losses of HNO3 in the Rosemount inlet of the MOZAIC instrument. Larger transient deviations were observed during periods after calibrations and when the aircraft entered the stratosphere. The time lag of the MOZAIC instrument observed in these instances is in accordance with the time constant of the MOZAIC inlet line determined in the laboratory for HNO3.

Poor survival on an artificial diet of two genotypes of the aphid Myzus persicae: a fitness cost of insecticide resistance?

A fully susceptible genotype (4106A) of Myzus persicae survived the longest on an artificial diet and, in several of the eight replicates, monitoring was terminated when the culture was still thriving. A genotype with elevated carboxylesterase FE4 at the R3 level (800F) had a mean survival of only 98.13 days, whereas 794J, which combines R3 E4 carboxylesterase with target-site resistance (knockdown resistance), survived for the even shorter mean time of 84.38 days. The poorer survival of the two genotypes with extremely elevated carboxylesterase-resistance was not the result of a reluctance to transfer to new diet at each diet change. Although available for only two replicates, a revertant clone of 794J (794Jrev), which has the same genotype as 794J but the amplified E4 genes are not expressed leading to a fully susceptible phenotype, did not appear to survive any better than this clone. This suggests that the poor survival on an artificial diet of the extreme-carboxylesterase genotypes is not the result of the cost of over-producing the enzyme. The frequency of insecticide-resistant genotypes is low in the population until insecticide is applied, indicating that they have reduced fitness, although this does not necessarily reflect a direct cost of expressing the resistance mechanism.

Phase calibration of the EISCAT Svalbard Radar interferometer using optical satellite signatures

The link between natural ion-line enhancements in radar spectra and auroral activity has been the subject of recent studies but conclusions have been limited by the spatial and temporal resolution previously available. The next challenge is to use shorter sub-second integration times in combination with interferometric programmes to resolve spatial structure within the main radar beam, and so relate enhanced filaments to individual auroral rays. This paper presents initial studies of a technique, using optical and spectral satellite signatures, to calibrate the received phase of a signal with the position of the scattering source along the interferometric baseline of the EISCAT Svalbard Radar. It is shown that a consistent relationship can be found only if the satellite passage through the phase fringes is adjusted from the passage predicted by optical tracking. This required adjustment is interpreted as being due to the vector between the theoretical focusing points of the two antennae, i.e. the true radar baseline, differing from the baseline obtained by survey between the antenna foot points. A method to obtain a measurement of the true interferometric baseline using multiple satellite passes is outlined.

Direct observation by time-resolved infrared spectroscopy of the bright and the dark excited states of the [Ru(phen)2(dppz)]2+ light-switch compound in solution and when bound to DNA

The [Ru(phen)2(dppz)]2+ complex (1) is non-emissive in water but is highly luminescent in organic solvents or when bound to DNA, making it a useful probe for DNA binding. To date, a complete mechanistic explanation for this “light-switch” effect is still lacking. With this in mind we have undertaken an ultrafast time resolved infrared (TRIR) study of 1 and directly observe marker bands between 1280–1450 cm-1, which characterise both the emissive “bright” and the non-emissive “dark” excited states of the complex, in CD3CN and D2O respectively. These characteristic spectral features are present in the [Ru(dppz)3]2+ solvent light-switch complex but absent in [Ru(phen)3]2+, which is luminescent in both solvents. DFT calculations show that the vibrational modes responsible for these characteristic bands are predominantly localised on the dppz ligand. Moreover, they reveal that certain vibrational modes of the “dark” excited state couple with vibrational modes of two coordinating water molecules, and through these to the bulk solvent, thus providing a new insight into the mechanism of the light-switch effect. We also demonstrate that the marker bands for the “bright” state are observed for both L- and D enantiomers of 1 when bound to DNA and that photo-excitation of the complex induces perturbation of the guanine and cytosine carbonyl bands. This perturbation is shown to be stronger for the L enantiomer, demonstrating the different binding site properties of the two enantiomers and the ability of this technique to determine the identity and nature of the binding site of such intercalators.

