Evaluating the Potential of Using 5-Azacytidine as an Epimutagen

A number of early flowering lines were induced when 5-azacytidine was applied to germinating flax (Linum usitatissimum L.) seed. The genetics of these lines indicate that the induced changes are epigenetic and probably result from demethylation of the genomic DNA at loci that affect flowering age. Although the growth and development of three stable early flowering lines are altered and the percentage of filled seed was reduced in all three lines compared with controls, measures of seed productivity demonstrated that harvest index was unaffected in two of the lines. In the third, harvest index was lower than normal and both seed set per capsule and seed mass per 100 seed were reduced. Furthermore, six generations after induction this line began to display relatively high levels of polyembryony. The late appearance of this twinning and other aspects related to working with lines induced by 5-azacytidine and using 5-azacytidine as an epimutagen are discussed

Selenium interactions with algae: Chemical processes at biological uptake sites, bioaccumulation, and intracellular metabolism

Selenium (Se) uptake by primary producers is the most variable and important step in determining Se concentrations at higher trophic levels in aquatic food webs. We gathered data available about the Se bioaccumulation at the base of aquatic food webs and analyzed its relationship with Se concentrations in water. This important dataset was separated into lotic and lentic systems to provide a reliable model to estimate Se in primary producers from aqueous exposure. We observed that lentic systems had higher organic selenium and selenite concentrations than in lotic systems and selenate concentrations were higher in lotic environments. Selenium uptake by algae is mostly driven by Se concentrations, speciation and competition with other anions, and is as well influenced by pH. Based on Se species uptake by algae in the laboratory, we proposed an accurate mechanistic model of competition between sulfate and inorganic Se species at algal uptake sites. Intracellular Se transformations and incorporation into selenoproteins as well as the mechanisms through which Se can induce toxicity in algae has also been reviewed. We provided a new tool for risk assessment strategies to better predict accumulation in primary consumers and consequently to higher trophic levels, and we identified some research needs that could fill knowledge gaps

Critical point network for drainage between rough surfaces

In this paper, we present a network method for computing two-phase flows between two rough surfaces with significant contact areas. Low-capillary number drainage is investigated here since one-phase flows have been previously investigated in other contributions. An invasion percolation algorithm is presented for modeling slow displacement of a wetting fluid by a non wetting one between two rough surfaces. Short-correlated Gaussian process is used to model random rough surfaces.The algorithm is based on a network description of the fracture aperture field. The network is constructed from the identification of critical points (saddles and maxima) of the aperture field. The invasion potential is determined from examining drainage process in a flat mini-channel. A direct comparison between numerical prediction and experimental visualizations on an identical geometry has been performed for one realization of an artificial fracture with a moderate fractional contact area of about 0.3. A good agreement is found between predictions and observations

Formalizing and Modeling Enterprise Architecture (EA) Principles with Goal-oriented Requirements Language (GRL)

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A synthesis of atmospheric mercury depletion event chemistry in the atmosphere and snow

It was discovered in 1995 that, during the spring time, unexpectedly low concentrations of gaseous elemental mercury (GEM) occurred in the Arctic air. This was surprising for a pollutant known to have a long residence time in the atmosphere; however conditions appeared to exist in the Arctic that promoted this depletion of mercury (Hg). This phenomenon is termed atmospheric mercury depletion events (AMDEs) and its discovery has revolutionized our understanding of the cycling of Hg in Polar Regions while stimulating a significant amount of research to understand its impact to this fragile ecosystem. Shortly after the discovery was made in Canada, AMDEs were confirmed to occur throughout the Arctic, sub-Artic and Antarctic coasts. It is now known that, through a series of photochemically initiated reactions involving halogens, GEM is converted to a more reactive species and is subsequently associated to particles in the air and/or deposited to the polar environment. AMDEs are a means by which Hg is transferred from the atmosphere to the environment that was previously unknown. In this article we review Hg research taken place in Polar Regions pertaining to AMDEs, the methods used to collect Hg in different environmental media, research results of the current understanding of AMDEs from field, laboratory and modeling work, how Hg cycles around the environment after AMDEs, gaps in our current knowledge and the future impacts that AMDEs may have on polar environments. The research presented has shown that while considerable improvements in methodology to measure Hg have been made but the main limitation remains knowing the speciation of Hg in the various media. The processes that drive AMDEs and how they occur are discussed. As well, the role that the snow pack and the sea ice play in the cycling of Hg is presented. It has been found that deposition of Hg from AMDEs occurs at marine coasts and not far inland and that a fraction of the deposited Hg does not remain in the same form in the snow. Kinetic studies undertaken have demonstrated that bromine is the major oxidant depleting Hg in the atmosphere. Modeling results demonstrate that there is a significant deposition of Hg to Polar Regions as a result of AMDEs. Models have also shown that Hg is readily transported to the Arctic from source regions, at times during springtime when this environment is actively transforming Hg from the atmosphere to the snow and ice surfaces. The presence of significant amounts of methyl Hg in snow in the Arctic surrounding AMDEs is important because this species is the link between the environment and impacts to wildlife and humans. Further, much work on methylation and demethylation processes has occurred but these processes are not yet fully understood. Recent changes in the climate and sea ice cover in Polar Regions are likely to have strong effects on the cycling of Hg in this environment; however more research is needed to understand Hg processes in order to formulate meaningful predictions of these changes

