DNA methylation in Drosophila melanogaster may depend on lineage heterogeneity

DNA methylation has been discovered in Drosophila only recently. Current evidence indicates that de novo methylation patterns in drosophila are maintained in a different way compared to vertebrates and plants. As the genomic role and determinants of DNA methylation are poorly understood in invertebrates, its link with several factors has been suggested. In this study, we tested for the putative link between DNA methylation patterns in Drosophila melanogaster and radiation or the activity of P transposon. Neither of the links was apparent from the results, however, we obtained some hints on a possible link between DNA methylation pattern and genomic heterogeneity of fly lineages.Метилирование ДНК описано у дрозофилы сравнительно недавно. Современные данные свидетельствуют о том, что механизмы метилирования de novo у дрозофилы отличаются от таковых у позвоночных животных и растений. Поскольку на сегодня роль метилирования у беспозвоночных окончательно не выяснена, этот процесс связывают с несколькими факторами. В настоящем исследовании проверена потенциальная связь между метилированием ДНК у дрозофилы, радиоактивным загрязнением и активностью Р транспозона. Наличие такой связи не подтверждено полученными результатами. В то же время получены свидетельства возможной связи метилирования ДНК с гетерогенностью популяций.Метилування ДНК було описано у дрозофіли досить недавно. Сучасні дані свідчать про те, що механізми метилування de novo у дрозофіли відрізняються від таких у хребетних тварин та рослин. Оскільки зараз роль метилування у безхребетних остаточно не з’ясована, цей процес пов’язують з кількома факторами. В даному дослідженні перевірено потенційний зв’язок між метилуванням ДНК у дрозофіли, радіоактивним забрудненням та активністю Р транспозона. Наявність такого зв’язку не підтверджено одержаними результатами. Натомість отримано дані, що свідчать про можливий зв’язок метилування ДНК з гетерогенністю популяцій

Elevated frequency of abnormalities in barn swallows from Chernobyl

Ever since the Chernobyl accident in 1986, that contaminated vast areas in surrounding countries with radiation, abnormalities and birth defects have been reported in human populations. Recently, several studies suggested that the elevated frequency of such abnormalities can be attributed to poverty and stress in affected human populations. Here, we present long-term results for a free-living population of barn swallows, Hirundo rustica, demonstrating the presence of 11 morphological abnormalities in populations around Chernobyl, but much less frequently in an uncontaminated Ukrainian control population and three more distant control populations. The presence of these abnormalities in barn swallows is associated with reduced viability. These findings demonstrate a link between morphological abnormalities and radiation in an animal population that cannot be attributed to poverty and stress. The most parsimonious hypothesis for abnormalities in animal and human populations alike is that the effects are caused by the same underlying cause, viz. radiation derived from the Chernobyl accident

Wiregrass (Aristida beyrichiana) may limit woody plant encroachment in longleaf pine (Pinus palustris) ecosystems

Wiregrass (Aristida beyrichiana) is a dominant groundcover species that facilitates fire in southeastern U.S.A. pine savannas, thereby limiting woody plant cover and maintaining a herbaceous dominated understory. In December 1993 two of us planted a plot of wiregrass (Aristida beyrichiana) in the midst of fire-maintained little bluestem (Schizachyrium scoparium) longleaf pine (Pinus palustris) savanna in the outer Coastal Plain of South Carolina. The plot and the surrounding area burned three times in the following 20 y. Vegetation sampling carried out in late summer 2013 indicated wiregrass dominated the plot and the majority of little bluestem had disappeared. The wiregrass plot was comparatively open and grass dominated, whereas the surrounding formerly bluestem dominated stand had filled in with loblolly pine (Pinus taeda) saplings as well as hardwood trees and shrubs. In addition wiregrass had reproduced and established away from the original planted area, most noticeably within a soil-disturbed plow line. A subsequent prescribed fire in spring 2014 burned with higher intensity within the wiregrass plot than in the surrounding area. Our observations suggest suppression of woody plant encroachment by dense wiregrass in pine savannas even during long fire free periods, which should reduce the likelihood of transition to hardwood dominated ecosystems

Evolutionary aspects of population structure for molecular and quantitative traits in the freshwater snail Radix balthica.

Detecting the action of selection in natural populations can be achieved using the QST-FST comparison that relies on the estimation of FST with neutral markers, and QST using quantitative traits potentially under selection. QST higher than FST suggests the action of directional selection and thus potential local adaptation. In this article, we apply the QST-FST comparison to four populations of the hermaphroditic freshwater snail Radix balthica located in a floodplain habitat. In contrast to most studies published so far, we did not detect evidence of directional selection for local optima for any of the traits we measured: QST calculated using three different methods was never higher than FST. A strong inbreeding depression was also detected, indicating that outcrossing is probably predominant over selfing in the studied populations. Our results suggest that in this floodplain habitat, local adaptation of R. balthica populations may be hindered by genetic drift, and possibly altered by uneven gene flow linked to flood frequency

Broad-scale patterns of body size in squamate reptiles of Europe and North America

Aim To document geographical interspecific patterns of body size of European and North American squamate reptile assemblages and explore the relationship between body size patterns and environmental gradients. Location North America and western Europe. Methods We processed distribution maps for native species of squamate reptiles to document interspecific spatial variation of body size at a grain size of 110 x 110 km. We also examined seven environmental variables linked to four hypotheses possibly influencing body size gradients. We used simple and multiple regression, evaluated using information theory, to identify the set of models best supported by the data. Results Europe is characterized by clear latitudinal trends in body size, whereas geographical variation in body size in North America is complex. There is a consistent association of mean body size with measures of ambient energy in both regions, although lizards increase in size northwards whereas snakes show the opposite pattern. Our best models accounted for almost 60% of the variation in body size of lizards and snakes within Europe, but the proportions of variance explained in North America were less than 20%. Main conclusions Although body size influences the energy balance of thermoregulating ectotherms, inconsistent biogeographical patterns and contrasting associations with energy in lizards and snakes suggest that no single mechanism can explain variation of reptile body size in the northern temperate zone

