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Henckes N.,French National Center for Scientific Research
International Journal of Epidemiology | Year: 2014

This article uses archival as well as published materials to trace the development of psychiatric epidemiology in France from 1945 to 1980. Although a research programme in this field was launched in the early 1960s at the National Institute of Medical Research (INH, later renamed INSERM), psychiatric epidemiology remained an embryonic field in France during the next two decades. French researchers in this field were hampered by limited resources, but their work was primarily characterized by a deep engagement with the epistemological challenges of psychiatric epidemiology. The history of French psychiatric epidemiology in the 1960s and 1970s can be seen as an attempt to create a specifically French way of doing psychiatric epidemiology research. In the first part of this article, the author relates this unique history to internal professional dynamics during the development of psychiatric research and, more broadly, to the biomedical institutional context in which epidemiological work was being done. The next part of this article examines the conditions under which the INH research team framed epidemiological research in psychiatry in the 1960s. The last part focuses on INH's flagship psychiatric epidemiology programme, developed in cooperation with pioneers of French community psychiatry in Paris's 13th arrondissement in the 1960s. © The Author 2014; all rights reserved.


Drancourt M.,French National Center for Scientific Research
Clinical Microbiology and Infection | Year: 2010

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) initiated a revolution in the identification of organisms grown on solid medium, including bacteria and fungi. Rapid identification of organisms responsible for septicaemia, which are typically grown in broth, is now expanding the field of application. Despite the fact that there are fewer than ten reports in the literature, published data indicate that MALDI-TOF MS yields accurate identification of blood-borne organisms in ≥80% of cases for inocula of >107 organisms/mL. A major current limitation is failure to accurately identify Streptococcus pneumoniae among viridans steptococci. Identification is achieved in <2 h, sharply reducing the turn-around time for communication of identification to the clinician. Further progress in handling protocols and automation, and extraction of antibiotic resistance data from the MALDI-TOF MS spectra, will further push this emerging approach as the standard one in the laboratory diagnosis of septicaemia, paving the way to application in further clinical situations and clinical specimens. © 2010 The Author. Clinical Microbiology and Infection © 2010 European Society of Clinical Microbiology and Infectious Diseases.


Janin Y.L.,Institute Pasteur Paris | Janin Y.L.,French National Center for Scientific Research
Chemical Reviews | Year: 2012

A pyrazole nucleus halogenation, if possible regioselective, is often the first step of many syntheses of more elaborated derivatives. Concerning the preparation of 3/5-halogenated derivatives with electrophilic reagents, this usually requires the 4 position to be substituted. Otherwise, halogenation will first take place on position 4 and then on the other ones, usually at higher temperature and/or using stronger reaction conditions. One approach to avoid the faster 4-halogenation of pyrazoles is to undertake C-5 halogenation of suitably N-substituted pyrazole anions. Dehydroxyhalogenation of 3/5-hydroxypyrazoles is probably one of the most obvious preparations of 3/5-chloro- or 3/5- bromopyrazoles using reagents such as phosphorus oxychloride or phosphorus oxybromide. Preparation of 1-substituted 3-halogenopyrazoles by the Sandmeyer reaction is also possible. Cycloaddition between sydnones and halogenated dipole leads to 3-halogenopyrazoles.


Galam S.,French National Center for Scientific Research
Physica A: Statistical Mechanics and its Applications | Year: 2010

Public debates driven by incomplete scientific data where nobody can claim absolute certainty, due to the current state of scientific knowledge, are studied. The cases of evolution theory, global warming and H1N1 pandemic influenza are investigated. The first two are of controversial impact while the third is more neutral and resolved. To adopt a cautious balanced attitude based on clear but inconclusive data appears to be a lose-out strategy. In contrast overstating arguments with incorrect claims which cannot be scientifically refuted appears to be necessary but not sufficient to eventually win a public debate. The underlying key mechanisms of these puzzling and unfortunate conclusions are identified using the Galam sequential probabilistic model of opinion dynamics (Galam, 2002 [4], Galam, 2005 [18], Galam and Jacobs, 2007 [19]). It reveals that the existence of inflexible agents and their respective proportions are the instrumental parameters to determine the faith of incomplete scientific data in public debates. Acting on one's own inflexible proportion modifies the topology of the flow diagram, which in turn can make irrelevant initial supports. On the contrary focusing on open-minded agents may be useless given some topologies. When the evidence is not as strong as claimed, the inflexibles rather than the data are found to drive the opinion of the population. The results shed a new but disturbing light on designing adequate strategies to win a public debate. © 2010 Elsevier B.V. All rights reserved.


Kim H.J.,Korea University | Lee M.H.,Korea University | Mutihac L.,University of Bucharest | Vicens J.,French National Center for Scientific Research | Kim J.S.,Korea University
Chemical Society Reviews | Year: 2012

The present critical review reports on recent developments of optical nanoparticles based on the association of gold, silver, silica and quantum dots and calixarenes. These hybrid organic-inorganic compounds characterized by a thick organic layer self-assembled on the surface of a core of mineral surface atoms take advantage of the supramolecular recognition of luminescent calixarenes to fabricate nanodevices of nanoparticle size, capable of detecting metal cations, polyaromatic hydrocarbons and pesticides. Also presented is an explanation of the involvement of such nanoparticles in biochemical systems. This critical review provides an overview of their preparation, the manner in which they are characterized, and their use (108 references). © 2012 The Royal Society of Chemistry.


Genin S.,French National Institute for Agricultural Research | Genin S.,French National Center for Scientific Research | Denny T.P.,University of Georgia
Annual Review of Phytopathology | Year: 2012

Ralstonia solanacearum is a major phytopathogen that attacks many crops and other plants over a broad geographical range. The extensive genetic diversity of strains responsible for the various bacterial wilt diseases has in recent years led to the concept of an R. solanacearum species complex. Genome sequencing of more than 10 strains representative of the main phylogenetic groups has broadened our knowledge of the evolution and speciation of this pathogen and led to the identification of novel virulence-associated functions. Comparative genomic analyses are now opening the way for refined functional studies. The many molecular determinants involved in pathogenicity and host-range specificity are described, and we also summarize current understanding of their roles in pathogenesis and how their expression is tightly controlled by an intricate virulence regulatory network. © 2012 by Annual Reviews. All rights reserved.


Souriau A.,French National Center for Scientific Research
Earth and Planetary Science Letters | Year: 2015

A layer of reduced P-velocity gradient with thickness of about 100-200 km has been identified at the base of the liquid core from seismological methods. It has been interpreted as a dense layer resulting from partial re-melting of the inner core, which is depleted in light elements with respect to the liquid core during freezing. In an attempt to specify where freezing and re-melting occur, the structure of this basal layer is investigated with the seismological core phase PKPbc which has its turning point in the lower third of the outer core. The large PKPbc data set of the EHB catalog distributed by the International Seismological Centre is analyzed. In order to compensate for the uneven distribution of the data and to minimize the influence of mantle heterogeneities, the travel time anomalies are binned inside equal area and equal azimuth sectors sampling the base of the liquid core at different depths. Most of the observed variations in the binned travel time residuals are not significant according to their confidence level. The only features which could be significant are a large patch with a velocity increase of about 0.5% located at the top of the basal layer beneath the eastern hemisphere, and the complementary velocity decrease beneath the western hemisphere and the South pole. This observation suggests that some freezing or re-melting processes occur at the top of the basal layer with a hemispherical dissymmetry. If confirmed, it may give strong constraints on the fate of the light elements during the freezing and re-melting process and on their interaction with the basal layer and the overlying liquid core. © 2015 Elsevier B.V.


Auzely-Velty R.,French National Center for Scientific Research
Comptes Rendus Chimie | Year: 2011

The supramolecular assemblies based on polysaccharides modified by cyclodextrins (CDs) and/or hydrophobic guest molecules have inspired interesting developments in the biomedical, pharmaceutical and cosmetic fields. This review will update the recent progress in the design, synthesis and study of such supramolecular structures. Preliminary studies demonstrated that such systems, based on the physical cross-linking of biopolymers through CD inclusion complexation, have potential as injectable hydrogels for the controlled release of drugs. Their nanoscale association also lead to the formation of original particles and films which pave the way to new applications in drug delivery and tissue engineering. © 2010 Académie des sciences.


