Persistence of Viruses by qPCR Downstream of Three Effluent-Dominated Rivers in the Western United States

This study was designed to determine the quantitative polymerase chain reaction (qPCR) signal persistence of viruses in three effluent-dominated streams. Samples were collected from the effluent outfall of three wastewater treatment plants in the Western United States and downstream at different locations. All samples were tested for the presence of pepper mild mottle virus (PMMoV), adenoviruses, norovirus GI and GII, Aichi virus, and enteroviruses using qPCR. PMMoV was detected most frequently in 54/57 (94.7%) samples, followed by adenoviruses which was detected in 21/57 (36.8%) samples. PMMoV was detected at all locations downstream and up to 32 km from the discharge point. This study demonstrated that the detection signal of PMMoV was able to persist in wastewater discharges to a greater degree than human enteric viruses in effluent-dominated rivers.     

Preservation of ancient DNA in thermally damaged archaeological bone

Evolutionary biologists are increasingly relying on ancient DNA from archaeological animal bones to study processes such as domestication and population dispersals. As many animal bones found on archaeological sites are likely to have been cooked, the potential for DNA preservation must be carefully considered to maximise the chance of amplification success. Here, we assess the preservation of mitochondrial DNA in a medieval cattle bone assemblage from Coppergate, York, UK. These bones have variable degrees of thermal alterations to bone collagen fibrils, indicative of cooking. Our results show that DNA preservation is not reliant on the presence of intact collagen fibrils. In fact, a greater number of template molecules could be extracted from bones with damaged collagen. We conclude that moderate heating of bone may enhance the retention of DNA fragments. Our results also indicate that ancient DNA preservation is highly variable, even within a relatively recent assemblage from contexts conducive to organic preservation, and that diagenetic parameters based on protein diagenesis are not always useful for predicting ancient DNA survival.     

Effects of sheltering fish on growth of their host corals

Stony corals are the foundation species of tropical reefs, and their structures can harbor a diverse range of mutualist taxa that can confer important benefits, including provision of nutrients. Prominent among the associates of branching coral in the genus Pocillopora are groups of zooplanktivorous damselfishes that take refuge in the coral to avoid their predators. In field and laboratory experiments, we explored the effects of colonies of resident damselfishes on growth of their host corals. Laboratory studies revealed a positive relationship between biomass of fish and output of ammonium. In the field, levels of ammonium were significantly elevated in the water surrounding the branches of Pocillopora occupied by colonies of damselfish, particularly in time periods following active feeding by the fish. Experimental manipulation of the presence of fish on host corals during a month-long field experiment revealed that corals hosting fish grew significantly more than those that lacked fish, and coral growth was positively correlated with the biomass of resident fish. The Pocillopora colonies in the field experiment varied in the degree of openness of their branching structure, and dye studies indicated that this affected their ability to retain waterborne nutrients. Together with biomass of resident fish, colony openness explained 76% of the variation in coral growth rate during the experiment. Corals can exhibit considerable morphological variability, and mutualistic fish respond to colony architecture during habitat selection, with some species preferring more open-branched forms. This makes it likely that corals may face tradeoffs in attracting resident fish and in retaining the nutrients they provide.     

Assessment of 222Rn emanation from ore body and backfill tailings in low-grade underground uranium mine

This paper presents a comparative study of ²²²Rn emanation from the ore and backfill tailings in an underground uranium mine located at Jaduguda, India. The effects of surface area, porosity, ²²⁶Ra and moisture contents on ²²²Rn emanation rate were examined. The study revealed that the bulk porosity of backfill tailings is more than two orders of magnitude than that of the ore. The geometric mean radon emanation rates from the ore body and backfill tailings were found to be 10.01?×?10^?3 and 1.03 Bq m^?2 s^?1, respectively. Significant positive linear correlations between ²²²Rn emanation rate and the ²²⁶Ra content of ore and tailings were observed. For normalised ²²⁶Ra content, the ²²²Rn emanation rate from tailings was found to be 283 times higher than the ore due to higher bulk porosity and surface area. The relative radon emanation from the tailings with moisture fraction of 0.14 was found to be 2.4 times higher than the oven-dried tailings. The study suggested that the mill tailings used as a backfill material significantly contributes to radon emanation as compared to the ore body itself and the ²²⁶Ra content and bulk porosity are the dominant factors for radon emanation into the mine atmosphere.     

A global empirical typology of anthropogenic drivers of environmental change in deltas

It is broadly recognized that river delta systems around the world are under threat from a range of anthropogenic activities. These activities occur at the local delta scale, at the regional river and watershed scale, and at the global scale. Tools are needed to support generalization of results from case studies in specific deltas. Here, we present a methodology for quantitatively constructing an empirical typology of anthropogenic change in global deltas. Utilizing a database of environmental change indicators, each associated with increased relative sea-level rise and coastal wetland loss, a clustering analysis of 48 global deltas provides a quantitative assessment of systems experiencing similar or dissimilar sources and degrees of anthropogenic stress. By identifying quantitatively similar systems, we hope to improve the transferability of scientific results across systems, and increase the effectiveness of delta management best practices. Both K-Means and Affinity Propagation clustering algorithms find similar clusters, with relative stability across small changes in K-Means cluster number. High-latitude deltas appear similar, in terms of anthropogenic environmental stress, to several low-population, low-latitude systems, including the Amazon delta, despite substantially different climatic regimes. Highly urbanized deltas in Southeast Asia form a distinct cluster. By providing a quantitative boundary between groups of delta systems, this approach may also be useful for assessing future delta change and sustainability given projected population growth, urbanization, and economic development trends.     

LES validation of urban flow,part I: flow statistics and frequency distributions

Essential prerequisites for a thorough model evaluation are the availability of problem-specific, quality-controlled reference data and the use of model-specific comparison methods. The work presented here is motivated by the striking lack of proportion between the increasing use of large-eddy simulation (LES) as a standard technique in micro-meteorology and wind engineering and the level of scrutiny that is commonly applied to assess the quality of results obtained. We propose and apply an in-depth, multi-level validation concept that is specifically targeted at the time-dependency of mechanically induced shear-layer turbulence. Near-surface isothermal turbulent flow in a densely built-up city serves as the test scenario for the approach. High-resolution LES data are evaluated based on a comprehensive database of boundary-layer wind-tunnel measurements. From an exploratory data analysis of mean flow and turbulence statistics, a high level of agreement between simulation and experiment is apparent. Inspecting frequency distributions of the underlying instantaneous data proves to be necessary for a more rigorous assessment of the overall prediction quality. From velocity histograms local accuracy limitations due to a comparatively coarse building representation as well as particular strengths of the model to capture complex urban flow features with sufficient accuracy are readily determined. However, the analysis shows that further crucial information about the physical validity of the LES needs to be obtained through the comparison of eddy statistics, which is focused on in part II. Compared with methods that rely on single figures of merit, the multi-level validation strategy presented here supports conclusions about the simulation quality and the model’s fitness for its intended range of application through a deeper understanding of the unsteady structure of the flow.