Volume I. Introduction to DUNE

The preponderance of matter over antimatter in the early universe, the dynamics of the supernovae that produced the heavy elements necessary for life, and whether protons eventually decay—these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our universe, its current state, and its eventual fate. The Deep Underground Neutrino Experiment (DUNE) is an international world-class experiment dedicated to addressing these questions as it searches for leptonic charge-parity symmetry violation, stands ready to capture supernova neutrino bursts, and seeks to observe nucleon decay as a signature of a grand unified theory underlying the standard model. The DUNE far detector technical design report (TDR) describes the DUNE physics program and the technical designs of the single- and dual-phase DUNE liquid argon TPC far detector modules. This TDR is intended to justify the technical choices for the far detector that flow down from the high-level physics goals through requirements at all levels of the Project. Volume I contains an executive summary that introduces the DUNE science program, the far detector and the strategy for its modular designs, and the organization and management of the Project. The remainder of Volume I provides more detail on the science program that drives the choice of detector technologies and on the technologies themselves. It also introduces the designs for the DUNE near detector and the DUNE computing model, for which DUNE is planning design reports. Volume II of this TDR describes DUNE\u27s physics program in detail. Volume III describes the technical coordination required for the far detector design, construction, installation, and integration, and its organizational structure. Volume IV describes the single-phase far detector technology. A planned Volume V will describe the dual-phase technology

Deep Underground Neutrino Experiment (DUNE), far detector technical design report, volume III: DUNE far detector technical coordination

The preponderance of matter over antimatter in the early universe, the dynamics of the supernovae that produced the heavy elements necessary for life, and whether protons eventually decay—these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our universe, its current state, and its eventual fate. The Deep Underground Neutrino Experiment (DUNE) is an international world-class experiment dedicated to addressing these questions as it searches for leptonic charge-parity symmetry violation, stands ready to capture supernova neutrino bursts, and seeks to observe nucleon decay as a signature of a grand unified theory underlying the standard model. The DUNE far detector technical design report (TDR) describes the DUNE physics program and the technical designs of the single- and dual-phase DUNE liquid argon TPC far detector modules. Volume III of this TDR describes how the activities required to design, construct, fabricate, install, and commission the DUNE far detector modules are organized and managed. This volume details the organizational structures that will carry out and/or oversee the planned far detector activities safely, successfully, on time, and on budget. It presents overviews of the facilities, supporting infrastructure, and detectors for context, and it outlines the project-related functions and methodologies used by the DUNE technical coordination organization, focusing on the areas of integration engineering, technical reviews, quality assurance and control, and safety oversight. Because of its more advanced stage of development, functional examples presented in this volume focus primarily on the single-phase (SP) detector module

Highly-parallelized simulation of a pixelated LArTPC on a GPU

The rapid development of general-purpose computing on graphics processing units (GPGPU) is allowing the implementation of highly-parallelized Monte Carlo simulation chains for particle physics experiments. This technique is particularly suitable for the simulation of a pixelated charge readout for time projection chambers, given the large number of channels that this technology employs. Here we present the first implementation of a full microphysical simulator of a liquid argon time projection chamber (LArTPC) equipped with light readout and pixelated charge readout, developed for the DUNE Near Detector. The software is implemented with an end-to-end set of GPU-optimized algorithms. The algorithms have been written in Python and translated into CUDA kernels using Numba, a just-in-time compiler for a subset of Python and NumPy instructions. The GPU implementation achieves a speed up of four orders of magnitude compared with the equivalent CPU version. The simulation of the current induced on 10^3 pixels takes around 1 ms on the GPU, compared with approximately 10 s on the CPU. The results of the simulation are compared against data from a pixel-readout LArTPC prototype

Limited scope for maternal effects in aphid defence against parasitoids

1. A mother’s environment frequently affects her offspring’s phenotype. Such maternal effects may be adaptive, in particular with respect to pathogens or parasites, for example if maternal exposure increases offspring resistance. 2. In aphids, maternal effects are likely to occur as a result of their telescoping generations. This study investigated whether maternal effects influence the susceptibility of the peach-potato aphid, Myzus persicae (Sulzer) (Hemiptera: Aphididae), to its parasitoid Diaeretiella rapae (M’Intosh) (Hymenoptera: Braconidae: Aphidiinae). 3. In a first experiment, susceptibility was compared among offspring of aphid mothers that had either no contact to parasitoids, had contact but were not attacked, or were attacked but not mummified. Mothers from the last group had successfully resisted the parasitoid. 4. In a second experiment using two different clones, maternal and progeny environment were manipulated by rearing each generation either on a benign (radish) or a more stressful host plant (silver beet) before progeny exposure to parasitoids. 5. The first experiment revealed no significant effect of the maternal treatment on offspring susceptibility to parasitoids and thus no evidence for trans-generational defence. In the second experiment, maternal environment effects were also weak, yet with a trend towards less susceptible offspring of aphid mothers reared on the more stressful plant. However, there was a significant difference among clones and a strong clone × progeny host plant interaction, illustrating that the outcome of a parasitoid attack may be determined by a complex interplay of genetic and environmental factors. 6. Overall, the results suggest that there is limited scope for maternal effects in aphid defence against parasitoids