Smooth and compactly supported viscous sub-cell shock capturing for Discontinuous Galerkin methods

In this work, a novel artificial viscosity method is proposed using smooth and compactly supported viscosities. These are derived by revisiting the widely used piecewise constant artificial viscosity method of Persson and Peraire as well as the piecewise linear refinement of Klöckner et al. with respect to the fundamental design criteria of conservation and entropy stability. Further investigating the method of modal filtering in the process, it is demonstrated that this strategy has inherent shortcomings, which are related to problems of Legendre viscosities to handle shocks near element boundaries. This problem is overcome by introducing certain functions from the fields of robust reprojection and mollififers as viscosity distributions. To the best of our knowledge, this is proposed for the first time in this work. The resulting $C_0^\infty$ artificial viscosity method is demonstrated to provide sharper profiles, steeper gradients and a higher resolution of small-scale features while still maintaining stability of the method

Different histories but similar genetic diversity and structure for black walnut in Indiana and Missouri

—Missouri and Indiana have markedly different histories of glaciation and recolonization by forest trees. These states also differ in land use patterns and degree of anthropogenic landscape change such as forest fragmentation. To determine the overall effects of these and other demographic differences on the levels of genetic diversity and structure in black walnut (Juglans nigra L.) more than 550 total black walnut trees from nine populations in Indiana and 10 in Missouri were sampled and analyzed using 12 nuclear microsatellite loci. Although genetic diversity parameters such as allelic richness and expected heterozygosity were high overall, they varied little among populations and their mean values for the two states were not significantly different. Pairwise genetic distance values between all population pairs ranged from 0.012-0.159, but no significant pattern of isolation by distance was detected. The estimate of the degree of genetic differentiation between states (FPT = 0.0009) was very small and not significant, indicating that differences between states explained an inconsequential portion of the total variance. The observed low levels of local and regional genetic structure indicate that high levels of pollen flow have buffered black walnut from the genetic consequences of founder effects and genetic drift in both geologic and recent time scales

Phylogenomic and functional characterization of an evolutionary conserved cytochrome P450-based insecticide detoxification mechanism in bees

This is the final version. Available on open access from the National Academy of Sciences via the DOI in this recordData Availability: All study data are included in the article and/or SI Appendix.The regulatory process for assessing the risks of pesticides to bees relies heavily on the use of the honeybee, Apis mellifera, as a model for other bee species. However, the validity of using A. mellifera as a surrogate for other Apis and non-Apis bees in pesticide risk assessment has been questioned. Related to this line of research, recent work on A. mellifera has shown that specific P450 enzymes belonging to the CYP9Q subfamily act as critically important determinants of insecticide sensitivity in this species by efficiently detoxifying certain insecticide chemotypes. However, the extent to which the presence of functional orthologs of these enzymes is conserved across the diversity of bees is unclear. Here we used a phylogenomic approach to identify > 100 putative CYP9Q functional orthologs across 75 bee species encompassing all major bee families. Functional analysis of 26 P450s from 20 representative bee species revealed that P450-mediated detoxification of certain systemic insecticides, including the neonicotinoid thiacloprid and the butenolide flupyradifurone, is conserved across all major bee pollinator families. However, our analyses also reveal that CYP9Q-related genes are not universal to all bee species, with some Megachilidae species lacking such genes. Thus, our results reveal an evolutionary conserved capacity to metabolize certain insecticides across all major bee families while identifying a small number of bee species where this function may have been lost. Furthermore, they illustrate the potential of a toxicogenomic approach to inform pesticide risk assessment for nonmanaged bee species by predicting the capability of bee pollinator species to break down synthetic insecticides.Biotechnology & Biological Sciences Research Council (BBSRC

A toxicogenomics approach reveals characteristics supporting the honey bee (Apis mellifera L.) safety profile of the butenolide insecticide flupyradifurone

