High throughput genomic analysis of Helicobacter pylori within-host diversity

Helicobacter pylori is a globally significant human pathogen and is the causative agent of a wide range of diverse gastroduodenal diseases such as gastritis, peptic ulceration and gastric adenocarcinoma. Antimicrobial resistance is a growing problem, with H. pylori recently listed as one of the top ten antibiotic resistant pathogens of global concern by the World Health Organisation. This species has been shown to be a globally diverse pathogen expressing large genetic variation, even within geographically clustered sub populations. Furthermore, individuals infected with H. pylori are thought to harbour unique and diverse populations of quasispecies, but diversity between and within different niches of the human stomach and the process of bacterial adaptation to, and infection persistence within each niche are not yet well understood. This study utilises whole genome deep population and single colony sequencing to quantify and characterise the within- and between-niche genetic diversity of H. pylori populations from paired antrum and corpus biopsies from the stomachs of individual patients. This revealed extensive genetic diversity both within and between different niches of the same stomach. Subsets of highly variable genes including outer membrane proteins, restriction modification systems, DNA repair, chemotaxis and virulence associated genes were observed. In addition, this study investigated the between niche (antrum versus corpus) antimicrobial resistance profiles of individual patients. The within and between niche (antrum and corpus) diversity of two sequential datasets were also investigated and results from the same patient before and after failed eradication therapy were compared. For one sequential dataset there was a big increase in H. pylori allelic diversity both within and between niches of the patient's stomach approximately five months after failed eradication therapy

Improving the stability of organosiloxane smectic A liquid crystal random lasers using redox dopants

This report is focus on the development of liquid crystal (LC) vis ible - light scattering devices for random lasers. These light - scattering devices are based upon binary mixtures that consist of an organosiloxane smectic A LC and a wide temperature range nematogen LC. Both the temperature range of the smectic A phase and t he dielectric anisotropy of the binary mixture are increased compared with that of the neat organosiloxane compound. In the latter case, the increase in the dielectric anisotropy results in a reduction of the magnitude of the electric field required to ind uce a clear state. Furthermore, it is found that the electric field threshold continues to decrease with increasing concentration of the nematic compound. For the random laser devices, the pyrromethene 597 laser dye was added to a mixture that was optimize d for scattering and it was found that the absorption properties of the dye becomes unstable in the presence of the electro - hydrodynamic instabilities that are required to generate scattering in the LC cells. This is believed to be due to electro - chemical reactions that occur at the electrodes. To avoid dye degradation and ensure repeatable electro - optic behaviour, a reduction - oxidation (redox) couple is dispersed within the dye - doped binary mixture. It is shown that the addition of redox dopants helps to s tabilize the dye in the scattering mixtures, and also increases the long - term repeatability of the scattering behaviour. Finally, we conclude by characterizing the random laser emission of the dye - doped binary mixture and demonstrate improved stability.This is the author accepted manuscript. The final published version is available at http://www.sciencedirect.com/science/article/pii/S0925346715000816

Neutrophil-Associated Central Nervous System Inflammation in Tuberculous Meningitis Immune Reconstitution Inflammatory Syndrome.

Background. The immunopathogenesis of tuberculosis-associated immune reconstitution inflammatory syndrome (IRIS) remains incompletely understood, and we know of only 1 disease site-specific study of the underlying immunology; we recently showed that Mycobacterium tuberculosis culture positivity and increased neutrophils in the cerebrospinal fluid (CSF) of patients with tuberculous meningitis (TBM) are associated with TBM-IRIS. In this study we investigated inflammatory mediators at the disease site in patients with TBM-IRIS. Methods. We performed lumbar puncture at 3–5 time points in human immunodeficiency virus (HIV)–infected patients with TBM (n = 34), including at TBM diagnosis, at initiation of antiretroviral therapy (ART) (day 14), 14 days after ART initiation, at presentation of TBM-IRIS, and 14 days thereafter. We determined the concentrations of 40 mediators in CSF (33 paired with blood) with Luminex or enzyme-linked immunosorbent assays. Findings were compared between patients who developed TBM-IRIS (n = 16) and those who did not (TBM-non-IRIS; n = 18). Results. At TBM diagnosis and 2 weeks after ART initiation, TBM-IRIS was associated with severe, compartmentalized inflammation in the CSF, with elevated concentrations of cytokines, chemokines, neutrophil-associated mediators, and matrix metalloproteinases, compared with TBM-non-IRIS. Patients with TBM-non-IRIS whose CSF cultures were positive for M. tuberculosis at TBM diagnosis (n = 6) showed inflammatory responses similar to those seen in patients with TBM-IRIS at both time points. However, at 2 weeks after ART initiation, S100A8/A9 was significantly increased in patients with TBM-IRIS, compared with patients with TBM-non-IRIS whose cultures were positive at baseline. Conclusions. A high baseline M. tuberculosis antigen load drives an inflammatory response that manifests clinically as TBM-IRIS in most, but not all, patients with TBM. Neutrophils and their mediators, especially S100A8/A9, are closely associated with the central nervous system inflammation that characterizes TBM-IRIS

