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International audience; In hypothetical accidental conditions, zirconium-based nuclear fuel claddings can absorb high hydrogen contents (up to several thousand wppm) and be exposed to high temperatures (βZr phase temperature range) before being cooled. This paper thoroughly investigates the microstructural and microchemical evolutions that take place in such conditions. Two zirconium-based alloys and unalloyed zirconium were pre-charged with hydrogen at various contents up to 3300 wppm and heat-treated at 1000 or 850 °C. Neutron diffraction analyses were performed in situ upon slow cooling from 700 °C and at room temperature. In the materials containing 3300 wppm of hydrogen, βZr progressively transforms into αZr during slow cooling then extensively transforms into αZr and δZrH2-x hydrides precipitate via a eutectoid reaction. Thermodynamic predictions at equilibrium are in good agreement with the experimental results. However, depending on the cooling scenario and the average hydrogen content, the precipitation of γZrH hydrides, potentially metastable, is evidenced below 350 °C and a significant amount of hydrogen can remain in solid solution in αZr. These metallurgical evolutions and the evolution of the different phase lattice parameters are strongly influenced by the partitioning of oxygen and hydrogen (revealed by electron probe and elastic recoil detection microanalyses) that occurs during the βZr to αZr transformation and hydride precipitation.

International audience; The emergence of non-native fungal pathogens is a growing threat to global health, biodiversity, conservation biology, food security and the global economy. Moreover, a thorough understanding of the spread and emergence of pathogens among invasive and native host populations, as well as genetic analysis of the structure of co-invasive host populations, is crucial in terms of conservation biology and management strategies. Here we com-bined extensive catchment sampling, molecular detection tools and genomic signatures to i) assess the prevalence of the rosette agent Sphaerothecum destruens in invasive and native fish populations in contrasting french regions, and ii) characterize the genetic diversity and population structure of its co-invasive and asymptomatic carrier Pseudorasbora parva. Although S. destruens was not detected in all the fish collected its presence in contrasting freshwater ecosystems suggests that the disease may already be widespread in France. Furthermore, our results show that the detection of S. destruens DNA in its asymptomatic carrier P. parva is still limited. Finally, we found that P. parva populations show a homogeneous genetic and geographical structuring, which raises the possibility of the occurrence of successive introduction events in France from their native and invasive range.

Additional file of Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX Titanium pyrosequencing

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Additional file 4: Representativeness of genome features using the equiprobability model. Representativeness of genome features using the equiprobability model in the case of Apis mellifera (A) and Danio rerio (B) for each of the six considered two-way tables chromosome × chromosomic region, chromosome × length of sequences, chromosome × microsatellite motifs, chromosomic region × length of sequences, chromosomic region × microsatellite motifs and length of sequences × microsatellite motifs. "Stat" refers to the overall χ2 statistic for the test of independence between the two variables defining the table. For each cell of the table: a red dot corresponds to an observed number significantly higher than expected under the hypothesis of independence between the two variables defining the table; a blue dot corresponds to an observed number significantly lower than expected under the hypothesis of independence between the two variables defining the table; absence of circle means a non-significant deviation. The size of the dot is inversely-proportional to the P-value, the scaling being made to the six considered tables so that the comparison of sizes between tables is meaningful. For cell tests, Benjamini-Hochberg20 correction for multiple tests was performed. (PDF 4 MB)

Authors’ original file for figure 4

Authors’ original file for figure 1

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Additional file 2: Representativeness of genome distribution after digestion with Rsa I. Representativeness of genome distribution after digestion with Rsa I in the case of Apis mellifera (A) and Danio rerio (B) for each of the six considered two-way tables: chromosome × chromosomic region, chromosome × length of sequences, chromosome × microsatellite motifs, chromosomic region × length of sequences, chromosomic region × microsatellite motifs and length of sequences × microsatellite motifs. "Stat" refers to the overall χ2 statistic for the test of independence between the two variables defining the table. For each cell of the table: a red dot corresponds to an observed number significantly higher than expected under the hypothesis of independence between the two variables defining the table, a blue dot corresponds to an observed number significantly lower than expected under the hypothesis of independence between the two variables defining the table; absence of dot means a non-significant deviation. The size of the dot is inversely-proportional to the P-value. The scaling is computed for the six considered tables so comparison of significance between tables is meaningful. For cell tests, Benjamini-Hochberg20 correction for multiple tests was performed. (PDF 3 MB)

