Focus on high energy particles and atmospheric processes

The letters published in the ‘Focus issue on high energy particles and atmospheric processes’ serve to broaden the discussion about the influence of high energy particles on the atmosphere beyond their possible effects on clouds and climate. These letters link climate and meteorological processes with atmospheric electricity, atmospheric chemistry, high energy physics and aerosol science from the smallest molecular cluster ions through to liquid droplets. Progress in such a disparate and complex topic is very likely to benefit from continued interdisciplinary interactions between traditionally distinct science areas

CHASE-PL Climate Projection dataset over Poland – bias adjustment of EURO-CORDEX simulations

The CHASE-PL (Climate change impact assessment for selected sectors in Poland) Climate Projections – Gridded Daily Precipitation and Temperature dataset 5 km (CPLCP-GDPT5) consists of projected daily minimum and maximum air temperatures and precipitation totals of nine EURO-CORDEX regional climate model outputs bias corrected and downscaled to a 5 km  ×  5 km grid. Simulations of one historical period (1971–2000) and two future horizons (2021–2050 and 2071–2100) assuming two representative concentration pathways (RCP4.5 and RCP8.5) were produced. We used the quantile mapping method and corrected any systematic seasonal bias in these simulations before assessing the changes in annual and seasonal means of precipitation and temperature over Poland. Projected changes estimated from the multi-model ensemble mean showed that annual means of temperature are expected to increase steadily by 1 °C until 2021–2050 and by 2 °C until 2071–2100 assuming the RCP4.5 emission scenario. Assuming the RCP8.5 emission scenario, this can reach up to almost 4 °C by 2071–2100. Similarly to temperature, projected changes in regional annual means of precipitation are expected to increase by 6 to 10 % and by 8 to 16 % for the two future horizons and RCPs, respectively. Similarly, individual model simulations also exhibited warmer and wetter conditions on an annual scale, showing an intensification of the magnitude of the change at the end of the 21st century. The same applied for projected changes in seasonal means of temperature showing a higher winter warming rate by up to 0.5 °C compared to the other seasons. However, projected changes in seasonal means of precipitation by the individual models largely differ and are sometimes inconsistent, exhibiting spatial variations which depend on the selected season, location, future horizon, and RCP. The overall range of the 90 % confidence interval predicted by the ensemble of multi-model simulations was found to likely vary between −7 % (projected for summer assuming the RCP4.5 emission scenario) and +40 % (projected for winter assuming the RCP8.5 emission scenario) by the end of the 21st century. Finally, this high-resolution bias-corrected product can serve as a basis for climate change impact and adaptation studies for many sectors over Poland. The CPLCP-GDPT5 dataset is publicly available at http://dx.doi.org/10.4121/uuid:e940ec1a-71a0-449e-bbe3-29217f2ba31d

The emergence of classical BSE from atypical/Nor98 scrapie

Atypical/Nor98 scrapie (AS) is a prion disease of small ruminants. Currently there are no efficient measures to control this form of prion disease, and, importantly, the zoonotic potential and the risk that AS might represent for other farmed animal species remains largely unknown. In this study, we investigated the capacity of AS to propagate in bovine PrP transgenic mice. Unexpectedly, the transmission of AS isolates originating from 5 different European countries to bovine PrP mice resulted in the propagation of the classical BSE (c-BSE) agent. Detection of prion seeding activity in vitro by protein misfolding cyclic amplification (PMCA) demonstrated that low levels of the c-BSE agent were present in the original AS isolates. C-BSE prion seeding activity was also detected in brain tissue of ovine PrP mice inoculated with limiting dilutions (endpoint titration) of ovine AS isolates. These results are consistent with the emergence and replication of c-BSE prions during the in vivo propagation of AS isolates in the natural host. These data also indicate that c-BSE prions, a known zonotic agent in humans, can emerge as a dominant prion strain during passage of AS between different species. These findings provide an unprecedented insight into the evolution of mammalian prion strain properties triggered by intra- and interspecies passage. From a public health perspective, the presence of c-BSE in AS isolates suggest that cattle exposure to small ruminant tissues and products could lead to new occurrences of c-BSE

A statistical downscaling framework for environmental mapping

In recent years, knowledge extraction from data has become increasingly popular, with many numerical forecasting models, mainly falling into two major categories—chemical transport models (CTMs) and conventional statistical methods. However, due to data and model variability, data-driven knowledge extraction from high-dimensional, multifaceted data in such applications require generalisations of global to regional or local conditions. Typically, generalisation is achieved via mapping global conditions to local ecosystems and human habitats which amounts to tracking and monitoring environmental dynamics in various geographical areas and their regional and global implications on human livelihood. Statistical downscaling techniques have been widely used to extract high-resolution information from regional-scale variables produced by CTMs in climate model. Conventional applications of these methods are predominantly dimensional reduction in nature, designed to reduce spatial dimension of gridded model outputs without loss of essential spatial information. Their downside is twofold—complete dependence on unlabelled design matrix and reliance on underlying distributional assumptions. We propose a novel statistical downscaling framework for dealing with data and model variability. Its power derives from training and testing multiple models on multiple samples, narrowing down global environmental phenomena to regional discordance through dimensional reduction and visualisation. Hourly ground-level ozone observations were obtained from various environmental stations maintained by the US Environmental Protection Agency, covering the summer period (June–August 2005). Regional patterns of ozone are related to local observations via repeated runs and performance assessment of multiple versions of empirical orthogonal functions or principal components and principal fitted components via an algorithm with fully adaptable parameters. We demonstrate how the algorithm can be extended to weather-dependent and other applications with inherent data randomness and model variability via its built-in interdisciplinary computational power that connects data sources with end-users

