Fungal speciation using quantitative polymerase chain reaction (QPCR) in patients with and without chronic rhinosinusitis.

Objectives/hypothesisThe objectives of this study were to determine the mycology of the middle meatus using an endoscopically guided brush sampling technique and polymerase chain reaction laboratory processing of nasal mucous; to compare the mycology of the middle meatus in patients with sinus disease with subjects without sinus disease; to compare the responses on two standardized quality-of-life survey forms between patients with and without sinusitis; and to determine whether the presence of fungi in the middle meatus correlates with responses on these data sets.Study designThe authors conducted a single-blind, prospective, cross-sectional study.MethodsPatients with sinus disease and a control group without sinus disease were enrolled in the study. A disease-specific, validated Sinonasal Outcomes Test survey (SNOT-20) was completed by the subjects and a generalized validated Medical Outcomes Short Form 36 Survey (SF-36) was also completed. An endoscopically guided brush sampling of nasal mucous was obtained from the middle meatus. Fungal specific quantitative polymerase chain reaction (QPCR) was performed on the obtained sample to identify one of 82 different species of fungus in the laboratory. Statistical analysis was used to categorize the recovered fungal DNA and to crossreference this information with the outcomes surveys.ResultsThe fungal recovery rate in the study was 45.9% in patients with sinus disease and 45.9% in control subjects. Patients with chronic rhinosinusitis had a mean SNOT-20 score of 1.80 versus the control group mean score of 0.77 (P < .0001). SF-36 data similarly showed a statistically significant difference between diseased and control populations with controls scoring a mean of 80.37 and patients with chronic rhinosinusitis scoring a mean of 69.35 for a P value of .02. However, no statistical significance could be ascribed to the presence or absence of fungi recovered, the type of fungi recovered, or the possible impact of fungi on the quality-of-life survey results.ConclusionThe recovery rate of fungi from the middle meatus of patients with chronic rhinosinusitis and a control population without chronic rhinosinusitis is 45.9% using QPCR techniques. No direct causation with regard to fungal species or presence was proven; however, a species grouping for future studies is proposed based on trends in this data and other reports. Disease-specific outcomes surveys revealed a statistically significant difference between the two groups

Conceptual Approaches to Alternate Methods in Toxicological Testing

Due to public pressure, in vivo methods of toxicity testing is being attempted to be replaced by in vitro methods, such as cell and organ culture, computer modelling and modified LD50 tests using lesser number of animals. Specifically in the case of Draize eye irritancy test using rabbits, a number of refinements have been incorporated by different workers, mainly use of a local anaesthetic which will reduce animal distress without vitiating the test results. The author recommends exploration of new avenues for testing based on the advances in cell biology

The First Forty Years of the Alternatives Approach: Refining, Reducing, and Replacing the Use of Laboratory Animals

The concept of the Three Rs— reduction, refinement, and replacement of animal use in biomedical experimentation—stems from a project launched in 1954 by a British organization, the Universities Federation for Animal Welfare (UFAW). UFAW commissioned William Russell and Rex Burch to analyze the status of humane experimental techniques involving animals. In 1959 these scientists published a book that set out the principles of the Three Rs, which came to be known as alternative methods. Initially, Russell and Burch’s book was largely ignored, but their ideas were gradually picked up by the animal protection community in the 1960s and early ’70s. In the ’80s, spurred by public pressure, the alternatives approach was incorporated into national legislation throughout the developed countries and embraced by industry in Europe and America. Government centers devoted to the validation and regulatory acceptance of alternative methods were established during the ’90s. By 2000 the use of animals in research had fallen by up to fifty percent from its high in the 1970s

Increased risk of HIV and other drug-related harms associated with injecting in public places: national bio-behavioural survey of people who inject drugs