Hennebelle P.,French National Center for Scientific Research
Astronomy and Astrophysics | Year: 2012

Context. It is believed that the majority of stars form in clusters. Therefore it is likely that the gas physical conditions that prevail in forming clusters largely determine the properties of stars that form, in particular, the initial mass function (IMF). Aims. We develop an analytical model to account for the formation of low-mass clusters and the formation of stars within clusters. Methods. The formation of clusters is determined by an accretion rate, the virial equilibrium, as well as energy and thermal balance. For this, both molecular and dust cooling are considered using published rates. The star distribution is computed within the cluster using the physical conditions inferred from this model and the Hennebelle & Chabrier theory. Results. Our model reproduces well the mass-size relation of low-mass clusters (up to a few ≈ 10 3M of stars corresponding to about five times more gas) and an IMF that is i) very close to the Chabrier IMF, ii) weakly dependent on the mass of the clusters, iii) relatively robust to (i.e. not too steeply dependent on) variations in physical quantities such as accretion rate, radiation, and cosmic ray abundances. Conclusions. The weak dependence of the mass distribution of stars on the cluster mass results from the compensation between varying clusters densities, velocity dispersions, and temperatures that are all inferred from first physical principles. This constitutes a possible explanation for the apparent universality of the IMF within the Galaxy, although variations with the local conditions may certainly be observed. © 2012 ESO.


Grandati Y.,French National Center for Scientific Research
Annals of Physics | Year: 2012

In some recent articles, we developed a new systematic approach to generate solvable rational extensions of primary translationally shape invariant potentials. In this generalized SUSYQM partnership, the DBTs are built on the excited states Riccati-Schrödinger (RS) functions regularized via specific discrete symmetries of the considered potential. In the present paper, we prove that this scheme can be extended in a multistep formulation. Applying this scheme to the isotonic oscillator, we obtain new towers of regular rational extensions of this potential which are strictly isospectral to it. We give explicit expressions for their eigenstates which are associated to the recently discovered exceptional Laguerre polynomials and show explicitly that these extensions inherit the shape invariance properties of the original potential. © 2012 Elsevier Inc.


Dubois D.,French National Center for Scientific Research
Fuzzy Sets and Systems | Year: 2011

We try to provide a tentative assessment of the role of fuzzy sets in decision analysis. We discuss membership functions, aggregation operations, linguistic variables, fuzzy intervals and the valued preference relations they induce. The importance of the notion of bipolarity and the potential of qualitative evaluation methods are also pointed out. We take a critical standpoint on the state-of-the-art, in order to highlight the actual achievements and question what is often considered debatable by decision scientists observing the fuzzy decision analysis literature. © 2011 Elsevier B.V. All rights reserved.


Chavanis P.H.,French National Center for Scientific Research
Astronomy and Astrophysics | Year: 2012

We study the growth of perturbations in an expanding Newtonian universe with Bose-Einstein condensate (BEC) dark matter. We first ignore special relativistic effects and derive a differential equation that governs the evolution of the density contrast in the linear regime. This equation, which takes quantum pressure and self-interaction into account, can be solved analytically in several cases. We argue that an attractive self-interaction can enhance the Jeans instability and fasten the formation of structures. Then, we take pressure effects (coming from special relativity) into account in the evolution of the cosmic fluid and add the contribution of radiation, baryons, and dark energy (cosmological constant). For BEC dark matter with repulsive self-interaction (positive pressure) the scale factor increases more rapidly than in the standard ΛCDM model where dark matter is pressureless, while it increases less rapidly for BEC dark matter with attractive self-interaction (negative pressure). We study the linear development of the perturbations in these two cases and show that the perturbations grow faster in BEC dark matter than in pressureless dark matter. Finally, we consider a "dark fluid" with a generalized equation of state p = (αρ + kρ 2) c 2 having a component p = kρ 2c 2 similar to BEC dark matter and a component p = αρc 2 mimicking the effect of the cosmological constant (dark energy). We find optimal parameters that give good agreement with the standard ΛCDM model that assumes a finite cosmological constant. © 2012 ESO.


Armijo J.,French National Center for Scientific Research
Physical Review Letters | Year: 2012

We report the first direct observation of collective quantum fluctuations in a continuous field. Shot-to-shot atom number fluctuations in small subvolumes of a weakly interacting, ultracold atomic 1D cloud are studied using in situ absorption imaging and statistical analysis of the density profiles. In the cloud centers, well in the quantum quasicondensate regime, the ratio of chemical potential to thermal energy is μ/k BT 4, and, owing to high resolution, up to 20% of the microscopically observed fluctuations are quantum phonons. Within a nonlocal analysis at variable observation length, we observe a clear deviation from a classical field prediction, which reveals the emergence of dominant quantum fluctuations at short length scales, as the thermodynamic limit breaks down. © 2012 American Physical Society.


Narison S.,French National Center for Scientific Research
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2012

We reconsider the extraction of the gluon condensates {left double angle bracket;αsG2{right double angle bracket}, {left double angle bracket;g3fabcG3{right double angle bracket} and the MS running quark masses mc,b from different Mn(Q2) moments and their ratios by including PT corrections to order αs3, NPT terms up to {left double angle bracket;G4{right double angle bracket} and using stability criteria of the results versus the degree n (number of Q2-derivative). We explicitly show that the spectral part of the lowest moment M1(0) depends strongly (as expected) on its high-energy (continuum) contribution, which is minimized for Mn≥3-4(0). Using higher moments and the correlations of {left double angle bracket;αsG2{right double angle bracket} with {left double angle bracket;g3fabcG3{right double angle bracket} and {left double angle bracket;G4{right double angle bracket}, we obtain {left double angle bracket;αsG2{right double angle bracket}=(7.0±1.3)×10-2GeV4 and {left double angle bracket;g3fabcG3{right double angle bracket}=(8.8±5.5)GeV2×{left double angle bracket;αsG2{right double angle bracket}, while our analysis favours a modified precise factorisation for {left double angle bracket;G4{right double angle bracket}. Using the previous results, we re-determine mc(mc) and find that the commonly used M1(0) lowest moment tends to overestimate its value compared to the ones from higher moments where stable values of mc(mc) versus the variations of n and the continuum models are reached. These features can indicate that the quoted errors of mc,b from M1(0) may have been underestimated. Our best results from different high-n moments and their ratios are: mc(mc)=1261(16)MeV and mb(mb)=4171(14)MeV, in excellent agreement with results obtained in Narison (2010) [1] using some judicious choices of ratios of moments. © 2011 Elsevier B.V.


Dejardin J.,French National Center for Scientific Research
Trends in Genetics | Year: 2015

Pericentromeric DNA represents a large fraction of the mammalian genome that is usually assembled into heterochromatin. Recent advances have revealed that the composition of pericentromeric heterochromatin is surprisingly dynamic. Indeed, high levels of histone H3 trimethylation on lysine 9 (H3K9me3) and DNA methylation normally characterize the repressive environment of this region. However, in specific tissues and in cancer cells, Polycomb proteins can occupy pericentromeric heterochromatin and act as a molecular sink for transcriptional regulators. Restoring heterochromatin methylation marks could, thus, be an important way to bring back normal gene expression programs in disease. Here, I discuss the potential mechanisms by which Polycomb complexes are recruited to pericentromeric DNA. Pericentromeric heterochromatin adopts distinct epigenetic signatures upon developmental cues or in pathological conditions such as cancer. H3K9me3 and DNA methylation represent the most common state of this heterochromatin and perturbing this regulation allows for Polycomb group protein recruitment at pericentromeres. Recent work has provided important molecular details on how Polycomb factors are recruited to this locus, and a key requisite is DNA hypomethylation. Understanding how PcG proteins bind to pericentromeric heterochromatin will give insights into how PcG proteins target their genes, and will also help understanding the function of pericentromeres in the control of gene expression. © 2015 Elsevier Ltd.