Recent oppositely directed trends in solar climate forcings and the global mean surface air temperature. II. Different reconstructions of the total solar irradiance variation and dependence on response time scale

We have previously placed the solar contribution to recent global warming in context using observations and without recourse to climate models. It was shown that all solar forcings of climate have declined since 1987. The present paper extends that analysis to include the effects of the various time constants with which the Earth’s climate system might react to solar forcing. The solar input waveform over the past 100 years is defined using observed and inferred galactic cosmic ray fluxes, valid for either a direct effect of cosmic rays on climate or an effect via their known correlation with total solar irradiance (TSI), or for a combination of the two. The implications, and the relative merits, of the various TSI composite data series are discussed and independent tests reveal that the PMOD composite used in our previous paper is the most realistic. Use of the ACRIM composite, which shows a rise in TSI over recent decades, is shown to be inconsistent with most published evidence for solar influences on pre-industrial climate. The conclusions of our previous paper, that solar forcing has declined over the past 20 years while surface air temperatures have continued to rise, are shown to apply for the full range of potential time constants for the climate response to the variations in the solar forcings.

A comparison of the active surveillance of scrapie in the European Union

The abattoir and the fallen stock surveys constitute the active surveillance component aimed at improving the detection of scrapie across the European Union. Previous studies have suggested the occurrence of significant differences in the operation of the surveys across the EU. In the present study we assessed the standardisation of the surveys throughout time across the EU and identified clusters of countries with similar underlying characteristics allowing comparisons between them. In the absence of sufficient covariate information to explain the observed variability across countries, we modelled the unobserved heterogeneity by means of non-parametric distributions on the risk ratios of the fallen stock over the abattoir survey. More specifically, we used the profile likelihood method on 2003, 2004 and 2005 active surveillance data for 18 European countries on classical scrapie, and on 2004 and 2005 data for atypical scrapie separately. We extended our analyses to include the limited covariate information available, more specifically, the proportion of the adult sheep population sampled by the fallen stock survey every year. Our results show that the between-country heterogeneity dropped in 2004 and 2005 relative to that of 2003 for classical scrapie. As a consequence, the number of clusters in the last two years was also reduced indicating the gradual standardisation of the surveillance efforts across the EU. The crude analyses of the atypical data grouped all the countries in one cluster and showed non-significant gain in the detection of this type of scrapie by any of the two sources. The proportion of the population sampled by the fallen stock appeared significantly associated with our risk ratio for both types of scrapie, although in opposite directions: negative for classical and positive for atypical. The initial justification for the fallen stock, targeting a high-risk population to increase the likelihood of case finding, appears compromised for both types of scrapie in some countries.

The kinetics of the gas-phase decomposition of the 2-methyl-2-butoxyl and 2-methyl-2-pentoxyl radicals

The kinetics of the title reactions have been studied by relative-rate methods as a function of temperature. Relative-rate coefficients for the two decomposition channels of 2-methyl-2-butoxyl have been measured at five different temperatures between 283 and 345 K and the observed temperature dependence is consistent with the results of some previous experimental studies. The kinetics of the two decomposition channels of 2-methyl-2-pentoxyl have also been investigated, as a function of temperature, relative to the estimated rate of isomerisation of this radical. Room-temperature rate coefficient data for the two decomposition channels of both 2-methyl-2-pentoxyl and 2-methyl-2-butxoyl (after combining the relative rate coefficient for this latter with a value for the rate coefficient of the major channel, extrapolated from the data presented by Batt et al., Int. J. Chem. Kinet., 1978, 10, 931) are shown to be consistent with a non-linear kinetic correlation, for alkoxyl radical decomposition rate data, previously presented by this laboratory (Johnson et al., Atmos. Environ., 2004, 38, 1755-1765).

An efficient numerical scheme for the two-dimensional shallow water equations using arithmetic averaging

A finite difference scheme based on flux difference splitting is presented for the solution of the two-dimensional shallow water equations of ideal fluid flow. A linearised problem, analogous to that of Riemann for gas dynamics is defined, and a scheme, based on numerical characteristic decomposition is presented for obtaining approximate solutions to the linearised problem, and incorporates the technique of operator splitting. An average of the flow variables across the interface between cells is required, and this average is chosen to be the arithmetic mean for computational efficiency leading to arithmetic averaging. This is in contrast to usual ‘square root’ averages found in this type of Riemann solver, where the computational expense can be prohibitive. The method of upwind differencing is used for the resulting scalar problems, together with a flux limiter for obtaining a second order scheme which avoids nonphysical, spurious oscillations. An extension to the two-dimensional equations with source terms is included. The scheme is applied to the one-dimensional problems of a breaking dam and reflection of a bore, and in each case the approximate solution is compared to the exact solution of ideal fluid flow. The scheme is also applied to a problem of stationary bore generation in a channel of variable cross-section. Finally, the scheme is applied to two other dam-break problems, this time in two dimensions with one having cylindrical symmetry. Each approximate solution compares well with those given by other authors.