IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana.

DNA methylation is an epigenetic mark affecting genes and transposons. Screening for mutants that fail to establish DNA methylation yielded two we termed "involved in de novo" (idn) 1 and 2. IDN1 encodes DMS3, an SMC-related protein, and IDN2 encodes a previously unknown double-stranded RNA-binding protein with homology to SGS3. IDN1 and IDN2 control de novo methylation and small interfering RNA (siRNA)-mediated maintenance methylation and are components of the RNA-directed DNA methylation pathway

Thermal/structural analyses of several hydrogen-cooled leading-edge concepts for hypersonic flight vehicles

The aerodynamic heating at high flight Mach numbers, when shock interference heating is included, can be extremely high and can exceed the capability of most conventional metallic and potential ceramic materials available. Numerical analyses of the heat transfer and thermal stresses are performed on three actively cooled leading-edge geometries (models) made of three different materials to address the issue of survivability in a hostile environment. These analyses show a mixture of results from one configuration to the next. Results for each configuration are presented and discussed. Combinations of enhanced internal film coefficients and high material thermal conductivity of copper and tungsten are predicted to maintain the maximum wall temperature for each concept within acceptable operating limits. The exception is the TD nickel material which is predicted to melt for most cases. The wide range of internal impingement film coefficients (based on correlations) for these conditions can lead to a significant uncertainty in expected leading-edge wall temperatures. The equivalent plastic strain, inherent in each configuration which results from the high thermal gradients, indicates a need for further cyclic analysis to determine component life

Concept design of a fast sail assisted feeder container ship

An environmentally sustainable fast sail-assisted feeder-container ship concept, with a maximum speed of 25 knots, has been developed for the 2020 South East Asian and Caribbean container markets. The use of low-carbon and zero-sulphur fuel (liquefied natural gas) and improvements in operational efficiency (cargo handling and scheduling) mean predicted Green house gas emissions should fall by 42% and 40% in the two selected operational regions. The adoption of a Multi-wing sail system reduces power requirement by up to 6% at the lower ship speed of 15 knots. The predicted daily cost savings are respectively 27% and 33% in South East Asian and the Caribbean regions.Two hull forms with a cargo capacity of 1270TEU utilising different propulsion combinations were initially developed to meet operational requirements. Analysis & tank testing of different hydrodynamic phenomena has enabled identification of efficiency gains for each design. The final propulsion chosen is a contra-rotating podded drive arrangement. Wind tunnel testing improved Multi-wing sail performance by investigating wing spacing, wing stagger and sail-container interactions. The associated lift coefficient was increased by 32%. Whilst savings in sail-assisted power requirement are lower than initially predicted an unexpected identified benefit was motion damping.The fast feeder-container ship is a proposed as a viable future method of container transhipment

Assessing the applicability of the Revised Universal Soil Loss Equation (RUSLE) to Irish Catchments

Elevated suspended sediment concentrations in fluvial environments have important implications for system ecology and even small concentrations may have serious consequences for sensitive ecosystems or organisms, such as freshwater pearl mussels (<i>Margaritifera margaritifera</i>). Informed decision making is therefore required for land managers to understand and control soil erosion and sediment delivery to the river network. However, given that monitoring of sediment fluxes requires financial and human resources which are often limited at a national scale, sediment mobilisation and delivery models are commonly used for sediment yield estimation and management. The Revised Universal Soil Loss Equation (RUSLE) is the most widely used model for overland flow erosion and can, when combined with a sediment delivery ratio (SDR), provide reasonable sediment load estimations for a catchment. This paper presents RUSLE factors established from extant GIS and rainfall datasets that are incorporated into a flexible catchment modelling approach. We believe that this is the first time that results from a RUSLE application at a national scale are tested against measured sediment yield values available from Ireland. An initial assessment of RUSLE applied to Irish conditions indicates an overestimation of modelled sediment yield values for most of the selected catchments. Improved methods for model and SDR factors estimation are needed to account for Irish conditions and catchment characteristics. Nonetheless, validation and testing of the model in this study using observed values is an important step towards more effective sediment yield modelling tools for nationwide applications

MOSFiT: Modular open source fitter for transients

Much of the progress made in time-domain astronomy is accomplished by relating observational multi-wavelength time series data to models derived from our understanding of physical laws. This goal is typically accomplished by dividing the task in two: collecting data (observing), and constructing models to represent that data (theorizing). Owing to the natural tendency for specialization, a disconnect can develop between the best available theories and the best available data, potentially delaying advances in our understanding new classes of transients. We introduce MOSFiT: the Modular Open-Source Fitter for Transients, a Python-based package that downloads transient datasets from open online catalogs (e.g., the Open Supernova Catalog), generates Monte Carlo ensembles of semi-analytical light curve fits to those datasets and their associated Bayesian parameter posteriors, and optionally delivers the fitting results back to those same catalogs to make them available to the rest of the community. MOSFiT is designed to help bridge the gap between observations and theory in time-domain astronomy; in addition to making the application of existing models and creation of new models as simple as possible, MOSFiT yields statistically robust predictions for transient characteristics, with a standard output format that includes all the setup information necessary to reproduce a given result. As large-scale surveys such as LSST discover entirely new classes of transients, tools such as MOSFiT will be critical for enabling rapid comparison of models against data in statistically consistent, reproducible, and scientifically beneficial ways