Bienvenut W.V.,French National Center for Scientific Research
Molecular & cellular proteomics : MCP | Year: 2012

N-terminal modifications play a major role in the fate of proteins in terms of activity, stability, or subcellular compartmentalization. Such modifications remain poorly described and badly characterized in proteomic studies, and only a few comparison studies among organisms have been made available so far. Recent advances in the field now allow the enrichment and selection of N-terminal peptides in the course of proteome-wide mass spectrometry analyses. These targeted approaches unravel as a result the extent and nature of the protein N-terminal modifications. Here, we aimed at studying such modifications in the model plant Arabidopsis thaliana to compare these results with those obtained from a human sample analyzed in parallel. We applied large scale analysis to compile robust conclusions on both data sets. Our data show strong convergence of the characterized modifications especially for protein N-terminal methionine excision, co-translational N-α-acetylation, or N-myristoylation between animal and plant kingdoms. Because of the convergence of both the substrates and the N-α-acetylation machinery, it was possible to identify the N-acetyltransferases involved in such modifications for a small number of model plants. Finally, a high proportion of nuclear-encoded chloroplast proteins feature post-translational N-α-acetylation of the mature protein after removal of the transit peptide. Unlike animals, plants feature in a dedicated pathway for post-translational acetylation of organelle-targeted proteins. The corresponding machinery is yet to be discovered.


Bonnefon J.-F.,French National Center for Scientific Research
Behavioral and Brain Sciences | Year: 2011

Reasoning research has traditionally focused on the derivation of beliefs from beliefs, but it is increasingly turning to reasoning about decisions. In the absence of a single, entrenched normative model, the drive toward normativism is weaker in this new field than in its parent fields. The current balance between normativism and descriptivism is illustrated by three approaches to reasoning about decisions. © 2011 Cambridge University Press.


Le Guerroue E.,French National Center for Scientific Research
Comptes Rendus - Geoscience | Year: 2010

Carbonate δ13C values provide a useful monitor of changes in the global carbon cycle because they can record the burial ratio of organic to carbonate carbon. The most pronounced isotope excursions in the geologic record occur during the Neoproterozoic and have assumed a central role in the interpretation of biogeochemical events preceding the Ediacaran and Cambrian radiations. The most profound negative carbon isotope excursion is best recorded in the Ediacaran-aged Shuram Formation of Oman and has potential equivalents worldwide including the Wonoka Formation of South Australia and other sections in China, India, Siberia, Canada, Scandinavia and Brazil. All these excursions are less well understood than those in the Phanerozoic because of their unusual magnitude, long duration (> 1 Ma) and the difficulty in correlating Neoproterozoic basins to confirm independently that they do indeed record global change in the mixed ocean reservoir. Alternatively, these δ13C anomalies could reflect diachronous diagenetic processes. Currently none of these excursion are firmly time constrained and critical to their interpretation is a coherent reproducibility and synchroneity at the global ocean scale. Here we use available strontium isotope record as an independent chronometer to test the timing and synchroneity of the Shuram δ13C and its potential equivalents. The use of the 86Sr/87Sr ratio allows the reconstruction of a coherent, global δ13C record calibrated independently against time. The calibrated δ13C curve indicates that the Shuram negative anomaly spans several tens of millions of years and reaches values below -10‰. This carbon isotopic anomaly therefore represents a meaningful oceanographic event that fundamentally challenges our understanding of the carbon cycle as defined in the Phanerozoic. © 2010 Académie des sciences.


Narison S.,French National Center for Scientific Research
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2012

We test the convergence of the QCD exponential sum rules by including PT corrections to order αs3 and the NP contributions up to dimension D=8 condensates. Then, using the ratio of exponential sum rules where the QCD PT series is more convergent, we study the correlation between the gluon condensates 〈α sG 2〉 and 〈g 3f abcG 3〉. From charmonium systems and using the charm quark mass as input, we deduce: 〈g 3f abcG 3〉=(8.2±1.0)GeV 2×〈α sG 2〉 corresponding to 〈α sG 2〉=(7.5±2.0)×10 -2GeV 4. Using these results for the bottomium systems, we obtain: m̄b(m̄b)=4212(32)MeV, which is slightly higher but consistent within the errors with the ones from Q 2-moments and their ratios m̄b(m̄b)=4172(12)MeV. We are tempted to consider as a final result from the sum rules approaches, the average m̄b(m̄b)=4177(11)MeV of the two previous determinations. © 2011 Elsevier B.V.


Ribeyre C.,University of Geneva | Ribeyre C.,French National Center for Scientific Research | Shore D.,University of Geneva
Nature Structural and Molecular Biology | Year: 2012

Telomeres hide (or 'cap') chromosome ends from DNA-damage surveillance mechanisms that arrest the cell cycle and promote repair, but the checkpoint status of telomeres is not well understood. Here we characterize the response in Saccharomyces cerevisiae to DNA double-strand breaks (DSBs) flanked by varying amounts of telomeric repeat sequences (TG 1-3). We show that even short arrays of TG 1-3 repeats do not induce G2/M arrest. Both Rif1 and Rif2 are required for capping at short, rapidly elongating ends, yet are largely dispensable for protection of longer telomeric arrays. Rif1 and Rif2 act through parallel pathways to block accumulation of both RPA and Rad24, activators of checkpoint kinase Mec1 (ATR). Finally, we show that Rif function is correlated with an 'anticheckpoint' effect, in which checkpoint recovery at an adjacent unprotected end is stimulated, and we provide insight into the molecular mechanism of this phenomenon. © 2012 Nature America, Inc. All rights reserved.


Riviere G.,French National Center for Scientific Research
Geophysical Research Letters | Year: 2010

The dynamical link between the west Pacific (WP) teleconnection and Rossby wave breaking (RWB) events is analyzed during winter months using ERA40 reanalysis data from 1957 to 2002. The WP pattern which is characterized by latitudinal fluctuations of the Pacific jet is closely linked to variations in the nature of RWB, similarly to the North Atlantic Oscillation. More anticyclonic (cyclonic) RWBs than usual occur in the Central Pacific during the positive (negative) WP phase when the Pacific jet is more to the north (south) than usual. Time lag daily composites show that before the occurrence of an anticyclonic RWB event, WP anomalies close to the positive phase preexist that are then reinforced during the breaking leading to an increase of the WP index even few days after the peak of the event. Cyclonic RWB events have similar but opposite effects on the WP pattern since they trigger and maintain the negative phase. Finally, a comparison with the RWB anomalies of the Pacific-North American (PNA) teleconnection is provided. Copyright © 2010 by the American Geophysical Union.


Bonnefille R.,French National Center for Scientific Research
Global and Planetary Change | Year: 2010

