Metabolite and transcriptome analysis of Campylobacter jejuni in vitro growth reveals a stationary-phase physiological switch.

Campylobacter jejuni is a prevalent cause of food-borne diarrhoeal illness in humans. Understanding of the physiological and metabolic capabilities of the organism is limited. We report a detailed analysis of the C. jejuni growth cycle in batch culture. Combined transcriptomic, phenotypic and metabolic analysis demonstrates a highly dynamic 'stationary phase', characterized by a peak in motility, numerous gene expression changes and substrate switching, despite transcript changes that indicate a metabolic downshift upon the onset of stationary phase. Video tracking of bacterial motility identifies peak activity during stationary phase. Amino acid analysis of culture supernatants shows a preferential order of amino acid utilization. Proton NMR (1H-NMR) highlights an acetate switch mechanism whereby bacteria change from acetate excretion to acetate uptake, most probably in response to depletion of other substrates. Acetate production requires pta (Cj0688) and ackA (Cj0689), although the acs homologue (Cj1537c) is not required. Insertion mutants in Cj0688 and Cj0689 maintain viability less well during the stationary and decline phases of the growth cycle than wild-type C. jejuni, suggesting that these genes, and the acetate pathway, are important for survival.

Comparative study of the slurry erosion and free-fall particle erosion of aluminum

A study has been performed of the erosion of aluminium by silica sand particles at a velocity of 4.5 m s-1, both air-borne and in the form of a water-borne slurry. Measurements made under similar experimental conditions show that slurry erosion proceeds at a rate several times that of air-borne erosion, the ratio of the two rates depending strongly on the angle of impact. Sand particles become embedded into the metal surface during air-borne particle erosion, forming a composite layer of metal and silica, and provide the major cause of the difference in wear rate. The embedded particles giving rise to surface hardening and a significant reduction in the erosion rate. Embedment of erodent particles was not observed during slurry erosion. Lubrication of the impacting interfaces by water appears to have minimal effect on the wear of aluminium by slurry erosion.

Quantitative RNA-seq analysis of the campylobacter jejuni transcriptome

Campylobacter jejuni is the most common bacterial cause of foodborne disease in the developed world. Its general physiology and biochemistry, as well as the mechanisms enabling it to colonize and cause disease in various hosts, are not well understood, and new approaches are required to understand its basic biology. High-throughput sequencing technologies provide unprecedented opportunities for functional genomic research. Recent studies have shown that direct Illumina sequencing of cDNA (RNA-seq) is a useful technique for the quantitative and qualitative examination of transcriptomes. In this study we report RNA-seq analyses of the transcriptomes of C. jejuni (NCTC11168) and its rpoN mutant. This has allowed the identification of hitherto unknown transcriptional units, and further defines the regulon that is dependent on rpoN for expression. The analysis of the NCTC11168 transcriptome was supplemented by additional proteomic analysis using liquid chromatography-MS. The transcriptomic and proteomic datasets represent an important resource for the Campylobacter research community. © 2011 SGM.

Detached-eddy simulation of transonic flow past a fan-blade section

Detached-eddy simulation of transonic flow past a thin section of a fan blade has been carried out. The inflow Mach number is 1.03, and a bow shock forms upstream of the blade. The shock (corresponding to an adjacent blade) impinges on the suction-side boundary layer which causes separation and rapid transition to turbulence. The boundary layer later re-attaches near the trailing edge. The pressure-side boundary layer transitions near the leading edge and remains attached. Mean surface pressure shows basic agreement with a steady RANS calculation; strong shock motion in the DES is the major cause of discrepancy. Surface pressure spectra are investigated, and low-frequency two-dimensional disturbances associated with the shock motion are dominant. Removing the two-dimensional component from the spectra, the pressure-side three-dimensional spectra reproduce the spectral shape given by a correlation for flat-plate boundary layer wall-pressure spectra developed by Goody. 1 The suction-side disturbances produce similar high- and intermediate-frequency scalings despite substantially different boundary layer development. Near-wake results show that disturbance kinetic energy peaks at the suction-side inflection point of the mean profile, and that the energy is concentrated at low frequencies relative to the near-trailing edge surface pressure. Copyright © 2009 by the authors.

Unsteady ejectors: The effect of driver jet mark-space ratio

mark Unsteady ejectors can be driven by a wide range of driver jets. These vary from pulse detonation engines, which typically have a long gap between each slug of fluid exiting the detonation tube (mark-space ratios in the range 0.1-0.2) to the exit of a pulsejet where the mean mass flow rate leads to a much shorter gap between slugs (mark-space ratios in the range 2-3). The aim of this paper is to investigate the effect of mark-space ratio on the thrust augmentation of an unsteady ejector. Experimental testing was undertaken using a driver jet with a sinusoidal exit velocity profile. The mean value, amplitude and frequency of the velocity profile could be changed allowing the length to diameter ratio of the fluid slugs L/D and the mark-space ratio (the ratio of slug length to the spacing between slugs) L/S to be varied. The setup allowed L/S of the jet to vary from 0.8 to 2.3, while the L/D ratio of the slugs could take any values between 3.5 and 7.5. This paper shows that as the mark-space ratio of the driver jet is increased the thrust augmentation drops. Across the range of mark-space ratios tested, there is shown to be a drop in thrust augmentation of 0.1. The physical cause of this reduction in thrust augmentation is shown to be a decrease in the percentage time over which the ejector entrains ambient fluid. This is the direct result ofthe space between consecutive slugs in the driver jet decreasing. The one dimensional model reported in Heffer et al. [1] is extended to include the effect of varying L/S and is shown to accurately capture the experimentally measured behavior ofthe ejector. Copyright © 2010 by the American Institute of Aeronautics and Astronautics, Inc.

Centrifuge modelling of pile-soil interaction in liquefiable slopes

Piles passing through sloping liquefiable deposits are prone to lateral loading if these deposits liquefy and flow during earthquakes. These lateral loads caused by the relative soil-pile movement will induce bending in the piles and may result in failure of the piles or excessive pile-head displacement. Whilst the weak nature of the flowing liquefied soil would suggest that only small loads would be exerted on the piles, it is known from case histories that piles do fail owing to the influence of laterally spreading soils. It will be shown, based on dynamic centrifuge test data, that dilatant behaviour of soil close to the pile is the major cause of these considerable transient lateral loads which are transferred to the pile. This paper reports the results of geotechnical centrifuge tests in which models of gently sloping liquefiable sand with pile foundations passing through them were subjected to earthquake excitation. The soil close to the pile was instrumented with pore-pressure transducers and contact stress cells in order to monitor the interaction between soil and pile and to track the soil stress state both upslope and downslope of the pile. The presence of instrumentation measuring pore-pressure and lateral stress close to the pile in the research described in this paper gives the opportunity to better study the soil stress state close to the pile and to compare the loads measured as being applied to the piles by the laterally spreading soils with those suggested by the JRA design code. This test data shows that lateral stresses much greater than one might expect from calculations based on the residual strength of liquefied soil may be applied to piles in flowing liquefied slopes owing to the dilative behaviour of the liquefied soil. It is shown at least for the particular geometry studied that the current JRA design code can be un-conservative by a factor of three for these dilation-affected transient lateral loads.

New evidence for the origin and behaviour of deep ocean 'crusts'

In situ tests in deep waterWest African clays show crust-like shear strengths within the top few metres of sediment. Typical strength profiles show su rising from mud-line to 10 kPa to 15 kPa before dropping back to normally consolidated strengths of 3 kPa to 4 kPa by 1.5m to 2m depth. A Cam-shear device is used to better understand the mechanical behaviour of undisturbed crust samples under pipelines. Extremely variable peak and residual shear strengths are observed for a range of pipeline consolidation stresses and test shear rates, with residual strengths approximating zero. ESEM of undisturbed samples and wet-sieved samples from various core depths show the presence of numerous randomly-located groups of invertebrate faecal pellets. It is therefore proposed that the cause of strength variability during shear testing and, indeed, of the crust's origin, is the presence of random groups of faecal pellets within the sediment. © 2011 Taylor & Francis Group, London.

Identification of Cj1051c as a Major determinant for the restriction barrier of Campylobacter jejuni StrainNCTC11168

Campylobacter jejuni is a leading cause of human diarrheal illness in the world, and research on it has benefitted greatly by the completion of several genome sequences and the development of molecular biology tools. However, many hurdles remain for a full understanding of this unique bacterial pathogen. One of the most commonly used strains for genetic work with C. jejuni is NCTC11168. While this strain is readily transformable with DNA for genomic recombination, transformation with plasmids is problematic. In this study, we have identified a determinant of this to be cj1051c, predicted to encode a restriction-modification type IIG enzyme. Knockout mutagenesis of this gene resulted in a strain with a 1,000-fold-enhanced transformation efficiency with a plasmid purified from a C. jejuni host. Additionally, this mutation conferred the ability to be transformed by plasmids isolated from an Escherichia coli host. Sequence analysis suggested a high level of variability of the specificity domain between strains and that this gene may be subject to phase variation. We provide evidence that cj1051c is active in NCTC11168 and behaves as expected for a type IIG enzyme. The identification of this determinant provides a greater understanding of the molecular biology of C. jejuni as well as a tool for plasmid work with strain NCTC11168. © 2012, American Society for Microbiology.

The rise heights of low-and high-Froude-number turbulent axisymmetric fountains

We present the results of an experimental investigation across a broad range of source Froude numbers, 0. 4 ≤ Fr 0 ≤ 45, into the dynamics, morphology and rise heights of Boussinesq turbulent axisymmetric fountains in quiescent uniform environments. Typically, these fountains are thought to rise to an initial height, z i, before settling back and fluctuating about a lesser (quasi-) steady height, z ss. Our measurements show that this is not always the case and the ratio of the fountain's initial rise height to steady rise height, λ = z i/z ss, varies widely, 0. 5 ≈ λ ≈ 2, across the range of Fr 0 investigated. As a result of near-ideal start-up conditions provided by the experimental set-up we were consistently able to form a vortex at the fountain's front. This enabled new insights into two features of the initial rise of turbulent fountains. Firstly, for 1. 0 ≈ Fr 0 ≈ 1. 7 the initial rise height is less than the steady rise height. Secondly, for Fr 0 ≈ 5. 5, the vortex formed at the fountain's front pinches off, separates from the main body and rises high above the fountain; there is thus a third rise height to consider, namely, the maximum vortex rise height, z v. From our observations we propose classifying turbulent axisymmetric fountains into five regimes (as opposed to the current three regimes) and present detailed descriptions of the flow in each. Finally, based on an analysis of the rise height fluctuations and the width of fountains in (quasi-) steady state we provide further insight into the physical cause of height fluctuations. © 2011 Cambridge University Press.

Numerical study of soil heterogeneity effects on contaminant transport in unsaturated soil (model development and validation)

The movement of chemicals through soil to groundwater is a major cause of degradation of water resources. In many cases, serious human and stock health implications are associated with this form of pollution. The study of the effects of different factors involved in transport phenomena can provide valuable information to find the best remediation approaches. Numerical models are increasingly being used for predicting or analyzing solute transport processes in soils and groundwater. This article presents the development of a stochastic finite element model for the simulation of contaminant transport through soils with the main focus being on the incorporation of the effects of soil heterogeneity in the model. The governing equations of contaminant transport are presented. The mathematical framework and the numerical implementation of the model are described. The comparison of the results obtained from the developed stochastic model with those obtained from a deterministic method and some experimental results shows that the stochastic model is capable of predicting the transport of solutes in unsaturated soil with higher accuracy than deterministic one. The importance of the consideration of the effects of soil heterogeneity on contaminant fate is highlighted through a sensitivity analysis regarding the variance of saturated hydraulic conductivity as an index of soil heterogeneity. © 2011 John Wiley & Sons, Ltd.

End-of-range defects in germanium and their role in boron deactivation

We investigated the thermal evolution of end-of-range (EOR) defects in germanium and their impact on junction thermal stability. After solid-phase epitaxial regrowth of a preamorphized germanium layer, EOR defects exhibiting dislocation loop-like contrast behavior are present. These defects disappear during thermal annealing at 400 °C, while boron electrical deactivation occurs. After the whole defect population vanishes, boron reactivation is observed. These results indicate that germanium self-interstitials, released by EOR defects, are the cause of B deactivation. Unlike in Si, the whole deactivation/reactivation cycle in Ge is found to take place while the maximum active B concentration exceeds its solubility limit. © 2010 American Institute of Physics.

Study of thermal effects in bulk RE-BCO superconductors submitted to a variable magnetic field

When bulk RE-BCO superconductors are used as permanent magnets in engineering applications, they are likely to experience transient variations of the applied magnetic field. The resulting vortex motion may cause a significant temperature increase. As a consequence the initial trapped flux is reduced. In the present work, we first focus on the cause of a temperature increase. The temperature distribution within a superconducting finite cylinder subjected to an alternating magnetic field is theoretically predicted. Results are compared to experimental data obtained by two temperature sensors attached to a bulk YBCO pellet. Second, we consider curative methods for reducing the effect of heat flux on the temperature increase. Hall-probe mappings on YBCO samples maintained out of the thermal equilibrium are performed for two different morphologies : a plain single domain and a single domain with a regularly spaced hole array. The drilled single-domain displays a trapped induction which is weakly affected by the local heating while displaying a high trapped field. © 2006 IOP Publishing Ltd.

The Effect of Motivation on Movement: A Study of Bradykinesia in Parkinson's Disease

Background: Bradykinesia is a cardinal feature of Parkinson's disease (PD). Despite its disabling impact, the precise cause of this symptom remains elusive. Recent thinking suggests that bradykinesia may be more than simply a manifestation of motor slowness, and may in part reflect a specific deficit in the operation of motivational vigour in the striatum. In this paper we test the hypothesis that movement time in PD can be modulated by the specific nature of the motivational salience of possible action-outcomes. Methodology/Principal Findings: We developed a novel movement time paradigm involving winnable rewards and avoidable painful electrical stimuli. The faster the subjects performed an action the more likely they were to win money (in appetitive blocks) or to avoid a painful shock (in aversive blocks). We compared PD patients when OFF dopaminergic medication with controls. Our key finding is that PD patients OFF dopaminergic medication move faster to avoid aversive outcomes (painful electric shocks) than to reap rewarding outcomes (winning money) and, unlike controls, do not speed up in the current trial having failed to win money in the previous one. We also demonstrate that sensitivity to distracting stimuli is valence specific. Conclusions/Significance: We suggest this pattern of results can be explained in terms of low dopamine levels in the Parkinsonian state leading to an insensitivity to appetitive outcomes, and thus an inability to modulate movement speed in the face of rewards. By comparison, sensitivity to aversive stimuli is relatively spared. Our findings point to a rarely described property of bradykinesia in PD, namely its selective regulation by everyday outcomes. © 2012 Shiner et al.