Evidence that natural selection maintains genetic variation for sleep in Drosophila melanogaster.

BackgroundDrosophila melanogaster often shows correlations between latitude and phenotypic or genetic variation on different continents, which suggests local adaptation with respect to a heterogeneous environment. Previous phenotypic analyses of latitudinal clines have investigated mainly physiological, morphological, or life-history traits. Here, we studied latitudinal variation in sleep in D. melanogaster populations from North and Central America. In parallel, we used RNA-seq to identify interpopulation gene expression differences.ResultsWe found that in D. melanogaster the average nighttime sleep bout duration exhibits a latitudinal cline such that sleep bouts of equatorial populations are roughly twice as long as those of temperate populations. Interestingly, this pattern of latitudinal variation is not observed for any daytime measure of activity or sleep. We also found evidence for geographic variation for sunrise anticipation. Our RNA-seq experiment carried out on heads from a low and high latitude population identified a large number of gene expression differences, most of which were time dependent. Differentially expressed genes were enriched in circadian regulated genes and enriched in genes potentially under spatially varying selection.ConclusionOur results are consistent with a mechanistic and selective decoupling of nighttime and daytime activity. Furthermore, the present study suggests that natural selection plays a major role in generating transcriptomic variation associated with circadian behaviors. Finally, we identified genomic variants plausibly causally associated with the observed behavioral and transcriptomic variation

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

Wolbachia do not live by reproductive manipulation alone: infection polymorphism in Drosophila suzukii and D. subpulchrella

This is the peer reviewed version of the following article: Hamm, C. A., Begun, D. J., Vo, A., Smith, C. C. R., Saelao, P., Shaver, A. O., Jaenike, J. and Turelli, M. (2014), Wolbachia do not live by reproductive manipulation alone: infection polymorphism in Drosophila suzukii and D. subpulchrella. Mol Ecol, 23: 4871–4885. doi:10.1111/mec.12901, which has been published in final form at http://doi.org/10.1111/mec.12901. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.Drosophila suzukii recently invaded North America and Europe. Populations in Hawaii, California, New York and Nova Scotia are polymorphic for Wolbachia, typically with <20% infection frequency. The Wolbachia in D. suzukii, denoted wSuz, is closely related to wRi, the variant prevalent in continental populations of D. simulans. wSuz is also nearly identical to Wolbachia found in D. subpulchrella, plausibly D. suzukii's sister species. This suggests vertical Wolbachia transmission through cladogenesis (“cladogenic transmission”). The widespread occurrence of 7-20% infection frequencies indicates a stable polymorphism. wSuz is imperfectly maternally transmitted, with wild infected females producing on average 5-10% uninfected progeny. As expected from its low frequency, wSuz produces no cytoplasmic incompatibility (CI), i.e., no elevated embryo mortality when infected males mate with uninfected females, and no appreciable sex-ratio distortion. The persistence of wSuz despite imperfect maternal transmission suggests positive fitness effects. Assuming a balance between selection and imperfect transmission, we expect a fitness advantage on the order of 20%. Unexpectedly, Wolbachia-infected females produce fewer progeny than do uninfected females. We do not yet understand the maintenance of wSuz in D. suzukii. The absence of detectable CI in D. suzukii and D. subpulchrella makes it unlikely that CI-based mechanisms could be used to control this species without transinfection using novel Wolbachia. Contrary to their reputation as horizontally transmitted reproductive parasites, many Wolbachia infections are acquired through introgression or cladogenesis and many cause no appreciable reproductive manipulation. Such infections, likely to be mutualistic, may be central to understanding the pervasiveness of Wolbachia among arthropods

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

Efficient Algorithm on a Non-staggered Mesh for Simulating Rayleigh-Benard Convection in a Box

An efficient semi-implicit second-order-accurate finite-difference method is described for studying incompressible Rayleigh-Benard convection in a box, with sidewalls that are periodic, thermally insulated, or thermally conducting. Operator-splitting and a projection method reduce the algorithm at each time step to the solution of four Helmholtz equations and one Poisson equation, and these are are solved by fast direct methods. The method is numerically stable even though all field values are placed on a single non-staggered mesh commensurate with the boundaries. The efficiency and accuracy of the method are characterized for several representative convection problems.Comment: REVTeX, 30 pages, 5 figure

