The emergence of antimicrobial resistance threatens modern medicine and necessitates more personalized treatment of bacterial infections. Sequencing the whole genome of the pathogen(s) in a clinical sample offers one way to improve clinical microbiology diagnostic services, and has already been adopted for tuberculosis in some countries. A key weakness of a genetics clinical microbiology is it cannot return a result for rare or novel genetic variants and therefore predictive methods are required. Non-synonymous mutations in the S. aureusdfrB gene can be successfully classified as either conferring resistance (or not) by calculating their effect on the binding free energy of the antibiotic, trimethoprim. The underlying approach, alchemical free energy methods, requires large numbers of molecular dynamics simulations to be run. We show that a large number (N = 15) of binding free energies calculated from a series of very short (50 ps) molecular dynamics simulations are able to satisfactorily classify all seven mutations in our clinically derived testset. A result for a single mutation could therefore be returned in less than an hour, thereby demonstrating that this or similar methods are now sufficiently fast and reproducible for clinical use.

The relationship between base pair hydrogen bond proton transfer and the rate of spontaneous single point mutations at ambient temperatures and pressures in aqueous DNA is investigated. By using an ensemble-based multiscale computational modelling method, statistically robust rates of proton transfer for the A:T and G:C base pairs within a solvated DNA dodecamer are calculated. Several different proton transfer pathways are observed within the same base pair. It is shown that, in G:C, the double proton transfer tautomer is preferred, while the single proton transfer process is favoured in A:T. The reported range of rate coefficients for double proton transfer is consistent with recent experimental data. Notwithstanding the approximately 1000 times more common presence of single proton transfer products from A:T, observationally there is bias towards G:C to A:T mutations in a wide range of living organisms. We infer that the double proton transfer reactions between G:C base pairs have a negligible contribution towards this bias for the following reasons: (i) the maximum half-life of the G*:C* tautomer is in the range of picoseconds, which is significantly smaller than the milliseconds it takes for DNA to unwind during replication, (ii) statistically, the majority of G*:C* tautomers revert back to their canonical forms through a barrierless process, and (iii) the thermodynamic instability of the tautomers with respect to the canonical base pairs. Through similar reasoning, we also deduce that proton transfer in the A:T base pair does not contribute to single point mutations in DNA.

Forests increasingly will be used for carbon dioxide removal (CDR) as a natural climate solution, and the implementation of forest-based CDR presents a complex public policy challenge. In this paper, our goal is to review a range of policy tools in place to support use of forests for CDR and demonstrate how concepts from the policy design literature can inform our understanding of this domain. We explore how the utilization of different policy tools shapes our ability to use forests to mitigate and adapt to climate change and consider the challenges of policy mixes and integration, taking a close look at three areas of international forest policy, including the Kyoto Protocol's Clean Development Mechanism, Reducing Emissions from Deforestation and Forest Degradation (REDD+) and voluntary carbon offset markets. As it is our expertise, we then examine in detail the case of the USA as a country that lacks aggressive implementation of national climate policies but has potential to increase CDR through reforestation and existing forest management on both public and private land. For forest-based CDR to succeed, a wide array of policy tools will have to be implemented in a variety of contexts with an eye towards overcoming the challenges of policy design with regard to uncertainty in policy outcomes, policy coherence around managing forests for carbon simultaneously with other goals and integration across governance contexts and levels.

Understanding of the triggers and timing of the rise of complex life ca 2100 to 720 million years ago has expanded dramatically in recent years. This theme issue brings together diverse and novel geochemical and palaeontological data presented as part of the Royal Society ‘ The origin and rise of complex life: integrating models , geochemical and palaeontological data ’ discussion meeting held in September 2019. The individual papers offer prescient insights from multiple disciplines. Here we summarize their contribution towards the goal of the meeting; to create testable hypotheses for the differing roles of changing climate, oceanic redox, nutrient availability, and ecosystem feedbacks across this profound, but enigmatic, transitional period.

The half-billion-year history of animal evolution is characterized by decreasing rates of background extinction. Earth's increasing habitability for animals could result from several processes: (i) a decrease in the intensity of interactions among species that lead to extinctions; (ii) a decrease in the prevalence or intensity of geological triggers such as flood basalt eruptions and bolide impacts; (iii) a decrease in the sensitivity of animals to environmental disturbance; or (iv) an increase in the strength of stabilizing feedbacks within the climate system and biogeochemical cycles. There is no evidence that the prevalence or intensity of interactions among species or geological extinction triggers have decreased over time. There is, however, evidence from palaeontology, geochemistry and comparative physiology that animals have become more resilient to an environmental change and that the evolution of complex life has, on the whole, strengthened stabilizing feedbacks in the climate system. The differential success of certain phyla and classes appears to result, at least in part, from the anatomical solutions to the evolution of macroscopic size that were arrived at largely during Ediacaran and Cambrian time. Larger-bodied animals, enabled by increased anatomical complexity, were increasingly able to mix the marine sediment and water columns, thus promoting stability in biogeochemical cycles. In addition, body plans that also facilitated ecological differentiation have tended to be associated with lower rates of extinction. In this sense, Cambrian solutions to Cambrian problems have had a lasting impact on the trajectory of complex life and, in turn, fundamental properties of the Earth system.

Important evolutionary events such as the Cambrian Explosion have inspired many attempts at explanation: why do they happen when they do? What shapes them, and why do they eventually come to an end? However, much less attention has been paid to the idea of a ‘null hypothesis’—that certain features of such diversifications arise simply through their statistical structure. Such statistical features also appear to influence our perception of the timing of these events. Here, we show in particular that study of unusually large clades leads to systematic overestimates of clade ages from some types of molecular clocks, and that the size of this effect may be enough to account for the puzzling mismatches seen between these molecular clocks and the fossil record. Our analysis of the fossil record of the late Ediacaran to Cambrian suggests that it is likely to be recording a true evolutionary radiation of the bilaterians at this time, and that explanations involving various sorts of cryptic origins for the bilaterians do not seem to be necessary.

Sleep is vital for our physical, emotional and cognitive health. However, adolescents face many challenges where their sleep is concerned. This is reflected in their sleep patterns including the timing of their sleep and how much sleep they achieve on a regular basis: their sleep is characteristically delayed and short. Notably, insufficient sleep is associated with impairments in adolescent functioning. Endogenous and exogenous factors are known to affect sleep at this age. Alterations in the bioregulation of sleep, comprising the circadian timing system and the sleep/wake homeostatic system, represent the intrinsic mechanisms at work. Compounding this, environmental, psychosocial and lifestyle factors may contribute to shortened sleep. This review discusses the amount of sleep gained by adolescents and its implications, the challenges to adolescent sleep and the interventions introduced in an effort to prioritize sleep health in this important developmental period.

The European Working Time Directive (2003) has had a significant impact in reducing the total number of hours worked per week, as well as shift-lengths. There is, however, no agreement on optimal shift-lengths and day/night work balance in different medical specialities. Given the time it takes for clinical events to unfold, particularly in relation to labour, there may be advantages in retaining the 24 hours on-call shift for obstetricians--in the interests of patient care and training. Increasingly seen as a relic of the past, this shift-length merits further research, which should include the impact on clinician well-being.