Is There a Causal Association between Genotoxicity and the Imposex Effect?

There is a growing body of evidence that indicates common environmental pollutants are capable of disrupting reproductive and developmental processes by interfering with the actions of endogenous hormones. Many reports of endocrine disruption describe changes in the normal development of organs and tissues that are consistent with genetic damage, and recent studies confirm that many chemicals classified to have hormone-modulating effects also possess carcinogenic and mutagenic potential. To date, however, there have been no conclusive examples linking genetic damage with perturbation of endocrine function and adverse effects in vivo. Here, we provide the first evidence of DNA damage associated with the development of imposex (the masculinization of female gastropods considered to be the result of alterations to endocrine-mediated pathways) in the dog-whelk Nucella lapillus. Animals (n = 257) that displayed various stages of tributyltin (TBT)-induced imposex were collected from sites in southwest England, and their imposex status was determined by physical examination. Linear regression analysis revealed a very strong relationship (correlation coefficient of 0.935, p < 0.0001) between the degree of imposex and the extent of DNA damage (micronucleus formation) in hemocytes. Moreover, histological examination of a larger number of dog-whelks collected from sites throughout Europe confirmed the presence of hyperplastic growths, primarily on the vas deferens and penis in both TBT-exposed male snails and in females that exhibited imposex. A strong association was found between TBT body burden and the prevalence of abnormal growths, thereby providing compelling evidence to support the hypothesis that environmental chemicals that affect reproductive processes do so partly through DNA damage pathways

Effects of larval growth condition and water availability on desiccation resistance and its physiological basis in adult Anopheles gambiae sensu stricto

<p>Abstract</p> <p>Background</p> <p>Natural populations of the malaria mosquito <it>Anopheles gambiae </it>s.s. are exposed to large seasonal and daily fluctuations in relative humidity and temperature, which makes coping with drought a crucial aspect of their ecology.</p> <p>Methods</p> <p>To better understand natural variation in desiccation resistance in this species, the effects of variation in larval food availability and access to water as an adult on subsequent phenotypic quality and desiccation resistance of adult females of the Mopti chromosomal form were tested experimentally.</p> <p>Results</p> <p>It was found that, under normal conditions, larval food availability and adult access to water had only small direct effects on female wet mass, dry mass, and water, glycogen and body lipid contents corrected for body size. In contrast, when females subsequently faced a strong desiccation challenge, larval food availability and adult access to water had strong carry-over effects on most measured physiological and metabolic parameters, and affected female survival. Glycogen and water content were the most used physiological reserves in relative terms, but their usage significantly depended on female phenotypic quality. Adult access to water significantly influenced the use of water and body lipid reserves, which subsequently affected desiccation resistance.</p> <p>Conclusions</p> <p>These results demonstrate the importance of growth conditions and water availability on adult physiological status and subsequent resistance to desiccation.</p

Observation of bright polariton solitons in a semiconductor microcavity

Microcavity polaritons are composite half-light half-matter quasi-particles, which have recently been demonstrated to exhibit rich physical properties, such as non-equilibrium Bose-Einstein condensation, parametric scattering and superfluidity. At the same time, polaritons have some important advantages over photons for information processing applications, since their excitonic component leads to weaker diffraction and stronger inter-particle interactions, implying, respectively, tighter localization and lower powers for nonlinear functionality. Here we present the first experimental observations of bright polariton solitons in a strongly coupled semiconductor microcavity. The polariton solitons are shown to be non-diffracting high density wavepackets, that are strongly localised in real space with a corresponding broad spectrum in momentum space. Unlike solitons known in other matter-wave systems such as Bose condensed ultracold atomic gases, they are non-equilibrium and rely on a balance between losses and external pumping. Microcavity polariton solitons are excited on picosecond timescales, and thus have significant benefits for ultrafast switching and transfer of information over their light only counterparts, semiconductor cavity lasers (VCSELs), which have only nanosecond response time

Impact of Darker, Intermediate and Lighter Phenotypes of Body Melanization on Desiccation Resistance in Drosophila melanogaster

A possible link between melanization and desiccation resistance can be inferred if within population differences in melanization find significant correlations with desiccation resistance and its mechanistic basis i.e. rate of water loss/hr. Accordingly, darker, intermediate and lighter phenotypes of body melanization were analyzed in wild and laboratory reared Drosophila melanogaster L. (Diptera: Clyclorrapha) populations from highland and lowland sites located in close proximity at five different latitudinal locations (11.15 °N to 31.06°N) within the Indian subcontinent. In large population samples, occurrence of significant within population variability made it possible to assort non-overlapping phenotypes of body coloration (i.e. lighter (< 25%), intermediate (30 to 40%) and darker (> 45%)) for all the populations which were further investigated for desiccation resistance and rate of water loss/hr. Significantly, higher desiccation resistance but much reduced rate of water loss/hr were observed in darker and intermediate phenotypes in all the populations. By contrast, lighter phenotypes exhibited lower desiccation tolerance but higher rate of water loss/hr. A regression analysis between traits provided similar slope values for wild and laboratory populations. For all three physiological traits, predicted trait values from multiple regression analysis as a simultaneous function of annual average temperature and relative humidity, matched the observed values. We infer that parallel changes in melanization and desiccation resistance may result from decreasing annual average temperature and relative humidity along increasing latitude as well as altitude on the Indian subcontinent