This paper reviews information on past vegetation of tropical Africa during the Cenozoic, focused upon the last 10. Ma, a time spanning hominid record in Central and East Africa. Summary of palaeobotanical data collected at terrestrial sites are compared with new results on the long term evolution of the continental vegetation zones documented from marine pollen record of two deep sea cores recovered from the Atlantic and Indian Oceans.Section 2 includes a summary of modern distribution of vegetation belts in the African continent and a synthesis of the results of both macrobotanical (fossil wood, leaves and fruits) and microbotanical (mainly pollen) studies presented according to time scale and geographical location. The main features emphasized by the palaeobotanical results are 1) seasonal vegetation and climate documented as soon as the Eocene in Tanzania 2) well diversified forests existing in northern West Ethiopia during the Oligocene 3) high temporal and spatial variabilities of forests composition during the Miocene when deciduous Legume woodland was documented in Ethiopia whereas wetter evergreen forests existed in Western Kenya 4) lack of evidence for an evergreen forest belt, continuous from Western Congo to East Africa.Section 3 presents new original pollen data recovered from a long core in the Gulf of Aden documenting large scale past vegetation changes in East Africa during the last 11. Ma. These results are discussed in comparison with a summarized long pollen sequence previously published from a marine core offshore the Niger delta. This comparison illustrates variations in geographical distribution of large vegetation zone at the continental scale, through time.In Section 4, vegetation changes registered during the last 10Ma are discussed in relation with the results of isotopic studies and an updated presentation of hominids evolution in Africa. Several changes are shown in the marine records. An expansion of savanna/grassland is shown at 10Ma in East Africa, 3Ma earlier than in West Africa where it is documented at 7Ma. At large geographical scale, this first increase in grass pollen simultaneously to forest increase in the marine records is interpreting as reflecting wetter conditions over the continent. Indeed, under global humid conditions, savanna could spread over the desert areas in the Northern and Eastern directions. A forest phase is well documented in West Africa between 7.5 and 7Ma, but has not been shown in East Africa, mainly because of low resolution analysis of the DSDP East African record which needs further investigation for that period. A strong vegetation change took place between 6.3 and 6Ma. It was marked by a trend of important decrease tree cover of the vegetation, simultaneous in West and East Africa. At that time, very arid conditions shown by scarce tree cover occurred over the whole tropical region. This happened before (or at) the early beginning of the Messinian crisis. Generally arid conditions coincide with the accepted timing for the Chimpanzee/hominid split, and record of Sahelanthropus tchadensis in Chad and Orrorin tugenensis in Kenya, although these fossils were found under locally wooded environment. The period from 6 to 4Ma saw the appearance of Ardipithecus and diversification of Australopithecines occurring during a progressive increased tree cover in the broad-scale vegetation that culminated at 3.9Ma, during A. anamensis time and before the first appearance of Australopithecus afarensis. Important variations in the vegetation occurred between 4 and 3Ma, and many plant ecosystems were available to A. afarensis, a hominid which had a wide geographical distribution and persisted at Hadar under temporal climatic and environmental variability. The strongest and abrupt decline of forest pollen accompanied by an increase in the grass pollen was found at 2.7Ma, more pronounced in the West than in East Africa. It was accompanied by a significant increase in C4 grass proportions, well indicated in the Turkana region and likely explained by an increase in dry season length. Such marked changes correspond to the global climate change due to the establishment of the Arctic ice sheet that induced strong aridity in the tropics. Savanna expanded at the expense of rainforest, both in West and East Africa, whereas sub-desertic steppe expanded over savanna areas in the North. Mountain forests moved down slopes, closer to lowland sites in the Rift. Simultaneous faunal changes documented by the herbivores in the fauna, the appearance of early Homo and stone tools in the archaeological record of East Africa appear contemporaneous to local vegetation changes documented at terrestrial sites. © 2010 Elsevier B.V.


Benhamou S.,French National Center for Scientific Research
PLoS ONE | Year: 2011

Background: Although habitat use reflects a dynamic process, most studies assess habitat use statically as if an animal's successively recorded locations reflected a point rather than a movement process. By relying on the activity time between successive locations instead of the local density of individual locations, movement-based methods can substantially improve the biological relevance of utilization distribution (UD) estimates (i.e. the relative frequencies with which an animal uses the various areas of its home range, HR). One such method rests on Brownian bridges (BBs). Its theoretical foundation (purely and constantly diffusive movements) is paradoxically inconsistent with both HR settlement and habitat selection. An alternative involves movement-based kernel density estimation (MKDE) through location interpolation, which may be applied to various movement behaviours but lacks a sound theoretical basis. Methodology/Principal Findings: I introduce the concept of a biased random (advective-diffusive) bridge (BRB) and show that the MKDE method is a practical means to estimate UDs based on simplified (isotropically diffusive) BRBs. The equation governing BRBs is constrained by the maximum delay between successive relocations warranting constant within-bridge advection (allowed to vary between bridges) but remains otherwise similar to the BB equation. Despite its theoretical inconsistencies, the BB method can therefore be applied to animals that regularly reorientate within their HRs and adapt their movements to the habitats crossed, provided that they were relocated with a high enough frequency. Conclusions/Significance: Biased random walks can approximate various movement types at short times from a given relocation. Their simplified form constitutes an effective trade-off between too simple, unrealistic movement models, such as Brownian motion, and more sophisticated and realistic ones, such as biased correlated random walks (BCRWs), which are too complex to yield functional bridges. Relying on simplified BRBs proves to be the most reliable and easily usable way to estimate UDs from serially correlated relocations and raw activity information. © 2011 Simon Benhamou.


Maurange C.,Aix - Marseille University | Maurange C.,French National Center for Scientific Research
Current Topics in Developmental Biology | Year: 2012

The mechanisms underlying the temporal specification of neural stem cells (NSCs), a process by which a single progenitor can generate different types of neurons and glia in an invariant order, are still poorly understood in mammals. However, in the past decade, work on Drosophila NSCs, called neuroblasts, has identified a series of sequentially expressed transcription factors that lies at the heart of this phenomenon. Here, I highlight some key findings that illuminate the role of these transcription factors during development and the regulatory principles allowing them not only to promote neuronal diversity but also to control the final number of neurons in the different regions of the nervous system. Ultimately, and given recent evidences of evolutionary conservation, cracking the temporal specification code of Drosophila neuroblasts may provide new perspectives for the safe manipulation of human NSCs and their therapeutic use. © 2012 Elsevier Inc.


Simonelig M.,French National Center for Scientific Research
Cell Research | Year: 2012

Although overlooked for many years, alternative cleavage and polyadenylation (APA) is now emerging as a major mechanism of gene regulation. A recent study identifies poly(A)-binding protein nuclear 1 (PABPN1), a general factor of polyadenylation, as a suppressor of alternative poly(A) sites. © 2012 IBCB, SIBS, CAS All rights reserved.


Ramazashvili R.,French National Center for Scientific Research
Physical Review Letters | Year: 2010

I study magnetic quantum oscillations in antiferromagnetic conductors with small carrier pockets and show that combining the oscillation data with symmetry arguments and with the knowledge of the possible positions of the band extrema may allow us to greatly constrain or even uniquely determine the location of a detected carrier pocket in the Brillouin zone. © 2010 The American Physical Society.


Veenstra J.A.,French National Center for Scientific Research
General and Comparative Endocrinology | Year: 2010

The Lottia gigantea genome was prospected for the presence of genes coding neuropeptides and neurohormones. Four genes code insulin-related peptides: two genes code molluscan insulin-like growth hormones, one gene an insulin very similar to vertebrate insulin, and the fourth a peptide related to drosophila insulin-like peptide 7. Four other genes encode the cysteine-knot proteins GPA2/GPB5 and bursicon/parabursicon. Another 37 genes code for precursors of the following neuropeptides: achatin, APGWamide, allatostatin C, allatotropin, buccalin (perhaps an allatostatin A homolog), cerebrin, CCAP, conopressin, elevenin (the predicted neuropeptide made by abdominal neuron 11 in Aplysia), egg laying hormone (two genes), enterin, feeding circuit activating neuropeptide (FCAP), FFamide, FMRFamide, GGNG, a GnRH-like peptide, the newly discovered LASGLVamide, LFRFamide, LFRYamide, LRNFVamide, luqin, lymnokinin, myomodulin (two genes), the newly discovered NKY, NPY, pedal peptide (three genes), PKYMDT, pleurin, PXFVamide, small cardioactive peptides, tachykinins (two genes) and WWamide (an allatostatin B homolog). One gene was found to encode FWISamide, while about 20 closely related genes were found to encode WWFamide. These small neuropeptides appear homologous to the NdWFamide, which contains d-Trp; these genes are similar to the Aplysia gene encoding NWFamide. Some of these peptides had not been previously identified from mollusks, such as the predicted hormones similar to Drosophila and vertebrate insulins, bursicon, the putative proctolin homolog PKYMDT and allatostatin C. Together with neuropeptides which are likely homologs of other insect neuropeptides, such as cerebrin and WWamide, this shows that despite significant differences the molluscan and arthropod neuropeptidomes are more similar than generally recognized. © 2010 Elsevier Inc.


Lode T.,French National Center for Scientific Research
BioEssays | Year: 2011

Here, I propose a new hypothesis: sex originated from an archaic gene transfer process among prebiotic bubbles without the prerequisite for reproduction. This de-coupling from reproduction might make the thorny problem of accounting for the evolution of sex, despite the apparent advantages of parthenogenicity, more tractable. © 2011 WILEY Periodicals, Inc.


Brasselet E.,French National Center for Scientific Research
Physical Review Letters | Year: 2012

A Comment on the Letter by O. Emile and J. Emile, Phys. Rev. Lett. 106, 183904 (2011)PRLTAO0031-900710.1103/PhysRevLett.106.183904. The authors of the Letter offer a Reply. © 2012 American Physical Society.


