Non-random distribution of azole resistance across the global population of Aspergillus fumigatus

The emergence of azole resistance in the pathogenic fungus Aspergillus fumigatus has continued to increase, with the dominant resistance mechanisms, consisting of a 34-nucleotide tandem repeat (TR34)/L98H and TR46/Y121F/T289A, now showing a structured global distribution. Using hierarchical clustering and multivariate analysis of 4,049 A. fumigatus isolates collected worldwide and genotyped at nine microsatellite loci using analysis of short tandem repeats of A. fumigatus (STRAf), we show that A. fumigatus can be subdivided into two broad clades and that cyp51A alleles TR34/L98H and TR46/Y121F/T289A are unevenly distributed across these two populations. Diversity indices show that azole-resistant isolates are genetically depauperate compared to their wild-type counterparts, compatible with selective sweeps accompanying the selection of beneficial mutations. Strikingly, we found that azole-resistant clones with identical microsatellite profiles were globally distributed and sourced from both clinical and environmental locations, confirming that azole resistance is an international public health concern. Our work provides a framework for the analysis of A. fumigatus isolates based on their microsatellite profile, which we have incorporated into a freely available, user-friendly R Shiny application (AfumID) that provides clinicians and researchers with a method for the fast, automated characterization of A. fumigatus genetic relatedness. Our study highlights the effect that azole drug resistance is having on the genetic diversity of A. fumigatus and emphasizes its global importance upon this medically important pathogenic fungus. IMPORTANCE Azole drug resistance in the human-pathogenic fungus Aspergillus fumigatus continues to emerge, potentially leading to untreatable aspergillosis in immunosuppressed hosts. Two dominant, environmentally associated resistance mechanisms, which are thought to have evolved through selection by the agricultural application of azole fungicides, are now distributed globally. Understanding the effect that azole resistance is having on the genetic diversity and global population of A. fumigatus will help mitigate drug-resistant aspergillosis and maintain the azole class of fungicides for future use in both medicine and crop protection

A Comment on the Geometric Entropy and Conical Space

It has been recently pointed out that a definition of the geometric entropy using the partition function in a conical space does not in general lead to a positive definite quantity. For a scalar field model with a non-minimal coupling we clarify the origin of the anomalous behavior from the viewpoint of the canonical formulation.Comment: No Figures. To appear in Classical and Quantum Gravit

On partial order semantics for SAT/SMT-based symbolic encodings of weak memory concurrency

Concurrent systems are notoriously difficult to analyze, and technological advances such as weak memory architectures greatly compound this problem. This has renewed interest in partial order semantics as a theoretical foundation for formal verification techniques. Among these, symbolic techniques have been shown to be particularly effective at finding concurrency-related bugs because they can leverage highly optimized decision procedures such as SAT/SMT solvers. This paper gives new fundamental results on partial order semantics for SAT/SMT-based symbolic encodings of weak memory concurrency. In particular, we give the theoretical basis for a decision procedure that can handle a fragment of concurrent programs endowed with least fixed point operators. In addition, we show that a certain partial order semantics of relaxed sequential consistency is equivalent to the conjunction of three extensively studied weak memory axioms by Alglave et al. An important consequence of this equivalence is an asymptotically smaller symbolic encoding for bounded model checking which has only a quadratic number of partial order constraints compared to the state-of-the-art cubic-size encoding.Comment: 15 pages, 3 figure

Crystallization of recombinant Bacteroides fragilis glutamine synthetase (GlnN) isolated using a novel and rapid purification protocol

Glutamine synthetase enzymes (GSs) are large oligomeric enzymes that play a critical role in nitrogen metabolism in all forms of life. To date, no crystal structures exist for the family of large (1 MDa) type III GS enzymes, which only share 9% sequence identity with the well characterized GSI and GSII enzymes. Here we present a novel protocol for the isolation of untagged Bacteroides fragilis GlnN expressed in an auxotrophic Escherichia coli strain. The rapid and scalable two-step protocol utilized differential precipitation by divalent cations followed by affinity chromatography to produce suitable quantities of homogenous material for structural characterization. Subsequent optimizations to the sample stability and solubility led to the discovery of conditions for the production of the first diffraction quality crystals of a type III GS enzyme

Off-Diagonal Long-Range Order in Bose Liquids: Irrotational Flow and Quantization of Circulation

