Tuberculosis vaccine strain _Mycobacterium bovis_ BCG Russia is a natural _recA_ mutant

The current tuberculosis vaccine is a live vaccine derived from _Mycobacterium bovis_ and attenuated by serial _in vitro_ passaging. All vaccine substrains in use stem from one source, strain Bacille Calmette-Guérin. However, they differ in regions of genomic deletions, antigen expression levels, immunogenicity, and protective efficacy. As a RecA phenotype increases genetic stability and may contribute restricting the ongoing evolution of the various BCG substrains, we aimed to inactivate _recA_ by allelic replacement in BCG vaccine strains representing different phylogenetic lineages (Pasteur, Frappier, Denmark, Russia). Homologous gene replacement was successful in three out of four strains. However, only illegitimate recombination was observed in BCG substrain Russia. Sequence analyses of _recA_ revealed that a single nucleotide insertion in the 5' part of _recA_ led to a translational frameshift with an early stop codon making BCG Russia a natural _recA_ mutant. At the protein level BCG Russia failed to express RecA. According to phylogenetic analyses BCG Russia is an ancient vaccine strain most closely related to the parental _M. bovis_. Our data suggest that _recA_ inactivation in BCG Russia occurred early and is in part responsible for its high degree of genomic stability, resulting in a substrain that has less genetic alterations than other vaccine substrains with respect to _M. bovis_ AF2122/97 wild type

Tuberculosis vaccine strain Mycobacterium bovis BCG Russia is a natural recA mutant

BACKGROUND: The current tuberculosis vaccine is a live vaccine derived from Mycobacterium bovis and attenuated by serial in vitro passaging. All vaccine substrains in use stem from one source, strain Bacille Calmette-Guérin. However, they differ in regions of genomic deletions, antigen expression levels, immunogenicity, and protective efficacy. RESULTS: As a RecA phenotype increases genetic stability and may contribute restricting the ongoing evolution of the various BCG substrains while maintaining their protective efficacy, we aimed to inactivate recA by allelic replacement in BCG vaccine strains representing different phylogenetic lineages (Pasteur, Frappier, Denmark, Russia). Homologous gene replacement was achieved successfully in three out of four strains. However, only illegitimate recombination was observed in BCG substrain Russia. Sequence analyses of recA revealed that a single nucleotide insertion in the 5' part of recA led to a translational frameshift with an early stop codon making BCG Russia a natural recA mutant. At the protein level BCG Russia failed to express RecA. CONCLUSION: According to phylogenetic analyses BCG Russia is an ancient vaccine strain most closely related to the parental M. bovis. We hypothesize that recA inactivation in BCG Russia occurred early and is in part responsible for its high degree of genomic stability, resulting in a substrain that has less genetic alterations than other vaccine substrains with respect to M. bovis AF2122/97 wild-type

Be stars in and around young clusters in the Magellanic Clouds

We present the results of a search for Be stars in six fields centered on the young clusters NGC 330 and NGC 346 in the SMC, and NGC 1818, NGC 1948, NGC 2004 and NGC 2100 in the LMC. Be stars were identified by differencing R band and narrow-band Hα CCD images. Our comparatively large images provide substantial Be star populations both within the clusters and in their surrounding fields. Magnitudes, positions and finding charts are given for the 224 Be stars found. The fraction of Be stars to normal B stars within each cluster is found to vary significantly although the average ratio is similar to the average Be to B star ratio found in the Galaxy. In some clusters, the Be star population is weighted to magnitudes near the main sequence turn-off. The Be stars are redder in V-I than normal main-sequence stars of similar magnitude and the redness increases with increasing Hα emission strength

Opportunities for using spatial property assessment data in air pollution exposure assessments

BACKGROUND: Many epidemiological studies examining the relationships between adverse health outcomes and exposure to air pollutants use ambient air pollution measurements as a proxy for personal exposure levels. When pollution levels vary at neighbourhood levels, using ambient pollution data from sparsely located fixed monitors may inadequately capture the spatial variation in ambient pollution. A major constraint to moving toward exposure assessments and epidemiological studies of air pollution at a neighbourhood level is the lack of readily available data at appropriate spatial resolutions. Spatial property assessment data are widely available in North America and may provide an opportunity for developing neighbourhood level air pollution exposure assessments. RESULTS: This paper provides a detailed description of spatial property assessment data available in the Pacific Northwest of Canada and the United States, and provides examples of potential applications of spatial property assessment data for improving air pollution exposure assessment at the neighbourhood scale, including: (1) creating variables for use in land use regression modelling of neighbourhood levels of ambient air pollution; (2) enhancing wood smoke exposure estimates by mapping fireplace locations; and (3) using data available on individual building characteristics to produce a regional air pollution infiltration model. CONCLUSION: Spatial property assessment data are an extremely detailed data source at a fine spatial resolution, and therefore a source of information that could improve the quality and spatial resolution of current air pollution exposure assessments

