On the Evolvability of OXA-48. A comprehensive study of new functions within the β-lactamase OXA-48

Our understanding of how antimicrobial resistance enzymes evolve to expand their substrate spectrum is limited. OXA-48, an enzyme able to catalyse the hydrolysis of β-lactam drugs, has become one of the most successfully disseminating β-lactamases. Although OXA-48 hydrolyses penicillins with high efficiency, its activity towards oxyimino cephalosporins, such as ceftazidime, is limited. Thus, ceftazidime and the combination of ceftazidime and the β-lactamase inhibitor avibactam, which inhibits OXA-48, are possible treatment options for infections caused by OXA-48 producing pathogens. Here, different evolutionary protocols were employed to elucidate the role of both ceftazidime and ceftazidime-avibactam as drivers in the evolution of OXA-48. Laboratory evolution towards increasing drug concentrations and long-term experimental evolution under low drug concentrations demonstrated that OXA-48 can acquire mutations that increase resistance to both ceftazidime and ceftazidime-avibactam. Independent replicates of directed evolution further showed that OXA-48 mediated ceftazidime resistance can be improved by the acquisition of only a few mutations, resulting in distinct mutational trajectories. Crystallographic structures demonstrated that increased resistance was likely achieved by optimising substrate positioning and the pre-organisation of active site residues. In addition, molecular dynamics simulations exposed elevated flexibility of active site loops, which likely aided the accommodation of ceftazidime. Studying epistatic and pleiotropic effects during the adaptational process uncovered that mutations, initially conferring increased ceftazidime resistance, tended to exhibit strong trade-offs concerning functionality and thermostability. However, the functional trade-off towards other β-lactams, such penicillins and carbapenems, was strong but limited due to positive epistasis among mutational combinations. Taken together, OXA-48-mediated ceftazidime and ceftazidime-avibactam resistance can evolve through point mutations and distinct mutational pathways. The diversity of these pathways in combination with epistasis has implications for the genotypic and phenotypic predictability of resistance development, as many mutational highly epistatic solutions may exist within an enzyme

Double-averaged kinetic energy budgets in flows over mobile granular beds : insights from DNS data analysis

Acknowledgments The authors gratefully acknowledge the Centre for Information Services and High Performance Computing (ZIH), Dresden, the Jülich Supercomputing Centre (JSC) and the High Performance Computing Service (Maxwell) of the University of Aberdeen for providing computing time. The authors would like to thank Professor Francesco Ballio and two anonymous reviewers for their helpful comments that contributed to improving the final version of this manuscript. Funding This study was part of the research project “Hydrodynamic Transport in Ecologically Critical Heterogeneous interfaces” (HYTECH), the support of which, under the European Union's Seventh Framework Programme (Marie Curie PFP7-PEOPLE-2012-ITN, European Commission [grant agreement number 316546]), is gratefully acknowledged. Financial support was also provided by the grantsp3 10.13039/501100000266 Engineering and Physical Sciences Research Council (EPSRC), UK, [grant EP/K041088/1] and the German Research Foundation (DFG), [project FR 1593/5-2]. B. Vowinckel and R. Jain gratefully acknowledge the scholarships respectfully provided by the Alexander von Humboldt Foundation and Saxon Scholarship Program, Germany.Peer reviewedPublisher PD

Spinning Braid Group Representation and the Fractional Quantum Hall Effect

The path integral approach to representing braid group is generalized for particles with spin. Introducing the notion of {\em charged} winding number in the super-plane, we represent the braid group generators as homotopically constrained Feynman kernels. In this framework, super Knizhnik-Zamolodchikov operators appear naturally in the Hamiltonian, suggesting the possibility of {\em spinning nonabelian} anyons. We then apply our formulation to the study of fractional quantum Hall effect (FQHE). A systematic discussion of the ground states and their quasi-hole excitations is given. We obtain Laughlin, Halperin and Moore-Read states as {\em exact} ground state solutions to the respective Hamiltonians associated to the braid group representations. The energy gap of the quasi-excitation is also obtainable from this approach.Comment: (36 pages) e-mail [email protected]

Water uptake of subpollen aerosol particles: Hygroscopic growth, cloud condensation nuclei activation, and liquid-liquid phase separation

Pollen grains emitted from vegetation can release subpollen particles (SPPs) that contribute to the fine fraction of atmospheric aerosols and may act as cloud condensation nuclei (CCN), ice nuclei (IN), or aeroallergens. Here, we investigate and characterize the hygroscopic growth and CCN activation of birch, pine, and rapeseed SPPs. A high-humidity tandem differential mobility analyzer (HHTDMA) was used to measure particle restructuring and water uptake over a wide range of relative humidity (RH) from 2 % to 99.5 %, and a continuous flow CCN counter was used for size-resolved measurements of CCN activation at supersaturations (S) in the range of 0.2 % to 1.2 %. For both subsaturated and supersaturated conditions, effective hygroscopicity parameters, κ, were obtained by Köhler model calculations. Gravimetric and chemical analyses, electron microscopy, and dynamic light scattering measurements were performed to characterize further properties of SPPs from aqueous pollen extracts such as chemical composition (starch, proteins, DNA, and inorganic ions) and the hydrodynamic size distribution of water-insoluble material. All investigated SPP samples exhibited a sharp increase of water uptake and κ above ∼95 % RH, suggesting a liquid–liquid phase separation (LLPS). The HHTDMA measurements at RH >95 % enable closure between the CCN activation at water vapor supersaturation and hygroscopic growth at subsaturated conditions, which is often not achieved when hygroscopicity tandem differential mobility analyzer (HTDMA) measurements are performed at lower RH where the water uptake and effective hygroscopicity may be limited by the effects of LLPS. Such effects may be important not only for closure between hygroscopic growth and CCN activation but also for the chemical reactivity, allergenic potential, and related health effects of SPPs

Relaxation time for a dimer covering with height representation

This paper considers the Monte Carlo dynamics of random dimer coverings of the square lattice, which can be mapped to a rough interface model. Two kinds of slow modes are identified, associated respectively with long-wavelength fluctuations of the interface height, and with slow drift (in time) of the system-wide mean height. Within a continuum theory, the longest relaxation time for either kind of mode scales as the system size N. For the real, discrete model, an exact lower bound of O(N) is placed on the relaxation time, using variational eigenfunctions corresponding to the two kinds of continuum modes.Comment: 12 pages, LaTeX; 1 figure in PostScript file; to appear, J. Stat. Phys. Sections and subsections were reshuffled to improve presentation, some text added on quantum-dimer model, fully-frustrated Ising model, and application to general class of "height" model

Eisosome proteins assemble into a membrane scaffold

Membrane organization by eisosomes is mediated by self-assembly of its main components into a membrane-bound protein scaffold with lipid-binding specificity

Racial differences in systemic sclerosis disease presentation: a European Scleroderma Trials and Research group study

Objectives. Racial factors play a significant role in SSc. We evaluated differences in SSc presentations between white patients (WP), Asian patients (AP) and black patients (BP) and analysed the effects of geographical locations.Methods. SSc characteristics of patients from the EUSTAR cohort were cross-sectionally compared across racial groups using survival and multiple logistic regression analyses.Results. The study included 9162 WP, 341 AP and 181 BP. AP developed the first non-RP feature faster than WP but slower than BP. AP were less frequently anti-centromere (ACA; odds ratio (OR) = 0.4, P < 0.001) and more frequently anti-topoisomerase-I autoantibodies (ATA) positive (OR = 1.2, P = 0.068), while BP were less likely to be ACA and ATA positive than were WP [OR(ACA) = 0.3, P < 0.001; OR(ATA) = 0.5, P = 0.020]. AP had less often (OR = 0.7, P = 0.06) and BP more often (OR = 2.7, P < 0.001) diffuse skin involvement than had WP.AP and BP were more likely to have pulmonary hypertension [OR(AP) = 2.6, P < 0.001; OR(BP) = 2.7, P = 0.03 vs WP] and a reduced forced vital capacity [OR(AP) = 2.5, P < 0.001; OR(BP) = 2.4, P < 0.004] than were WP. AP more often had an impaired diffusing capacity of the lung than had BP and WP [OR(AP vs BP) = 1.9, P = 0.038; OR(AP vs WP) = 2.4, P < 0.001]. After RP onset, AP and BP had a higher hazard to die than had WP [hazard ratio (HR) (AP) = 1.6, P = 0.011; HR(BP) = 2.1, P < 0.001].Conclusion. Compared with WP, and mostly independent of geographical location, AP have a faster and earlier disease onset with high prevalences of ATA, pulmonary hypertension and forced vital capacity impairment and higher mortality. BP had the fastest disease onset, a high prevalence of diffuse skin involvement and nominally the highest mortality

Measurement of the top quark forward-backward production asymmetry and the anomalous chromoelectric and chromomagnetic moments in pp collisions at √s = 13 TeV

Abstract The parton-level top quark (t) forward-backward asymmetry and the anomalous chromoelectric (d̂ t) and chromomagnetic (μ̂ t) moments have been measured using LHC pp collisions at a center-of-mass energy of 13 TeV, collected in the CMS detector in a data sample corresponding to an integrated luminosity of 35.9 fb−1. The linearized variable AFB(1) is used to approximate the asymmetry. Candidate t t ¯ events decaying to a muon or electron and jets in final states with low and high Lorentz boosts are selected and reconstructed using a fit of the kinematic distributions of the decay products to those expected for t t ¯ final states. The values found for the parameters are AFB(1)=0.048−0.087+0.095(stat)−0.029+0.020(syst),μ̂t=−0.024−0.009+0.013(stat)−0.011+0.016(syst), and a limit is placed on the magnitude of | d̂ t| < 0.03 at 95% confidence level. [Figure not available: see fulltext.

MUSiC : a model-unspecific search for new physics in proton-proton collisions at root s=13TeV

Results of the Model Unspecific Search in CMS (MUSiC), using proton-proton collision data recorded at the LHC at a centre-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 35.9 fb(-1), are presented. The MUSiC analysis searches for anomalies that could be signatures of physics beyond the standard model. The analysis is based on the comparison of observed data with the standard model prediction, as determined from simulation, in several hundred final states and multiple kinematic distributions. Events containing at least one electron or muon are classified based on their final state topology, and an automated search algorithm surveys the observed data for deviations from the prediction. The sensitivity of the search is validated using multiple methods. No significant deviations from the predictions have been observed. For a wide range of final state topologies, agreement is found between the data and the standard model simulation. This analysis complements dedicated search analyses by significantly expanding the range of final states covered using a model independent approach with the largest data set to date to probe phase space regions beyond the reach of previous general searches.Peer reviewe