14 research outputs found

    The draft genome, transcriptome, and microbiome of Dermatophagoides farinae reveal a broad spectrum of dust mite allergens

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    © 2014 The Authors. Published by Elsevier Inc. Background A sequenced house dust mite (HDM) genome would advance our understanding of HDM allergens, a common cause of human allergies. Objective We sought to produce an annotated Dermatophagoides farinae draft genome and develop a combined genomic-transcriptomic-proteomic approach for elucidation of HDM allergens. Methods A D farinae draft genome and transcriptome were assembled with high-throughput sequencing, accommodating microbiome sequences. The allergen gene structures were validated by means of Sanger sequencing. The mite's microbiome composition was determined, and the predominant genus was validated immunohistochemically. The allergenicity of a ubiquinol-cytochrome c reductase binding protein homologue was evaluated with immunoblotting, immunosorbent assays, and skin prick tests. Results The full gene structures of 20 canonical allergens and 7 noncanonical allergen homologues were produced. A novel major allergen, ubiquinol-cytochrome c reductase binding protein-like protein, was found and designated Der f 24. All 40 sera samples from patients with mite allergy had IgE antibodies against rDer f 24. Of 10 patients tested, 5 had positive skin reactions. The predominant bacterial genus among 100 identified species was Enterobacter (63.4%). An intron was found in the 13.8-kDa D farinae bacteriolytic enzyme gene, indicating that it is of HDM origin. The Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed a phototransduction pathway in D farinae, as well as thiamine and amino acid synthesis pathways, which is suggestive of an endosymbiotic relationship between D farinae and its microbiome. Conclusion An HDM genome draft produced from genomic, transcriptomic, and proteomic experiments revealed allergen genes and a diverse endosymbiotic microbiome, providing a tool for further identification and characterization of HDM allergens and development of diagnostics and immunotherapeutic vaccines.Link_to_subscribed_fulltex

    Robust estimation of bacterial cell count from optical density

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    Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

    Theory of mind deficits and paranoid delusions in schizophrenia : a game theoretical investigation

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    published_or_final_versionPsychiatryMasterMaster of Philosoph

    Examining the impact of physical activity on sleep quality and executive functions in children with autism spectrum disorder: A randomized controlled trial

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    Sleep disturbance and executive dysfunction have been widely reported in children with autism spectrum disorder. While the positive impacts of physical activity on sleep quality and cognition are documented in children with typical development, similar studies in children with autism spectrum disorder are scarce. The objective of this study was to examine the impact of physical activity on sleep quality and cognition in children with autism spectrum disorder. A total of 40 children diagnosed with autism spectrum disorder (mean age = 9.95 years) were randomly assigned into two groups: physical activity intervention and control. Four sleep parameters (sleep efficiency, sleep onset latency, sleep duration, and wake after sleep onset) and two executive functions (inhibition control and working memory) were assessed. Results revealed a significant improvement in sleep efficiency, sleep onset latency, and sleep duration in the intervention group but not in the control group during weekdays. Moreover, a significant improvement in inhibitory control was shown in the intervention group but not in the control group. No significant improvement in working memory capacity was documented in either group (ps > 0.05). Our findings highlight the value of physical activity in improving sleep quality and cognition among children with autism spectrum disorder, but specific physical activity may be required to benefit individual executive functions
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