Large-scale genomics unveils the genetic architecture of psychiatric disorders

Family study results are consistent with genetic effects making substantial contributions to risk of psychiatric disorders such as schizophrenia, yet robust identification of specific genetic variants that explain variation in population risk had been disappointing until the advent of technologies that assay the entire genome in large samples. We highlight recent progress that has led to a better understanding of the number of risk variants in the population and the interaction of allele frequency and effect size. The emerging genetic architecture implies a large number of contributing loci (that is, a high genome-wide mutational target) and suggests that genetic risk of psychiatric disorders involves the combined effects of many common variants of small effect, as well as rare and de novo variants of large effect. The capture of a substantial proportion of genetic risk facilitates new study designs to investigate the combined effects of genes and the environment

Spatial variations in estimated chronic exposure to traffic-related air pollution in working populations: A simulation

<p>Abstract</p> <p>Background</p> <p>Chronic exposure to traffic-related air pollution is associated with a variety of health impacts in adults and recent studies show that exposure varies spatially, with some residents in a community more exposed than others. A spatial exposure simulation model (SESM) which incorporates six microenvironments (<it>home indoor</it>, <it>work indoor</it>, <it>other indoor</it>, <it>outdoor</it>, <it>in-vehicle to work </it>and <it>in-vehicle other</it>) is described and used to explore spatial variability in estimates of exposure to traffic-related nitrogen dioxide (not including indoor sources) for working people. The study models spatial variability in estimated exposure aggregated at the census tracts level for 382 census tracts in the Greater Vancouver Regional District of British Columbia, Canada. Summary statistics relating to the distributions of the estimated exposures are compared visually through mapping. Observed variations are explored through analyses of model inputs.</p> <p>Results</p> <p>Two sources of spatial variability in exposure to traffic-related nitrogen dioxide were identified. Median estimates of total exposure ranged from 8 μg/m³to 35 μg/m³of annual average hourly NO₂for workers in different census tracts in the study area. Exposure estimates are highest where ambient pollution levels are highest. This reflects the regional gradient of pollution in the study area and the relatively high percentage of time spent at home locations. However, for workers within the same census tract, variations were observed in the partial exposure estimates associated with time spent outside the residential census tract. Simulation modeling shows that some workers may have exposures 1.3 times higher than other workers residing in the same census tract because of time spent away from the residential census tract, and that time spent in work census tracts contributes most to the differences in exposure. Exposure estimates associated with the activity of commuting by vehicle to work were negligible, based on the relatively short amount of time spent in this microenvironment compared to other locations. We recognize that this may not be the case for pollutants other than NO_2.These results represent the first time spatially disaggregated variations in exposure to traffic-related air pollution within a community have been estimated and reported.</p> <p>Conclusion</p> <p>The results suggest that while time spent in the <it>home indoor </it>microenvironment contributes most to between-census tract variation in estimates of annual average exposures to traffic-related NO₂, time spent in the <it>work indoor </it>microenvironment contributes most to within-census tract variation, and time spent in transit by vehicle makes a negligible contribution. The SESM has potential as a policy evaluation tool, given input data that reflect changes in pollution levels or work flow patterns due to traffic demand management and land use development policy.</p

Neural tracking of visual periodic motion

Periodicity is a fundamental property of biological systems, including human movement systems. Periodic movements support displacements of the body in the environment as well as interactions and communication between individuals. Here, we use electroencephalography (EEG) to investigate the neural tracking of visual periodic motion, and more specifically, the relevance of spatiotemporal information contained at and between their turning points. We compared EEG responses to visual sinusoidal oscillations versus nonlinear Rayleigh oscillations, which are both typical of human movements. These oscillations contain the same spatiotemporal information at their turning points but differ between turning points, with Rayleigh oscillations having an earlier peak velocity, shown to increase an individual's capacity to produce accurately synchronized movements. EEG analyses highlighted the relevance of spatiotemporal information between the turning points by showing that the brain precisely tracks subtle differences in velocity profiles, as indicated by earlier EEG responses for Rayleigh oscillations. The results suggest that the brain is particularly responsive to velocity peaks in visual periodic motion, supporting their role in conveying behaviorally relevant timing information at a neurophysiological level. The results also suggest key functions of neural oscillations in the Alpha and Beta frequency bands, particularly in the right hemisphere. Together, these findings provide insights into the neural mechanisms underpinning the processing of visual periodic motion and the critical role of velocity peaks in enabling proficient visuomotor synchronization

Broad-Range 16S rRNA Gene Polymerase Chain Reaction for Diagnosis of Culture-Negative Bacterial Infections

