A radiation-hydrodynamics scheme valid from the transport to the diffusion limit

We present in this paper the numerical treatment of the coupling between hydrodynamics and radiative transfer. The fluid is modeled by classical conservation laws (mass, momentum and energy) and the radiation by the grey moment $M_1$ system. The scheme introduced is able to compute accurate numerical solution over a broad class of regimes from the transport to the diffusive limits. We propose an asymptotic preserving modification of the HLLE scheme in order to treat correctly the diffusion limit. Several numerical results are presented, which show that this approach is robust and have the correct behavior in both the diffusive and free-streaming limits. In the last numerical example we test this approach on a complex physical case by considering the collapse of a gas cloud leading to a proto-stellar structure which, among other features, exhibits very steep opacity gradients.Comment: 29 pages, submitted to Journal of Computational physic

Decay resistance against Coriolus versicolor in Sessile oak ( Quercus petraea Liebl.): analysis of the between-tree variability and correlations with extractives, tree growth and other basic wood properties

Abstract : Weight loss due to fungus Coriolus versicolor has been measured on 614 samples according to the NF EN 113 norm. Up to eight samples were cut at breast height (two opposite radii×four radial positions in heartwood) from 82 mature sessile oaks ( Quercus petraea Liebl.) originating from contrasting regions, silvicultural schedules and site qualities in France. The following points are addressed in the paper: (i) contribution to the total variability for weight loss of the effects "tree”, "position in the tree”, as well as their interaction; (ii) percentage of wood samples and trees in each of the five classes of natural durability defined by the norm NF EN 350-2; (iii) test of the effects of region, silvicultural schedule and site quality on weight loss and evaluating their contribution to the total variation; and (iv) correlations at tree level between weight loss and several traits related to tree growth and basic wood properties (density, swelling, grain angle, multiseriate wood rays characteristics, extractives content). The results are discussed with a view to aid the forest manager as well as the log/wood user to take advantage of the high level of between-tree variability observed as natural durability against C. versicolo

Symmetry of Magnetically Ordered Quasicrystals

The notion of magnetic symmetry is reexamined in light of the recent observation of long range magnetic order in icosahedral quasicrystals [Charrier et al., Phys. Rev. Lett. 78, 4637 (1997)]. The relation between the symmetry of a magnetically-ordered (periodic or quasiperiodic) crystal, given in terms of a ``spin space group,'' and its neutron diffraction diagram is established. In doing so, an outline of a symmetry classification scheme for magnetically ordered quasiperiodic crystals is provided. Predictions are given for the expected diffraction patterns of magnetically ordered icosahedral crystals, provided their symmetry is well described by icosahedral spin space groups.Comment: 5 pages. Accepted for publication in Phys. Rev. Letter

Évaluation des risques écologiques causés par des matériaux de dragage: roposition d'une approche adaptée aux dépôts en gravière en eau

