Metagenomics for the study of viruses in urban sewage as a tool for public health surveillance

The application of next-generation sequencing (NGS) techniques for the identification of viruses present in urban sewage has not been fully explored. This is partially due to a lack of reliable and sensitive protocols for studying viral diversity and to the highly complex analysis required for NGS data processing. One important step towards this goal is finding methods that can efficiently concentrate viruses from sewage samples. Here the application of a virus concentration method based on skimmed milk organic flocculation (SMF) using 10 L of sewage collected in different seasons enabled the detection of many viruses. However, some viruses, such as human adenoviruses, could not always be detected using metagenomics, even when quantitative PCR (qPCR) assessments were positive. A targeted metagenomic assay for adenoviruses was conducted and 59.41% of the obtained reads were assigned to murine adenoviruses. However, up to 20 different human adenoviruses (HAdV) were detected by this targeted assay being the most abundant HAdV-41 (29.24%) and HAdV-51 (1.63%). To improve metagenomics' sensitivity, two different protocols for virus concentration were comparatively analysed: an ultracentrifugation protocol and a lower-volume SMF protocol. The sewage virome contained 41 viral families, including pathogenic viral species from families Caliciviridae, Adenoviridae, Astroviridae, Picornaviridae, Polyomaviridae, Papillomaviridae and Hepeviridae. The contribution of urine to sewage metavirome seems to be restricted to a few specific DNA viral families, including the polyomavirus and papillomavirus species. In experimental infections with sewage in a rhesus macaque model, infective human hepatitis E and JC polyomavirus were identified. Urban raw sewage consists of the excreta of thousands of inhabitants; therefore, it is a representative sample for epidemiological surveillance purposes. The knowledge of the metavirome is of significance to public health, highlighting the presence of viral strains that are circulating within a population while acting as a complex matrix for viral discovery. (c) 2017 Elsevier B.V. All rights reserved

Insights into the Late Mesolithic toolkit: use-wear analysis of the notched blades. Case-studies from the Iberian Peninsula

During the last decades we have gained a considerable amount of data about the Mesolithic lithic toolkit in the Western Mediterranean. A large set of instruments probably existed for a variety of pur-poses: foraging practices (both hunting and fishing), food processing, crafting activities, etc. Dispos-able tools, scarcely elaborated, coexisted with formal and more complex instruments, often com-posed of multiple parts and realized on a variety of raw-materials (e.g. stone, shell or bone inserts; bone or wood hafts, etc.). In this paper we will consider one particular type of tool that appears in the Western Mediterranean starting from the Seventh-Sixth millennia BC: the notched and denticulated blades. We will consider and interpret from a functional viewpoint materials from five different Late Mesolithic contexts: the Cocina Cave and Vallmayor IX in the NE of the Peninsula, Artusia rock-shel-ters in Navarre and Atxoste and Mendandia rock-shelters in the Basque country

New insights into the neolithisation process in southwest Europe according to spatial density analysis from calibrated radiocarbon dates

The agricultural way of life spreads throughout Europe via two main routes: the Danube corridor and the Mediterranean basin. Current archaeological literature describes the arrival to the Western Mediterranean as a rapid process which involves both demic and cultural models, and in this regard, the dispersal movement has been investigated using mathematical models, where the key factors are time and space. In this work, we have created a compilation of all available radiocarbon dates for the whole of Iberia, in order to draw a chronological series of maps to illustrate temporal and spatial patterns in the neolithisation process. The maps were prepared by calculating the calibrated 14C date probability density curves, as a proxy to show the spatial dynamics of the last hunter-gatherers and first farmers. Several scholars have pointed out problems linked with the variability of samples, such as the overrepresentation of some sites, the degree of regional research, the nature of the dated samples and above all the archaeological context, but we are confident that the selected dates, after applying some filters and statistical protocols, constitute a good way to approach settlement spatial patterns in Iberia at the time of the neolithisation process

Evaluating natural capital performance of urban development through system dynamics: A case study from London.