No Detectable Fertility Benefit from a Single Additional Mating in Wild Stalk-Eyed Flies

Background: Multiple mating by female insects is widespread, and the explanation(s) for repeated mating by females has been the subject of much discussion. Females may profit from mating multiply through direct material benefits that increase their own reproductive output, or indirect genetic benefits that increase offspring fitness. One particular direct benefit that has attracted significant attention is that of fertility assurance, as females often need to mate multiply to achieve high fertility. This hypothesis has never been tested in a wild insect population.Methodology/Principal Findings: Female Malaysian stalk-eyed flies (Teleopsis dalmanni) mate repeatedly during their lifetime, and have been shown to be sperm limited under both laboratory and field conditions. Here we ask whether receiving an additional mating alleviates sperm limitation in wild females. In our experiment one group of females received a single additional mating, while a control group received an interrupted, and therefore unsuccessful, mating. Females that received an additional mating did not lay more fertilised eggs in total, nor did they lay proportionately more fertilised eggs. Female fertility declined significantly through time, demonstrating that females were sperm limited. However, receipt of an additional mating did not significantly alter the rate of this decline.Conclusions/Significance: Our data suggest that the fertility consequences of a single additional mating were small. We discuss this effect (or lack thereof), and suggest that it is likely to be attributed to small ejaculate size, a high proportion of failed copulations, and the presence of X-linked meiotic drive in this species

Warfarin-induced skin necrosis in HIV-1-infected patients with tuberculosis and venous thrombosis

Background. At the turn of the century, only 300 cases of warfarin-induced skin necrosis (WISN) had been reported. WISN is a rare but potentially fatal complication of warfarin therapy. There are no published reports of WISN occurring in patients with HIV-1 infection or tuberculosis (TB).Methods. We retrospectively reviewed cases of WISN presenting from April 2005 to July 2008 at a referral hospital in Cape Town, South Africa.Results. Six cases of WISN occurred in 973 patients receiving warfarin therapy for venous thrombosis (0.62%, 95% CI 0.25 - 1.37%). All 6 cases occurred in HIV-1-infected women (median age 30 years, range 27 - 42) with microbiologically confirmed TB and venous thrombosis. All were profoundly immunosuppressed (median CD4+ count at TB diagnosis49 cells/μl, interquartile range 23 - 170). Of the 3 patients receiving combination antiretroviral therapy, 2 had TB-IRIS (immune reconstitution inflammatory syndrome). The median interval from initiation of antituberculosis treatment to venous thrombosis was 37 days (range 0 - 150). The median duration of parallel heparin and warfarin therapy was 2days (range 1 - 6). WISN manifested 6 days (range 4 - 8) after initiation of warfarin therapy. The international normalised ratio (INR) at WISN onset was supra-therapeutic, median 5.6 (range 3.8 - 6.6). Sites of WISN included breasts, buttocks and thighs. Four of 6 WISN sites were secondarily infected with drug-resistant nosocomial bacteria (methicillin-resistant Staphylococcus aureus (MRSA), Acinetobacter, extendedspectrumβ-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae) 17 - 37 days after WISN onset. In 4 patients, the median interval from WISN onset to death was 43 days (range 25 - 45). One of the 2 patients who survived underwent bilateral mastectomies and extensive skin graftingat a specialist centre. Conclusion. This is one of the largest case series of WISN. We report a novel clinical entity: WISN in HIV-1 infected patients with TB and venous thrombosis. The occurrence of 6 WISN cases in a 40-month period may be attributed to (i) hypercoagulability, secondary to HIV-1 and TB; (ii) shortconcurrent heparin and warfarin therapy; and (iii) high loading doses of warfarin. Active prevention and appropriate management of WISN are likely to improve the dire morbidity and mortality of this unusual condition.S Afr Med J 2010; 100: 372-377

Prediction of Neonatal Respiratory Distress Biomarker Concentration by Application of Machine Learning to Mid-Infrared Spectra

The authors of this study developed the use of attenuated total reflectance Fourier transform infrared spectroscopy (ATR–FTIR) combined with machine learning as a point-of-care (POC) diagnostic platform, considering neonatal respiratory distress syndrome (nRDS), for which no POC currently exists, as an example. nRDS can be diagnosed by a ratio of less than 2.2 of two nRDS biomarkers, lecithin and sphingomyelin (L/S ratio), and in this study, ATR–FTIR spectra were recorded from L/S ratios of between 1.0 and 3.4, which were generated using purified reagents. The calibration of principal component (PCR) and partial least squares (PLSR) regression models was performed using 155 raw baselined and second derivative spectra prior to predicting the concentration of a further 104 spectra. A three-factor PLSR model of second derivative spectra best predicted L/S ratios across the full range (R2: 0.967; MSE: 0.014). The L/S ratios from 1.0 to 3.4 were predicted with a prediction interval of +0.29, −0.37 when using a second derivative spectra PLSR model and had a mean prediction interval of +0.26, −0.34 around the L/S 2.2 region. These results support the validity of combining ATR–FTIR with machine learning to develop a point-of-care device for detecting and quantifying any biomarker with an interpretable mid-infrared spectrum

