BCG Cell Imaging Using Scanning Probe Microscopy

Scanning tunneling microscopy (STM) and atomic force microscopy (AFM) were used to obtain images of the surface of whole, intact BCG (bacille Calmette Guerin, a mycobacterium) cells in air and under solution by immobilizing the cells onto glass slides (AFM only) or highly oriented pyrolytic graphite. The technique used for AFM imaging involved depositing a submonolayer of cells under a centrifugal force followed by fixation/dehydration using polar organic solvents. AFM images agree well with images from light and electron microscopy and showed large numbers of BCG cells in their distinctive cord arrangement. The AFM also proved useful for identifying extracellular microgranules which cannot be seen with light microscopy. For STM imaging, the hydrophobicity of BCG enabled strong adhesion from aqueous solution onto graphite. STM images of BCG could only be obtained while scanning in aqueous solution, and the cells showed a large variation in contrast when different samples were imaged. The STM provided greater detail of surface features than the AFM and was able to produce images of periodic layers corroborating observations made by transmission electron microscopy

Bacterial Signatures of Paediatric Respiratory Disease : An Individual Participant Data Meta-Analysis

Introduction: The airway microbiota has been linked to specific paediatric respiratory diseases, but studies are often small. It remains unclear whether particular bacteria are associated with a given disease, or if a more general, non-specific microbiota association with disease exists, as suggested for the gut. We investigated overarching patterns of bacterial association with acute and chronic paediatric respiratory disease in an individual participant data (IPD) meta-analysis of 16S rRNA gene sequences from published respiratory microbiota studies.Methods: We obtained raw microbiota data from public repositories or via communication with corresponding authors. Cross-sectional analyses of the paediatric (10 case subjects were included. Sequence data were processed using a uniform bioinformatics pipeline, removing a potentially substantial source of variation. Microbiota differences across diagnoses were assessed using alpha- and beta-diversity approaches, machine learning, and biomarker analyses.Results: We ultimately included 20 studies containing individual data from 2624 children. Disease was associated with lower bacterial diversity in nasal and lower airway samples and higher relative abundances of specific nasal taxa including Streptococcus and Haemophilus. Machine learning success in assigning samples to diagnostic groupings varied with anatomical site, with positive predictive value and sensitivity ranging from 43 to 100 and 8 to 99%, respectively.Conclusion: IPD meta-analysis of the respiratory microbiota across multiple diseases allowed identification of a non-specific disease association which cannot be recognised by studying a single disease. Whilst imperfect, machine learning offers promise as a potential additional tool to aid clinical diagnosis.Peer reviewe

Analytical methods for inferring functional effects of single base pair substitutions in human cancers

Cancer is a genetic disease that results from a variety of genomic alterations. Identification of some of these causal genetic events has enabled the development of targeted therapeutics and spurred efforts to discover the key genes that drive cancer formation. Rapidly improving sequencing and genotyping technology continues to generate increasingly large datasets that require analytical methods to identify functional alterations that deserve additional investigation. This review examines statistical and computational approaches for the identification of functional changes among sets of single-nucleotide substitutions. Frequency-based methods identify the most highly mutated genes in large-scale cancer sequencing efforts while bioinformatics approaches are effective for independent evaluation of both non-synonymous mutations and polymorphisms. We also review current knowledge and tools that can be utilized for analysis of alterations in non-protein-coding genomic sequence

Portrayals of the Holocaust in English history textbooks, 1991–2016: continuities, challenges and concerns

This study examines portrayals of the Holocaust in a sample of 21 secondary school history textbooks published in England between 1991 and 2016. Evaluated against internationally recognized criteria and guidelines, the content of most textbooks proved very problematic. Typically, textbooks failed to provide clear chronological and geographical frameworks and adopted simplistic Hitler-centric, perpetrator-oriented narratives. Furthermore, textbooks paid limited attention to pre-war Jewish life, the roots of antisemitism, the complicity of local populations and collaborationist regimes, and the impact of the Holocaust on people across Europe. Based on these critical findings, the article concludes by offering initial recommendations for textbook improvement