Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors

Epigenetic modifications on chromatin play important roles in regulating gene expression. Although chromatin states are often governed by multilayered structure, how individual pathways contribute to gene expression remains poorly understood. For example, DNA methylation is known to regulate transcription factor binding but also to recruit methyl-CpG binding proteins that affect chromatin structure through the activity of histone deacetylase complexes (HDACs). Both of these mechanisms can potentially affect gene expression, but the importance of each, and whether these activities are integrated to achieve appropriate gene regulation, remains largely unknown. To address this important question, we measured gene expression, chromatin accessibility, and transcription factor occupancy in wild-type or DNA methylation-deficient mouse embryonic stem cells following HDAC inhibition. We observe widespread increases in chromatin accessibility at retrotransposons when HDACs are inhibited, and this is magnified when cells also lack DNA methylation. A subset of these elements has elevated binding of the YY1 and GABPA transcription factors and increased expression. The pronounced additive effect of HDAC inhibition in DNA methylation-deficient cells demonstrates that DNA methylation and histone deacetylation act largely independently to suppress transcription factor binding and gene expression

Phosphorylation induces structural changes in the Autographa californica nucleopolyhedrovirus P10 protein

Baculoviruses encode a variety of auxiliary proteins that are not essential for viral replication but provide them with a selective advantage in nature. P10 is a 10 kDa auxiliary protein produced in the very-late phase of gene transcription by Autographa californica multiple nucleopolyhedrovirus (AcMNPV). The P10 protein forms cytoskeletal-like structures in the host cell that associate with microtubules varying from filamentous forms in the cytoplasm to aggregated peri-nuclear tubules that form a cage-like structure around the nucleus. These P10 structures may have a role in the release of occlusion bodies (OBs) and thus mediate horizontal transmission of the virus between insect hosts. Here it is demonstrated, using mass spectrometric analysis, that the C-terminus of P10 is phosphorylated during virus infection of cells in culture. Analysis of the P10 mutants encoded by recombinant baculoviruses in which putative phosphorylation residues were mutated to alanine showed that serine 93 is a site of phosphorylation. Confocal microscopy examination of the serine 93 mutant structures revealed an aberrant formation of the peri-nuclear tubules. Thus, phosphorylation of serine 93 may induce aggregation of filaments to form tubules. Together, these data suggest that the phosphorylation of serine 93 affects P10 structural conformation. IMPORTANCE The baculovirus P10 protein has been researched intensively since it was first observed in 1969, but its role during the viral infection remains unclear. It is conserved in the alphabaculoviruses and expressed at high levels during virus infection. Producing large amounts of a protein is wasteful for the virus unless it is advantageous for survival of its progeny and therefore P10 presents an enigma. As P10 polymerises to form organised cytoskeletal structures that co-localise with the host cell microtubules, the structural relationship of the protein with the host cell may present a key to help understand the function and importance of this protein. This study addresses the importance of the structural changes in P10 during infection and how they may be governed by phosphorylation. The P10 structures affected by phosphorylation are closely associated with the viral progeny and thus, potentially, be responsible for its dissemination and survival

Exoplanets and SETI

The discovery of exoplanets has both focused and expanded the search for extraterrestrial intelligence. The consideration of Earth as an exoplanet, the knowledge of the orbital parameters of individual exoplanets, and our new understanding of the prevalence of exoplanets throughout the galaxy have all altered the search strategies of communication SETI efforts, by inspiring new "Schelling points" (i.e. optimal search strategies for beacons). Future efforts to characterize individual planets photometrically and spectroscopically, with imaging and via transit, will also allow for searches for a variety of technosignatures on their surfaces, in their atmospheres, and in orbit around them. In the near-term, searches for new planetary systems might even turn up free-floating megastructures.Comment: 9 page invited review. v2 adds some references and v3 has other minor additions and modification

Collapse of superconductivity in a hybrid tin-graphene Josephson junction array

When a Josephson junction array is built with hybrid superconductor/metal/superconductor junctions, a quantum phase transition from a superconducting to a two-dimensional (2D) metallic ground state is predicted to happen upon increasing the junction normal state resistance. Owing to its surface-exposed 2D electron gas and its gate-tunable charge carrier density, graphene coupled to superconductors is the ideal platform to study the above-mentioned transition between ground states. Here we show that decorating graphene with a sparse and regular array of superconducting nanodisks enables to continuously gate-tune the quantum superconductor-to-metal transition of the Josephson junction array into a zero-temperature metallic state. The suppression of proximity-induced superconductivity is a direct consequence of the emergence of quantum fluctuations of the superconducting phase of the disks. Under perpendicular magnetic field, the competition between quantum fluctuations and disorder is responsible for the resilience at the lowest temperatures of a superconducting glassy state that persists above the upper critical field. Our results provide the entire phase diagram of the disorder and magnetic field-tuned transition and unveil the fundamental impact of quantum phase fluctuations in 2D superconducting systems.Comment: 25 pages, 6 figure

Religiosity and decreased risk of substance use disorders: is the effect mediated by social support or mental health status?

