Semi-quantitative, duplexed qPCR assay for the detection of leishmania spp. using bisulphite conversion technology

© 2019 by the authors. Leishmaniasis is caused by the flagellated protozoan Leishmania, and is a neglected tropical disease (NTD), as defined by theWorld Health Organisation (WHO). Bisulphite conversion technology converts all genomic material to a simplified form during the lysis step of the nucleic acid extraction process, and increases the efficiency of multiplex quantitative polymerase chain reaction (qPCR) reactions. Through utilization of qPCR real-time probes, in conjunction with bisulphite conversion, a new duplex assay targeting the 18S rDNA gene region was designed to detect all Leishmania species. The assay was validated against previously extracted DNA, from seven quantitated DNA and cell standards for pan-Leishmania analytical sensitivity data, and 67 cutaneous clinical samples for cutaneous clinical sensitivity data. Specificity was evaluated by testing 76 negative clinical samples and 43 bacterial, viral, protozoan and fungal species. The assay was also trialed in a side-by-side experiment against a conventional PCR (cPCR), based on the Internal transcribed spacer region 1 (ITS1 region). Ninety-seven percent of specimens from patients that previously tested positive for Leishmania were positive for Leishmania spp. with the bisulphite conversion assay, and a limit of detection (LOD) of 10 copies per PCR was achieved, while the LOD of the ITS1 methodology was 10 cells/1000 genomic copies per PCR. This method of rapid, accurate and simple detection of Leishmania can lead to improved diagnosis, treatment and public health outcomes

A model of hyphal tip growth involving microtubule-based transport

We propose a simple model for mass transport within a fungal hypha and its subsequent growth. Inspired by the role of microtubule-transported vesicles, we embody the internal dynamics of mass inside a hypha with mutually excluding particles progressing stochastically along a growing one-dimensional lattice. The connection between long range transport of materials for growth, and the resulting extension of the hyphal tip has not previously been addressed in the modelling literature. We derive and analyse mean-field equations for the model and present a phase diagram of its steady state behaviour, which we compare to simulations. We discuss our results in the context of the filamentous fungus, Neurospora crassa.Comment: 5 pages, 5 figure

Candida albicans colonization and dissemination from the murine gastrointestinal tract : the influence of morphology and Th17 immunity

This article is protected by copyright. All rights reserved. This work was supported by the Wellcome Trust (086558, 080088, 102705), a Wellcome Trust Strategic Award (097377) and a studentship from the University of Aberdeen. D.K. was supported by grant 5R01AI083344 from the National Institute of Allergy and Infectious Diseases and by a Voelcker Young Investigator Award from the Max and Minnie Tomerlin Voelcker Fund.Peer reviewedPublisher PD

Hormonal regulation of alveolarization: structure-function correlation

BACKGROUND: Dexamethasone (Dex) limits and all-trans-retinoic acid (RA) promotes alveolarization. While structural changes resulting from such hormonal exposures are known, their functional consequences are unclear. METHODS: Neonatal rats were treated with Dex and/or RA during the first two weeks of life or were given RA after previous exposure to Dex. Morphology was assessed by light microscopy and radial alveolar counts. Function was evaluated by plethysmography at d13, pressure volume curves at d30, and exercise swim testing and arterial blood gases at both d15 and d30. RESULTS: Dex-treated animals had simplified lung architecture without secondary septation. Animals given RA alone had smaller, more numerous alveoli. Concomitant treatment with Dex + RA prevented the Dex-induced changes in septation. While the results of exposure to Dex + RA were sustained, the effects of RA alone were reversed two weeks after treatment was stopped. At d13, Dex-treated animals had increased lung volume, respiratory rate, tidal volume, and minute ventilation. On d15, both RA- and Dex-treated animals had hypercarbia and low arterial pH. By d30, the RA-treated animals resolved this respiratory acidosis, but Dex-treated animals continued to demonstrate blood gas and lung volume abnormalities. Concomitant RA treatment improved respiratory acidosis, but failed to normalize Dex-induced changes in pulmonary function and lung volumes. No differences in exercise tolerance were noted at either d15 or d30. RA treatment after the period of alveolarization also corrected the effects of earlier Dex exposure, but the structural changes due to RA alone were again lost two weeks after treatment. CONCLUSION: We conclude that both RA- and corticosteroid-treatments are associated with respiratory acidosis at d15. While RA alone-induced changes in structure andrespiratory function are reversed, Dex-treated animals continue to demonstrate increased respiratory rate, minute ventilation, tidal and total lung volumes at d30. Concomitant treatment with Dex + RA prevents decreased septation induced by Dex alone and results in correction of hypercarbia. However, these animals continue to have abnormal pulmonary function and lung volumes. Increased septation as a result of RA treatment alone is reversed upon discontinuation of treatment. These data suggest that Dex + RA treatment results in improved gas exchange likely secondary to normalized septation

