A dynamic and intricate regulatory network determines Pseudomonas aeruginosa virulence

Pseudomonas aeruginosa is a metabolically versatile bacterium that is found in a wide range of biotic and abiotic habitats. It is a major human opportunistic pathogen causing numerous acute and chronic infections. The critical traits contributing to the pathogenic potential of P. aeruginosa are the production of a myriad of virulence factors, formation of biofilms and antibiotic resistance. Expression of these traits is under stringent regulation, and it responds to largely unidentified environmental signals. This review is focused on providing a global picture of virulence gene regulation in P. aeruginosa. In addition to key regulatory pathways that control the transition from acute to chronic infection phenotypes, some regulators have been identified that modulate multiple virulence mechanisms. Despite of a propensity for chaotic behaviour, no chaotic motifs were readily observed in the P. aeruginosa virulence regulatory network. Having a ‘birds-eye’ view of the regulatory cascades provides the forum opportunities to pose questions, formulate hypotheses and evaluate theories in elucidating P. aeruginosa pathogenesis. Understanding the mechanisms involved in making P. aeruginosa a successful pathogen is essential in helping devise control strategies.     

Inhibition of acid production in Streptococcus mutans R9: Inhibition constants and reversibility

Abstract The pac gene encoding the penicillin G acylase (PGA) of Bacillus megaterium ATCC 14945 has been cloned in Escherichia coli HB101 ( proA, leuB ) using a selective minimal medium containing phenylacetyl-L-leucine instead of L-leucine. The nucleotide sequence of this gene has been determined and contains an open reading frame of 2406 nucleotides. The deduced amino acid sequence shows significant similarity with other β-lactam acylases. Although the PGA of B. megaterium is extracellular, the enzyme produced in E. coli appears to have a cytoplasmic localization.     

Vertebral Bomb Radiocarbon Suggests Extreme Longevity in White Sharks

Conservation and management efforts for white sharks (Carcharodon carcharias) remain hampered by a lack of basic demographic information including age and growth rates. Sharks are typically aged by counting growth bands sequentially deposited in their vertebrae, but the assumption of annual deposition of these band pairs requires testing. We compared radiocarbon (Δ¹⁴C) values in vertebrae from four female and four male white sharks from the northwestern Atlantic Ocean (NWA) with reference chronologies documenting the marine uptake of ¹⁴C produced by atmospheric testing of thermonuclear devices to generate the first radiocarbon age estimates for adult white sharks. Age estimates were up to 40 years old for the largest female (fork length [FL]: 526 cm) and 73 years old for the largest male (FL: 493 cm). Our results dramatically extend the maximum age and longevity of white sharks compared to earlier studies, hint at possible sexual dimorphism in growth rates, and raise concerns that white shark populations are considerably more sensitive to human-induced mortality than previously thought.     

Natural and Unanticipated Modifiers of RNAi Activity in Caenorhabditis elegans

Organisms used as model genomics systems are maintained as isogenic strains, yet evidence of sequence differences between independently maintained wild-type stocks has been substantiated by whole-genome resequencing data and strain-specific phenotypes. Sequence differences may arise from replication errors, transposon mobilization, meiotic gene conversion, or environmental or chemical assault on the genome. Low frequency alleles or mutations with modest effects on phenotypes can contribute to natural variation, and it has proven possible for such sequences to become fixed by adapted evolutionary enrichment and identified by resequencing. Our objective was to identify and analyze single locus genetic defects leading to RNAi resistance in isogenic strains of Caenorhabditis elegans. In so doing, we uncovered a mutation that arose de novo in an existing strain, which initially frustrated our phenotypic analysis. We also report experimental, environmental, and genetic conditions that can complicate phenotypic analysis of RNAi pathway defects. These observations highlight the potential for unanticipated mutations, coupled with genetic and environmental phenomena, to enhance or suppress the effects of known mutations and cause variation between wild-type strains.     