This study defines the role of 16S ribosomal RNA (rRNA) gene polymerase chain reaction (PCR) for diagnosis of culture-negative bacterial infections. Our data show that 16S rRNA PCR is particularly valuable for identification of pathogens in patients pretreated with antibiotic

BALL-SNP: combining genetic and structural information to identify candidate non-synonymous single nucleotide polymorphisms

Background: High-throughput genetic testing is increasingly applied in clinics. Next-Generation Sequencing (NGS) data analysis however still remains a great challenge. The interpretation of pathogenicity of single variants or combinations of variants is crucial to provide accurate diagnostic information or guide therapies. Methods: To facilitate the interpretation of variants and the selection of candidate non-synonymous polymorphisms (nsSNPs) for further clinical studies, we developed BALL-SNP. Starting from genetic variants in variant call format (VCF) files or tabular input, our tool, first, visualizes the three-dimensional (3D) structure of the respective proteins from the Protein Data Bank (PDB) and highlights mutated residues, automatically. Second, a hierarchical bottom up clustering on the nsSNPs within the 3D structure is performed to identify nsSNPs, which are close to each other. The modular and flexible implementation allows for straightforward integration of different databases for pathogenic and benign variants, but also enables the integration of pathogenicity prediction tools. The collected background information of all variants is presented below the 3D structure in an easily interpretable table format. Results: First, we integrated different data resources into BALL-SNP, including databases containing information on genetic variants such as ClinVar or HUMSAVAR; third party tools that predict stability or pathogenicity in silico such as I-Mutant2.0; and additional information derived from the 3D structure such as a prediction of binding pockets. We then explored the applicability of BALL-SNP on the example of patients suffering from cardiomyopathies. Here, the analysis highlighted accumulation of variations in the genes JUP, VCL, and SMYD2. Conclusion: Software solutions for analyzing high-throughput genomics data are important to support diagnosis and therapy selection. Our tool BALL-SNP, which is freely available at http://www.ccb.uni-saarland.de/BALL-SNP , combines genetic information with an easily interpretable and interactive, graphical representation of amino acid changes in proteins. Thereby relevant information from databases and computational tools is presented. Beyond this, proximity to functional sites or accumulations of mutations with a potential collective effect can be discovered

Optimizing mycobacteria molecular diagnostics: No decontamination! Human DNA depletion? Greener storage at 4 °C!

INTRODUCTION Tuberculosis (TB) is an infectious disease caused by the group of bacterial pathogens Mycobacterium tuberculosis complex (MTBC) and is one of the leading causes of death worldwide. Timely diagnosis and treatment of drug-resistant TB is a key pillar of WHO's strategy to combat global TB. The time required to carry out drug susceptibility testing (DST) for MTBC via the classic culture method is in the range of weeks and such delays have a detrimental effect on treatment outcomes. Given that molecular testing is in the range of hours to 1 or 2 days its value in treating drug resistant TB cannot be overstated. When developing such tests, one wants to optimize each step so that tests are successful even when confronted with samples that have a low MTBC load or contain large amounts of host DNA. This could improve the performance of the popular rapid molecular tests, especially for samples with mycobacterial loads close to the limits of detection. Where optimizations could have a more significant impact is for tests based on targeted next generation sequencing (tNGS) which typically require higher quantities of DNA. This would be significant as tNGS can provide more comprehensive drug resistance profiles than the relatively limited resistance information provided by rapid tests. In this work we endeavor to optimize pre-treatment and extraction steps for molecular testing. METHODS We begin by choosing the best DNA extraction device by comparing the amount of DNA extracted by five commonly used devices from identical samples. Following this, the effect that decontamination and human DNA depletion have on extraction efficiency is explored. RESULTS The best results were achieved (i.e., the lowest Ct values) when neither decontamination nor human DNA depletion were used. As expected, in all tested scenarios the addition of decontamination to our workflow substantially reduced the yield of DNA extracted. This illustrates that the standard TB laboratory practice of applying decontamination, although being vital for culture-based testing, can negatively impact the performance of molecular testing. As a complement to the above experiments, we also considered the best Mycobacterium tuberculosis DNA storage method to optimize molecular testing carried out in the near- to medium-term. Comparing Ct values following three-month storage at 4 °C and at -20 °C and showed little difference between the two. DISCUSSION In summary, for molecular diagnostics aimed at mycobacteria this work highlights the importance of choosing the right DNA extraction device, indicates that decontamination causes significant loss of mycobacterial DNA, and shows that samples preserved for further molecular testing can be stored at 4 °C, just as well at -20 °C. Under our experimental settings, human DNA depletion gave no significant improvement in Ct values for the detection of MTBC