One misdated sequence of rabbit hemorrhagic disease virus prevents accurate estimation of its nucleotide substitution rate

BACKGROUND: The literature is ripe with phylogenetic estimates of nucleotide substitution rates, especially of measurably evolving species such as RNA viruses. However, it is not known how robust these rate estimates are to inaccuracies in the data, particularly in sampling dates that are used for molecular clock calibration. Here we report on the rate of evolution of the emerging pathogen Rabbit hemorrhagic disease virus (RHDV), which has significantly different rates of evolution for the same outer capsid (VP60) gene published in the literature. In an attempt to reconcile the conflicting data and further elucidate details of RHDV ’s evolutionary history, we undertook fresh Bayesian analyses and employed jackknife control methods to produce robust substitution rate and time to most recent common ancestor (TMRCA) estimates for RHDV based on the VP60 and RNA-dependent RNA polymerase genes. RESULTS: Through these control methods, we were able to identify a single misdated taxon, a passaged lab strain used for vaccine production, which was responsible for depressing the RHDV capsid gene’s rate of evolution by 65%. Without this isolate, the polymerase and the capsid protein genes had nearly identical rates of evolution: 1.90x10(-3) nucleotide substitutions/site/year, ns/s/y, (95% highest probability density (HPD) 1.25x10(-3)-2.55x10(-3)) and 1.91x10(-3) ns/s/y (95% HPD 1.50x10(-3)-2.34x10(-3)), respectively. CONCLUSIONS: After excluding the misdated taxon, both genes support a significantly higher substitution rate as well as a relatively recent emergence of RHDV, and obviate the need for previously hypothesized decades of unobserved diversification of the virus. The control methods show that using even one misdated taxon in a large dataset can significantly skew estimates of evolutionary parameters and suggest that it is better practice to use smaller datasets composed of taxa with unequivocal isolation dates. These jackknife controls would be useful for future tip-calibrated rate analyses that include taxa with ambiguous dates of isolation

Targeted surveillance strategies for efficient detection of novel antibiotic resistance variants.

Genotype-based diagnostics for antibiotic resistance represent a promising alternative to empiric therapy, reducing inappropriate antibiotic use. However, because such assays infer resistance based on known genetic markers, their utility will wane with the emergence of novel resistance. Maintenance of these diagnostics will therefore require surveillance to ensure early detection of novel resistance variants, but efficient strategies to do so remain undefined. We evaluate the efficiency of targeted sampling approaches informed by patient and pathogen characteristics in detecting antibiotic resistance and diagnostic escape variants in Neisseria gonorrhoeae, a pathogen associated with a high burden of disease and antibiotic resistance and the development of genotype-based diagnostics. We show that patient characteristic-informed sampling is not a reliable strategy for efficient variant detection. In contrast, sampling informed by pathogen characteristics, such as genomic diversity and genomic background, is significantly more efficient than random sampling in identifying genetic variants associated with resistance and diagnostic escape

Future Scenarios as a Research Tool: Investigating Climate Change Impacts, Adaptation Options and Outcomes for the Great

Abstract Climate change is a significant future driver of change in coastal social-ecological systems. Our knowledge of impacts, adaptation options, and possible outcomes for marine environments and coastal industries is expanding, but remains limited and uncertain. Alternative scenarios are a way to explore potential futures under a range of conditions. We developed four alternative future scenarios for the Great Barrier Reef and its fishing and tourism industries positing moderate and more extreme (2-3°C above pre-industrial temperatures) warming for 2050 and contrasting 'limited' and 'ideal' ecological and social adaptation. We presented these scenarios to representatives of key stakeholder groups to assess the perceived viability of different social adaptation options to deliver desirable outcomes under varied contexts

Managing fisheries for maximum nutrient yield

Wild-caught fish are a bioavailable source of nutritious food that, if managed strategically, could enhance diet quality for billions of people. However, optimising nutrient production from the sea has not been a priority, hindering development of nutrition-sensitive policies. With fisheries management increasingly effective at rebuilding stocks and regulating sustainable fishing, we can now begin to integrate nutritional outcomes within existing management frameworks. Here, we develop a conceptual foundation for managing fisheries for multispecies Maximum Nutrient Yield (mMNY). We empirically test our approach using size-based models of North Sea and Baltic Sea fisheries and show that mMNY is predicted by the relative contribution of nutritious species to total catch and their vulnerability to fishing, leading to trade-offs between catch and specific nutrients. Simulated nutrient yield curves suggest that vitamin D, which is deficient in Northern European diets, was underfished at fishing levels that returned maximum catch weights. Analysis of global catch data shows there is scope for nutrient yields from most of the world's marine fisheries to be enhanced through nutrient-sensitive fisheries management. With nutrient composition data now widely available, we expect our mMNY framework to motivate development of nutrient-based reference points in specific contexts, such as data-limited fisheries. Managing for mMNY alongside policies that promote access to fish could help close nutrient gaps for coastal populations, maximising the contribution of wild-caught fish to global food and nutrition security