Une procédure d'évaluation des risques pour l'écosystème aquatique engendrés par un dépôt de matériaux de dragage dans une gravière type a été élaborée, et testée avec des échantillons de sédiments d'un canal du Nord-Est de la France. La procédure comporte une étape d'évaluation sommaire des risques, à partir de quotients des concentrations mesurées par les critères de danger correspondants, et une étape d'évaluation détaillée où des essais de toxicité et de lixiviation en colonnes sont mis en œuvre. Le scénario testé retient trois hypothèses, qui concernent (a) les effets sur les peuplements d'invertébrés benthiques, représentés notamment par Hyalella azteca et Chironomus riparius, (b) les effets sur les peuplements d'organismes pélagiques, représentés par Chlorella vulgaris, Ceriodaphnia dubia, et Brachionus calyciflorus, et (c) la pollution de la nappe alluviale associée. Différentes modalités d'exposition (essais normalisés, microcosmes) ont été testées. Dans le contexte particulier des trois sédiments étudiés, ces hypothèses se sont avérées plus ou moins discriminantes, la pollution de la nappe étant la plus sensible. Des améliorations de la procédure doivent être envisagées qui concernent à la fois la formulation des hypothèses (risques à court et long terme sur les organismes pélagiques), et les protocoles d'essai, tant pour les organismes du sédiment (rôle de la nourriture notamment) que pour les essais de lixiviation en colonnes.When contaminated by metals or synthetic organic compounds, dredged sediments may have negative impacts on receiving ecosystems. Therefore, there is a need for an operational risk assessment approach. Such a framework is proposed for dredged material deposits in open gravel quarries, which is a rather common means of disposal in France. The first step of the assessment relies upon chemical characterisation of the sediments; the resulting concentrations are divided by "probable effect concentrations" and pooled together, in order to calculate a global hazard quotient. According to the value of this quotient, several decisions can be taken: (a) undertake a detailed risk assessment, (b) dispose of the materials without further constraints, or (c) in case of uncertainty, do some biological testing (with Hyalella azteca and Chironomus riparius) in order to allow decisions. The second step is a detailed ecological risk assessment. Three different assessment endpoints have been proposed, which are (1) the deposit should have no effect on the structure and abundance of benthic invertebrates in the quarry, (2) it should have no long term effect on pelagic species, and (3) it should not cause groundwater pollution, as such quarries are in fact cross sections of shallow alluvial groundwater aquifers. A fourth assessment endpoint should be introduced, regarding health risks for recreational uses, including fishing, but this endpoint was not implemented in the current version of the approach. The analysis phase includes aquatic bioassays (bacteria - Metplate TM-, algae, microcrustaceans Ceriodaphnia dubia, rotifers Brachionus calyciflorus), and leaching assays in columns under ascendant flow.The proposed approach was tested with 3 sediments from a canal located in the north-eastern region of France. Microcosm assays were introduced in parallel to the proposed tests, in order to explore alternatives to standardised bioassays. According to their hazard quotient, the 3 sediments showed a contamination gradient; one of them should not have entered the detailed risk assessment phase, while another would have been further tested with H. azteca and C. riparius. In that case, this latter sediment would not have entered the detailed phase either, as it was not toxic to these species. However, the detailed risk assessment approach was applied to the three sediments, so as to test completely the relevance of the framework.The three sediments were not significantly toxic to either C. riparius or H. azteca. However, some effects were observed in microcosms, including genotoxicity to molluscs. In this case, no risk characterisation could be made. Pore waters extracted from the three sediments were not toxic or slightly toxic to bacteria, algae, and C. dubia; an EC10 value could be determined only for B. calyciflorus. Therefore, due to exposure calculations, it seems there is a risk to pelagic species. However, as 3 bioassays out of 4 were negative or inconclusive, a refinement step would seem to be necessary. The highest concentrations of cadmium, copper, chromium, nickel and zinc were measured in the first lixiviates of the most contaminated sediment. Yet, even in that case, the total extracted fraction remained less than 10% of the total load. This fraction was below 1% for the other sediments, whatever the metal. Maximum concentrations and predicted concentrations at 1 year were compared to drinking water standards. This comparison showed a real risk of degrading groundwater quality for that most contaminated sediment, and a transient risk due to cadmium and nickel for the following one on the contamination gradient.Considering these results, the design of the first step of the proposed assessment approach may be discussed, as one sediment which would not have been assessed in depth according to its hazard quotient did show a risk to pelagic species. This discrepancy underlines the fact that some sediment toxicity may exist below the lowest threshold. As it would be unrealistic to enter systematically into detailed risk assessments, the proposed thresholds in the decision diagram must be pragmatic compromises rather than absolutely safe boundaries. Moreover, protocol improvements are needed for sediment toxicity bioassays. Chronic endpoints are preferable, as they are more sensitive and more relevant. Another issue is related to the role of additional food: not adding food may increase the apparent toxicity, but the sediment organic content, which is an alternative food source, may also be a contaminant carrier. Furthermore, the second assessment endpoint (risk to pelagic species) should be reformulated, as it includes in fact two different questions. Short-term risks related to the deposition phase could be assessed with standardised bioassays like C. dubia survival and reproduction and algal growth, while longer term risks related to contaminant diffusion could be assessed with microcosms. Genotoxic effects were observed at rather high levels, as compared to published results. This result stresses the interest of introducing sensitive and early markers in the risk assessment process, although their real meaning for ecosystems is not yet fully elucidated. Finally, the leaching tests in columns are not completely satisfactory, as the column filling implies that one must first dry the sediments, which will alter their structure. Other application trials along with field validation studies should be carried out prior to the introduction of this scenario in operational or regulatory frameworks

Expression and trans-specific polymorphism of self-incompatibility RNases in Coffea (Rubiaceae)

