The genomic basis of rapid adaptation to antibiotic combination therapy in Pseudomonas aeruginosa

Combination therapy is a common antibiotic treatment strategy that aims at minimizing the risk of resistance evolution in several infectious diseases. Nonetheless, evidence supporting its efficacy against the nosocomial opportunistic pathogen Pseudomonas aeruginosa remains elusive. Identification of the possible evolutionary paths to resistance in multidrug environments can help to explain treatment outcome. For this purpose, we here performed whole-genome sequencing of 127 previously evolved populations of P. aeruginosa adapted to sublethal doses of distinct antibiotic combinations and corresponding single-drug treatments, and experimentally characterized several of the identified variants. We found that alterations in the regulation of efflux pumps are the most favored mechanism of resistance, regardless of the environment. Unexpectedly, we repeatedly identified intergenic variants in the adapted populations, often with no additional mutations and usually associated with genes involved in efflux pump expression, possibly indicating a regulatory function of the intergenic regions. The experimental analysis of these variants demonstrated that the intergenic changes caused similar increases in resistance against single and multidrug treatments as those seen for efflux regulatory gene mutants. Surprisingly, we could find no substantial fitness costs for a majority of these variants, most likely enhancing their competitiveness toward sensitive cells, even in antibiotic-free environments. We conclude that the regulation of efflux is a central target of antibiotic-mediated selection in P. aeruginosa and that, importantly, changes in intergenic regions may represent a usually neglected alternative process underlying bacterial resistance evolution, which clearly deserves further attention in the future

Bottleneck size and selection level reproducibly impact evolution of antibiotic resistance

During antibiotic treatment, the evolution of bacterial pathogens is fundamentally affected by bottlenecks and varying selection levels imposed by the drugs. Bottlenecks—that is, reductions in bacterial population size—lead to an increased influence of random effects (genetic drift) during bacterial evolution, and varying antibiotic concentrations during treatment may favour distinct resistance variants. Both aspects influence the process of bacterial evolution during antibiotic therapy and thereby treatment outcome. Surprisingly, the joint influence of these interconnected factors on the evolution of antibiotic resistance remains largely unexplored. Here we combine evolution experiments with genomic and genetic analyses to demonstrate that bottleneck size and antibiotic-induced selection reproducibly impact the evolutionary path to resistance in pathogenic Pseudomonas aeruginosa, one of the most problematic opportunistic human pathogens. Resistance is favoured—expectedly—under high antibiotic selection and weak bottlenecks, but—unexpectedly—also under low antibiotic selection and severe bottlenecks. The latter is likely to result from a reduced probability of losing favourable variants through drift under weak selection. Moreover, the absence of high resistance under low selection and weak bottlenecks is caused by the spread of low-resistance variants with high competitive fitness under these conditions. We conclude that bottlenecks, in combination with drug-induced selection, are currently neglected key determinants of pathogen evolution and outcome of antibiotic treatment

Dependence of Turbulent and Mesoscale Velocity Variances on Scale and Stability

The scale dependence of velocity variances is studied using data collected from a grassland site, a heather site, and four forested sites. The dependence of velocity variances on averaging time, used to define the fluctuation quantities, is modeled. The crosswind velocity variance is emphasized, because it is more difficult to model than the other two components and is crucial input for applications such as dispersion modeling. The distinction between turbulence and mesoscale variances is examined in detail. Because mesoscale and turbulence motions are governed by different physics, meaningful study of the behavior of velocity variances requires adequate separation of turbulence and mesoscale motions from data. For stable conditions, the horizontal velocity variances near the surface exhibit a spectral gap, here corresponding to a very slow or nonexistent increase of variance with increasing averaging time. This “gap region,” when it occurs, allows separation of mesoscale and turbulence motions; however, the averaging times corresponding to this gap vary substantially with stability. A choice of typical averaging times for defining turbulent perturbations, such as 5 or 10 min, leads to the capture of significant mesoscale motions for very stable conditions and contributes to the disagreement with turbulence similarity theory. For unstable motions, the gap region for the horizontal velocity variances shrinks or becomes poorly defined, because large convective eddies tend to “fill in” the gap between turbulence and mesoscale motions. The formulation developed here allows turbulence and mesoscale motions to overlap into the same intermediate timescales. The mesoscale variances are less predictable, because a wide variety of physical processes contribute to mesoscale motions. Their magnitude and range of timescales vary substantially among sites. The variation of the behavior of turbulence variances among sites is significant but substantially less than that for the mesoscale motions

Исследование датчиков рН и удельной электрической проводимости фирмы WTW в системе автоматизированного контроля качества очистки сточных вод

We demonstrate the suitability of microcavities based on circular grating resonators (CGRs) as fast switches. This type of optical resonator is characterized by a high quality factor and very small mode volume. The waveguide-coupled CGRs are fabricated with silicon-on-insulator technology compatible with standard complementary metal-oxide semiconductor (CMOS) processing. The linear optical properties of the CGRs are investigated by transmission spectroscopy. From 3D finite-difference time-domain simulations of isolated CGRs, we identify the measured resonances. We probe the spatial distribution and the parasitic losses of a resonant optical mode with scanning near-field optical microscopy. We observe fast all-optical switching within a few picoseconds by optically generating free charge carriers within the cavity. (C) 2009 Optical Society of Americ