Statistical Power of Model Selection Strategies for Genome-Wide Association Studies

Genome-wide association studies (GWAS) aim to identify genetic variants related to diseases by examining the associations between phenotypes and hundreds of thousands of genotyped markers. Because many genes are potentially involved in common diseases and a large number of markers are analyzed, it is crucial to devise an effective strategy to identify truly associated variants that have individual and/or interactive effects, while controlling false positives at the desired level. Although a number of model selection methods have been proposed in the literature, including marginal search, exhaustive search, and forward search, their relative performance has only been evaluated through limited simulations due to the lack of an analytical approach to calculating the power of these methods. This article develops a novel statistical approach for power calculation, derives accurate formulas for the power of different model selection strategies, and then uses the formulas to evaluate and compare these strategies in genetic model spaces. In contrast to previous studies, our theoretical framework allows for random genotypes, correlations among test statistics, and a false-positive control based on GWAS practice. After the accuracy of our analytical results is validated through simulations, they are utilized to systematically evaluate and compare the performance of these strategies in a wide class of genetic models. For a specific genetic model, our results clearly reveal how different factors, such as effect size, allele frequency, and interaction, jointly affect the statistical power of each strategy. An example is provided for the application of our approach to empirical research. The statistical approach used in our derivations is general and can be employed to address the model selection problems in other random predictor settings. We have developed an R package markerSearchPower to implement our formulas, which can be downloaded from the Comprehensive R Archive Network (CRAN) or http://bioinformatics.med.yale.edu/group/

Markedly Divergent Tree Assemblage Responses to Tropical Forest Loss and Fragmentation across a Strong Seasonality Gradient

We examine the effects of forest fragmentation on the structure and composition of tree assemblages within three seasonal and aseasonal forest types of southern Brazil, including evergreen, Araucaria, and deciduous forests. We sampled three southernmost Atlantic Forest landscapes, including the largest continuous forest protected areas within each forest type. Tree assemblages in each forest type were sampled within 10 plots of 0.1 ha in both continuous forests and 10 adjacent forest fragments. All trees within each plot were assigned to trait categories describing their regeneration strategy, vertical stratification, seed-dispersal mode, seed size, and wood density. We detected differences among both forest types and landscape contexts in terms of overall tree species richness, and the density and species richness of different functional groups in terms of regeneration strategy, seed dispersal mode and woody density. Overall, evergreen forest fragments exhibited the largest deviations from continuous forest plots in assemblage structure. Evergreen, Araucaria and deciduous forests diverge in the functional composition of tree floras, particularly in relation to regeneration strategy and stress tolerance. By supporting a more diversified light-demanding and stress-tolerant flora with reduced richness and abundance of shade-tolerant, old-growth species, both deciduous and Araucaria forest tree assemblages are more intrinsically resilient to contemporary human-disturbances, including fragmentation-induced edge effects, in terms of species erosion and functional shifts. We suggest that these intrinsic differences in the direction and magnitude of responses to changes in landscape structure between forest types should guide a wide range of conservation strategies in restoring fragmented tropical forest landscapes worldwide

Cone visual pigments of monotremes: Filling the phylogenetic gap

We have determined the sequence and genomic organization of the genes encoding the cone visual pigment of the platypus (Ornithorhynchus anatinus) and the echidna (Tachyglossus aculeatus), and inferred their spectral properties and evolutionary pathways. We prepared platypus and echidna retinal RNA and used primers of the middle-wave-sensitive (MWS), long-wave-sensitive (LWS), and short-wave sensitive (SWS1) pigments corresponding to coding sequences that are highly conserved among mammals; to PCR amplify the corresponding pigment sequences. Amplification from the retinal RNA revealed the expression of LWS pigment mRNA that is homologous in sequence and spectral properties to the primate LWS visual pigments. However, we were unable to amplify the mammalian SWS1 pigment from these two species, indicating this gene was lost prior to the echidna-platypus divergence ~21 MYA. Subsequently, when the platypus genome sequence became available, we found an LWS pigment gene in a conserved genomic arrangement that resembles the primate pigment, but, surprisingly we found an adjacent (~20 kb) SWS2 pigment gene within this conserved genomic arrangement. We obtained the same result after sequencing the echidna genes. The encoded SWS2 pigment is predicted to have a wavelength of maximal absorption of about 440 nm, and is paralogous to SWS pigments typically found in reptiles, birds, and fish but not in mammals. This study suggests the locus control region (LCR) has played an important role in the conservation of photo receptor gene arrays and the control of their spatial and temporal expression in the retina in all mammals. In conclusion, a duplication event of an ancestral cone visual pigment gene, followed by sequence divergence and selection gave rise to the LWS and SWS2 visual pigments. So far, the echidna and platypus are the only mammals that share the gene structure of the LWS-SWS2 pigment gene complex with reptiles, birds and fishes.Matthew J. Wakefield, Mark Anderson, Ellen Chang, Ke-Jun Wei, Rajinder Kaul, Jennifer A. Marshall Graves, Frank Grutzner and Samir S. Dee