Geraads D.,French National Center for Scientific Research
Quaternary International | Year: 2010

North-western Africa, today included in the Palaearctic realm, is well separated from the Ethiopian province by the Sahara, but the distribution of large mammals shows that these biogeographic domains cannot simply be extrapolated to the late Cenozoic. In the latest Miocene and earliest Pliocene, there were close connections with central Africa, but also remarkable similarities with East Africa, in some instances reaching the species level. There is no evidence of northern influence among large mammals, although several small mammals had a wide range in the Mediterranean. East African or pan-African forms are also largely predominant in the well sampled Late Pliocene, their low diversity resulting probably from local environmental conditions. There are but a few immigrants from Eurasia, mostly carnivores. During the Early Pleistocene, limited exchanges occurred with the Middle East, but many more with the rest of Africa. By the Middle Pleistocene similarities with East Africa reached their climax, and it is only with the latest part of this period that some northern immigrants put a Palaearctic stamp on this fauna, the "Ethiopian" character of which decreased by extinction of many of its elements. © 2009 Elsevier Ltd and INQUA.


Salotti J.M.,French National Center for Scientific Research
Acta Astronautica | Year: 2012

We present a revised version of our scenario for human missions to Mars. The idea is to take into consideration the difficulties and constraints for entry, descent and landing by splitting the heavy vehicle into two smaller ones. The standard capsule shape is thus possible for aerocapture and landing on Mars. It is suggested to use the largest possible diameter such that the ballistic coefficient is minimized and the lift to drag ratio is kept small. The maneuvers for the descent and landing are then simplified and the risks are minimized. The scenario has been modified to cope with the new constraints. Different options have been taken into account. It is possible to land a small Mars ascent vehicle or to reuse the habitat lander for Mars ascent. All options perform as well as the others for the criterion of the initial mass in low Earth orbit. However, reusing the habitat lander allows a significant reduction of the size of the Earth return vehicle, which otherwise requires a huge launching capability. © 2012 Elsevier Ltd. All rights reserved.


Felix M.A.,French National Center for Scientific Research
BMC biology | Year: 2012

The nematode Caenorhabditis elegans is a major model organism in laboratory biology. Very little is known, however, about its ecology, including where it proliferates. In the past, C. elegans was mainly isolated from human-made compost heaps, where it was overwhelmingly found in the non-feeding dauer diapause stage. C. elegans and C. briggsae were found in large, proliferating populations in rotting plant material (fruits and stems) in several locations in mainland France. Both species were found to co-occur in samples isolated from a given plant species. Population counts spanned a range from one to more than 10,000 Caenorhabditis individuals on a single fruit or stem. Some populations with an intermediate census size (10 to 1,000) contained no dauer larvae at all, whereas larger populations always included some larvae in the pre-dauer or dauer stages. We report on associated micro-organisms, including pathogens. We systematically sampled a spatio-temporally structured set of rotting apples in an apple orchard in Orsay over four years. C. elegans and C. briggsae were abundantly found every year, but their temporal distributions did not coincide. C. briggsae was found alone in summer, whereas both species co-occurred in early fall and C. elegans was found alone in late fall. Competition experiments in the laboratory at different temperatures show that C. briggsae out-competes C. elegans at high temperatures, whereas C. elegans out-competes C. briggsae at lower temperatures. C. elegans and C. briggsae proliferate in the same rotting vegetal substrates. In contrast to previous surveys of populations in compost heaps, we found fully proliferating populations with no dauer larvae. The temporal sharing of the habitat by the two species coincides with their temperature preference in the laboratory, with C. briggsae populations growing faster than C. elegans at higher temperatures, and vice at lower temperatures.


Salles J.-M.,French National Center for Scientific Research
Comptes Rendus - Biologies | Year: 2011

The evaluation of ecosystems and biodiversity has become an important field of investigation for economists. Although their interest has been largely motivated by the search for arguments in favour of broader conservation policies, both the methods and the meaning of the results remain controversial. This article aims at clarifying the interest and limitations of these works, by revisiting a number of issues, such as the economic qualification of the services that human societies take from biodiversity and ecological systems in general, the specificities of their contribution to human well-being and the consequences of a valuation of biodiversity based on ecosystem services. We conclude with a discussion of the purposes of evaluations: improving public policies or creating new markets? © 2011 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.


Sausset F.,CEA Saclay Nuclear Research Center | Tarjus G.,French National Center for Scientific Research
Physical Review Letters | Year: 2010

We investigate the characteristic length scales associated with the glass transition phenomenon. By studying an atomic glass-forming liquid in negatively curved space, for which the local order is well identified and the amount of frustration opposing the spatial extension of this order is tunable, we provide insight into the structural origin of the main characteristics of the dynamics leading to glass formation. We find that the structural length and the correlation length characterizing the increasing heterogeneity of the dynamics grow together as temperature decreases. However, the system eventually enters a regime in which the former saturates as a result of frustration whereas dynamic correlations keep building up. © 2010 The American Physical Society.


Bento N.,French National Center for Scientific Research
International Journal of Hydrogen Energy | Year: 2010

This article addresses the issue of the diffusion of hydrogen cars in the market, particularly the competition with electric cars for the replacement of conventional vehicles. Using the multi-technological competition model developed by Le Bas and Baron-Sylvester's (Diffusion technologique non binaire et schéma épidémiologique. Une reconsidération. Economie Appliquée 1995; tome XLVIII(3):71-101), it is shown that the early deployment of plug-in hybrid vehicles - the only electric technology which can compete with fuel cell cars in the multipurpose vehicle field - risks closing the market for hydrogen in the future. Moreover, the advent of the hydrogen vehicle depends on the rapid advancements in fuel cell technologies, as well as on the existence of an infrastructure with a sufficient coverage. © 2009 Professor T. Nejat Veziroglu. Published by Elsevier Ltd. All rights reserved.


Narison S.,French National Center for Scientific Research
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2013

Using recent values of the QCD (non-) perturbative parameters given in Table 1, we reconsider the extraction of fB and the on-shell mass Mb from HQET Laplace spectral sum rules known to N2LO PT series and including dimension 7 condensates in the OPE. We especially study the convergence of the PT series, the effects on "different spectral sum rules data" of the continuum threshold and subtraction point varied in a larger range than in the existing literature and include in the error an estimate of the N3LO PT series based on a geometric growth of the PT series. We obtain the Renormalization Group Invariant (RGI) universal coupling: f̂B∞=0.416(60)GeV3/2 in the static limit Mb→∞ and the physical decay constant including 1/Mb corrections: fBhqet=199(29)MeV. Using the ratio of sum rules, we obtain, to order αs2, the running mass m-b(m-b)=4213(59)MeV. The previous results are in good agreement with the ones from QCD spectral sum rules (QSSR) in full QCD to the same order from the same channel Narison (2013) [1]: fBqcd=206(7)MeV and m-b(m-b)qcd=4236(69)MeV. © 2013 Elsevier B.V.


James G.,French National Center for Scientific Research
Journal of Nonlinear Science | Year: 2012

We study the propagation of an unusual type of periodic travelling waves in chains of identical beads interacting via Hertz's contact forces. Each bead periodically undergoes a compression phase followed by free flight, due to special properties of Hertzian interactions (fully nonlinear under compression and vanishing in the absence of contact). We prove the existence of such waves close to binary oscillations, and numerically continue these solutions when their wavelength is increased. In the long wave limit, we observe their convergence towards shock profiles consisting of small compression regions close to solitary waves, alternating with large domains of free flight where bead velocities are small. We give formal arguments to justify this asymptotic behavior, using a matching technique and previous results concerning solitary wave solutions. The numerical finding of such waves implies the existence of compactons, i.e. compactly supported compression waves propagating at a constant velocity, depending on the amplitude and width of the wave. The beads are stationary and separated by equal gaps outside the wave, and each bead reached by the wave is shifted by a finite distance during a finite time interval. Below a critical wave number, we observe fast instabilities of the periodic travelling waves, leading to a disordered regime. © Springer Science+Business Media, LLC 2012.