Background: Whilst injecting drugs in public places is considered a proxy for high risk behaviour among people who inject drugs (PWID), studies quantifying its relationship with multiple drug-related harms are lacking and none have examined this in the context of an ongoing HIV outbreak (located in Glasgow, Scotland). We aimed to: 1) estimate the prevalence of public injecting in Scotland and associated risk factors; and 2) estimate the association between public injecting and HIV, current HCV, overdose, and skin and soft tissue infections (SSTI). Methods: Cross-sectional, bio-behavioural survey (including dried blood spot testing to determine HIV and HCV infection) of 1469 current PWID (injected in last 6 months) recruited by independent interviewers from 139 harm reduction services across Scotland during 2017–18. Primary outcomes were: injecting in a public place (yes/no); HIV infection; current HCV infection; self-reported overdose in the last year (yes/no) and SSTI the last year (yes/no). Multi-variable logistic regression was used to determine factors associated with public injecting and to estimate the association between public injecting and drug-related harms (HIV, current HCV, overdose and SSTI). Results: Prevalence of public injecting was 16% overall in Scotland and 47% in Glasgow city centre. Factors associated with increased odds of public injecting were: recruitment in Glasgow city centre (aOR=5.45, 95% CI 3.48–8.54, p<0.001), homelessness (aOR=3.68, 95% CI 2.61–5.19, p<0.001), high alcohol consumption (aOR=2.42, 95% CI 1.69–3.44, p<0.001), high injection frequency (≥4 per day) (aOR=3.16, 95% CI 1.93–5.18, p<0.001) and cocaine injecting (aOR=1.46, 95% CI 1.00 to 2.13, p = 0.046). Odds were lower for those receiving opiate substitution therapy (OST) (aOR=0.37, 95% CI 0.24 to 0.56, p<0.001) and older age (per year increase) (aOR=0.97, 95% CI 0.95 to 0.99, p = 0.013). Public injecting was associated with an increased risk of HIV infection (aOR=2.11, 95% CI 1.13–3.92, p = 0.019), current HCV infection (aOR=1.49, 95% CI 1.01–2.19, p = 0.043), overdose (aOR=1.59, 95% CI 1.27–2.01, p<0.001) and SSTI (aOR=1.42, 95% CI 1.17–1.73, p<0.001). Conclusions: These findings highlight the need to address the additional harms observed among people who inject in public places and provide evidence to inform proposals in the UK and elsewhere to introduce facilities that offer safer drug consumption environments

Unbalanced Charge Distribution as a Determinant for Dependence of a Subset of Escherichia coli Membrane Proteins on the Membrane Insertase YidC

Membrane proteins are involved in numerous essential cell processes, including transport, gene regulation, motility, and metabolism. To function properly, they must be inserted into the membrane and folded correctly. YidC, an essential protein in Escherichia coli with homologues in other bacteria, Archaea, mitochondria, and chloroplasts, functions by incompletely understood mechanisms in the insertion and folding of certain membrane proteins. Using a genome-scale approach, we identified 69 E. coli membrane proteins that, in the absence of YidC, exhibited aberrant localization by microscopy. Further examination of a subset revealed biochemical defects in membrane insertion in the absence of YidC, indicating their dependence on YidC for proper membrane insertion or folding. Membrane proteins possessing an unfavorable distribution of positively charged residues were significantly more likely to depend on YidC for membrane insertion. Correcting the charge distribution of a charge-unbalanced YidC-dependent membrane protein abrogated its requirement for YidC, while perturbing the charge distribution of a charge-balanced YidC-independent membrane protein rendered it YidC dependent, demonstrating that charge distribution can be a necessary and sufficient determinant of YidC dependence. These findings provide insights into a mechanism by which YidC promotes proper membrane protein biogenesis and suggest a critical function of YidC in all organisms and organelles that express it

Predictions for the Cosmogenic Neutrino Flux in Light of New Data from the Pierre Auger Observatory

The Pierre Auger Observatory (PAO) has measured the spectrum and composition of the ultrahigh energy cosmic rays with unprecedented precision. We use these measurements to constrain their spectrum and composition as injected from their sources and, in turn, use these results to estimate the spectrum of cosmogenic neutrinos generated in their propagation through intergalactic space. We find that the PAO measurements can be well fit if the injected cosmic rays consist entirely of nuclei with masses in the intermediate (C, N, O) to heavy (Fe, Si) range. A mixture of protons and heavier species is also acceptable but (on the basis of existing hadronic interaction models) injection of pure light nuclei (p, He) results in unacceptable fits to the new elongation rate data. The expected spectrum of cosmogenic neutrinos can vary considerably, depending on the precise spectrum and chemical composition injected from the cosmic ray sources. In the models where heavy nuclei dominate the cosmic ray spectrum and few dissociated protons exceed GZK energies, the cosmogenic neutrino flux can be suppressed by up to two orders of magnitude relative to the all-proton prediction, making its detection beyond the reach of current and planned neutrino telescopes. Other models consistent with the data, however, are proton-dominated with only a small (1-10%) admixture of heavy nuclei and predict an associated cosmogenic flux within the reach of upcoming experiments. Thus a detection or non-detection of cosmogenic neutrinos can assist in discriminating between these possibilities.Comment: 10 pages, 7 figure