Self-incompatibility (SI) is widespread in the angiosperms, but identifying the biochemical components of SI mechanisms has proven to be difficult in most lineages. Coffea (coffee; Rubiaceae) is a genus of old-world tropical understory trees in which the vast majority of diploid species utilize a mechanism of gametophytic self-incompatibility (GSI). The S-RNase GSI system was one of the first SI mechanisms to be biochemically characterized, and likely represents the ancestral Eudicot condition as evidenced by its functional characterization in both asterid (Solanaceae, Plantaginaceae) and rosid (Rosaceae) lineages. The S-RNase GSI mechanism employs the activity of class III RNase T2 proteins to terminate the growth of "self" pollen tubes. Here, we investigate the mechanism of Coffea GSI and specifically examine the potential for homology to S-RNase GSI by sequencing class III RNase T2 genes in populations of 14 African and Madagascan Coffea species and the closely related self-compatible species Psilanthus ebracteolatus. Phylogenetic analyses of these sequences aligned to a diverse sample of plant RNase T2 genes show that the Coffea genome contains at least three class III RNase T2 genes. Patterns of tissue-specific gene expression identify one of these RNase T2 genes as the putative Coffea S-RNase gene. We show that populations of SI Coffea are remarkably polymorphic for putative S-RNase alleles, and exhibit a persistent pattern of trans-specific polymorphism characteristic of all S-RNase genes previously isolated from GSI Eudicot lineages. We thus conclude that Coffea GSI is most likely homologous to the classic Eudicot S-RNase system, which was retained since the divergence of the Rubiaceae lineage from an ancient SI Eudicot ancestor, nearly 90 million years ago.United States National Science Foundation [0849186]; Society of Systematic Biologists; American Society of Plant Taxonomists; Duke University Graduate Schoolinfo:eu-repo/semantics/publishedVersio

Gut Bacterial Communities in the Giant Land Snail Achatina fulica and Their Modification by Sugarcane-Based Diet

The invasive land snail Achatina fulica is one of the most damaging agricultural pests worldwide representing a potentially serious threat to natural ecosystems and human health. This species is known to carry parasites and harbors a dense and metabolically active microbial community; however, little is known about its diversity and composition. Here, we assessed for the first time the complexity of bacterial communities occurring in the digestive tracts of field-collected snails (FC) by using culture-independent molecular analysis. Crop and intestinal bacteria in FC were then compared to those from groups of snails that were reared in the laboratory (RL) on a sugarcane-based diet. Most of the sequences recovered were novel and related to those reported for herbivorous gut. Changes in the relative abundance of Bacteroidetes and Firmicutes were observed when the snails were fed a high-sugar diet, suggesting that the snail gut microbiota can influence the energy balance equation. Furthermore, this study represents a first step in gaining a better understanding of land snail gut microbiota and shows that this is a complex holobiont system containing diverse, abundant and active microbial communities

Quantification of lentiviral vector copy numbers in individual hematopoietic colony-forming cells shows vector dose-dependent effects on the frequency and level of transduction

Lentiviral vectors are effective tools for gene transfer and integrate variable numbers of proviral DNA copies in variable proportions of cells. The levels of transduction of a cellular population may therefore depend upon experimental parameters affecting the frequency and/or the distribution of vector integration events in this population. Such analysis would require measuring vector copy numbers (VCN) in individual cells. To evaluate the transduction of hematopoietic progenitor cells at the single-cell level, we measured VCN in individual colony-forming cell (CFC) units, using an adapted quantitative PCR (Q-PCR) method. The feasibility, reproducibility and sensitivity of this approach were tested with characterized cell lines carrying known numbers of vector integration. The method was validated by correlating data in CFC with gene expression or with calculated values, and was found to slightly underestimate VCN. In spite of this, such Q-PCR on CFC was useful to compare transduction levels with different infection protocols and different vectors. Increasing the vector concentration and re-iterating the infection were two different strategies that improved transduction by increasing the frequency of transduced progenitor cells. Repeated infection also augmented the number of integrated copies and the magnitude of this effect seemed to depend on the vector preparation. Thus, the distribution of VCN in hematopoietic colonies may depend upon experimental conditions including features of vectors. This should be carefully evaluated in the context of ex vivo hematopoietic gene therapy studies