International Geomagnetic Reference Field: the 12th generation

The 12th generation of the International Geomagnetic Reference Field (IGRF) was adopted in December 2014 by the Working Group V-MOD appointed by the International Association of Geomagnetism and Aeronomy (IAGA). It updates the previous IGRF generation with a definitive main field model for epoch 2010.0, a main field model for epoch 2015.0, and a linear annual predictive secular variation model for 2015.0-2020.0. Here, we present the equations defining the IGRF model, provide the spherical harmonic coefficients, and provide maps of the magnetic declination, inclination, and total intensity for epoch 2015.0 and their predicted rates of change for 2015.0-2020.0. We also update the magnetic pole positions and discuss briefly the latest changes and possible future trends of the Earth’s magnetic fiel

Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome

<p>Abstract</p> <p>Background</p> <p>One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for <it>Quercus robur</it>, its characterization and an analysis of BAC end sequences.</p> <p>Results</p> <p>The <it>Eco</it>RI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while <it>ab initio </it>repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of <it>Arabidopsis thaliana</it>, <it>Vitis vinifera </it>and <it>Populus trichocarpa</it>. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of <it>V. vinifera.</it></p> <p>Conclusions</p> <p>This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak.</p

Gene Expression Profiles Characterize Inflammation Stages in the Acute Lung Injury in Mice

Acute Lung Injury (ALI) carries about 50 percent mortality and is frequently associated with an infection (sepsis). Life-support treatment with mechanical ventilation rescues many patients, although superimposed infection or multiple organ failure can result in death. The outcome of a patient developing sepsis depends on two factors: the infection and the pre-existing inflammation. In this study, we described each stage of the inflammation process using a transcriptional approach and an animal model. Female C57BL6/J mice received an intravenous oleic acid injection to induce an acute lung injury (ALI). Lung expression patterns were analyzed using a 9900 cDNA mouse microarray (MUSV29K). Our gene-expression analysis revealed marked changes in the immune and inflammatory response metabolic pathways, notably lipid metabolism and transcription. The early stage (1 hour–1.5 hours) is characterized by a pro-inflammatory immune response. Later (3 hours–4 hours), the immune cells migrate into inflamed tissues through interaction with vascular endothelial cells. Finally, at late stages of lung inflammation (18 hours–24 hours), metabolism is deeply disturbed. Highly expressed pro-inflammatory cytokines activate transcription of many genes and lipid metabolism. In this study, we described a global overview of critical events occurring during lung inflammation which is essential to understand infectious pathologies such as sepsis where inflammation and infection are intertwined. Based on these data, it becomes possible to isolate the impact of a pathogen at the transcriptional level from the global gene expression modifications resulting from the infection associated with the inflammation

Between but not within species variation in the distribution of fitness effects

New mutations provide the raw material for evolution and adaptation. The distribution of fitness effects (DFE) describes the spectrum of effects of new mutations that can occur along a genome, and is therefore of vital interest in evolutionary biology. Recent work has uncovered striking similarities in the DFE between closely related species, prompting us to ask whether there is variation in the DFE among populations of the same species, or among species with different degrees of divergence, i.e., whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterised the DFE for multiple species, and for each species, multiple populations, and investigated the factors potentially influencing the DFE, such as demography, population divergence and genetic background. We find statistical support for there being variation in the DFE at the species level, even among relatively closely related species. However, we find very little difference at the population level, suggesting that differences in the DFE are primarily driven by deep features of species biology, and that evolutionarily recent events, such as demographic changes and local adaptation, have little impact

Etude du transcriptome du mutant de la levure dna2-1 vieillissant prématurement à l'aide d'un nouveau système permettant l'analyse comparative du puces à ADN