The negative association between religiosity (religious beliefs and church attendance) and the likelihood of substance use disorders is well established, but the mechanism(s) remain poorly understood. We investigated whether this association was mediated by social support or mental health status. We utilized cross-sectional data from the 2002 National Survey on Drug Use and Health (n = 36,370). We first used logistic regression to regress any alcohol use in the past year on sociodemographic and religiosity variables. Then, among individuals who drank in the past year, we regressed past year alcohol abuse/dependence on sociodemographic and religiosity variables. To investigate whether social support mediated the association between religiosity and alcohol use and alcohol abuse/dependence we repeated the above models, adding the social support variables. To the extent that these added predictors modified the magnitude of the effect of the religiosity variables, we interpreted social support as a possible mediator. We also formally tested for mediation using path analysis. We investigated the possible mediating role of mental health status analogously. Parallel sets of analyses were conducted for any drug use, and drug abuse/dependence among those using any drugs as the dependent variables. The addition of social support and mental health status variables to logistic regression models had little effect on the magnitude of the religiosity coefficients in any of the models. While some of the tests of mediation were significant in the path analyses, the results were not always in the expected direction, and the magnitude of the effects was small. The association between religiosity and decreased likelihood of a substance use disorder does not appear to be substantively mediated by either social support or mental health status

A life-course and time perspective on the construct validity of psychological distress in women and men. Measurement invariance of the K6 across gender

<p>Abstract</p> <p>Background</p> <p>Psychological distress is a widespread indicator of mental health and mental illness in research and clinical settings. A recurrent finding from epidemiological studies and population surveys is that women report a higher mean level and a higher prevalence of psychological distress than men. These differences may reflect, to some extent, cultural norms associated with the expression of distress in women and men. Assuming that these norms differ across age groups and that they evolve over time, one would expect gender differences in psychological distress to vary over the life-course and over time. The objective of this study was to investigate the construct validity of a psychological distress scale, the K6, across gender in different age groups and over a twelve-year period.</p> <p>Methods</p> <p>This study is based on data from the Canadian National Population Health Survey (C-NPHS). Psychological distress was assessed with the K6, a scale developed by Kessler and his colleagues. Data were examined through multi-group confirmatory factor analyses. Increasing levels of measurement and structural invariance across gender were assessed cross-sectionally with data from cycle 1 (n = 13019) of the C-NPHS and longitudinally with cycles 1 (1994-1995), 4 (2000-2001) and 7 (2006-2007).</p> <p>Results</p> <p>Higher levels of measurement and structural invariance across gender were reached only after the constraint of equivalence was relaxed for various parameters of a few items of the K6. Some items had a different pattern of gender non invariance across age groups and over the course of the study. Gender differences in the expression of psychological distress may vary over the lifespan and over a 12-year period without markedly affecting the construct validity of the K6.</p> <p>Conclusions</p> <p>This study confirms the cross-gender construct validity of psychological distress as assessed with the K6 despite differences in the expression of some symptoms in women and in men over the life-course and over time. Findings suggest that the higher mean level of psychological distress observed in women reflects a true difference in distress and is unlikely to be gender-biased. Gender differences in psychological distress are an important public health and clinical issue and further researches are needed to decipher the factors underlying these differences.</p

Divergent allocation of sperm and the seminal proteome along a competition gradient in Drosophila melanogaster

Sperm competition favors large, costly ejaculates, and theory predicts the evolution of allocation strategies that enable males to plastically tailor ejaculate expenditure to sperm competition threat. While greater sperm transfer in response to a perceived increase in the risk of sperm competition is well-supported, we have a poor understanding of whether males (i) respond to changes in perceived intensity of sperm competition, (ii) use the same allocation rules for sperm and seminal fluid, and (iii) experience changes in current and future reproductive performance as a result of ejaculate compositional changes. Combining quantitative proteomics with fluorescent sperm labeling, we show that Drosophila melanogaster males exercise independent control over the transfer of sperm and seminal fluid proteins (SFPs) under different levels of male–male competition. While sperm transfer peaks at low competition, consistent with some theoretical predictions based on sperm competition intensity, the abundance of transferred SFPs generally increases at high competition levels. However, we find that clusters of SFPs vary in the directionality and sensitivity of their response to competition, promoting compositional change in seminal fluid. By tracking the degree of decline in male mating probability and offspring production across successive matings, we provide evidence that ejaculate compositional change represents an adaptive response to current sperm competition, but one that comes at a cost to future mating performance. Our work reveals a previously unknown divergence in ejaculate component allocation rules, exposes downstream costs of elevated ejaculate investment, and ultimately suggests a central role for ejaculate compositional plasticity in sexual selection

Non-fatal disease burden for subtypes of depressive disorder: population-based epidemiological study

Background: Major depression is the leading cause of non-fatal disease burden. Because major depression is not a homogeneous condition, this study estimated the non-fatal disease burden for mild, moderate and severe depression in both single episode and recurrent depression. All estimates were assessed from an individual and a population perspective and presented as unadjusted, raw estimates and as estimates adjusted for comorbidity. Methods: We used data from the first wave of the second Netherlands-Mental-Health-Survey-and-Incidence-Study (NEMESIS-2, n = 6646; single episode Diagnostic and Statistical Manual (DSM)-IV depression, n = 115; recurrent depression, n = 246). Disease burden from an individual perspective was assessed as 'disability weight * time spent in depression' for each person in the dataset. From a population perspective it was assessed as 'disability weight * time spent in depression *number of people affected'. The presence of mental disorders was assessed with the Composite International Diagnostic Interview (CIDI) 3.0. Results: Single depressive episodes emerged as a key driver of disease burden from an individual perspective. From a population perspective, recurrent depressions emerged as a key driver. These findings remained unaltered after adjusting for comorbidity. Conclusions: The burden of disease differs between the subtype of depression and depends much on the choice of perspective. The distinction between an individual and a population perspective may help to avoid misunderstandings between policy makers and clinicians. © 2016 Biesheuvel-Leliefeld et al