BaitFisher: A software package for multispecies target DNA enrichment probe design

Christoph Urs Mayer [et al.]Target DNA enrichment combined with high-throughput sequencing technologies is a powerful approach to probing a large number of loci in genomes of interest. However, software algorithms that explicitly consider nucleotide sequence information of target loci in multiple reference species for optimizing design of target enrichment baits to be applicable across a wide range of species have not been developed. Here we present an algorithm that infers target DNA enrichment baits from multiple nucleotide sequence alignments. By applying clustering methods and the combinatorial 1-center sequence optimization to bait design, we are able to minimize the total number of baits required to efficiently probe target loci in multiple species. Consequently, more loci can be probed across species with a given number of baits. Using transcript sequences of 24 apoid wasps (Hymenoptera: Crabronidae, Sphecidae) from the 1KITE project and the gene models of Nasonia vitripennis, we inferred 57,650, 120-bp-long baits for capturing 378 coding sequence sections of 282 genes in apoid wasps. Illumina reduced-representation library sequencing confirmed successful enrichment of the target DNA when applying these baits to DNA of various apoid wasps. The designed baits furthermore enriched a major fraction of the target DNA in distantly related Hymenoptera, such as Formicidae and Chalcidoidea, highlighting the baits' broad taxonomic applicability. The availability of baits with broad taxonomic applicability is of major interest in numerous disciplines, ranging from phylogenetics to biodiversity monitoring. We implemented our new approach in a software package, called BaitFisher, which is open source and freely available at https://github.com/cmayer/BaitFisher-package.git.C.B. is a “Ramon y Cajal” fellow supported by the Spanish Ministry of Science and Education (MEC) (RYC-2014-15615).Peer Reviewe

Widespread pesticide distribution in the European atmosphere questions their degradability in air

Risk assessment of pesticide impacts on remote ecosystems makes use of model-estimated degradation in air. Recent studies suggest these degradation rates to be overestimated, questioning current pesticide regulation. Here, we investigated the concentrations of 76 pesticides in Europe at 29 rural, coastal, mountain, and polar sites during the agricultural application season. Overall, 58 pesticides were observed in the European atmosphere. Low spatial variation of 7 pesticides suggests continental-scale atmospheric dispersal. Based on concentrations in free tropospheric air and at Arctic sites, 22 pesticides were identified to be prone to long-range atmospheric transport, which included 15 substances approved for agricultural use in Europe and 7 banned ones. Comparison between concentrations at remote sites and those found at pesticide source areas suggests long atmospheric lifetimes of atrazine, cyprodinil, spiroxamine, tebuconazole, terbuthylazine, and thiacloprid. In general, our findings suggest that atmospheric transport and persistence of pesticides have been underestimated and that their risk assessment needs to be improved

Benchmarking of reactive transport codes for 2D simulations with mineral dissolution–precipitation reactions and feedback on transport parameters

Porosity changes due to mineral dissolution–precipitation reactions in porous media and the resulting impact on transport parameters influence the evolution of natural geological environments or engineered underground barrier systems. In the absence of long-term experimental studies, reactive transport codes are used to evaluate the long-term evolution of engineered barrier systems and waste disposal in the deep underground. Examples for such problems are the long-term fate of CO2 in saline aquifers and mineral transformations that cause porosity changes at clay–concrete interfaces. For porosity clogging under a diffusive transport regime and for simple reaction networks, the accuracy of numerical codes can be verified against analytical solutions. For clogging problems with more complex chemical interactions and transport processes, numerical benchmarks are more suitable to assess model performance, the influence of thermodynamic data, and sensitivity to the reacting mineral phases. Such studies increase confidence in numerical model descriptions of more complex, engineered barrier systems. We propose a reactive transport benchmark, considering the advective–diffusive transport of solutes; the effect of liquid-phase density on liquid flow and advective transport; kinetically controlled dissolution–precipitation reactions causing porosity, permeability, and diffusivity changes; and the formation of a solid solution. We present and analyze the results of five participating reactive transport codes (i.e., CORE2D, MIN3P-THCm, OpenGeoSys-GEM, PFLOTRAN, and TOUGHREACT). In all cases, good agreement of the results was obtained

Treatment of resistant fever: New method of local cerebral cooling

BACKGROUND: Fever in neurocritical care patients is common and has a negative impact on neurological outcome. The purpose of this prospective observational study was (1) to evaluate the practicability of cooling with newly developed neck pads in the daily setting of neurointensive care unit (NICU) patients and (2) to evaluate its effectiveness as a surrogate endpoint to indicate the feasibility of neck cooling as a new method for intractable fever. METHODS: Nine patients with ten episodes of intractable fever and aneurysmal subarachnoid hemorrhage were treated with one of two different shapes of specifically adapted cooling neck pads. Temperature values of the brain, blood, and urinary bladder were taken close meshed after application of the cooling neck pads up to hour 8. RESULTS: The brain, blood, and urinary bladder temperatures decreased significantly from hour 0 to a minimum in hour 5 (P < 0.01). After hour 5, instead of continuous cooling in all the patients, the temperature of all the three sites remounted. CONCLUSION: This study showed the practicability of local cooling for intractable fever using the newly developed neck pads in the daily setting of NICU patients