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

Global Prevalence and Mental Health Outcomes of Intimate Partner Violence Among Women: A Systematic Review and Meta-Analysis

The aim of this systematic review was to assess the magnitude of the association between types of intimate partner violence (IPV) and mental health outcomes and shed light on the large variation in IPV prevalence rates between low- to middle-income countries and high-income countries. The study is a systematic review and meta-analysis. The following databases were searched for this study: Cochrane, MEDLINE, EMBASE, PsycINFO, Cumulative Index to Nursing and Allied Health Literature, and the Applied Social Sciences Index and Abstracts. The inclusion criteria for this study are as follows: quantitative studies published from 2012 to 2020 on IPV exposure in women aged 16+, using validated measures. Random effects meta-analyses and subgroup analysis exploring heterogeneity across population groups in different economic contexts are used in this study. In all, 201 studies were included with 250,599 women, primarily from high-income countries. Higher prevalence rates were reported for women’s lifetime IPV than past year IPV. Lifetime psychological violence was the most prevalent form of IPV. Women in the community reported the highest prevalence for physical, psychological, and sexual violence in the past year compared to clinical groups. Perinatal women were most likely to have experienced lifetime physical IPV. Prevalence rates differed significantly (p = .037 to <.001) for “any IPV” and all subtypes by income country level. Meta-analysis suggested increased odds for all mental health outcomes associated with IPV including depression (odds ratio [OR] = 2.04–3.14), posttraumatic stress disorder (PTSD) (OR = 2.15–2.66), and suicidality (OR = 2.17–5.52). Clinical and community populations were exposed to high prevalence of IPV and increased likelihood of depression, PTSD, and suicidality. Future research should seek to understand women’s perspectives on service/support responses to IPV to address their mental health needs. Work with IPV survivors should be carried out to develop bespoke services to reduce IPV in groups most at risk such as pregnant and/or help-seeking women

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

Global Prevalence and Mental Health Outcomes of Intimate Partner Violence Among Women: A Systematic Review and Meta-Analysis

The aim of this systematic review was to assess the magnitude of the association between types of intimate partner violence (IPV) and mental health outcomes and shed light on the large variation in IPV prevalence rates between low- to middle-income countries and high-income countries. The study is a systematic review and meta-analysis. The following databases were searched for this study: Cochrane, MEDLINE, EMBASE, PsycINFO, Cumulative Index to Nursing and Allied Health Literature, and the Applied Social Sciences Index and Abstracts. The inclusion criteria for this study are as follows: quantitative studies published from 2012 to 2020 on IPV exposure in women aged 16+, using validated measures. Random effects meta-analyses and subgroup analysis exploring heterogeneity across population groups in different economic contexts are used in this study. In all, 201 studies were included with 250,599 women, primarily from high-income countries. Higher prevalence rates were reported for women’s lifetime IPV than past year IPV. Lifetime psychological violence was the most prevalent form of IPV. Women in the community reported the highest prevalence for physical, psychological, and sexual violence in the past year compared to clinical groups. Perinatal women were most likely to have experienced lifetime physical IPV. Prevalence rates differed significantly (p = .037 to <.001) for “any IPV” and all subtypes by income country level. Meta-analysis suggested increased odds for all mental health outcomes associated with IPV including depression (odds ratio [OR] = 2.04–3.14), posttraumatic stress disorder (PTSD) (OR = 2.15–2.66), and suicidality (OR = 2.17–5.52). Clinical and community populations were exposed to high prevalence of IPV and increased likelihood of depression, PTSD, and suicidality. Future research should seek to understand women’s perspectives on service/support responses to IPV to address their mental health needs. Work with IPV survivors should be carried out to develop bespoke services to reduce IPV in groups most at risk such as pregnant and/or help-seeking women