Numerical Approximation of the Transport Equation: Comparison of Five Positive Definite Algorithms

IIASA's Regional Acidification INformation and Simulation (RAINS) model will be used to develop and assess international control strategies to reduce emissions of acidifying pollutants. These strategies will involve the expenditure of large sum of money; it is important, therefore, to assess the effect of uncertainties in the model on its results. An important component of the RAINS model is its atmospheric transport component; this paper reports the results of examining several algorithms for solution of the atmospheric transport equation. It also represents a joint effort between IIASA scientists and those in the Institute of Meteorology and Water Management in Warsaw and Central Institute for Meteorology and Geodynamics in Vienna

Airborne nitrogen deposition to the Baltic Sea: past trends, source allocation and future

Despite significant reductions in nitrogen emissions achieved in Europe during the last three decades, eutrophication remains an environmental concern in the Baltic Sea basin. Recently, a number of comprehensive modelling studies have been conducted for the HELCOM Commission to inform the 2021 update of the Baltic Sea Action Plan. The calculations have focused on trends in airborne nitrogen deposition to the Baltic Sea and its nine sub-basins during the 2000-2017 period, the identification and ranking of the main contributors to deposition, as well as future projections for 2030, assuming compliance with the Gothenburg Protocol and the EU NEC Directive. This paper synthesizes the main results from these studies and puts them into the context of maximum allowable nutrient inputs to the Baltic Sea. According to our results, the airborne annual deposition to the Baltic Sea in 2017 amounted to 122.6 Gg(N) of oxidized nitrogen and 105.3 Gg(N) of reduced nitrogen, corresponding to a decrease since 2000 by, respectively, 39% and 11%. In order to filter out the large inter-annual variability due to meteorology and to better reflect trends in emissions, weather-normalized depositions of nitrogen have been calculated as well, according to which the decreases since 2000 amount to 35%, 7% and 25% for oxidized, reduced and total nitrogen, respectively. In 2017, Germany, Poland and Denmark were the most important contributors to airborne deposition of total (oxidized + reduced) nitrogen to the Baltic Sea. Agriculture contributed most to reduced nitrogen deposition, while the transport sector contributed most to oxidized nitrogen deposition. Agriculture in Germany was the single-most important contributor to nitrogen deposition to the Baltic Sea basin in 2017 (accounting for about 15% of the total), but there are numerous other important sectoral contributions. Emissions of nitrogen from the nine HELCOM Contracting Parties contributed 49%, 76% and 61% to oxidized, reduced and total nitrogen deposition, respectively. Assuming full compliance with the EU NEC Directive and the Gothenburg Protocol, significant further reductions in nitrogen deposition can be achieved by 2030, down to an annual deposition of 72.7 Gg(N) and 84.7 Gg(N) of oxidized and reduced nitrogen, respectively

A molecular insight into algal-oomycete warfare : cDNA analysis of Ectocarpus siliculosus infected with the basal oomycete Eurychasma dicksonii

Peer reviewedPublisher PD

A GIS model-based assessment of the environmental distribution of g-hexachlorocyclohexane in European soils and waters

The MAPPE GIS based multimedia model is used to produce a quantitative description of the behaviour of γ-hexachlorocyclohexane (γ-HCH) in Europe, with emphasis on continental surface waters. The model is found to reasonably reproduce γ-HCH distributions and variations along the years in atmosphere and soil; for continental surface waters, concentrations were reasonably well predicted for year 1995, when lindane was still used in agriculture, while for 2005, assuming severe restrictions in use, yields to substantial underestimation. Much better results were yielded when same mode of release as in 1995 was considered, supporting the conjecture that for γ-HCH, emission data rather that model structure and parameterization can be responsible for wrong estimation of concentrations. Future research should be directed to improve the quality of emission data. Joint interpretation of monitoring and modelling results, highlights that lindane emissions in Europe, despite the marked decreasing trend, persist beyond the provisions of existing legislation. An spatially-explicit multimedia modelling strategy was applied to describe the historical distribution of γ-HCH in European soils and surface waters

The RNAi machinery controls distinct responses to environmental signals in the basal fungus Mucor circinelloides

BACKGROUND: RNA interference (RNAi) is a conserved mechanism of genome defence that can also have a role in the regulation of endogenous functions through endogenous small RNAs (esRNAs). In fungi, knowledge of the functions regulated by esRNAs has been hampered by lack of clear phenotypes in most mutants affected in the RNAi machinery. Mutants of Mucor circinelloides affected in RNAi genes show defects in physiological and developmental processes, thus making Mucor an outstanding fungal model for studying endogenous functions regulated by RNAi. Some classes of Mucor esRNAs map to exons (ex-siRNAs) and regulate expression of the genes from which they derive. To have a broad picture of genes regulated by the silencing machinery during vegetative growth, we have sequenced and compared the mRNA profiles of mutants in the main RNAi genes by using RNA-seq. In addition, we have achieved a more complete phenotypic characterization of silencing mutants.  RESULTS: Deletion of any main RNAi gene provoked a deep impact in mRNA accumulation at exponential and stationary growth. Genes showing increased mRNA levels, as expected for direct ex-siRNAs targets, but also genes with decreased expression were detected, suggesting that, most probably, the initial ex-siRNA targets regulate the expression of other genes, which can be up- or down-regulated. Expression of 50% of the genes was dependent on more than one RNAi gene in agreement with the existence of several classes of ex-siRNAs produced by different combinations of RNAi proteins. These combinations of proteins have also been involved in the regulation of different cellular processes. Besides genes regulated by the canonical RNAi pathway, this analysis identified processes, such as growth at low pH and sexual interaction that are regulated by a dicer-independent non-canonical RNAi pathway.  CONCLUSION: This work shows that the RNAi pathways play a relevant role in the regulation of a significant number of endogenous genes in M. circinelloides during exponential and stationary growth phases and opens up an important avenue for in-depth study of genes involved in the regulation of physiological and developmental processes in this fungal model

