Genome of Drosophila suzukii, the spotted wing drosophila.

Drosophila suzukii Matsumura (spotted wing drosophila) has recently become a serious pest of a wide variety of fruit crops in the United States as well as in Europe, leading to substantial yearly crop losses. To enable basic and applied research of this important pest, we sequenced the D. suzukii genome to obtain a high-quality reference sequence. Here, we discuss the basic properties of the genome and transcriptome and describe patterns of genome evolution in D. suzukii and its close relatives. Our analyses and genome annotations are presented in a web portal, SpottedWingFlyBase, to facilitate public access

Energetic particle induced intra-seasonal variability of ozone inside the Antarctic polar vortex observed in satellite data

Measurements from 2002 to 2011 by three independent satellite instruments, namely MIPAS, SABER, and SMR on board the ENVISAT, TIMED, and Odin satellites are used to investigate the intra-seasonal variability of stratospheric and mesospheric O3 volume mixing ratio (vmr) inside the Antarctic polar vortex due to solar and geomagnetic activity. In this study, we individually analysed the relative O3 vmr variations between maximum and minimum conditions of a number of solar and geomagnetic indices (F10.7 cm solar radio flux, Ap index, >= 2 MeV electron flux). The indices are 26-day averages centred at 1 April, 1 May, and 1 June while O3 is based on 26-day running means from 1 April to 1 November at altitudes from 20 to 70 km. During solar quiet time from 2005 to 2010, the composite of all three instruments reveals an apparent negative O3 signal associated to the geomagnetic activity (Ap index) around 1 April, on average reaching amplitudes between -5 and -10% of the respective O3 background. The O3 response exceeds the significance level of 95% and propagates downwards throughout the polar winter from the stratopause down to ~ 25 km. These observed results are in good qualitative agreement with the O3 vmr pattern simulated with a three-dimensional chemistry-transport model, which includes particle impact ionisation

Energetic particle induced intra-seasonal variability of ozone inside the Antarctic polar vortex observed in satellite data

Measurements from 2002 to 2011 by three independent satellite instruments, namely MIPAS, SABER, and SMR on board the ENVISAT, TIMED, and Odin satellites are used to investigate the intra-seasonal variability of stratospheric and mesospheric O3 volume mixing ratio (vmr) inside the Antarctic polar vortex due to solar and geomagnetic activity. In this study, we individually analysed the relative O3 vmr variations between maximum and minimum conditions of a number of solar and geomagnetic indices (F10.7 cm solar radio flux, Ap index, >= 2 MeV electron flux). The indices are 26-day averages centred at 1 April, 1 May, and 1 June while O3 is based on 26-day running means from 1 April to 1 November at altitudes from 20 to 70 km. During solar quiet time from 2005 to 2010, the composite of all three instruments reveals an apparent negative O3 signal associated to the geomagnetic activity (Ap index) around 1 April, on average reaching amplitudes between -5 and -10% of the respective O3 background. The O3 response exceeds the significance level of 95% and propagates downwards throughout the polar winter from the stratopause down to ~ 25 km. These observed results are in good qualitative agreement with the O3 vmr pattern simulated with a three-dimensional chemistry-transport model, which includes particle impact ionisation

Energetic particle induced inter-annual variability of ozone inside the Antarctic polar vortex observed in satellite data

Measurements from 2002-2011 by three independent satellite instruments, namely MIPAS, SABER, and SMR on board the ENVISAT, TIMED, and Odin satellites are used to investigate the inter-annual variability of stratospheric and mesospheric O3 volume mixing ratio (vmr) inside the Antarctic polar vortex due to solar and geomagnetic activity. In this study, we individually analysed the relative O3 vmr variations between maximum and minimum conditions of a number of solar and geomagnetic indices (F10.7 cm solar radio flux, Ap index, >= 2 MeV electron flux). The indices are 26 day averages centred at 1 April, 1 May, and 1 June while O3 is based on 26 day running means from 1 April-1 November at altitudes from 20-70 km. During solar quiet time from 2005-2010, the composite of all three instruments reveals an apparent negative O3 feedback associated to the geomagnetic activity (Ap index) around 1 April, on average reaching amplitudes between -5 and -10% of the respective O3 background. The O3 response exceeds the significance level of 95% and propagates downwards throughout the polar winter from the stratopause down to ~ 25 km. These observed results are in good qualitative agreement with the O3 vmr pattern simulated with a three-dimensional chemistry-transport model, which includes particle impact ionisation

In silico assessment of potential druggable pockets on the surface of α1-Antitrypsin conformers

The search for druggable pockets on the surface of a protein is often performed on a single conformer, treated as a rigid body. Transient druggable pockets may be missed in this approach. Here, we describe a methodology for systematic in silico analysis of surface clefts across multiple conformers of the metastable protein α1-antitrypsin (A1AT). Pathological mutations disturb the conformational landscape of A1AT, triggering polymerisation that leads to emphysema and hepatic cirrhosis. Computational screens for small molecule inhibitors of polymerisation have generally focused on one major druggable site visible in all crystal structures of native A1AT. In an alternative approach, we scan all surface clefts observed in crystal structures of A1AT and in 100 computationally produced conformers, mimicking the native solution ensemble. We assess the persistence, variability and druggability of these pockets. Finally, we employ molecular docking using publicly available libraries of small molecules to explore scaffold preferences for each site. Our approach identifies a number of novel target sites for drug design. In particular one transient site shows favourable characteristics for druggability due to high enclosure and hydrophobicity. Hits against this and other druggable sites achieve docking scores corresponding to a Kd in the µM–nM range, comparing favourably with a recently identified promising lead. Preliminary ThermoFluor studies support the docking predictions. In conclusion, our strategy shows considerable promise compared with the conventional single pocket/single conformer approach to in silico screening. Our best-scoring ligands warrant further experimental investigation

Lattice Boltzmann simulations in microfluidics: probing the no-slip boundary condition in hydrophobic, rough, and surface nanobubble laden microchannels

In this contribution we review recent efforts on investigations of the effect of (apparent) boundary slip by utilizing lattice Boltzmann simulations. We demonstrate the applicability of the method to treat fundamental questions in microfluidics by investigating fluid flow in hydrophobic and rough microchannels as well as over surfaces covered by nano- or microscale gas bubbles.Comment: 11 pages, 6 figure

3D visualization processes for recreating and studying organismal form

The study of biological form is a vital goal of evolutionary biology and functional morphology. We review an emerging set of methods that allow scientists to create and study accurate 3D models of living organisms and animate those models for biomechanical and fluid dynamic analyses. The methods for creating such models include 3D photogrammetry, laser and CT-scanning, and 3D software. New multi-camera devices can be used to create accurate 3D models of living animals in the wild and captivity. New websites and virtual reality/augmented reality devices now enable the visualization and sharing of these data. We provide examples of these approaches for animals ranging from large whales to lizards and show applications for several areas: Natural history collections; body condition/scaling, bioinspired robotics, computational fluids dynamics (CFD), machine learning, and education. We provide two data sets to demonstrate the efficacy of CFD and machine learning approaches and conclude with a prospectus