Quantifying marine snow as a food choice for zooplankton using stable silicon isotope tracers

Aggregates of biogenic origin >0.5 mm, known as marine snow,represent a concentrated potential source of food for zooplankton.Little is known, however, about whether aggregates are commonlygrazed by zooplankton in the field. While previous laboratorystudies have shown that the euphausiid Euphausia pacifica, andthe copepod, Calanus pacificus, common crustacean zooplankters,consume marine snow if it is the only food source available,it is not known if euphausiids will select marine snow in thepresence of edible dispersed cells, as readily occurs in nature.To examine this question, we offered E. pacifica the diatom,Nitzschia angularis in aggregated and dispersed form as preysimultaneously. Aggregates and dispersed food contained identicalcell types so that differing prey quality, taste or motilitywould not be a factor. A new method was developed to track foodsources by labeling the frustules of aggregated cells with differentnaturally occurring, but rare, stable isotopes of silicon, ³⁰Siand ²⁹Si. Food selection was then estimated by measuring theisotopic composition of silica within fecal pellets producedby animals feeding on mixtures of the two labeled foods. Resultsindicate that E. pacifica consumed both aggregates and dispersedcells, even when more cells were made available in dispersedform than in aggregated form. This suggests that aggregatesmay indeed be a food source in the field, even when dispersedcells are relatively abundant. The method of labeling diatomcells with stable isotopes of silica may prove useful for futuregrazing experiments to distinguish identical cell types.     

Genome‐wide association study of word reading: Overlap with risk genes for neurodevelopmental disorders

Reading disabilities (RD) are the most common neurocognitive disorder, affecting 5% to 17% of children in North America. These children often have comorbid neurodevelopmental/psychiatric disorders, such as attention deficit/hyperactivity disorder (ADHD). The genetics of RD and their overlap with other disorders is incompletely understood. To contribute to this, we performed a genome‐wide association study (GWAS) for word reading. Then, using summary statistics from neurodevelopmental/psychiatric disorders, we computed polygenic risk scores (PRS) and used them to predict reading ability in our samples. This enabled us to test the shared aetiology between RD and other disorders. The GWAS consisted of 5.3 million single nucleotide polymorphisms (SNPs) and two samples; a family‐based sample recruited for reading difficulties in Toronto (n = 624) and a population‐based sample recruited in Philadelphia [Philadelphia Neurodevelopmental Cohort (PNC)] (n = 4430). The Toronto sample SNP‐based analysis identified suggestive SNPs (P ~ 5 × 10^?7) in the ARHGAP23 gene, which is implicated in neuronal migration/axon pathfinding. The PNC gene‐based analysis identified significant associations (P < 2.72 × 10^?6) for LINC00935 and CCNT1, located in the region of the KANSL2/CCNT1/LINC00935/SNORA2B/SNORA34/MIR4701/ADCY6 genes on chromosome 12q, with near significant SNP‐based analysis. PRS identified significant overlap between word reading and intelligence (R² = 0.18, P = 7.25 × 10^?181), word reading and educational attainment (R² = 0.07, P = 4.91 × 10^?48) and word reading and ADHD (R² = 0.02, P = 8.70 × 10^?6; threshold for significance = 7.14 × 10^?3). Overlap was also found between RD and autism spectrum disorder (ASD) as top‐ranked genes were previously implicated in autism by rare and copy number variant analyses. These findings support shared risk between word reading, cognitive measures, educational outcomes and neurodevelopmental disorders, including ASD.     

How to Report Record Open‐Circuit Voltages in Lead‐Halide Perovskite Solar Cells

Open‐circuit voltages of lead‐halide perovskite solar cells are improving rapidly and are approaching the thermodynamic limit. Since many different perovskite compositions with different bandgap energies are actively being investigated, it is not straightforward to compare the open‐circuit voltages between these devices as long as a consistent method of referencing is missing. For the purpose of comparing open‐circuit voltages and identifying outstanding values, it is imperative to use a unique, generally accepted way of calculating the thermodynamic limit, which is currently not the case. Here a meta‐analysis of methods to determine the bandgap and a radiative limit for open‐circuit voltage is presented. The differences between the methods are analyzed and an easily applicable approach based on the solar cell quantum efficiency as a general reference is proposed.