Sureau C.,Laboratoire Of Virologie Moleculaire | Sureau C.,French National Center for Scientific Research | Salisse J.,Laboratoire Of Virologie Moleculaire
Hepatology | Year: 2013

Two determinants of infectivity have been identified in the hepatitis B virus (HBV) envelope proteins: a pre-S1 receptor-binding site and an uncharacterized determinant in the antigenic loop (AGL), which is structurally related to the antigenic a-determinant. Infection would proceed through virus attachment to cell surface heparan sulfate (HS) proteoglycans (HSPGs) before pre-S1 engages a specific receptor for uptake. Using heparin binding and in vitro infection assays with hepatitis D virus as a surrogate for HBV, we established that HS binding is mediated by the AGL. Electrostatic interaction was shown to depend upon AGL residues R122 and K141, because their substitution with alanine modified the virus net-charge and prevented binding to heparin, attachment to hepatocytes, and infection. In addition to R122 and K141, the HS binding determinant was mapped to cysteines and prolines, which also define the conformational a-determinant. The importance of AGL conformation was further demonstrated by the concomitant loss of a-determinant and heparin binding upon treatment of viral particles with membrane-impermeable reducing agent. Furthermore, envelope proteins extracted from the viral membrane with a nonionic detergent were shown to conserve the a-determinant but to lose heparin affinity/avidity. Conclusion: Our findings support a model in which attachment of HBV to HSPGs is mediated by the AGL HS binding site, including only two positively charged residues (R122 and K141) positioned precisely in a three-dimensional AGL structure that is stabilized by disulfide bonds. HBV envelope proteins would individually bind to HS with low affinity, but upon their clustering in the viral membrane, they would reach sufficient avidity for a stable interaction between virus and cell surface HSPGs. Our data provide new insight into the HBV entry pathway, including the opportunity to design antivirals directed to the AGL-HS interaction. © 2012 American Association for the Study of Liver Diseases.


Grandati Y.,French National Center for Scientific Research
Annals of Physics | Year: 2011

Combining recent results on rational solutions of the Riccati-Schrödinger equations for shape invariant potentials to the finite difference Bäcklund algorithm and specific symmetries of the isotonic potential, we show that it is possible to generate the three infinite sets (L1, L2 and L3 families) of regular rational solvable extensions of this potential in a very direct and transparent way. © 2011 Elsevier Inc.


Jaffrin M.Y.,French National Center for Scientific Research
Annual Review of Fluid Mechanics | Year: 2011

This article reviews the use of various techniques for membrane filtration, such as Dean and Taylor vortices, pulsatile flows, and dynamic filtration, which can generate high shear rates more efficiently than cross-flow filtration. In dynamic filtration, shear rates are generated not by a pump, but by moving parts or by vibrations. The most successful application of Taylor vortices has been plasma collection from donors in transfusion centers by microfiltration (MF), using small rotating cylindrical filters. Industrial dynamic filtration modules consist of metal disks with vanes or blades rotating between circular flat membranes or rotating ceramic membrane disks. These systems can be operated at high rotation speeds in order to produce very high permeate fluxes, or they can be operated at low speeds and save energy as compared with cross-flow filtration for the same flux. Vibrating modules (i.e., vibratory shear-enhanced processing) consist of a stack of circular membranes oscillating around a vertical shaft at its resonant frequency. While instabilities created by Dean vortices and pulsatile flows are mostly efficient in laminar flow and in MF and ultrafiltration, the benefits of high shear dynamic filtration are even more impressive in nanofiltration and reverse osmosis, as the reduction in concentration polarization not only increases permeate flux as compared with cross-flow filtration, but also decreases microsolute transmission.


De Rafael E.,French National Center for Scientific Research
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2011

We reconsider the Constituent Chiral Quark Model of Manohar and Georgi in the presence of SU(3)L×SU(3)R external sources. As recently emphasized by Weinberg, the corresponding effective Lagrangian is renormalizable in the large- Nc limit. We show, however, that the number of the required counterterms depends crucially on the value of gA and it is minimized for gA=1. We then find that with a rather small value for the constituent quark mass, which we fix phenomenologically to MQ=(190±40) MeV, the model reproduces rather well the values of several well-known low-energy constants. We also comment on the limitations of the model as well as on a few exceptional applications, to more complicated low-energy observables, where one can expect the model to make reasonably good predictions. © 2011 Elsevier B.V.


Berthier L.,CNRS Charles Coulomb Laboratory | Biroli G.,CEA Saclay Nuclear Research Center | Biroli G.,French National Center for Scientific Research
Reviews of Modern Physics | Year: 2011

A theoretical perspective is provided on the glass transition in molecular liquids at thermal equilibrium, on the spatially heterogeneous and aging dynamics of disordered materials, and on the rheology of soft glassy materials. We start with a broad introduction to the field and emphasize its connections with other subjects and its relevance. The important role played by computer simulations in studying and understanding the dynamics of systems close to the glass transition at the molecular level is given. The recent progress on the subject of the spatially heterogeneous dynamics that characterizes structural relaxation in materials with slow dynamics is reviewed. The main theoretical approaches are presented describing the glass transition in supercooled liquids, focusing on theories that have a microscopic, statistical mechanics basis. We describe both successes and failures and critically assess the current status of each of these approaches. The physics of aging dynamics in disordered materials and the rheology of soft glassy materials are then discussed, and recent theoretical progress is described. For each section, an extensive overview is given of the most recent advances, but we also describe in some detail the important open problems that will occupy a central place in this field in the coming years. © 2011 American Physical Society.


Antiviral monoclonal antibodies (mAbs) represent promising therapeutics. However, most mAbs-based immunotherapies conducted so far have only considered the blunting of viral propagation and not other possible therapeutic effects independent of virus neutralization, namely the modulation of the endogenous immune response. As induction of long-term antiviral immunity still remains a paramount challenge for treating chronic infections, we have asked here whether neutralizing mAbs can, in addition to blunting viral propagation, exert immunomodulatory effects with protective outcomes. Supporting this idea, we report here that mice infected with the FrCas(E) murine retrovirus on day 8 after birth die of leukemia within 4-5 months and mount a non-protective immune response, whereas those rapidly subjected to short immunotherapy with a neutralizing mAb survive healthy and mount a long-lasting protective antiviral immunity with strong humoral and cellular immune responses. Interestingly, the administered mAb mediates lysis of infected cells through an antibody-dependent cell cytotoxicity (ADCC) mechanism. In addition, it forms immune complexes (ICs) with infected cells that enhance antiviral CTL responses through Fc gammaR-mediated binding to dendritic cells (DCs). Importantly, the endogenous antiviral antibodies generated in mAb-treated mice also display the same properties, allowing containment of viral propagation and enhancement of memory cellular responses after disappearance of the administered mAb. Thus, our data demonstrate that neutralizing antiviral mAbs can act as immunomodulatory agents capable of stimulating a protective immunity lasting long after the end of the treatment. They also show an important role of infected-cells/antibody complexes in the induction and the maintenance of protective immunity through enhancement of both primary and memory antiviral T-cell responses. They also indicate that targeting infected cells, and not just viruses, by antibodies can be crucial for elicitation of efficient, long-lasting antiviral T-cell responses. This must be considered when designing antiviral mAb-based immunotherapies.


Havaux M.,French Atomic Energy Commission | Havaux M.,French National Center for Scientific Research | Havaux M.,Aix - Marseille University
Plant Journal | Year: 2014

Carotenoids are known to play important roles in plants as antioxidants, accessory light-harvesting pigments, and attractants for pollinators and seed dispersers. A new function for carotenoids has recently emerged, which relates to the response of plants to environmental stresses. Reactive oxygen species, especially singlet oxygen, produced in the chloroplasts under stress conditions, can oxidize carotenoids leading to a variety of oxidized products, including aldehydes, ketones, endoperoxides and lactones. Some of those carotenoid derivatives, such as volatile β-cyclocitral, derived from the oxidation of β-carotene, are reactive electrophile species that are bioactive and can induce changes in gene expression leading to acclimation to stress conditions. This review summarizes the current knowledge on the non-enzymatic oxidation of carotenoids, the bioactivity of the resulting cleavage compounds and their functions as stress signals in plants. © 2013 The Author The Plant Journal © 2013 John Wiley & Sons Ltd.


Simonelig M.,French National Center for Scientific Research
RNA biology | Year: 2011

The primary function of the piRNA pathway is to repress the expression and transposition of transposable elements. However, the piRNA pathway has additional biological and developmental functions. These functions are either a consequence of transposon regulation, or they result from direct roles of transposable elements in chromosome structure and gene regulation through piRNAs. Recent data have extended the functions of transposable elements in gene regulation, revealing a trans-acting role of transposable element piRNAs in the control of gene expression. Over the last few years, extensive studies on the piRNA pathway have rapidly increased our understanding of the relationships between transposable elements and the host genome, and of the essential role of transposable elements in biological and developmental processes.