Genomic diversity of Helicobacter pylori populations from different regions of the human stomach

Individuals infected with Helicobacter pylori harbor unique and diverse populations of quasispecies, but diversity between and within different regions of the human stomach and the process of bacterial adaptation to each location are not yet well understood. We applied whole-genome deep sequencing to characterize the within- and between-stomach region genetic diversity of H. pylori populations from paired antrum and corpus biopsies of 15 patients, along with single biopsies from one region of an additional 3 patients, by scanning allelic diversity. We combined population deep sequencing with more conventional sequencing of multiple H. pylori single colony isolates from individual biopsies to generate a unique dataset. Single colony isolates were used to validate the scanning allelic diversity pipelines. We detected extensive population allelic diversity within the different regions of each patient’s stomach. Diversity was most commonly found within non-coding, hypothetical, outer membrane, restriction modification system, virulence, lipopolysaccharide biosynthesis, efflux systems, and chemotaxis-associated genes. Antrum and corpus populations from the same patient grouped together phylogenetically, indicating that most patients were initially infected with a single strain, which then diversified. Single colonies from the antrum and corpus of the same patients grouped into distinct clades, suggesting mechanisms for within-location adaptation across multiple H. pylori isolates from different patients. The comparisons made available by combined sequencing and analysis of isolates and populations enabled comprehensive analysis of the genetic changes associated with H. pylori diversification and stomach region adaptation

Mycobacterium tuberculosis cords within lymphatic endothelial cells to evade host immunity

The ability of Mycobacterium tuberculosis to form serpentine cords is intrinsically related to its virulence, but specifically how M. tuberculosis cording contributes to pathogenesis remains obscure. Here, we show that several M. tuberculosis clinical isolates form intracellular cords in primary human lymphatic endothelial cells (hLECs) in vitro and in the lymph nodes of patients with tuberculosis. We identified via RNA-Seq a transcriptional program that activated, in infected-hLECs, cell survival and cytosolic surveillance of pathogens pathways. Consistent with this, cytosolic access was required for intracellular M. tuberculosis cording. Mycobacteria lacking ESX-1 type VII secretion system or phthiocerol dimycocerosates expression, which failed to access the cytosol, were indeed unable to form cords within hLECs. Finally, we show that M. tuberculosis cording is a size-dependent mechanism used by the pathogen to avoid its recognition by cytosolic sensors and evade either resting or IFN-γ–induced hLEC immunity. These results explain the long-standing association between M. tuberculosis cording and virulence and how virulent mycobacteria use intracellular cording as strategy to successfully adapt and persist in the lymphatic tracts

Hybrid graphene nematic liquid crystal light scattering device.

A hybrid graphene nematic liquid crystal (LC) light scattering device is presented. This device exploits the inherent poly-crystallinity of chemical vapour deposited (CVD) graphene films to induce directional anchoring and formation of LC multi-domains. This thereby enables efficient light scattering without the need for crossed polarisers or separate alignment layers/additives. The hybrid LC device exhibits switching thresholds at very low electric fields (< 1 V μm(-1)) and repeatable, hysteresis free characteristics. This exploitation of LC alignment effects on CVD graphene films enables a new generation of highly efficient nematic LC scattering displays as well as many other possible applications.Funding from the EPSRC (Grant No. EP/K016636/1, GRAPHTED) is acknowledged. P.R.K. acknowledges funding from Cambridge Commonwealth Trust (CCT) and the Lindemann Trust Fellowship. A.A.K would like to thank the Higher Education of Pakistan (HEC) and the CCT for financial support. A.C.V. acknowledges funding from the Cambridge Conacyt Scholarship and the Roberto Rocca Fellowship. A.K. would like to thank the Luys Educational Foundation and Hovnanian Foundation for scholarships.This is the author accepted manuscript. The final version is available from the Royal Society of Chemistry via http://dx.doi.org/10.1039/c5nr04094

Optimization of a total acid hydrolysis based protocol for the quantification of carbohydrate in macroalgae

Accurate quantification of carbohydrate content of biomass is crucial for many bio-refining applications. The standardised NREL two stage complete acid hydrolysis protocol was evaluated for its suitability towards seaweeds, as the protocol was originally developed for lignocellulosic feedstocks. The compositional differences between the major polysaccharides in seaweeds and terrestrial plants, and seaweed’s less recalcitrant nature, could suggest the NREL based protocol may be too extreme. Underestimations of carbohydrate content through the degradation of liberated sugars into furan compounds may yield erroneous data. An optimised analysis method for carbohydrate quantification in the brown seaweed L. digitata was thus developed and evaluated. Results from this study revealed stage 1 of the assay was crucial for optimisation however stage 2 proved to be less crucial. The newly optimised protocol for L. digitata yielded 210 mg of carbohydrate per g of biomass compared to a yield of only 166 mg/g from the original NREL protocol. Use of the new protocol on two other species of seaweed also gave consistent results; higher carbohydrate and significantly lower sugar degradation products generation than the original protocol. This study demonstrated the importance of specific individual optimisations of the protocol for accurate sugar quantification, particularly for different species of seawee