Analysis of multiple single nucleotide polymorphisms closely positioned in the ovine PRNP gene using linear fluorescent probes and melting curve analysis

<p>Abstract</p> <p>Background</p> <p>Resistance and susceptibility to scrapie has been associated with single nucleotide polymorphisms located within codons 136, 154 and 171 of the ovine prion protein gene (<it>PRNP</it>). Dual-labelled HyBeacon probes were developed to analyse single and clustered polymorphisms within these and neighbouring codons.</p> <p>Methods</p> <p>Extracted DNAs and unpurified blood samples were genotyped with respect to polymorphisms in <it>PRNP </it>codons 136, 141, 154 and 171. PCR amplicons were investigated using a LightTyper instrument, measuring the stability of probe/target hybridisation through peak melting temperatures and determining the sequence of nucleotides at polymorphic sites.</p> <p>Results</p> <p>The performance of HyBeacon assays was evaluated in a validation study comparing genotypes with those obtained using a primer extension assay (Sequenom MassEXTEND) analysed on a MALDI-ToF mass spectrometer. Over 12,000 sheep samples were successfully genotyped, reliably detecting A¹³⁶, V¹³⁶, T¹³⁶, T¹³⁷, L¹⁴¹, F¹⁴¹R¹⁵⁴, H¹⁵⁴, L¹⁶⁸, R¹⁷¹, Q¹⁷¹, H¹⁷¹and K¹⁷¹sequence variants using only 4 HyBeacon probes.</p> <p>Conclusion</p> <p>HyBeacon assays provide an extremely robust and accurate method for the analysis of single and clustered <it>PRNP </it>polymorphisms in a high-throughput format. The flexibility of the diagnostic tests ensures that samples are correctly genotyped even in the presence of additional sequence variations that flank the polymorphisms of interest. Such sequence variations may also be neutralised using universal bases such as 5-nitroindole if required.</p

Atypical/Nor98 Scrapie Infectivity in Sheep Peripheral Tissues

Atypical/Nor98 scrapie was first identified in 1998 in Norway. It is now considered as a worldwide disease of small ruminants and currently represents a significant part of the detected transmissible spongiform encephalopathies (TSE) cases in Europe. Atypical/Nor98 scrapie cases were reported in ARR/ARR sheep, which are highly resistant to BSE and other small ruminants TSE agents. The biology and pathogenesis of the Atypical/Nor98 scrapie agent in its natural host is still poorly understood. However, based on the absence of detectable abnormal PrP in peripheral tissues of affected individuals, human and animal exposure risk to this specific TSE agent has been considered low. In this study we demonstrate that infectivity can accumulate, even if no abnormal PrP is detectable, in lymphoid tissues, nerves, and muscles from natural and/or experimental Atypical/Nor98 scrapie cases. Evidence is provided that, in comparison to other TSE agents, samples containing Atypical/Nor98 scrapie infectivity could remain PrPSc negative. This feature will impact detection of Atypical/Nor98 scrapie cases in the field, and highlights the need to review current evaluations of the disease prevalence and potential transmissibility. Finally, an estimate is made of the infectivity loads accumulating in peripheral tissues in both Atypical/Nor98 and classical scrapie cases that currently enter the food chain. The results obtained indicate that dietary exposure risk to small ruminants TSE agents may be higher than commonly believed

Robust projections of Fire Weather Index in the Mediterranean using statistical downscaling

The effect of climate change on wildfires constitutes a serious concern in fire-prone regions with complex fire behavior such as the Mediterranean. The coarse resolution of future climate projections produced by General Circulation Models (GCMs) prevents their direct use in local climate change studies. Statistical downscaling techniques bridge this gap using empirical models that link the synoptic-scale variables from GCMs to the local variables of interest (using e.g. data from meteorological stations). In this paper, we investigate the application of statistical downscaling methods in the context of wildfire research, focusing in the Canadian Fire Weather Index (FWI), one of the most popular fire danger indices. We target on the Iberian Peninsula and Greece and use historical observations of the FWI meteorological drivers (temperature, humidity, wind and precipitation) in several local stations. In particular, we analyze the performance of the analog method, which is a convenient first choice for this problem since it guarantees physical and spatial consistency of the downscaled variables, regardless of their different statistical properties. First we validate the method in perfect model conditions using ERA-Interim reanalysis data. Overall, not all variables are downscaled with the same accuracy, with the poorest results (with spatially averaged daily correlations below 0.5) obtained for wind, followed by precipitation. Consequently, those FWI components mostly relying on those parameters exhibit the poorest results. However, those deficiencies are compensated in the resulting FWI values due to the overall high performance of temperature and relative humidity. Then, we check the suitability of the method to downscale control projections (20C3M scenario) from a single GCM (the ECHAM5 model) and compute the downscaled future fire danger projections for the transient A1B scenario. In order to detect problems due to non-stationarities related to climate change, we compare the results with those obtained with a Regional Climate Model (RCM) driven by the same GCM. Although both statistical and dynamical projections exhibit a similar pattern of risk increment in the first half of the 21st century, they diverge during the second half of the century. As a conclusion, we advocate caution in the use of projections for this last period, regardless of the regionalization technique applied.We are grateful to the Spanish Meteorological Agency (AEMET) and to the Hellenic National Meteorological Service (HNMS) for providing the observational data used in this study. We would also like to thank Erik van Meijgaard from the Royal Netherlands Meteorological Institute for making available ENSEMBLES RACMO2 climate model output verifying at 12:00 UTC and to the Max Planck Institute for providing the appropriate data for the ECHAM5 model used in this work. This work was partly funded by European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreements 243888 (FUME Project) and from Spanish Ministry MICINN under grant EXTREMBLES (CGL2010-21869). We thank tw