Natural capital plays a central role in urban functioning, reducing flooding, mitigating urban heat island effects, reducing air pollution, and improving urban biodiversity through provision of habitat space. There is also evidence on the role played by blue and green space in improving physical and mental health, reducing the burden on the health care service. Yet from an urban planning and development view, natural capital may be considered a nice to have, but not essential element of urban design; taking up valuable space which could otherwise be used for traditional built environment uses. While urban natural capital is largely recognised as a positive element, its benefits are difficult to measure both in space and time, making its inclusion in urban (re)development difficult to justify. Here, using a London case study and information provided by key stakeholders, we present a system dynamics (SD) modelling framework to assess the natural capital performance of development and aid design evaluation. A headline indicator: Natural Space Performance, is used to evaluate the capacity of natural space to provide ecosystem services, providing a semi-quantitative measure of system wide impacts of change within a combined natural, built and social system. We demonstrate the capacity of the model to explore how combined or individual changes in development design can affect natural capital and the provision of ecosystem services, for example, biodiversity or flood risk. By evaluating natural capital and ecosystem services over time, greater justification for their inclusion in planning and development can be derived, providing support for increased blue and green space within cities, improving urban sustainability and enhancing quality of life. Furthermore, the application of a SD approach captures key interactions between variables over time, showing system evolution while highlighting intervention opportunities

Be-10-derived Himalayan denudation rates and sediment budgets in the Ganga basin

The Himalayas represent the archetype of mountain building due to active continental collision and are considered in many studies as the locus of intense interactions between climate, denudation and tectonics. Estimates of modern denudation rates across the entire range remain, however, relatively sparse. In this study, in situ-produced cosmogenic Be-10 concentrations were measured in detritic quartz in order to determine basin-scale denudation rates for the central part of the Himalayan range. River sand was sampled over several years in the main trans-Himalayan rivers, from the Himalayan front to the Ganga outlet in Bangladesh. The calculated Be-10 denudation rates of the trans-Himalayan river basins range from 0.5 to 2.4 mm yr(-1) (average 1.3 mm yr(-1)) and vary by up to a factor of 3 between sampling years. These denudation rates strongly contrast with the 0.007 mm yr(-1) denudation rate of southern tributary basins draining the Indian craton. This work also shows that in the Ganga basin, no systematic evolution of average Be-10 concentrations is observed during floodplain transfer, implying that distal samples can be used to estimate the integrated denudation rate of the whole central Himalayan range. Samples from the Ganga in Bangladesh display remarkably low variability in Be-10 concentration, implying an average Himalayan denudation rate of 1.0-1.1 mm yr(-1). However, within the floodplain, several samples suggest a recent perturbation of sediment transport dynamics with a recent increase in the relative sediment contribution from southern tributaries. The Himalayan sediment flux, deduced from the Be-10 denudation rate of the range, is 610 +/- 230 Mt yr(-1). This flux is consistent, within uncertainty, with sediment fluxes derived from sediment gauging. The similarity of the two flux estimates suggests that Himalayan erosion fluxes have remained stable over the last centuries, even if the large uncertainties associated with each method hamper more precise assessments

Paleo-erosion rates in Central Asia since 9 Ma: A transient increase at the onset of Quaternary glaciations?

Erosion is a fundamental player of the interactions existing between internal geodynamics and climate, in particular through its influence on the carbon dioxide budget. However, long term (> Ma) erosion rates, estimated indirectly from sediment budget, remain poorly constrained. While some studies suggest that worldwide erosion rates increased at the Plio-Pleistocene climatic transition (~4–2 Ma), the validity of this observation and its significance is a matter of debate due to potential biases of the sedimentary record and to the influence of sea level fall on the global sedimentary flux to marginal basins. In the present study, we estimate erosion rates over the last ~9 Ma using in situ produced cosmogenic ^(10)Be concentrations measured in magnetostratigraphically dated continental sediments. We focus on an intracontinental endorheic watershed draining the northern Tianshan in Central Asia, a key region regarding the ongoing debate. While erosion rates between 0.1 and 1 mm·yr^(−1) are derived from most of our record, they reach values as high as ~2.5 mm·yr^(−1) from 2.5 to 1.7 Ma. Then, after 1.7 Ma, recent andmodern erosion rates fell below 1 mm·yr^(−1). This temporary increase is correlated with the onset of Quaternary ice ages and suggests that global climate had a significant and transient impact on erosion