Cette these decrit une methode originale de comparaison automatique d'experiences de transcriptome appliquee a la determination des causes du vieillissement de l'organisme eucaryote modele: Saccharomyces cerevisiae. Les experiences de transcriptome, qui peuvent etre realisees a l'aide de microarrays, permettent au biologiste d'etudier simultanement les variations globales d'expression de milliers de genes dans de nombreuses conditions experimentales. Ces experiences a grande echelle realisees a haut-debit generent une quantite importante de donnees. En consequence, les biologistes ont besoin d'outils informatiques pour les interpreter. L'utilisation de microarrays pour l'etude des causes du vieillissement chez la levure nous a permis d'identifier les outils informatiques necessaires a l'interpretation des donnees de transcriptome. Independemment de son interet biologique, le vieillissement est un probleme particulierement bien adapte a une double approche biologique et informatique. Nous avons analyse le transcriptome des cellules de levure au cours de leur vieillissement. Deux souches ont ete etudiees: l'une d'elles est une souche sauvage et l'autre un mutant, dna2-1, vieillissant prematurement, et dont la replication de l'ADN est deficiente. Plusieurs outils existants d'analyse de donnees microarrays nous ont permis d'interpreter nos resultats. Nous avons constate un stockage d'energie associe au vieillissement: les genes impliques dans la gluconeogenese, le cycle du glyoxylate, le metabolisme lipidique, et la production de glycogene sont actives dans les vieilles cellules. Nous avons egalement observe une reponse generalisee au stress connue sous le nom ESR (Reponse Environnementale au Stress) decrite auparavant dans d'autres etudes. De plus, Nous avons observe l'induction d'un ensemble de genes qui reparent l'ADN et connus sous le nom de signature de degradation de l'ADN. Plusieurs genes ayant un role dans la production d'energie sont actives dans la souche mutante dna2-1. La reponse au vieillissement observee chez dna2-1 est similaire a celle decrite dans un mutant dont la telomerase est disfonctionnelle (TDR). Elle est constituee par un ensemble de genes dont l'expression change durant la senescence cellulaire. Ces resultats suggerent indirectement que les cellules agees repondent a une instabilite du genome. Le travail d'interpretation de ces donnees nous a permis d'identifier des besoins informatiques specifiques parmis lesquels la necessite de comparer des experiences microarray de facon automatique. Pour cette raison, nous avons developpe, dans la deuxieme partie de cette these, une methode permettant de comparer des experiences microarray de facon automatique. Cette methode originale repose sur une ontologie pour experiences microarrays associee a un modele de cout evaluant le degre de compatibilite de deux experiences. La validation de cette methode a conduit au developpement d'une plateforme de test, Malako, qui associe les outils informatiques classiques d'analyses de donnees microarray a un systeme de comparaison automatique d'experiences microarray.BORDEAUX1-BU Sciences-Talence (335222101) / SudocSudocFranceF

The Transcriptome of Prematurely Aging Yeast Cells Is Similar to That of Telomerase-deficient Cells

To help define the pathologies associated with yeast cells as they age, we analyzed the transcriptome of young and old cells isolated by elutriation, which allows isolation of biochemical quantities of old cells much further advanced in their life span than old cells prepared by the biotin-streptavidin method. Both 18-generation-old wild-type yeast and 8-generation-old cells from a prematurely aging mutant (dna2-1), with a defect in DNA replication, were evaluated. Genes involved in gluconeogenesis, the glyoxylate cycle, lipid metabolism, and glycogen production are induced in old cells, signifying a shift toward energy storage. We observed a much more extensive generalized stress response known as the environmental stress response (ESR), than observed previously in biotin-streptavidin-isolated cells, perhaps because the elutriated cells were further advanced in their life span. In addition, there was induction of DNA repair genes that fall in the so-called DNA damage “signature” set. In the dna2-1 mutant, energy production genes were also induced. The response in the dna2-1 strain is similar to the telomerase delete response, genes whose expression changes during cellular senescence in telomerase-deficient cells. We propose that these results suggest, albeit indirectly, that old cells are responding to genome instability

Projet Big Dry, Ruptures et continuité dans le peuplement de l’Afrique à la fin du Pléistocène : paléoanthropologie, paléoenvironnement et archéologies comparées du Rift et du Nil dans leur cadre continental.

International audienc

Discovering genes involved in ecological speciation in European white oaks using an RNAseq approach

National audienc