Cavalli G.,French National Center for Scientific Research
Nature Genetics | Year: 2015

The three-dimensional organization of the genome has an important role in orchestrating gene expression, but its regulation is poorly understood. Now, a new study uncovers a major role for Polycomb components of the PRC1 complex in organizing physical networks of genes that are co-repressed to maintain pluripotency. © 2015 Nature America, Inc.


Albertin W.,French National Center for Scientific Research
Proceedings. Biological sciences / The Royal Society | Year: 2012

Polyploidy is a major evolutionary process in eukaryotes-particularly in plants and, to a less extent, in animals, wherein several past and recent whole-genome duplication events have been described. Surprisingly, the incidence of polyploidy in other eukaryote kingdoms, particularly within fungi, remained largely disregarded by the scientific community working on the evolutionary consequences of polyploidy. Recent studies have significantly increased our knowledge of the occurrence and evolutionary significance of fungal polyploidy. The ecological, structural and functional consequences of polyploidy in fungi are reviewed here and compared with the knowledge acquired with conventional plant and animal models. In particular, the genus Saccharomyces emerges as a relevant model for polyploid studies, in addition to plant and animal models.


Merrifield C.J.,French National Center for Scientific Research | Kaksonen M.,Cell biology and biophysics unit
Cold Spring Harbor Perspectives in Biology | Year: 2014

Up to 60 different proteins are recruited to the site of clathrin-mediated endocytosis in an ordered sequence. These accessory proteins have roles during all the different stages of clathrin-mediated endocytosis. First, they participate in the initiation of the endocytic event, thereby determining when and where endocytic vesicles are made; later they are involved in the maturation of the clathrin coat, recruitment of specific cargo molecules, bending of the membrane, and finally in scission and uncoating of the nascent vesicle. In addition, many of the accessory components are involved in regulating and coupling the actin cytoskeleton to the endocytic membrane. We will discuss the different accessory components and their various roles. Most of the data comes from studies performed with cultured mammalian cells or yeast cells. The process of endocytosis is well conserved between these different organisms, but there are also many interesting differences that may shed light on the mechanistic principles of endocytosis. © 2014 Cold Spring Harbor Laboratory Press. All rights reserved.


Louapre P.,French National Center for Scientific Research
PloS one | Year: 2012

Clonal plants spreading horizontally and forming a network structure of ramets exhibit complex growth patterns to maximize resource uptake from the environment. They respond to spatial heterogeneity by changing their internode length or branching frequency. Ramets definitively root in the soil but stay interconnected for a varying period of time thus allowing an exchange of spatial and temporal information. We quantified the foraging response of clonal plants depending on the local soil quality sampled by the rooting ramet (i.e. the present information) and the resource variability sampled by the older ramets (i.e. the past information). We demonstrated that two related species, Potentilla reptans and P. anserina, responded similarly to the local quality of their environment by decreasing their internode length in response to nutrient-rich soil. Only P. reptans responded to resource variability by decreasing its internode length. In both species, the experience acquired by older ramets influenced the plastic response of new rooted ramets: the internode length between ramets depended not only on the soil quality locally sampled but also on the soil quality previously sampled by older ramets. We quantified the effect of the information perceived at different time and space on the foraging behavior of clonal plants by showing a non-linear response of the ramet rooting in the soil of a given quality. These data suggest that the decision to grow a stolon or to root a ramet at a given distance from the older ramet results from the integration of the past and present information about the richness and the variability of the environment.


Lalonde S.V.,French National Center for Scientific Research | Konhauser K.O.,University of Alberta
Proceedings of the National Academy of Sciences of the United States of America | Year: 2015

The Great Oxidation Event (GOE) is currently viewed as a protracted process during which atmospheric oxygen increased above ∼10-5 times the present atmospheric level (PAL). This threshold represents an estimated upper limit for sulfur isotope mass-independent fractionation (S-MIF), an Archean signature of atmospheric anoxia that begins to disappear from the rock record at 2.45 Ga. However, an increasing number of papers have suggested that the timing for oxidative continental weathering, and by conventional thinking the onset of atmospheric oxygenation, was hundreds of million years earlier than previously thought despite the presence of S-MIF. We suggest that this apparent discrepancy can be resolved by the earliest oxidative-weathering reactions occurring in benthic and soil environments at profound redox disequilibrium with the atmosphere, such as biological soil crusts and freshwater microbial mats covering riverbed, lacustrine, and estuarine sediments. We calculate that oxygenic photosynthesis in these millimeter-thick ecosystems provides sufficient oxidizing equivalents to mobilize sulfate and redox-sensitive trace metals from land to the oceans while the atmosphere itself remained anoxic with its attendant S-MIF signature. As continental freeboard increased significantly between 3.0 and 2.5 Ga, the chemical and isotopic signatures of benthic oxidative weathering would have become more globally significant from a mass-balance perspective. These observations help reconcile evidence for pre-GOE oxidative weathering with the history of atmospheric chemistry, and support the plausible antiquity of a terrestrial biosphere populated by cyanobacteria well before the GOE.


Villeval M.C.,University of Lyon | Villeval M.C.,French National Center for Scientific Research
Science | Year: 2012

Women's willingness to compete can be increased through appropriate affirmative action.


Veenstra J.A.,French National Center for Scientific Research
Insect Biochemistry and Molecular Biology | Year: 2010

The twelve sequenced Drosophila genomes show the vast majority of neurohormone and neuropeptide genes to be very well conserved. Nonetheless, the gene encoding the hormone neuroparsin has undergone significant evolution. Although Drosophila melanogaster has one of the best known genomes, no neuroparsin gene can be detected in either the assembled genome or any of the individual sequencing traces. This gene is similarly absent from the genomes of other species in the melanogaster subgroup, even though it is present in the genomes of eight other Drosophila species. Transgenes in which the promotor of the Drosophila ananassae neuroparsin gene drives expression of gal4 show no expression in D. melanogaster. The hypothesis that this gene has been lost from the melanogaster subgroup is also supported by the neuroparsin gene of Drosophila auraria. In this species, of which the genome has not been sequenced, but which stands phylogenetically between D. ananassae and D. melanogaster, the predicted neuroparsin has lost half its normal size, including four of the twelve conserved cysteine residues. These findings demonstrate that a hormone which plays important regulatory roles in development and reproduction in hemimetabola and is important in mosquito reproduction, has lost its relevance in the melanogaster subgroup of the genus Drosophila. If the essential role of neuroparsin in larval hemimetabola is to ensure the gradual progression from a larval into an adult form during development, that role might become superfluous in some holometabola. In mosquitoes the role of neuroparsin in reproduction appears similar to that of the insulin-related hormones. Perhaps the combination of the development of a complete metamorphosis and a redundant role in reproduction made neuroparsin dispensable in some Drosophila species. © 2010 Elsevier Ltd. All rights reserved.


Fossati P.,French National Center for Scientific Research
European Neuropsychopharmacology | Year: 2012

Different models of emotion highlight the role of strategic brain regions in emotion identification, response and regulation. Cortical, subcortical and limbic structures constitute the emotional brain. In this short review, we focus on the function of the amygdala and medial prefrontal cortex. Both regions have reciprocal connections and are densely connected with cortical and subcortical structures. Beyond its classical role in fear processing, the amygdala is considered as a region that detects salient and personally relevant stimuli in cooperation with ventral and dorsal medial prefrontal cortex. Amygdala and medial prefrontal cortex are also engaged in the processing of socially relevant stimuli. Our review emphasized the overlap between the emotional and the social brain. Adopting a socio-affective neuroscience perspective is a promising perspective to identify new pathophysiological pathways in the study of emotion and mental disorders, especially major depressive disorder. © 2012 Elsevier B.V. and ECNP.


