1,318 research outputs found

    Possible surface plasmon polariton excitation under femtosecond laser irradiation of silicon

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    The mechanisms of ripple formation on silicon surface by femtosecond laser pulses are investigated. We demonstrate the transient evolution of the density of the excited free-carriers. As a result, the experimental conditions required for the excitation of surface plasmon polaritons are revealed. The periods of the resulting structures are then investigated as a function of laser parameters, such as the angle of incidence, laser fluence, and polarization. The obtained dependencies provide a way of better control over the properties of the periodic structures induced by femtosecond laser on the surface of a semiconductor material.Comment: 11 pages, 8 figures, accepted for publication in Journal of Applied Physic

    A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

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    Strain-specific genomic diversity in the Mycobacterium tuberculosis complex (MTBC) is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Several systems have been proposed to classify MTBC strains into distinct lineages and families. Here, we investigate single-nucleotide polymorphisms (SNPs) as robust (stable) markers of genetic variation for phylogenetic analysis. We identify ~92k SNP across a global collection of 1,601 genomes. The SNP-based phylogeny is consistent with the gold-standard regions of difference (RD) classification system. Of the ~7k strain-specific SNPs identified, 62 markers are proposed to discriminate known circulating strains. This SNP-based barcode is the first to cover all main lineages, and classifies a greater number of sublineages than current alternatives. It may be used to classify clinical isolates to evaluate tools to control the disease, including therapeutics and vaccines whose effectiveness may vary by strain type

    Multiscale modeling of the effective viscoplastic behavior of Mg 2 SiO 4 wadsleyite: bridging atomic and polycrystal scales

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    The viscoplastic behavior of polycrystalline Mg2SiO4 wadsleyite aggregates, a major high pressure phase of the mantle transition zone of the Earth (depth range: 410–520 km), is obtained by properly bridging several scale transition models. At the very fine nanometric scale corresponding to the dislocation core structure, the behavior of thermally activated plastic slip is modeled for strain-rates relevant for laboratory experimental conditions, at high pressure and for a wide range of temperatures, based on the Peierls–Nabarro–Galerkin model. Corresponding single slip reference resolved shear stresses and associated constitutive equations are deduced from Orowan’s equation in order to describe the average viscoplastic behavior at the grain scale, for the easiest slip systems. These data have been implemented in two grain-polycrystal scale transition models, a mean-field one (the recent Fully-Optimized Second-Order Viscoplastic Self-Consistent scheme of [1]) allowing rapid evaluation of the effective viscosity of polycrystalline aggregates, and a full-field (FFT based [2, 3]) method allowing investigating stress and strain-rate localization in typical microstructures and heterogeneous activation of slip systems within grains. Calculations have been performed at pressure and temperatures relevant for in-situ conditions. Results are in very good agreement with available mechanical tests conducted at strain-rates typical for laboratory experiments.This work was supported by the European Research Council under the Seventh Framework Programme (FP 7), ERC (grant number 290424 RheoMan) and under the Horizon 2020 research and innovation programme (grant number 787198 TimeMan)

    Synthetic long non-coding RNAs [SINEUPs] rescue defective gene expression in vivo

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    Non-coding RNAs provide additional regulatory layers to gene expression as well as the potential to being exploited as therapeutic tools. Non-coding RNA-based therapeutic approaches have been attempted in dominant diseases, however their use for treatment of genetic diseases caused by insufficient gene dosage is currently more challenging. SINEUPs are long antisense non-coding RNAs that up-regulate translation in mammalian cells in a gene-specific manner, although, so far evidence of SINEUP efficacy has only been demonstrated in in vitro systems. We now show that synthetic SINEUPs effectively and specifically increase protein levels of a gene of interest in vivo. We demonstrated that SINEUPs rescue haploinsufficient gene dosage in a medakafish model of a human disorder leading to amelioration of the disease phenotype. Our results demonstrate that SINEUPs act through mechanisms conserved among vertebrates and that SINEUP technology can be successfully applied in vivo as a new research and therapeutic tool for gene-specific up-regulation of endogenous functional proteins

    Développement d'outils microbiologiques et chimiques permettant d'identifier l'origine des pollutions fécales dans les eaux de baignades