A conserved fungal glycosyltransferase facilitates pathogenesis of plants by enabling hyphal growth on solid surfaces

Article Authors Metrics Comments Related Content Abstract Author summary Introduction Results and discussion Conclusions Methods Supporting information Acknowledgments References Reader Comments (0) Media Coverage (0) Figures Abstract Pathogenic fungi must extend filamentous hyphae across solid surfaces to cause diseases of plants. However, the full inventory of genes which support this is incomplete and many may be currently concealed due to their essentiality for the hyphal growth form. During a random T-DNA mutagenesis screen performed on the pleomorphic wheat (Triticum aestivum) pathogen Zymoseptoria tritici, we acquired a mutant unable to extend hyphae specifically when on solid surfaces. In contrast “yeast-like” growth, and all other growth forms, were unaffected. The inability to extend surface hyphae resulted in a complete loss of virulence on plants. The affected gene encoded a predicted type 2 glycosyltransferase (ZtGT2). Analysis of >800 genomes from taxonomically diverse fungi highlighted a generally widespread, but discontinuous, distribution of ZtGT2 orthologues, and a complete absence of any similar proteins in non-filamentous ascomycete yeasts. Deletion mutants of the ZtGT2 orthologue in the taxonomically un-related fungus Fusarium graminearum were also severely impaired in hyphal growth and non-pathogenic on wheat ears. ZtGT2 expression increased during filamentous growth and electron microscopy on deletion mutants (ΔZtGT2) suggested the protein functions to maintain the outermost surface of the fungal cell wall. Despite this, adhesion to leaf surfaces was unaffected in ΔZtGT2 mutants and global RNAseq-based gene expression profiling highlighted that surface-sensing and protein secretion was also largely unaffected. However, ΔZtGT2 mutants constitutively overexpressed several transmembrane and secreted proteins, including an important LysM-domain chitin-binding virulence effector, Zt3LysM. ZtGT2 likely functions in the synthesis of a currently unknown, potentially minor but widespread, extracellular or outer cell wall polysaccharide which plays a key role in facilitating many interactions between plants and fungi by enabling hyphal growth on solid matrices

Carbohydrate-active enzymes from the zygomycete fungus Rhizopus oryzae: a highly specialized approach to carbohydrate degradation depicted at genome level

<p>Abstract</p> <p>Background</p> <p><it>Rhizopus oryzae </it>is a zygomycete filamentous fungus, well-known as a saprobe ubiquitous in soil and as a pathogenic/spoilage fungus, causing Rhizopus rot and mucomycoses.</p> <p>Results</p> <p>Carbohydrate Active enzyme (CAZy) annotation of the <it>R. oryzae </it>identified, in contrast to other filamentous fungi, a low number of glycoside hydrolases (GHs) and a high number of glycosyl transferases (GTs) and carbohydrate esterases (CEs). A detailed analysis of CAZy families, supported by growth data, demonstrates highly specialized plant and fungal cell wall degrading abilities distinct from ascomycetes and basidiomycetes. The specific genomic and growth features for degradation of easily digestible plant cell wall mono- and polysaccharides (starch, galactomannan, unbranched pectin, hexose sugars), chitin, chitosan, β-1,3-glucan and fungal cell wall fractions suggest specific adaptations of <it>R. oryzae </it>to its environment.</p> <p>Conclusions</p> <p>CAZy analyses of the genome of the zygomycete fungus <it>R. oryzae </it>and comparison to ascomycetes and basidiomycete species revealed how evolution has shaped its genetic content with respect to carbohydrate degradation, after divergence from the Ascomycota and Basidiomycota.</p

An Osmotic Model of the Growing Pollen Tube

Pollen tube growth is central to the sexual reproduction of plants and is a longstanding model for cellular tip growth. For rapid tip growth, cell wall deposition and hardening must balance the rate of osmotic water uptake, and this involves the control of turgor pressure. Pressure contributes directly to both the driving force for water entry and tip expansion causing thinning of wall material. Understanding tip growth requires an analysis of the coordination of these processes and their regulation. Here we develop a quantitative physiological model which includes water entry by osmosis, the incorporation of cell wall material and the spreading of that material as a film at the tip. Parameters of the model have been determined from the literature and from measurements, by light, confocal and electron microscopy, together with results from experiments made on dye entry and plasmolysis in Lilium longiflorum. The model yields values of variables such as osmotic and turgor pressure, growth rates and wall thickness. The model and its predictive capacity were tested by comparing programmed simulations with experimental observations following perturbations of the growth medium. The model explains the role of turgor pressure and its observed constancy during oscillations; the stability of wall thickness under different conditions, without which the cell would burst; and some surprising properties such as the need for restricting osmotic permeability to a constant area near the tip, which was experimentally confirmed. To achieve both constancy of pressure and wall thickness under the range of conditions observed in steady-state growth the model reveals the need for a sensor that detects the driving potential for water entry and controls the deposition rate of wall material at the tip