Late Ediacaran Redox Stability and Metazoan Evolution

The Neoproterozoic arrival of animals fundamentally changed Earth's biological and geochemical trajectory. Since the early description of Ediacaran and Cambrian animal fossils, a vigorous debate has emerged about the drivers underpinning their seemingly rapid radiation. Some argue for predation and ecology as central to diversification, whereas others point to a changing chemical environment as the trigger. In both cases, questions of timing and feedbacks remain unresolved. Through these debates, the last fifty years of work has largely converged on the concept that a change in atmospheric oxygen levels, perhaps manifested indirectly as an oxygenation of the deep ocean, was causally linked to the initial diversification of large animals. What has largely been absent, but is provided in this study, is a multi-proxy stratigraphic test of this hypothesis. Here, we describe a coupled geochemical and paleontological investigation of Neoproterozoic sedimentary rocks from northern Russia. In detail, we provide iron speciation data, carbon and sulfur isotope compositions, and major element abundances from a predominantly siliciclastic succession (spanning>1000 m) sampled by the Kel'tminskaya-1 drillcore. Our interpretation of these data is consistent with the hypothesis that the $pO_2$ threshold required for diversification of animals with high metabolic oxygen demands was crossed prior to or during the Ediacaran Period. Redox stabilization of shallow marine environments was, however, also critical and only occurred about 560 million years ago (Ma), when large motile bilaterians first enter the regional stratigraphic record. In contrast, neither fossils nor geochemistry lend support to the hypothesis that ecological interactions altered the course of evolution in the absence of environmental change. Together, the geochemical and paleontological records suggest a coordinated transition from low oxygen oceans sometime before the Marinoan (~635 Ma) ice age, through better oxygenated but still redox-unstable shelves of the early Ediacaran Period, to the fully and persistently oxygenated marine environments characteristic of later Ediacaran successions that preserve the first bilaterian macrofossils and trace fossils.Earth and Planetary SciencesOrganismic and Evolutionary Biolog

Degenerate weakly nonlinear elastic plane waves

Weakly nonlinear plane waves are considered in hyperelastic crystals. Evolution equations are derived at a quadratically nonlinear level for the amplitudes of quasi-longitudinal and quasi-transverse waves propagating in arbitrary anisotropic media. The form of the equations obtained depends upon the direction of propagation relative to the crystal axes. A single equation is found for all propagation directions for quasi-longitudinal waves, but a pair of coupled equations occurs for quasi-transverse waves propagating along directions of degeneracy, or acoustic axes. The coupled equations involve four material parameters but they simplify if the wave propagates along an axis of material symmetry. Thus, only two parameters arise for propagation along an axis of two-fold symmetry, and one for a three-fold axis. The transverse wave equations decouple if the axis is four-fold or higher. In the absence of a symmetry axis it is possible that the evolution equations of the quasi-transverse waves decouple if the third order elastic moduli satisfy a certain identity. The theoretical results are illustrated with explicit examples.Comment: 18 pages, no figure

Genetic Reporter System for Positioning of Proteins at the Bacterial Pole

Spatial organization within bacteria is fundamental to many cellular processes, although the basic mechanisms underlying localization of proteins to specific sites within bacteria are poorly understood. The study of protein positioning has been limited by a paucity of methods that allow rapid large-scale screening for mutants in which protein positioning is altered. We developed a genetic reporter system for protein localization to the pole within the bacterial cytoplasm that allows saturation screening for mutants in Escherichia coli in which protein localization is altered. Utilizing this system, we identify proteins required for proper positioning of the Shigella autotransporter IcsA. Autotransporters, widely distributed bacterial virulence proteins, are secreted at the bacterial pole. We show that the conserved cell division protein FtsQ is required for localization of IcsA and other autotransporters to the pole. We demonstrate further that this system can be applied to the study of proteins other than autotransporters that display polar positioning within bacterial cells.Molecular and Cellular Biolog

Doppler-free ion imaging of hydrogen molecules produced in bimolecular reactions

Abstract We report on the use of two-color Doppler-free [(1 + 1 0 ) + 1/1 0 ] resonance enhanced multiphoton ionization (REMPI) for threedimensional imaging of state-selected product molecules from bimolecular reactions. We demonstrate the viability of this method by measuring differential cross sections for the reaction H + D 2 ! D + HD(v 0 = 1,j 0 = 1,5,8) at 1.7 eV collision energy. We achieve higher resolution allowing us to observe oscillations that were not resolved by previous experiments; these oscillations agree closely with quantum mechanical calculations