X-ray Fluorescence Particle Size and Scattering Angle Considerations Preparatory Experiments for the Calibration and Interpretation of C1XS Data

ISRO’s Chandrayaan-1 mission to the Moon is due to be launched in April 2008. Part of its payload is C1XS, a compact X-ray fluorescence (XRF) spectrometer which will provide high quality elemental mapping of the lunar surface [1]. In flight, the input source (solar X-ray spectrum) will be measured by the accompanying XSM payload [2]. An ‘in-house’ IDL XRF modelling code (referred to as the ‘C1XS XRF code’ [3]), which is based on the methods of [4], will be used to convert the C1XS data from X-ray fluxes into elemental ratios and abundances. This study outlines a plan of testing the accuracy and robustness of the code, using XRF spectral data from well characterised geological samples. We aim to quantify how XRF intensity varies with changing particle size and phase angle (θ in Fig. 1) geometry, in order to simulate changes in the solar aspect angle (angle between the Sun, the lunar surface and the detectors), as well as surface topography. These issues have previously been studied within a materials science context e.g. [5 – 9], but rarely but rarely for heterogeneous, geological samples [10 – 12]

Identification of a Latitude Gradient in the Prevalence of Primary Biliary Cholangitis

Introduction: The prevalence of primary biliary cholangitis (PBC) reported in different countries varies significantly and seems to have a latitudinal gradient with the highest prevalence reported in higher latitudes, as has been observed with other autoimmune diseases. This study aimed to determine whether there is a latitudinal gradient of PBC prevalence in Australia using 2 methods of case ascertainment.Methods: We investigated the latitudinal variation of PBC prevalence across the states and territories of Australia (latitudinal range 18.0°-42.7°S) using pathology-based (private pathology antimitochondrial antibody results and PBC-specific prescription databases (prescriptions for ursodeoxycholic acid, the only publicly subsidized treatment for this disease).Results: PBC prevalence was significantly positively associated with latitude, and the postcodes in the highest quintile of latitude (encompassing the south coastal areas of the Australian mainland and Tasmania; latitude range -37.75° to -42.72°) had a prevalence estimate that was 1.78 times higher using the pathology-based prevalence estimation than those in the lowest quintile (encompassing tropical and southern Queensland; latitude range -18.02° to -27.59°). Comparing prevalence estimates between states/territories, the result was 2.53 and 2.21 times higher in Tasmania compared with Queensland when using the pathology-based and prescription-based methods, respectively.Discussion: Using 2 different case-ascertainment methods, we have demonstrated that prevalence estimates of PBC vary significantly with latitude in Australia. Further studies are needed to determine whether factors such as variations in ultraviolet radiation exposure and/or vitamin D levels are responsible for this observation and to investigate the latitudinal prevalence of PBC in other populations

The time course of auditory and language-specific mechanisms in compensation for sibilant assimilation

Models of spoken-word recognition differ on whether compensation for assimilation is language-specific or depends on general auditory processing. English and French participants were taught words that began or ended with the sibilants /s/ and /∫/. Both languages exhibit some assimilation in sibilant sequences (e.g., /s/ becomes like [∫] in dress shop and classe chargée), but they differ in the strength and predominance of anticipatory versus carryover assimilation. After training, participants were presented with novel words embedded in sentences, some of which contained an assimilatory context either preceding or following. A continuum of target sounds ranging from [s] to [∫] was spliced into the novel words, representing a range of possible assimilation strengths. Listeners' perceptions were examined using a visual-world eyetracking paradigm in which the listener clicked on pictures matching the novel words. We found two distinct language-general context effects: a contrastive effect when the assimilating context preceded the target, and flattening of the sibilant categorization function (increased ambiguity) when the assimilating context followed. Furthermore, we found that English but not French listeners were able to resolve the ambiguity created by the following assimilatory context, consistent with their greater experience with assimilation in this context. The combination of these mechanisms allows listeners to deal flexibly with variability in speech forms