Evidence of a Massive Stellar Disruption in the X-ray Spectrum of ASASSN-14li

The proximity and duration of the tidal disruption event (TDE) ASASSN-14li led to the discovery of narrow, blue-shifted absorption lines in X-rays and UV. The gas seen in X-ray absorption is consistent with bound material close to the apocenter of elliptical orbital paths, or with a disk wind similar to those seen in Seyfert-1 active galactic nuclei. We present a new analysis of the deepest high-resolution XMM-Newton and Chandra spectra of ASASSN-14li. Driven by the relative strengths of He-like and H-like charge states, the data require [N/C] > 2.4, in qualitative agreement with UV spectral results. Flows of the kind seen in the X-ray spectrum of ASASSN-14li were not clearly predicted in simulations of TDEs; this left open the possibility that the observed absorption might be tied to gas released in prior AGN activity. However, the abundance pattern revealed in this analysis points to a single star rather than a standard AGN accretion flow comprised of myriad gas contributions. The simplest explanation of the data is likely that a moderately massive star (M ~ 3 Msun) with significant CNO processing was disrupted. An alternative explanation is that a lower mass star was disrupted that had previously been stripped of its envelope. We discuss the strengths and limitations of our analysis and these interpretations.Comment: Accepted for publication in ApJ Letter

A multi-organ transcriptome resource for the Burmese Python (Python molurus bivittatus)

<p>Abstract</p> <p>Background</p> <p>Snakes provide a unique vertebrate system for studying a diversity of extreme adaptations, including those related to development, metabolism, physiology, and venom. Despite their importance as research models, genomic resources for snakes are few. Among snakes, the Burmese python is the premier model for studying extremes of metabolic fluctuation and physiological remodelling. In this species, the consumption of large infrequent meals can induce a 40-fold increase in metabolic rate and more than a doubling in size of some organs. To provide a foundation for research utilizing the python, our aim was to assemble and annotate a transcriptome reference from the heart and liver. To accomplish this aim, we used the 454-FLX sequencing platform to collect sequence data from multiple cDNA libraries.</p> <p>Results</p> <p>We collected nearly 1 million 454 sequence reads, and assembled these into 37,245 contigs with a combined length of 13,409,006 bp. To identify known genes, these contigs were compared to chicken and lizard gene sets, and to all Genbank sequences. A total of 13,286 of these contigs were annotated based on similarity to known genes or Genbank sequences. We used gene ontology (GO) assignments to characterize the types of genes in this transcriptome resource. The raw data, transcript contig assembly, and transcript annotations are made available online for use by the broader research community.</p> <p>Conclusion</p> <p>These data should facilitate future studies using pythons and snakes in general, helping to further contribute to the utilization of snakes as a model evolutionary and physiological system. This sequence collection represents a major genomic resource for the Burmese python, and the large number of transcript sequences characterized should contribute to future research in this and other snake species.</p

Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa

This is the publisher’s final pdf. The article is copyrighted by the New Phytologist Trust and published by John Wiley & Sons, Inc. It can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291469-8137. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work.•Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. For example, the detection of reliable phenotype–genotype associations and molecular signatures of selection requires a detailed knowledge about genome-wide patterns of allele frequency variation, linkage disequilibrium and recombination.\ud •We resequenced 16 genomes of the model tree Populus trichocarpa and genotyped 120 trees from 10 subpopulations using 29 213 single-nucleotide polymorphisms.\ud •Significant geographic differentiation was present at multiple spatial scales, and range-wide latitudinal allele frequency gradients were strikingly common across the genome. The decay of linkage disequilibrium with physical distance was slower than expected from previous studies in Populus, with r² dropping below 0.2 within 3–6 kb. Consistent with this, estimates of recent effective population size from linkage disequilibrium (N[subscript e] ≈ 4000–6000) were remarkably low relative to the large census sizes of P. trichocarpa stands. Fine-scale rates of recombination varied widely across the genome, but were largely predictable on the basis of DNA sequence and methylation features.\ud •Our results suggest that genetic drift has played a significant role in the recent evolutionary history of P. trichocarpa. Most importantly, the extensive linkage disequilibrium detected suggests that genome-wide association studies and genomic selection in undomesticated populations may be more feasible in Populus than previously assumed

A novel method for the genome-wide high resolution analysis of DNA damage

DNA damage occurs via endogenous and exogenous genotoxic agents and compromises a genome’s integrity. Knowing where damage occurs within a genome is crucial to understanding the repair mechanisms which protect this integrity. This paper describes a new development based on microarray technology which uses ultraviolet light induced DNA damage as a paradigm to determine the position and frequency of DNA damage and its subsequent repair throughout the entire yeast genome