On the basis of gauge invariance, it is proven in an elementary and straightforward manner, but without invoking any {\it ad hoc} assumption, that the existence of off-diagonal long-range order in one-particle reduced density matrix in Bose liquids implies both the irrotational flow in a simply connected region and the quantization of circulation in a multiply connected region, the two fundamental properties of a Bose superfluid. The origin for both is the phase coherence of condensate wave-functions. Some relevant issues are also addressed.Comment: Revtex, 4 pages, no figure

An evaluation of a nurse led unit: an action research study

This study is an exemplar of working in a participatory way with members of the public and health and social care practitioners as co-researchers. A Nurse Consultant Older People working in a nurse-led bed, intermediate care facility in a community hospital acted as joint project lead with an academic researcher. From the outset, members of the public were part of a team of 16 individuals who agreed an evaluation focus and were involved in all stages of the research process from design through to dissemination. An extensive evaluation reflecting all these stakeholders’ preferences was undertaken. Methods included research and audit including: patient and carer satisfaction questionnaire surveys, individual interviews with patients, carers and staff, staff surveys, graffiti board, suggestion box, first impressions questionnaire, patient tracking and a bed census. A key aim of the study has been capacity building of the research team members which has also been evaluated. In terms of impact, the co-researchers have developed research skills and knowledge, grown in confidence, developed in ways that have impacted elsewhere in their lives, developed posters, presented at conferences and gained a better understanding of the NHS. The evaluation itself has provided useful information on the processes and outcomes of intermediate care on the ward which was used to further improve the service

Growth, processing, and optical properties of epitaxial Er_2O_3 on silicon

Erbium-doped materials have been investigated for generating and amplifying light in low-power chip-scale optical networks on silicon, but several effects limit their performance in dense microphotonic applications. Stoichiometric ionic crystals are a potential alternative that achieve an Er^(3+) density 100× greater. We report the growth, processing, material characterization, and optical properties of single-crystal Er_2O_3 epitaxially grown on silicon. A peak Er^(3+) resonant absorption of 364 dB/cm at 1535nm with minimal background loss places a high limit on potential gain. Using high-quality microdisk resonators, we conduct thorough C/L-band radiative efficiency and lifetime measurements and observe strong upconverted luminescence near 550 and 670 nm

MARDy: Mycology Antifungal Resistance Database

This is the final version. Available from the publisher via the DOI in this record.Summary: The increase of antifungal drug resistance is a major global human health concern and threatens agriculture and food security; in order to tackle these concerns, it is important to understand the mechanisms that cause antifungal resistance. The curated Mycology Antifungal Resistance Database (MARDy) is a web-service of antifungal drug resistance mechanisms, including amino acid substitutions, tandem repeat sequences and genome ploidy. MARDy is implemented on a Linux, Apache, MySQL and PHP web development platform and includes a local installation of BLASTn of the database of curated genes.Antimicrobial Research Collaborative (ARC)Natural Environment Research Council (NERC

Conformational flexibility of the oncogenic protein LMO2 primes the formation of the multi-protein transcription complex

LMO2 was discovered via chromosomal translocations in T-cell leukaemia and shown normally to be essential for haematopoiesis. LMO2 is made up of two LIM only domains (thus it is a LIM-only protein) and forms a bridge in a multi-protein complex. We have studied the mechanism of formation of this complex using a single domain antibody fragment that inhibits LMO2 by sequestering it in a non-functional form. The crystal structure of LMO2 with this antibody fragment has been solved revealing a conformational difference in the positioning and angle between the two LIM domains compared with its normal binding. This contortion occurs by bending at a central helical region of LMO2. This is a unique mechanism for inhibiting an intracellular protein function and the structural contusion implies a model in which newly synthesized, intrinsically disordered LMO2 binds to a partner protein nucleating further interactions and suggests approaches for therapeutic targeting of LMO2

Correlated Wave-Functions and the Absence of Long Range Order in Numerical Studies of the Hubbard Model

We present a formulation of the Constrained Path Monte Carlo (CPMC) method for fermions that uses trial wave-functions that include many-body effects. This new formulation allows us to implement a whole family of generalized mean-field states as constraints. As an example, we calculated superconducting pairing correlation functions for the two-dimensional repulsive Hubbard model using a BCS trial state as the constraint. We compared the results with the case where a free-electron trial wave-function is used. We found that the correlation functions are independent of which state is used as the constraint, which reaffirms the results previously found by Zhang et. al regarding the suppression of long range pairing correlations as the system size increases.Comment: 15 pages, 3 figures, submitted to Phys. Rev.