Reviews and syntheses: Effects of permafrost thaw on Arctic aquatic ecosystems

The Arctic is a water-rich region, with freshwater systems covering about 16 % of the northern permafrost landscape. Permafrost thaw creates new freshwater ecosystems, while at the same time modifying the existing lakes, streams, and rivers that are impacted by thaw. Here, we describe the current state of knowledge regarding how permafrost thaw affects lentic (still) and lotic (moving) systems, exploring the effects of both thermokarst (thawing and collapse of ice-rich permafrost) and deepening of the active layer (the surface soil layer that thaws and refreezes each year). Within thermokarst, we further differentiate between the effects of thermokarst in lowland areas vs. that on hillslopes. For almost all of the processes that we explore, the effects of thaw vary regionally, and between lake and stream systems. Much of this regional variation is caused by differences in ground ice content, topography, soil type, and permafrost coverage. Together, these modifying factors determine (i) the degree to which permafrost thaw manifests as thermokarst, (ii) whether thermokarst leads to slumping or the formation of thermokarst lakes, and (iii) the manner in which constituent delivery to freshwater systems is altered by thaw. Differences in thaw-enabled constituent delivery can be considerable, with these modifying factors determining, for example, the balance between delivery of particulate vs. dissolved constituents, and inorganic vs. organic materials. Changes in the composition of thaw-impacted waters, coupled with changes in lake morphology, can strongly affect the physical and optical properties of thermokarst lakes. The ecology of thaw-impacted lakes and streams is also likely to change; these systems have unique microbiological communities, and show differences in respiration, primary production, and food web structure that are largely driven by differences in sediment, dissolved organic matter, and nutrient delivery. The degree to which thaw enables the delivery of dissolved vs. particulate organic matter, coupled with the composition of that organic matter and the morphology and stratification characteristics of recipient systems will play an important role in determining the balance between the release of organic matter as greenhouse gases (CO2and CH4), its burial in sediments, and its loss downstream. The magnitude of thaw impacts on northern aquatic ecosystems is increasing, as is the prevalence of thaw-impacted lakes and streams. There is therefore an urgent need to quantify how permafrost thaw is affecting aquatic ecosystems across diverse Arctic landscapes, and the implications of this change for further climate warming.Additional co-authors: G. MacMillan, M. Rautio, K. M. Walter Anthony, and K. P. Wicklan

Enhancing Goal-based Requirements Consistency: an Argumentation-based Approach

International audienceRequirements engineering research has for long recognized the leading role of goals as requirement artifacts during the requirements engineering specification processes. Given the large number of artifacts created during the requirements specification and the continuous evolution of these artifacts, reasoning about them remains a challenging task. Moreover, the rising complexity of the target domain under consideration during the requirements engineering process as well as the growth of geographically distributed projects explain why the number of collected requirements as well as their complexity also increase. In this context, providing support to stakeholders in achieving a common understanding of a set of goal-based requirements, in consolidating them and keeping them consistent over time is another challenging task. In this paper, we propose an approach to detect consistent sets of goal-based requirements and maintain their consistency over time. Our approach relies on argumentation theory which allows to detect the conflicts among elements called arguments. In particular, we rely on meta-argumentation, which instantiates abstract argumentation frameworks, where requirements are represented as arguments and the standard Dung-like argumentation framework is extended with additional relations between goal-based requirements

A consensus protocol for the recovery of mercury methylation genes from metagenomes

Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes