TNOs are Cool: A survey of the trans-Neptunian region. VIII. Combined Herschel PACS and SPIRE observations of nine bright targets at 70–500 μm

International audienceAims. Trans-Neptunian objects (TNOs) are bodies populating the Kuiper belt and they are believed to retain the most pristine and least altered material of the solar system. The Herschel open time key programme entitled “TNOs are Cool: A survey of the trans-Neptunian region” has been awarded 373 h to investigate the albedo, size distribution and thermal properties of TNOs and Centaurs. Here we focus on the brightest targets observed by both the PACS and SPIRE multiband photometers: the dwarf planet Haumea, six TNOs (Huya, Orcus, Quaoar, Salacia, 2002 UX25, and 2002 TC302), and two Centaurs (Chiron and Chariklo).Methods. Flux densities are derived from PACS and SPIRE instruments using optimised data reduction methods. The spectral energy distribution obtained with the Herschel PACS and SPIRE instruments over 6 bands (centred at 70, 100, 160, 250, 350, and 500 μm), with Spitzer-MIPS at 23.7 and 71.4 μm, and with WISE at 11.6 and 22.1 μm in the case of 10199 Chariklo, has been modelled with the NEATM thermal model in order to derive the albedo, diameter, and beaming factor. For the Centaurs Chiron and Chariklo and for the 1000 km sized Orcus and Quaoar, a thermophysical model was also run to better constrain their thermal properties.Results. We derive the size, albedo, and thermal properties, including thermal inertia and surface emissivity, for the 9 TNOs and Centaurs. Several targets show a significant decrease in their spectral emissivity longwards of ~300 μm and especially at 500 μm. Using our size estimations and the mass values available in the literature, we also derive the bulk densities for the binaries Quaoar/Weywot (2.18-0.36+0.43 g/cm3), Orcus/Vanth (1.53-0.13+0.15 g/cm3), and Salacia/Actea (1.29-0.23+0.29 g/cm3). Quaoar’s density is similar to that of the other dwarf planets Pluto and Haumea, and its value implies high contents of refractory materials mixed with ices

Simulation aux grandes échelles: instabilités thermo-acoustiques, combustion diphasique et couplages multi-physiques

La combustion turbulente, que ce soit dans des configurations de laboratoire ou dans des configurations réelles industrielles, met en oeuvre un nombre important de physiques fortement couplées: chimie, turbulence, multi-phasique, thermique, etc. Pour répondre aux demandes de plus en plus exigeantes des concepteurs, qui doivent proposer des solutions concurrentielles tout en respectant les contraintes environnementales de bruit et d'émission de polluants, la simulation numérique est devenue incontournable. Plus précisément, la simulation maintenant utilisée comme outil de conception, doit être fiable et précise. Dans le domaine de la combustion turbulente, à fort caractère instationnaire, la Simulation aux Grandes Echelles (SGE) s'est récemment imposée. Cette technique s'est en effet avérée capable de prédire finement le comportement des brûleurs dans des environnements complexes, et permet aujourd'hui d'aborder des problématiques encore mal maîtrisées telles que les instabilités thermo-acoustiques ou la combustion diphasique. On donne ici quelques exemples de problèmes encore ouverts dans ce domaine

Profiling allele-specific gene expression in brains from individuals with autism spectrum disorder reveals preferential minor allele usage.

One fundamental but understudied mechanism of gene regulation in disease is allele-specific expression (ASE), the preferential expression of one allele. We leveraged RNA-sequencing data from human brain to assess ASE in autism spectrum disorder (ASD). When ASE is observed in ASD, the allele with lower population frequency (minor allele) is preferentially more highly expressed than the major allele, opposite to the canonical pattern. Importantly, genes showing ASE in ASD are enriched in those downregulated in ASD postmortem brains and in genes harboring de novo mutations in ASD. Two regions, 14q32 and 15q11, containing all known orphan C/D box small nucleolar RNAs (snoRNAs), are particularly enriched in shifts to higher minor allele expression. We demonstrate that this allele shifting enhances snoRNA-targeted splicing changes in ASD-related target genes in idiopathic ASD and 15q11-q13 duplication syndrome. Together, these results implicate allelic imbalance and dysregulation of orphan C/D box snoRNAs in ASD pathogenesis

Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages

This study provides the proof of principle that probing the host and the microbe transcriptomes simultaneously is a valuable means to accessing unique information on host pathogen interactions. Our results also underline the extraordinary plasticity of host cell and pathogen responses to infection, and provide a solid framework to further understand the complex mechanisms involved in immunity to M. tuberculosis and in mycobacterial adaptation to different intracellular environments

Inheritance of an Epigenetic Mark: The CpG DNA Methyltransferase 1 Is Required for De Novo Establishment of a Complex Pattern of Non-CpG Methylation

