On the mechanistic nature of epistasis in a canonical cis -regulatory element

Understanding the relation between genotype and phenotype remains a major challenge. The difficulty of predicting individual mutation effects, and particularly the interactions between them, has prevented the development of a comprehensive theory that links genotypic changes to their phenotypic effects. We show that a general thermodynamic framework for gene regulation, based on a biophysical understanding of protein-DNA binding, accurately predicts the sign of epistasis in a canonical cis-regulatory element consisting of overlapping RNA polymerase and repressor binding sites. Sign and magnitude of individual mutation effects are sufficient to predict the sign of epistasis and its environmental dependence. Thus, the thermodynamic model offers the correct null prediction for epistasis between mutations across DNA-binding sites. Our results indicate that a predictive theory for the effects of cis-regulatory mutations is possible from first principles, as long as the essential molecular mechanisms and the constraints these impose on a biological system are accounted for

The factors driving evolved herbicide resistance at a national scale

Repeated use of xenobiotic chemicals has selected for the rapid evolution of resistance threatening health and food security at a global scale. Strategies for preventing the evolution of resistance include cycling and mixtures of chemicals and diversification of management. We currently lack large-scale studies that evaluate the efficacy of these different strategies for minimizing the evolution of resistance. Here we use a national scale dataset of occurrence of the weed Alopecurus myosuroides (Blackgrass) in the UK to address this. Weed densities are correlated with assays of evolved resistance, supporting the hypothesis that resistance is driving weed abundance at a national scale. Resistance was correlated with the frequency of historical herbicide applications suggesting that evolution of resistance is primarily driven by intensity of exposure to herbicides, but was unrelated directly to other cultural techniques. We find that populations resistant to one herbicide are likely to show resistance to multiple herbicide classes. Finally, we show that the economic costs of evolved resistance are considerable: loss of control through resistance can double the economic costs of weeds. This research highlights the importance of managing threats to food production and healthcare systems using an evolutionarily informed approach in a proactive not reactive manner

A high-resolution versatile focused ion implantation platform for nanoscale engineering

The ability to spatially control and modify material properties on the nanoscale, including within nanoscale objects themselves, is a fundamental requirement for the development of advanced nanotechnologies. The development of a platform for nanoscale advanced materials engineering (P-NAME) designed to meet this demand is demonstrated. P-NAME delivers a high-resolution focused ion beam system with a coincident scanning electron microscope and secondary electron detection of single-ion implantation events. The isotopic mass-resolution capability of the P-NAME system for a wide range of ion species is demonstrated, offering access to the implantation of isotopes that are vital for nanomaterials engineering and nanofunctionalization. The performance of the isotopic mass selection is independently validated using secondary ion mass spectrometry (SIMS) for a number of species implanted into intrinsic silicon. The SIMS results are shown to be in good agreement with dynamic ion implantation simulations, demonstrating the validity of this simulation approach. The wider performance capabilities of P-NAME, including sub-10 nm ion beam imaging resolution and the ability to perform direct-write ion beam doping and nanoscale ion lithography, are also demonstrated

The Open Anchoring Quest Dataset: Anchored Estimates from 96 Studies on Anchoring Effects

People’s estimates are biased toward previously considered numbers (anchoring). We have aggregated all available data from anchoring studies that included at least two anchors into one large dataset. Data were standardized to comprise one estimate per row, coded according to a wide range of variables, and are available for download and analyses online (https://metaanalyses.shinyapps.io/OpAQ/). Because the dataset includes both original and meta-data it allows for fine-grained analyses (e.g., correlations of estimates for different tasks) but also for meta-analyses (e.g., effect sizes for anchoring effects)

Failures to replicate a key result of the selective accessibility theory of anchoring

Numerical anchoring effects describe the assimilative effect of a previously presented number on subsequent numerical estimates. Such effects are robust and consequential. A number of different accounts have been proposed to explain these effects. What is currently unclear is under which situations different mechanisms play more or less critical roles. An extant test from the literature is proposed as a ‘signature test’ for the operation of selective accessibility mechanisms. Four experiments were conducted to ascertain the evidence for selective accessibility with this test, tests that subsequently failed. A fifth experiment employed a different methodology, and again failed to show evidence for selective accessibility. Subsequent discussion suggests that the robustness of anchoring effects is remarkable, but the theoretical basis for some previous tests of the selective accessibility account of anchoring is shaky, and we advise against its use in this capacity

Gene amplification as a form of population-level gene expression regulation

Organisms cope with change by taking advantage of transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. Here, we investigate whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using real-time monitoring of gene-copy-number mutations in Escherichia coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy-number and, therefore, expression-level polymorphisms. This amplification-mediated gene expression tuning (AMGET) occurs on timescales that are similar to canonical gene regulation and can respond to rapid environmental changes. Mathematical modelling shows that amplifications also tune gene expression in stochastic environments in which transcription-factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune the expression of any gene, without leaving any genomic signature