The variational Bayesian approach to fitting mixture models to circular wave direction data

The emerging variational Bayesian (VB) technique for approximate Bayesian statistical inference is a nonsimulation- based and time-efficient approach. It provides a useful, practical alternative to other Bayesian statistical approaches such as Markov chain Monte Carlo–based techniques, particularly for applications involving large datasets. This article reviews the increasingly popular VB statistical approach and illustrates how it can be used to fit Gaussian mixture models to circular wave direction data. This is done by taking the straightforward approach of padding the data; this method involves adding a repeat of a complete cycle of the data to the existing dataset to obtain a dataset on the real line. The padded dataset can then be analyzed using the standard VB technique. This results in a practical, efficient approach that is also appropriate for modeling other types of circular, or directional, data such as wind direction

Formulation of surface heat flux: application to BOREAS

The aerodynamic temperature is required for prediction of the surface heat flux using Monin-Obukhov similarity. This "fictitious" temperature is not systematically equal to the actual air temperature near the surface and is not directly available from observations or in numerical models. The aerodynamic temperature is normally replaced with either the canopy air temperature or the surface radiation temperature, sometimes accompanied by adjustment of the thermal roughness length or specification of an excess resistance. In this study, the relationship between the aerodynamic temperature and the surface radiation temperature is examined in terms of the surface energy budget and simple representation of canopy structure. Previous inconsistencies are discussed. The observed behavior of the aerodynamic temperature is studied using Canadian Twin Otter aircraft data from BOREAS over nine different forested and nonforested sites. Variation of the behavior of the aerodynamic temperature between different parts of the boreal forest is found to be strongly correlated with the red reflectance

The Critical Richardson Number and Limits of Applicability of Local Similarity Theory in the Stable Boundary Layer

Measurements of atmospheric turbulence made over the Arctic pack ice during the Surface Heat Budget of the Arctic Ocean experiment (SHEBA) are used to determine the limits of applicability of Monin-Obukhov similarity theory (in the local scaling formulation) in the stable atmospheric boundary layer. Based on the spectral analysis of wind velocity and air temperature fluctuations, it is shown that, when both of the gradient Richardson number, Ri, and the flux Richardson number, Rf, exceed a 'critical value' of about 0.20 - 0.25, the inertial subrange associated with the Richardson-Kolmogorov cascade dies out and vertical turbulent fluxes become small. Some small-scale turbulence survives even in this supercritical regime, but this is non-Kolmogorov turbulence, and it decays rapidly with further increasing stability. Similarity theory is based on the turbulent fluxes in the high-frequency part of the spectra that are associated with energy-containing/flux-carrying eddies. Spectral densities in this high-frequency band diminish as the Richardson-Kolmogorov energy cascade weakens; therefore, the applicability of local Monin-Obukhov similarity theory in stable conditions is limited by the inequalities Ri < Ri_cr and Rf < Rf_cr. However, it is found that Rf_cr = 0.20 - 0.25 is a primary threshold for applicability. Applying this prerequisite shows that the data follow classical Monin-Obukhov local z-less predictions after the irrelevant cases (turbulence without the Richardson-Kolmogorov cascade) have been filtered out.Comment: Boundary-Layer Meteorology (Manuscript submitted: 16 February 2012; Accepted: 10 September 2012

Energy- and flux-budget (EFB) turbulence closure model for the stably stratified flows. Part I: Steady-state, homogeneous regimes

We propose a new turbulence closure model based on the budget equations for the key second moments: turbulent kinetic and potential energies: TKE and TPE (comprising the turbulent total energy: TTE = TKE + TPE) and vertical turbulent fluxes of momentum and buoyancy (proportional to potential temperature). Besides the concept of TTE, we take into account the non-gradient correction to the traditional buoyancy flux formulation. The proposed model grants the existence of turbulence at any gradient Richardson number, Ri. Instead of its critical value separating - as usually assumed - the turbulent and the laminar regimes, it reveals a transition interval, 0.1< Ri <1, which separates two regimes of essentially different nature but both turbulent: strong turbulence at Ri<<1; and weak turbulence, capable of transporting momentum but much less efficient in transporting heat, at Ri>1. Predictions from this model are consistent with available data from atmospheric and lab experiments, direct numerical simulation (DNS) and large-eddy simulation (LES).Comment: 40 pages, 6 figures, Boundary-layer Meteorology, resubmitted, revised versio

Formation of Large-Scale Semi-Organized Structures in Turbulent Convection

A new mean-field theory of turbulent convection is developed. This theory predicts the convective wind instability in a shear-free turbulent convection which causes formation of large-scale semi-organized fluid motions in the form of cells or rolls. Spatial characteristics of these motions, such as the minimum size of the growing perturbations and the size of perturbations with the maximum growth rate, are determined. This study predicts also the existence of the convective shear instability in a sheared turbulent convection which results in generation of convective shear waves with a nonzero hydrodynamic helicity. Increase of shear promotes excitation of the convective shear instability. Applications of the obtained results to the atmospheric turbulent convection and the laboratory experiments on turbulent convection are discussed. This theory can be applied also for the describing a mesogranular turbulent convection in astrophysics.Comment: 16 pages, 10 figures, REVTEX4, PHYSICAL REVIEW E, v. 67, in press (2003