Variations on a theme: diversification of cuticular hydrocarbons in a clade of cactophilic Drosophila

<p>Abstract</p> <p>Background</p> <p>We characterized variation and chemical composition of epicuticular hydrocarbons (CHCs) in the seven species of the <it>Drosophila buzzatii </it>cluster with gas chromatography/mass spectrometry. Despite the critical role of CHCs in providing resistance to desiccation and involvement in communication, such as courtship behavior, mating, and aggregation, few studies have investigated how CHC profiles evolve within and between species in a phylogenetic context. We analyzed quantitative differences in CHC profiles in populations of the <it>D. buzzatii </it>species cluster in order to assess the concordance of CHC differentiation with species divergence.</p> <p>Results</p> <p>Thirty-six CHC components were scored in single fly extracts with carbon chain lengths ranging from C₂₉to C₃₉, including methyl-branched alkanes, <it>n</it>-alkenes, and alkadienes. Multivariate analysis of variance revealed that CHC amounts were significantly different among all species and canonical discriminant function (CDF) analysis resolved all species into distinct, non-overlapping groups. Significant intraspecific variation was found in different populations of <it>D. serido </it>suggesting that this taxon is comprised of at least two species. We summarized CHC variation using CDF analysis and mapped the first five CHC canonical variates (CVs) onto an independently derived <it>period </it>(<it>per</it>) gene + chromosome inversion + mtDNA COI gene for each sex. We found that the COI sequences were not phylogenetically informative due to introgression between some species, so only <it>per </it>+ inversion data were used. Positive phylogenetic signal was observed mainly for CV1 when parsimony methods and the test for serial independence (TFSI) were used. These results changed when no outgroup species were included in the analysis and phylogenetic signal was then observed for female CV3 and/or CV4 and male CV4 and CV5. Finally, removal of divergent populations of <it>D. serido </it>significantly increased the amount of phylogenetic signal as up to four out of five CVs then displayed positive phylogenetic signal.</p> <p>Conclusions</p> <p>CHCs were conserved among species while quantitative differences in CHC profiles between populations and species were statistically significant. Most CHCs were species-, population-, and sex-specific. Mapping CHCs onto an independently derived phylogeny revealed that a significant portion of CHC variation was explained by species' systematic affinities indicating phylogenetic conservatism in the evolution of these hydrocarbon arrays, presumptive waterproofing compounds and courtship signals as in many other drosophilid species.</p

The Born supremacy: quantum advantage and training of an Ising Born machine

The search for an application of near-term quantum devices is widespread. Quantum Machine Learning is touted as a potential utilisation of such devices, particularly those which are out of the reach of the simulation capabilities of classical computers. In this work, we propose a generative Quantum Machine Learning Model, called the Ising Born Machine (IBM), which we show cannot, in the worst case, and up to suitable notions of error, be simulated efficiently by a classical device. We also show this holds for all the circuit families encountered during training. In particular, we explore quantum circuit learning using non-universal circuits derived from Ising Model Hamiltonians, which are implementable on near term quantum devices. We propose two novel training methods for the IBM by utilising the Stein Discrepancy and the Sinkhorn Divergence cost functions. We show numerically, both using a simulator within Rigetti's Forest platform and on the Aspen-1 16Q chip, that the cost functions we suggest outperform the more commonly used Maximum Mean Discrepancy (MMD) for differentiable training. We also propose an improvement to the MMD by proposing a novel utilisation of quantum kernels which we demonstrate provides improvements over its classical counterpart. We discuss the potential of these methods to learn `hard' quantum distributions, a feat which would demonstrate the advantage of quantum over classical computers, and provide the first formal definitions for what we call `Quantum Learning Supremacy'. Finally, we propose a novel view on the area of quantum circuit compilation by using the IBM to `mimic' target quantum circuits using classical output data only.Comment: v3 : Close to journal published version - significant text structure change, split into main text & appendices. See v2 for unsplit version; v2 : Typos corrected, figures altered slightly; v1 : 68 pages, 39 Figures. Comments welcome. Implementation at https://github.com/BrianCoyle/IsingBornMachin

‘What happens when you intuit?’: Understanding human resource practitioners’ subjective experience of intuition through a novel linguistic method

The objective of this research was to understand the phenomenon of intuition from the perspective of the intuitor. Against a background of a steadily growing interest in intuition in managerial decision research, and inclining towards a phenomenological stance, the research used a novel linguistic method based on ‘de-nominalization’ to access participants’ (124 human resource practitioners) experiences of intuition. Based on an analysis of responses to the question ‘what happens when you intuit?’ the article: defines intuition based on participants’ subjective experiences; reveals the subjective experience of intuition as comprising three phases - ‘intuiting’, ‘intuition’, and ‘implementing’; uncovers two aspects of intuitive affect - ‘bodily awareness’ and ‘cognitive awareness’; establishes that participants use primary metaphors to articulate their experiences of intuition. The article outlines the theoretical implications and practical relevance of these findings, and makes suggestions for further qualitative phenomenological studies of intuition