Securing a just space for small-scale fisheries in the blue economy

The vast developmental opportunities offered by the world\u27s coasts and oceans have attracted the attention of governments, private enterprises, philanthropic organizations, and international conservation organizations. High-profile dialogue and policy decisions on the future of the ocean are informed largely by economic and ecological research. Key insights from the social sciences raise concerns for food and nutrition security, livelihoods and social justice, but these have yet to gain traction with investors and the policy discourse on transforming ocean governance. The largest group of ocean-users - women and men who service, fish and trade from small-scale fisheries (SSF) - argue that they have been marginalized from the dialogue between international environmental and economic actors that is determining strategies for the future of the ocean. Blue Economy or Blue Growth initiatives see the ocean as the new economic frontier and imply an alignment with social objectives and SSF concerns. Deeper analysis reveals fundamental differences in ideologies, priorities and approaches. We argue that SSF are being subtly and overtly squeezed for geographic, political and economic space by larger scale economic and environmental conservation interests, jeopardizing the substantial benefits SSF provide through the livelihoods of millions of women and men, for the food security of around four billion consumers globally, and in the developing world, as a key source of micro-nutrients and protein for over a billion low-income consumers. Here, we bring insights from social science and SSF to explore how ocean governance might better account for social dimensions of fisheries

The Erotic and the Vulgar: Visual Culture and Organized Labor's Critique of U.S. Hegemony in Occupied Japan

This essay engages the colonial legacy of postwar Japan by arguing that the political cartoons produced as part of the postwar Japanese labor movement’s critique of U.S. cultural hegemony illustrate how gendered discourses underpinned, and sometimes undermined, the ideologies formally represented by visual artists and the organizations that funded them. A significant component of organized labor’s propaganda rested on a corpus of visual media that depicted women as icons of Japanese national culture. Japan’s most militant labor unions were propagating anti-imperialist discourses that invoked an engendered/endangered nation that accentuated the importance of union roles for men by subordinating, then eliminating, union roles for women

Principles for transformative ocean governance

With a focus on oceans, we collaborated across ecological, social and legal disciplines to respond to the United Nations call for transformation in the ‘2030 Agenda for Sustainable Development’. We developed a set of 13 principles that strategically and critically connect transformative ocean research to transformative ocean governance (complementing the UN Decade for Ocean Science). We used a rigorous, iterative and transparent consensus-building approach to define the principles, which can interact in supporting, neutral or sometimes conflicting ways. We recommend that the principles could be applied as a comprehensive set and discuss how to learn from their interactions, particularly those that reveal hidden tensions. The principles can bring and keep together partnerships for innovative ocean action. This action must respond to the many calls to reform current ocean-use practices which are based on economic growth models that have perpetuated inequities and fuelled conflict and environmental decline

Clinical impairment in premanifest and early Huntington's disease is associated with regionally specific atrophy.

TRACK-HD is a multicentre longitudinal observational study investigating the use of clinical assessments and 3-Tesla magnetic resonance imaging as potential biomarkers for future therapeutic trials in Huntington's disease (HD). The cross-sectional data from this large well-characterized dataset provide the opportunity to improve our knowledge of how the underlying neuropathology of HD may contribute to the clinical manifestations of the disease across the spectrum of premanifest (PreHD) and early HD. Two hundred and thirty nine gene-positive subjects (120 PreHD and 119 early HD) from the TRACK-HD study were included. Using voxel-based morphometry (VBM), grey and white matter volumes were correlated with performance in four domains: quantitative motor (tongue force, metronome tapping, and gait); oculomotor [anti-saccade error rate (ASE)]; cognition (negative emotion recognition, spot the change and the University of Pennsylvania smell identification test) and neuropsychiatric measures (apathy, affect and irritability). After adjusting for estimated disease severity, regionally specific associations between structural loss and task performance were found (familywise error corrected, P < 0.05); impairment in tongue force, metronome tapping and ASE were all associated with striatal loss. Additionally, tongue force deficits and ASE were associated with volume reduction in the occipital lobe. Impaired recognition of negative emotions was associated with volumetric reductions in the precuneus and cuneus. Our study reveals specific associations between atrophy and decline in a range of clinical modalities, demonstrating the utility of VBM correlation analysis for investigating these relationships in HD

Theoretical Overview: The New Mesons

After commenting on the state of contemporary hadronic physics and spectroscopy, I highlight four areas where the action is: searching for the relevant degrees of freedom, mesons with beauty and charm, chiral symmetry and the D_{sJ} levels, and X(3872) and the lost tribes of charmonium.Comment: 10 pages, uses jpconf.cls; talk at First Meeting of the APS Topical Group on Hadronic Physic