This is the final version. Available on open access from Elsevier via the DOI in this recordFlupyradifurone, a novel butenolide insecticide, selectively targets insect nicotinic acetylcholine receptors (nAChRs), comparable to structurally different insecticidal chemotypes such as neonicotinoids and sulfoximines. However, flupyradifurone was shown in acute toxicity tests to be several orders of magnitude less toxic to western honey bee (Apis mellifera L.) than many other insecticides targeting insect nAChRs. The underlying reasons for this difference in toxicity remains unknown and were investigated here. Pharmacokinetic studies after contact application of [14C]flupyradifurone to honey bees revealed slow uptake, with internalized compound degraded into a few metabolites that are all practically non-toxic to honey bees in both oral and contact bioassays. Furthermore, receptor binding studies revealed a lack of high-affinity binding of these metabolites to honey bee nAChRs. Screening of a library of 27 heterologously expressed honey bee cytochrome P450 enzymes (P450s) identified three P450s involved in the detoxification of flupyradifurone: CYP6AQ1, CYP9Q2 and CYP9Q3. Transgenic Drosophila lines ectopically expressing CYP9Q2 and CYP9Q3 were significantly less susceptible to flupyradifurone when compared to control flies, confirming the importance of these P450s for flupyradifurone metabolism in honey bees. Biochemical assays using the fluorescent probe substrate 7-benzyloxymethoxy-4-(trifluoromethyl)-coumarin (BOMFC) indicated a weak, non-competitive inhibition of BOMFC metabolism by flupyradifurone. In contrast, the azole fungicides prochloraz and propiconazole were strong nanomolar inhibitors of these flupyradifurone metabolizing P450s, explaining their highly synergistic effects in combination with flupyradifurone as demonstrated in acute laboratory contact toxicity tests of adult bees. Interestingly, the azole fungicide prothioconazole is only slightly synergistic in combination with flupyradifurone - an observation supported by molecular P450 inhibition assays. Such molecular assays have value in the prediction of potential risks posed to bees by flupyradifurone mixture partners under applied conditions. Quantitative PCR confirmed the expression of the identified P450 genes in all honey bee life-stages, with highest expression levels observed in late larvae and adults, suggesting honey bees have the capacity to metabolize flupyradifurone across all life-stages. These findings provide a biochemical explanation for the low intrinsic toxicity of flupyradifurone to honey bees and offer a new, more holistic approach to support bee pollinator risk assessment by molecular means

Genetic divergence in two tropical maize composites after four cycles of reciprocal recurrent selection

First published: 6 January 2017; Open Access JournalTwo tropical maize composites were subjected to four cycles of reciprocal recurrent selection to develop divergent inbred lines with good combining ability. This study was conducted to examine the extent of genetic diversity, changes in allele composition and genetic structure, of 100 randomly selected S1 lines each from the original (C0) and advanced (C4) selection cycles of TZL COMP3 and TZL COMP4, genotyped using single nucleotide polymorphism (SNP) markers. Results revealed that the proportion of alleles at both low and high frequencies decreased from C0 to C4, whereas those at intermediate frequencies increased at C4 in the two composites. More unique and other alleles were lost at C4 in TZL COMP3 relative to those in TZL COMP4. The changes in different measures of genetic diversity were either small or negligible with selection in the two composites. The proportion of markers departing from Hardy–Weinberg equilibrium (HWE) decreased with selection, whereas the total number of pairs of markers in linkage disequilibrium increased with selection in the two composites. Examination of changes in population structures using a model-based approach as well as cluster and multivariate analyses found a high degree of concordance in stratifying the 400 S1 lines into four non-overlapping groups corresponding to the two selection cycles each within the reciprocal composites. The observed molecular-based divergence between cycles within the same composite and the clear differentiation between the complementary composites highlight the importance of reciprocal recurrent selection for preserving genetic diversity for long-term selection. This increases the potential of the advanced selection cycles to sustain genetic gain in productivity of hybrids adapted to the savannas in West and Central Africa

Variable Expression of Cre Recombinase Transgenes Precludes Reliable Prediction of Tissue-Specific Gene Disruption by Tail-Biopsy Genotyping

The Cre/loxP-system has become the system of choice for the generation of conditional so-called knockout mouse strains, i.e. the tissue-specific disruption of expression of a certain target gene. We here report the loss of expression of Cre recombinase in a transgenic mouse strain with increasing number of generations. This eventually led to the complete abrogation of gene expression of the inserted Cre cDNA while still being detectable at the genomic level. Conversely, loss of Cre expression caused an incomplete or even complete lack of disruption for the protein under investigation. As Cre expression in the tissue of interest in most cases cannot be addressed in vivo during the course of a study, our findings implicate the possibility that individual tail-biopsy genotypes may not necessarily indicate the presence or absence of gene disruption. This indicates that sustained post hoc analyses in regards to efficacy of disruption for every single study group member may be required

High-Resolution 3D Structure Determination of Kaliotoxin by Solid-State NMR Spectroscopy

High-resolution solid-state NMR spectroscopy can provide structural information of proteins that cannot be studied by X-ray crystallography or solution NMR spectroscopy. Here we demonstrate that it is possible to determine a protein structure by solid-state NMR to a resolution comparable to that by solution NMR. Using an iterative assignment and structure calculation protocol, a large number of distance restraints was extracted from 1H/1H mixing experiments recorded on a single uniformly labeled sample under magic angle spinning conditions. The calculated structure has a coordinate precision of 0.6 Å and 1.3 Å for the backbone and side chain heavy atoms, respectively, and deviates from the structure observed in solution. The approach is expected to be applicable to larger systems enabling the determination of high-resolution structures of amyloid or membrane proteins