The pangenomic diversity in Burkholderia pseudomallei is high, with approximately 5.8% of the genome consisting of genomic islands. Genomic islands are known hotspots for recombination driven primarily by site-specific recombination associated with tRNAs. However, recombination rates in other portions of the genome are also high, a feature we expected to disrupt gene order. We analyzed the pangenome of 37 isolates of B. pseudomallei and demonstrate that the pangenome is ‘open’, with approximately 136 new genes identified with each new genome sequenced, and that the global core genome consists of 4568±16 homologs. Genes associated with metabolism were statistically overrepresented in the core genome, and genes associated with mobile elements, disease, and motility were primarily associated with accessory portions of the pangenome. The frequency distribution of genes present in between 1 and 37 of the genomes analyzed matches well with a model of genome evolution in which 96% of the genome has very low recombination rates but 4% of the genome recombines readily. Using homologous genes among pairs of genomes, we found that gene order was highly conserved among strains, despite the high recombination rates previously observed. High rates of gene transfer and recombination are incompatible with retaining gene order unless these processes are either highly localized to specific sites within the genome, or are characterized by symmetrical gene gain and loss. Our results demonstrate that both processes occur: localized recombination introduces many new genes at relatively few sites, and recombination throughout the genome generates the novel multi-locus sequence types previously observed while preserving gene order.

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Previous self-report survey research has demonstrated significant variation in social trust and neighborhood social ties between two neighborhoods of contrasting socioeconomic fortunes within the same English city. Residents in a deprived neighborhood reported that they trusted their neighbors less and had fewer social ties within the neighborhood than residents in an affluent neighborhood. We carried out direct behavioral observations in these neighborhoods to determine whether this difference was apparent in behavior on the streets. We found that people were less likely to be alone and adults were more likely to engage in social interactions with other adults in the deprived neighborhood than in the affluent neighborhood, indicating a more active social life. We argue that self-reports about social interactions are not simple objective descriptions of those interactions, but involve adding interpretation and meaning to them. We highlight the importance of observational data for exploring cultural differences within and between societies.

Prosociality is a central topic in positive psychology. An important but under-studied distinction can be made between active and reactive expressions. We suggest that the novel construct of social mindfulness represents active rather than reactive prosociality. Across four studies (N = 2,594), including a multi-wave representative sample spanning six years, social mindfulness is found to correlate with personality traits associated with prosocial and/or antisocial behavior. We find positive associations with empathy, social value orientation, and general prosocial behavior, and negative associations with moral disengagement and narcissism. Importantly, social mindfulness emerges as an active rather than a reactive characteristic that is more strongly related to HEXACO honesty-humility (active cooperation) than to HEXACO agreeableness (reactive cooperation). The association between social mindfulness and honesty-humility was found across measures six years apart. Given the well-established link between prosociality and wellbeing, emphasizing social mindfulness may be a good start to promote the latter. ARTICLE HISTORY

Nanopore sequencing, a novel genomics technology, has potential applications for routine biosurveillance, clinical diagnosis, and outbreak investigation of virus infections. Using rapid sequencing of unamplified RNA/cDNA hybrids, we identified Venezuelan equine encephalitis virus and Ebola virus in 3 hours from sample receipt to data acquisition, demonstrating a fieldable technique for RNA virus characterization.

Objectives: Test whether Moffitt’s theory of adolescence-limited offenders, which contends that as young people enter adult roles they exit the “maturity gap” of adolescence and desist from crime, still applies given the changed nature of the early adult years. Examine whether spending time in adult roles remains a driver of desistance, and whether today’s emerging adults are at risk of experiencing a maturity gap between how adult they feel and the reality of their social situation. Methods: Using longitudinal data from a Dutch general population sample aged 18 to 24 years, fixed-effects models were run examining the effect of within-person changes in time spent in adult roles on self-reported delinquency and moderation of this effect by feelings of adultness. Results: The more time spent in adult roles, the less delinquency respondents consequently reported. This effect was moderated: When spending more time in adult roles and feeling more adult, higher delinquency was reported than when spending more time in adult roles and feeling less adult. Conclusions: Today’s emerging adults desist from delinquency in response to taking on adult roles. Possible interpretations for the unexpected qualification of this conclusion are discussed, as well as limitations such as the simplicity of our feeling adult measure.

BackgroundThe detection of pathogens in complex sample backgrounds has been revolutionized by wide access to next-generation sequencing (NGS) platforms. However, analytical methods to support NGS platforms are not as uniformly available. Pathosphere (found at Pathosphere.org) is a cloud - based open - sourced community tool that allows for communication, collaboration and sharing of NGS analytical tools and data amongst scientists working in academia, industry and government. The architecture allows for users to upload data and run available bioinformatics pipelines without the need for onsite processing hardware or technical support.ResultsThe pathogen detection capabilities hosted on Pathosphere were tested by analyzing pathogen-containing samples sequenced by NGS with both spiked human samples as well as human and zoonotic host backgrounds. Pathosphere analytical pipelines developed by Edgewood Chemical Biological Center (ECBC) identified spiked pathogens within a common sample analyzed by 454, Ion Torrent, and Illumina sequencing platforms. ECBC pipelines also correctly identified pathogens in human samples containing arenavirus in addition to animal samples containing flavivirus and coronavirus. These analytical methods were limited in the detection of sequences with limited homology to previous annotations within NCBI databases, such as parvovirus. Utilizing the pipeline-hosting adaptability of Pathosphere, the analytical suite was supplemented by analytical pipelines designed by the United States Army Medical Research Insititute of Infectious Diseases and Walter Reed Army Institute of Research (USAMRIID-WRAIR). These pipelines were implemented and detected parvovirus sequence in the sample that the ECBC iterative analysis previously failed to identify.ConclusionsBy accurately detecting pathogens in a variety of samples, this work demonstrates the utility of Pathosphere and provides a platform for utilizing, modifying and creating pipelines for a variety of NGS technologies developed to detect pathogens in complex sample backgrounds. These results serve as an exhibition for the existing pipelines and web-based interface of Pathosphere as well as the plug-in adaptability that allows for integration of newer NGS analytical software as it becomes available.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0840-5) contains supplementary material, which is available to authorized users.

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