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    La pollution organique issue des effluents d'Ă©levage et des stations d'Ă©puration urbaines conduit Ă  un problĂšme essentiel de santĂ© publique liĂ© Ă  la contamination des eaux de surface oĂč s'exercent des activitĂ©s sensibles telles que la baignade. S'il est possible de dĂ©terminer les pollutions localisĂ©es liĂ©es Ă  un dysfonctionnement des systĂšmes de traitement, il est beaucoup plus difficile d'identifier les pollutions organiques diffuses qui participent pourtant majoritairement Ă  la dĂ©gradation de la qualitĂ© des eaux de surface. La problĂ©matique des pollutions diffuses est d'autant plus importante que la nouvelle rĂ©glementation europĂ©enne concernant les eaux de baignade (Directive 2006/7/CE) demande de constituer des profils de baignade qui nĂ©cessitent une identification et une hiĂ©rarchisation des sources de pollutions fĂ©cales. Le dĂ©nombrement de Escherichia coli et des entĂ©rocoques intestinaux stipulĂ© par les textes rĂ©glementaires europĂ©ens, reprĂ©sente actuellement le seul outil analytique permettant la mise en Ă©vidence d'une contamination fĂ©cale du milieu aquatique, sans toutefois diffĂ©rencier l'origine humaine ou animale de cette contamination. Il est donc nĂ©cessaire de dĂ©velopper de nouvelles mĂ©thodes de dĂ©tection de la pollution fĂ©cale qui puissent non seulement mettre en Ă©vidence une contamination mais aussi en indiquer l'origine. C'est d'ailleurs dans cet objectif que s'est dĂ©veloppĂ© depuis quelques annĂ©es, le concept de "Microbial Source Tracking" ("Traceurs de Sources Microbiennes") qui consiste Ă  identifier Ă  l'aide de marqueurs microbiologiques ou chimiques les sources de pollutions fĂ©cales. Dans ce contexte, six laboratoires de recherche se sont associĂ©s pour dĂ©velopper des techniques de traçage des contaminations fĂ©cales afin de proposer un outil opĂ©rationnel utilisable pour diffĂ©rencier les sources de pollution, de leur point d'Ă©mission jusqu'au milieu rĂ©cepteur final que constituent les eaux de surface. Les marqueurs qui ont fait l'objet de cette Ă©tude sont des molĂ©cules chimiques naturelles (stĂ©roĂŻdes, cafĂ©ine), des molĂ©cules de synthĂšse retrouvĂ©es dans les effluents de stations d'Ă©puration ou des rapports de fluorescence de la matiĂšre organique ainsi que des micro-organismes (bactĂ©riophages, bactĂ©ries). A la suite des dĂ©veloppements mĂ©thodologiques, plusieurs marqueurs ont Ă©tĂ© sĂ©lectionnĂ©s : - bactĂ©ries appartenant aux groupes bactĂ©riens dominants du tractus intestinal humain (Bifidobacterium adolescentis) et porcin (Lactobacillus amylovorus) ; - Bacteroidales spĂ©cifiques des humains, porcins et bovins (HF183, Pig-2-Bac, Rum-2-Bac); - gĂ©nogroupes humains des bactĂ©riophages F ARN spĂ©cifiques; - rapports de stĂ©roĂŻdes : coprostanol/(24ethylcoprostanol+coprostanol) (R1) et sitostanol/coprostanol (R2); - cafĂ©ine, benzophĂ©none et tri(2-chloroethyl)phosphate (TCEP)

    Cryptogamic ground covers as analogues for early terrestrial biospheres: Initiation and evolution of biologically mediated proto-soils

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    Modern cryptogamic ground covers (CGCs), comprising assemblages of bryophytes (hornworts, liverworts, mosses), fungi, bacteria, lichens and algae, are thought to resemble early divergent terrestrial communities. However, limited in-situ plant and other fossils in the rock record, and a lack of CGC-like soils reported in the pre-Silurian sedimentological record, have hindered understanding of the structure, composition, and interactions within the earliest CGCs. A key question is how the earliest CGC-like organisms drove weathering on primordial terrestrial surfaces (regolith), leading to the early stages of soil development as proto-soils, and subsequently contributing to large-scale biogeochemical shifts in the Earth System. Here, we employed a novel qualitative, quantitative and multi-dimensional imaging approach through X-ray micro-computed tomography, scanning electron, and optical microscopy to investigate whether different combinations of modern CGC organisms from primordial-like settings in Iceland develop organism-specific soil-forming features at the macro- and micro-scales. Additionally, we analysed CGCs growing on hard rocky substrates to investigate the initiation of weathering processes non-destructively in 3D. We show that thalloid CGC organisms (liverworts, hornworts) develop thin organic layers at the surface (<1 cm) with limited subsurface structural development, whereas leafy mosses and communities of mixed-organisms form profiles that are thicker (up to ~7 cm), structurally more complex, and more organic-rich. We term these thin layers and profiles proto-soils. Component analyses from X-ray micro-computed tomography data show that thickness and structure of these proto-soils are determined by the type of colonising organism(s), suggesting that the evolution of more complex soils through the Palaeozoic may have been driven by a shift in body plan of CGC-like organisms from flattened and appressed to upright and leafy. Our results provide a framework for identifying CGC-like proto-soils in the rock record and a new proxy for understanding organism-soil interactions in ancient terrestrial biospheres and their contribution to the early stages of soil-formation

    An ecosystem-based approach to assess the status of Mediterranean algae-dominated shallow rocky reefs.

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    A conceptual model was constructed for the functioning the algae-dominated rocky reef ecosystem of the Mediterranean Sea. The Ecosystem-Based Quality Index (reef-EBQI) is based upon this model. This index meets the objectives of the EU Marine Strategy Framework Directive. It is based upon (i) the weighting of each compartment, according to its importance in the functioning of the ecosystem; (ii) biological parameters assessing the state of each compartment; (iii) the aggregation of these parameters, assessing the quality of the ecosystem functioning, for each site; (iv) and a Confidence Index measuring the reliability of the index, for each site. The reef-EBQI was used at 40 sites in the northwestern Mediterranean. It constitutes an efficient tool, because it is based upon a wide set of functional compartments, rather than upon just a few species; it is easy and inexpensive to implement, robust and not redundant with regard to already existing indices

    TEAD and YAP regulate the enhancer network of human embryonic pancreatic progenitors.

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    The genomic regulatory programmes that underlie human organogenesis are poorly understood. Pancreas development, in particular, has pivotal implications for pancreatic regeneration, cancer and diabetes. We have now characterized the regulatory landscape of embryonic multipotent progenitor cells that give rise to all pancreatic epithelial lineages. Using human embryonic pancreas and embryonic-stem-cell-derived progenitors we identify stage-specific transcripts and associated enhancers, many of which are co-occupied by transcription factors that are essential for pancreas development. We further show that TEAD1, a Hippo signalling effector, is an integral component of the transcription factor combinatorial code of pancreatic progenitor enhancers. TEAD and its coactivator YAP activate key pancreatic signalling mediators and transcription factors, and regulate the expansion of pancreatic progenitors. This work therefore uncovers a central role for TEAD and YAP as signal-responsive regulators of multipotent pancreatic progenitors, and provides a resource for the study of embryonic development of the human pancreas
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