Severe infections emerge from commensal bacteria by adaptive evolution

Bacteria responsible for the greatest global mortality colonize the human microbiota far more frequently than they cause severe infections. Whether mutation and selection among commensal bacteria are associated with infection is unknown. We investigated de novo mutation in 1163 Staphylococcus aureus genomes from 105 infected patients with nose colonization. We report that 72% of infections emerged from the nose, with infecting and nose-colonizing bacteria showing parallel adaptive differences. We found 2.8-to-3.6-fold adaptive enrichments of protein-altering variants in genes responding to rsp, which regulates surface antigens and toxin production; agr, which regulates quorum-sensing, toxin production and abscess formation; and host-derived antimicrobial peptides. Adaptive mutations in pathogenesis-associated genes were 3.1-fold enriched in infecting but not nose-colonizing bacteria. None of these signatures were observed in healthy carriers nor at the species-level, suggesting infection-associated, short-term, within-host selection pressures. Our results show that signatures of spontaneous adaptive evolution are specifically associated with infection, raising new possibilities for diagnosis and treatment

A Net Energy Analysis of the Global Agriculture, Aquaculture, Fishing and Forestry System

The global agriculture, aquaculture, fishing and forestry (AAFF) energy system is subject to three unsustainable trends: (1) the approaching biophysical limits of AAFF; (2) the role of AAFF as a driver of environmental degradation; and (3) the long-term declining energy efficiency of AAFF due to growing dependence on fossil fuels. In response, we conduct a net energy analysis for the period 1971–2017 and review existing studies to investigate the global AAFF energy system and its vulnerability to the three unsustainable trends from an energetic perspective. We estimate the global AAFF system represents 27.9% of societies energy supply in 2017, with food energy representing 20.8% of societies total energy supply. We find that the net energy-return-on-investment (net EROI) of global AAFF increased from 2.87:1 in 1971 to 4.05:1 in 2017. We suggest that rising net EROI values are being fuelled in part by ‘depleting natures accumulated energy stocks’. We also find that the net energy balance of AAFF increased by 130% in this period, with at the same time a decrease in both the proportion of rural residents and also the proportion of the total population working in AAFF—which decreased from 19.8 to 10.3%. However, this comes at the cost of growing fossil fuel dependency which increased from 43.6 to 62.2%. Given the increasing probability of near-term fossil fuel scarcity, the growing impacts of climate change and environmental degradation, and the approaching biophysical limits of global AAFF, ‘Odum’s hoax’ is likely soon to be revealed

Gene expression patterns associated with blood-feeding in the malaria mosquito Anopheles gambiae

BACKGROUND: Blood feeding, or hematophagy, is a behavior exhibited by female mosquitoes required both for reproduction and for transmission of pathogens. We determined the expression patterns of 3,068 ESTs, representing ~2,000 unique gene transcripts using cDNA microarrays in adult female Anopheles gambiae at selected times during the first two days following blood ingestion, at 5 and 30 min during a 40 minute blood meal and at 0, 1, 3, 5, 12, 16, 24 and 48 hours after completion of the blood meal and compared their expression to transcript levels in mosquitoes with access only to a sugar solution. RESULTS: In blood-fed mosquitoes, 413 unique transcripts, approximately 25% of the total, were expressed at least two-fold above or below their levels in the sugar-fed mosquitoes, at one or more time points. These differentially expressed gene products were clustered using k-means clustering into Early Genes, Middle Genes, and Late Genes, containing 144, 130, and 139 unique transcripts, respectively. Several genes from each group were analyzed by quantitative real-time PCR in order to validate the microarray results. CONCLUSION: The expression patterns and annotation of the genes in these three groups (Early, Middle, and Late genes) are discussed in the context of female mosquitoes' physiological responses to blood feeding, including blood digestion, peritrophic matrix formation, egg development, and immunity

Structural and Process Quality of Danish Preschools : Direct and Indirect Associations With Children’s Growth in Language and Preliteracy Skills

Structural quality in childcare centers is considered a precondition for process quality, which in turn is related to children’s outcomes. However, the evidence on relations between structural and process quality is mixed. Moreover, despite strong theoretical claims, empirical evidence supporting the indirect relation of structural features through process quality on child outcomes is scarce. The current study contributes to the knowledge by (a) investigating the direct relations of structural teacher and classroom features with growth in children’s language and preliteracy skills in a sample of more than 3,000 children, (b) studying the associations of process quality with children’s outcomes using the widely used Classroom Assessment Scoring System Pre-K observational measure among more than 400 teachers, and (c) testing indirect effects of structural quality through process quality on growth in children’s skills. Process quality was generally directly positively associated with gains in children’s language and preliteracy skills, whereas structural quality showed few direct relations. In addition, the average level of children’s initial language and preliteracy skills were positively related to gains, as was classrooms’ proportion of non-Danish children (indirectly through process quality). The results illustrate the complexities of relations between structural and process quality and children’s outcomes and warrant further research

Structural and Process Quality of Danish Preschools : Direct and Indirect Associations With Children’s Growth in Language and Preliteracy Skills

Structural quality in childcare centers is considered a precondition for process quality, which in turn is related to children’s outcomes. However, the evidence on relations between structural and process quality is mixed. Moreover, despite strong theoretical claims, empirical evidence supporting the indirect relation of structural features through process quality on child outcomes is scarce. The current study contributes to the knowledge by (a) investigating the direct relations of structural teacher and classroom features with growth in children’s language and preliteracy skills in a sample of more than 3,000 children, (b) studying the associations of process quality with children’s outcomes using the widely used Classroom Assessment Scoring System Pre-K observational measure among more than 400 teachers, and (c) testing indirect effects of structural quality through process quality on growth in children’s skills. Process quality was generally directly positively associated with gains in children’s language and preliteracy skills, whereas structural quality showed few direct relations. In addition, the average level of children’s initial language and preliteracy skills were positively related to gains, as was classrooms’ proportion of non-Danish children (indirectly through process quality). The results illustrate the complexities of relations between structural and process quality and children’s outcomes and warrant further research