Additional file 3: Comparison of genome features using the equiprobability model Comparison of genome features using the equiprobability model in the case of Apis mellifera (A) and Danio rerio (B) for each of the four considered one-way tables: chromosome, chromosomic region, length of sequences and microsatellite motifs. For each table is figured in red the 95% confidence interval of the expected number of microsatellites under the equiprobability hypothesis, in black are figured observed numbers (genome distribution after digestion in silico with Rsa I). (PDF 2 MB)

The present note intends to challenge, based on field observations, the definition of treeline and argues for considering the upper occurrences of tree-species as an integrative result of historical and contemporary processes acting on high-altitude socio-ecosystems. A field survey of Pinus cembra growing above 2800 m asl was conducted, in an ecoregion of southwestern Alps, straddling France and Italy (Queyras-Mt Viso area). Pines were described (height, density) and their habitats were contextualized (altitude, slope degree and exposure, bedrock). Individuals of Pinus cembra are commonly growing between 2800 and 3200 m asl, generally on east-facing, steep and rocky slopes, with a pine density decreasing with altitude. Pines are generally dwarf-shaped, sometimes erected or prostrated. Their needles are half the size compared to those of pines growing in subalpine forests. Pine morphology indicates harsh growing conditions, notably strong wind, aridity and frost. These habitats constitute visually emerging objects attractive for the nutcracker caching behaviour. This setting acts as a positive passive driver for pine at high altitudes, which is further favoured by intense atmospheric moisture supplied by the east from the Po valley. Steep and rocky slopes exclude livestock, likely explaining why these pines are located in grass-less habitats. These tree clusters constitute remarkable “sky-island” populations. Larix decidua and Pinus uncinata were also recorded at exceptional altitudes but P. cembra is the most frequent species in high alpine conditions. These observations altogether highlight a complex pattern of tree-species line in the western Alps, and probably beyond.

Anisotropy of bulk magnetic properties and magnetic structure studies of a Tb

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Additional file 3: Breakdown of error rate variation using all available variables. For each plate, we used a logistic model to decipher the role of each selected variable in explaining the variation of error rate (see materials and methods). The figure is broken down by error type: a) insertions, b) deletions, c) mismatches and d) ambiguous base calls. We tested the deviance from the complete model by breaking down the model into the sum of three terms: the first exclusive to the single effect of the variable considered (in black), the second exclusive effect of the rest of the variables without the variable of interest (in gray) and the last expressing the sum of the effects of interactions between the variable considered and the other variables (in white). The contribution of each term (the proportion) for a considered variable can be viewed on the y-axis. Additional file 3 displays the results for plates #2 and #3 (results from the plate #1 are presented as Figure 2). (PDF 117 KB)

Additional file 2: Distribution of errors along the reference sequences. The blue line represents the proportion of sequences generated (y-axis) according to the sequence position (x-axis), using data obtained from the analysis of reference 5 reference sequences (excluding reference #3, which is displayed in Figure 1). The error rate for each type of error (insertions, deletions, mismatches and ambiguous base calls) is presented as a function of the sequence position (x-axis) and specific position on the y-axis. The position and length of homopolymers for each base is given on the x-axis to facilitate interpretation (green: A, red: T, black: G, blue: C). (PDF 265 KB)

Anisotropy of bulk magnetic properties and magnetic structure studies of a Tb2Pd2In single crystal by means of bulk magnetization methods and neutron diffraction techniques confirmed the antiferromagnetic order below the N el temperature 29.5 K. The collinear magnetic structure of Tb magnetic moments aligned along the tetragonal c axis is characterized by a propagation vector k 1 4, 1 4, 1 2 , yielding an equal moment structure with alternating coupling between nearest as well as next nearest Tb neighbors within the basal plane and antiferromagnetic coupling between the c axis neighbors. In the context of magnetism of R2T2X compounds, where R stands for rare earth or actinide element, such collinear structure with long wavelength periodicity represents a new type of magnetic structure.