Site-specific methylation of cytosines is a key epigenetic mark of vertebrate DNA. While a majority of the methylated residues are in the symmetrical (meC)pG:Gp(meC) configuration, a smaller, but significant fraction is found in the CpA, CpT and CpC asymmetric (non-CpG) dinucleotides. CpG methylation is reproducibly maintained by the activity of the DNA methyltransferase 1 (Dnmt1) on the newly replicated hemimethylated substrates (meC)pG:GpC. On the other hand, establishment and hereditary maintenance of non-CpG methylation patterns have not been analyzed in detail. We previously reported the occurrence of site- and allele-specific methylation at both CpG and non-CpG sites. Here we characterize a hereditary complex of non-CpG methylation, with the transgenerational maintenance of three distinct profiles in a constant ratio, associated with extensive CpG methylation. These observations raised the question of the signal leading to the maintenance of the pattern of asymmetric methylation. The complete non-CpG pattern was reinstated at each generation in spite of the fact that the majority of the sperm genomes contained either none or only one methylated non-CpG site. This observation led us to the hypothesis that the stable CpG patterns might act as blueprints for the maintenance of non-CpG DNA methylation. As predicted, non-CpG DNA methylation profiles were abrogated in a mutant lacking Dnmt1, the enzymes responsible for CpG methylation, but not in mutants defective for either Dnmt3a or Dnmt2

Phylogeny of Mycobacterium tuberculosis Beijing Strains Constructed from Polymorphisms in Genes Involved in DNA Replication, Recombination and Repair

The original publication is available at http:/www.plosone.orgBackground: The Beijing family is a successful group of M. tuberculosis strains, often associated with drug resistance and widely distributed throughout the world. Polymorphic genetic markers have been used to type particular M. tuberculosis strains. We recently identified a group of polymorphic DNA repair replication and recombination (3R) genes. It was shown that evolution of M. tuberculosis complex strains can be studied using 3R SNPs and a high-resolution tool for strain discrimination was developed. Here we investigated the genetic diversity and propose a phylogeny for Beijing strains by analyzing polymorphisms in 3R genes. Methodology/Principal Findings: A group of 3R genes was sequenced in a collection of Beijing strains from different geographic origins. Sequence analysis and comparison with the ones of non-Beijing strains identified several SNPs. These SNPs were used to type a larger collection of Beijing strains and allowed identification of 26 different sequence types for which a phylogeny was constructed. Phylogenetic relationships established by sequence types were in agreement with evolutionary pathways suggested by other genetic markers, such as Large Sequence Polymorphisms (LSPs). A recent Beijing genotype (Bmyc10), which included 60% of strains from distinct parts of the world, appeared to be predominant. Conclusions/Significance: We found SNPs in 3R genes associated with the Beijing family, which enabled discrimination of different groups and the proposal of a phylogeny. The Beijing family can be divided into different groups characterized by particular genetic polymorphisms that may reflect pathogenic features. These SNPs are new, potential genetic markers that may contribute to better understand the success of the Beijing family. © 2011 Mestre et al.Publishers' Versio

Evolution and Diversity of Clonal Bacteria: The Paradigm of Mycobacterium tuberculosis

International audienceBACKGROUND: Mycobacterium tuberculosis complex species display relatively static genomes and 99.9% nucleotide sequence identity. Studying the evolutionary history of such monomorphic bacteria is a difficult and challenging task. PRINCIPAL FINDINGS: We found that single-nucleotide polymorphism (SNP) analysis of DNA repair, recombination and replication (3R) genes in a comprehensive selection of M. tuberculosis complex strains from across the world, yielded surprisingly high levels of polymorphisms as compared to house-keeping genes, making it possible to distinguish between 80% of clinical isolates analyzed in this study. Bioinformatics analysis suggests that a large number of these polymorphisms are potentially deleterious. Site frequency spectrum comparison of synonymous and non-synonymous variants and Ka/Ks ratio analysis suggest a general negative/purifying selection acting on these sets of genes that may lead to suboptimal 3R system activity. In turn, the relaxed fidelity of 3R genes may allow the occurrence of adaptive variants, some of which will survive. Furthermore, 3R-based phylogenetic trees are a new tool for distinguishing between M. tuberculosis complex strains. CONCLUSIONS/SIGNIFICANCE: This situation, and the consequent lack of fidelity in genome maintenance, may serve as a starting point for the evolution of antibiotic resistance, fitness for survival and pathogenicity, possibly conferring a selective advantage in certain stressful situations. These findings suggest that 3R genes may play an important role in the evolution of highly clonal bacteria, such as M. tuberculosis. They also facilitate further epidemiological studies of these bacteria, through the development of high-resolution tools. With many more microbial genomes being sequenced, our results open the door to 3R gene-based studies of adaptation and evolution of other, highly clonal bacteria