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Additional file of Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing

Additional file 1: Number of sequences to correct erroneous positions. 1a: this file illustrates the number of sequences necessary to obtain a majority of correct sequences. The x-axis shows the error rate and the y-axis shows the number of sequences needed, according to three possible probabilities: 0.001 0.01 and 0.05. 1b the x-axis shows the error rate for a given position (ranging from 0 to 0.5); the y-axis shows the cumulative proportion of erroneous sequences sampled (ranging from 0 to 0.5) in the total sample. Sample size varies from 10 to 100, 500 and 1,000 sequences. For a given error rate and a cumulative proportion of erroneous sequences in the sample of size N, the probability of observing this combination is indicated in color: green: 1 to 0.95, blue: 0.95 to 0.8, yellow: 0.8 to 0.6, orange: 0.6 to 0.5, red: 0.5 to 0.4, gray: 0.4 to 0.2 and white: below 0.2. For example, if the error rate is 0.2, the probability of observing a cumulative proportion of erroneous sequences in the sample of between 0 and 0.2 ranges between 0.4 and 0.5 (red envelope). In this case, the probability of there being 20% erroneous sequences in the sample is between 0.4 and 0.5. If we consider the same error rate (0.2) with 40% erroneous sequences, then the probability ranges from 0.8 to 0.95 (blue envelope). If N increases, the variance of the probability envelopes decreases. (PDF 5 MB)

Additional file 4: Spatial localization of error rate variation. For each error type and the sequence length, the x-axis represents the spatial localization of 454 reads as x-coordinates and the y-axis represents the y-coordinates on the PT plate. The results presented in this additional data file 4 correspond to plates #2 and #3. The strips represent the regions. We display separately the four types of error (insertions, deletions, mismatches and ambiguous base calls) and the length of the generated sequences. Colors represent the ranges of error rates from 0 to 1 (or the length of the sequences from 0 to 500), using a sliding window (see materials and methods). (PDF 550 KB)

International audience; Augustin Augier's “Arbre botanique” (“botanical tree”) (1801), a diagram representing the natural order of plants in the shape of a family tree, is today a standard reference in histories of systematics and phylogenetic trees. The previously unidentified author was a nobleman from Saint-Tropez, a schoolteacher and a priest in the Société de l'Oratoire de Jésus et de Marie immaculée. His biography and two previously unnoticed publications, as well as his correspondence with the Institut national in Paris, are discussed. Knowledge of Augier's identity, his life and works sheds new light upon his taxonomic theories, and helps us to understand his “Arbre botanique”. Long before the tree was made into an icon of evolutionism, Augier used it to demonstrate the beauty and perfect order of divine creation.; En 1801, Augustin Augier publiait son “Arbre botanique”, diagramme représentant l'ordre naturel des plantes sous la forme d'un arbre généalogique, considéré aujourd'hui comme une référence de base par les historiens de la systématique et des arbres phylogénétiques. L'auteur, resté jusqu'ici inconnu, était un gentilhomme originaire de Saint-Tropez, enseignant et prêtre de la Société de l'Oratoire de Jésus et de Marie immaculée. Nous présentons sa première biographie ainsi que deux ouvrages inédits de lui et sa correspondance avec l'Institut national à Paris. La connaissance de l'identité d'Augier, de sa vie et de ses travaux, jette une nouvelle lumière sur ses théories taxonomiques et nous aide à comprendre son “Arbre botanique”. Longtemps avant que l'arbre ne devienne une icône de l’évolutionnisme, Augier l'utilisa pour démontrer la beauté et l'ordre parfait de la création divine.