Jones A.P.,French National Center for Scientific Research | Jones A.P.,University Paris - Sud
Astronomy and Astrophysics | Year: 2012

Context. The compositional properties of hydrogenated amorphous carbons are known to evolve in response to the local conditions. Aims. We present a model for low-temperature, amorphous hydrocarbon solids, based on the microphysical properties of random and defected networks of carbon and hydrogen atoms, that can be used to study and predict the evolution of their properties in the interstellar medium. Methods. We adopt an adaptable and prescriptive approach to model these materials, which is based on a random covalent network (RCN) model, extended here to a full compositional derivation (the eRCN model), and a defective graphite (DG) model for the hydrogen poorer materials where the eRCN model is no longer valid. Results. We provide simple expressions that enable the determination of the structural, infrared and spectral properties of amorphous hydrocarbon grains as a function of the hydrogen atomic fraction, X H. Structural annealing, resulting from hydrogen atom loss, results in a transition from H-rich, aliphatic-rich to H-poor, aromatic-rich materials. Conclusions. The model predicts changes in the optical properties of hydrogenated amorphous carbon dust in response to the likely UV photon-driven and/or thermal annealing processes resulting, principally, from the radiation field in the environment. We show how this dust component will evolve, compositionally and structurally in the interstellar medium in response to the local conditions. © 2012 ESO.


Aubret F.,French National Center for Scientific Research
Heredity | Year: 2015

Island colonisation by animal populations is often associated with dramatic shifts in body size. However, little is known about the rates at which these evolutionary shifts occur, under what precise selective pressures and the putative role played by adaptive plasticity on driving such changes. Isolation time played a significant role in the evolution of body size in island Tiger snake populations, where adaptive phenotypic plasticity followed by genetic assimilation fine-tuned neonate body and head size (hence swallowing performance) to prey size. Here I show that in long isolated islands (>6000 years old) and mainland populations, neonate body mass and snout-vent length are tightly correlated with the average prey body mass available at each site. Regression line equations were used to calculate body size values to match prey size in four recently isolated populations of Tiger snakes. Rates of evolution in body mass and snout-vent length, calculated for seven island snake populations, were significantly correlated with isolation time. Finally, rates of evolution in body mass per generation were significantly correlated with levels of plasticity in head growth rates. This study shows that body size evolution occurs at a faster pace in recently isolated populations and suggests that the level of adaptive plasticity for swallowing abilities may correlate with rates of body mass evolution. I hypothesise that, in the early stages of colonisation, adaptive plasticity and directional selection may combine and generate accelerated evolution towards an 'optimal' phenotype. © 2015 Macmillan Publishers Limited.


Morbidelli A.,French National Center for Scientific Research | Nesvorny D.,SWRI
Astronomy and Astrophysics | Year: 2012

Context. Understanding the growth of the cores of giant planets is a difficult problem. Recently, Lambrechts & Johansen (2012, A&A, 544, A32, LJ12) proposed a new model in which the cores grow by the accretion of pebble-size objects, as the latter drift towards the star due to gas drag. Aims. We investigate the dynamics of pebble-size objects in the vicinity of planetary embryos of 1 and 5 Earth masses and the resulting accretion rates. Methods. We use hydrodynamical simulations, in which the embryo influences the dynamics of the gas and the pebbles suffer gas drag according to the local gas density and velocities. Results. The pebble dynamics in the vicinity of the planetary embryo is non-trivial, and it changes significantly with the pebble size. Nevertheless, the accretion rate of the embryo that we measure is within an order of magnitude of the rate estimated in LJ12 and tends to their value with increasing pebble-size. Conclusions. The model by LJ12 has the potential to explain the rapid growth of giant planet cores. The actual accretion rates however, depend on the surface density of pebble size objects in the disk, which is unknown to date. ©2012 ESO.


Guerra M.F.,French National Center for Scientific Research
Radiation Physics and Chemistry | Year: 2014

Ancient gold items are important expressions of different aspects of past civilisations. By using non-destructive techniques of analysis and exam it is possible to obtain data kept within the objects morphology and within the materials employed, providing information, among others, on the manufacturing technologies, on the functions attributed to the objects, and on the sources of raw material exploited. This paper aims to give an overview of the questions raised by cultural heritage objects made with gold, and the role of science-based techniques applied to their study and authentication. Two examples serve to illustrate this: one concerns 19th century restorations of Etruscan objects and the other the provenance of Merovingian gold. © 2013 Elsevier Ltd.


de Tayrac M.,French National Center for Scientific Research
PloS one | Year: 2013

Recent studies have highlighted the heterogeneity of gliomas and demonstrated that molecular and genetic analysis could help in their classification and in the design of treatment protocols. In a previous study we have identified a 4-gene signature highly correlated with survival of glioma patients. The aim of this study is to confirm and extend these findings by investigating the expression of these genes at the protein level and their association with outcome of patients with high grade gliomas. Immunohistochemical staining for EDN/RB, HJURP, p60/CAF-1 and PDLI4 was studied on archive materials from 96 patients (64 glioblastomas and 32 grade III gliomas). The levels of all four proteins differed significantly between grade III and grade IV tumours. The levels of the EDN/RB, HJURP and p60/CAF-1 proteins were strongly associated with overall survival (p<0.001, p<0.001 and p=0.002, respectively), whereas the one of PDLI4 was not (P=0.11). A risk criterion defined as high levels of at least two of the EDN/RB, HJURP and p60/CAF-1 proteins accurately predicted the prognosis of patients. Multivariate analysis confirmed that this criterion was an independent negative prognostic marker (hazard ratio = 2.225; 95% CI, 1.248 to 3.966, p=0.007). The expression of the EDN/RB, HJURP, p60/CAF-1 and PDLI4 proteins is disrupted in high grade gliomas and increases in the levels of these proteins are closely linked to tumour aggressiveness and poor outcome.


Gounelle M.,French National Center for Scientific Research
Elements | Year: 2011

Recent results from the Stardust comet sample-return mission have confirmed the idea that there is a continuum between primitive small bodies in the outer main asteroid belt and comets. Indeed, the mineralogy as well as the chemical and oxygen isotope compositions of the dust from comet Wild 2 are very similar to those of carbonaceous chondrites, a class of meteorites allegedly derived from primitive, dark asteroids. Comets no longer represent extremely primitive samples of the early Solar System that are radically different from dark asteroids. We enter a new era in which comets and their siblings, the dark asteroids, are seen as a collection of individual objects whose geology can be studied. The most primitive of these objects, i.e. the ones that escaped thermal metamorphism or hydrothermal alteration, can help us decipher physicochemical processes in the interstellar medium and in the protoplanetary disk from which our Solar System formed.


Rumpel C.,French National Center for Scientific Research | Kogel-Knabner I.,TU Munich
Plant and Soil | Year: 2011

Despite their low carbon (C) content, most subsoil horizons contribute to more than half of the total soil C stocks, and therefore need to be considered in the global C cycle. Until recently, the properties and dynamics of C in deep soils was largely ignored. The aim of this review is to synthesize literature concerning the sources, composition, mechanisms of stabilisation and destabilization of soil organic matter (SOM) stored in subsoil horizons. Organic C input into subsoils occurs in dissolved form (DOC) following preferential flow pathways, as aboveground or root litter and exudates along root channels and/or through bioturbation. The relative importance of these inputs for subsoil C distribution and dynamics still needs to be evaluated. Generally, C in deep soil horizons is characterized by high mean residence times of up to several thousand years. With few exceptions, the carbon-to-nitrogen (C/N) ratio is decreasing with soil depth, while the stable C and N isotope ratios of SOM are increasing, indicating that organic matter (OM) in deep soil horizons is highly processed. Several studies suggest that SOM in subsoils is enriched in microbial-derived C compounds and depleted in energy-rich plant material compared to topsoil SOM. However, the chemical composition of SOM in subsoils is soil-type specific and greatly influenced by pedological processes. Interaction with the mineral phase, in particular amorphous iron (Fe) and aluminum (Al) oxides was reported to be the main stabilization mechanism in acid and near neutral soils. In addition, occlusion within soil aggregates has been identified to account for a great proportion of SOM preserved in subsoils. Laboratory studies have shown that the decomposition of subsoil C with high residence times could be stimulated by addition of labile C. Other mechanisms leading to destabilisation of SOM in subsoils include disruption of the physical structure and nutrient supply to soil microorganisms. One of the most important factors leading to protection of SOM in subsoils may be the spatial separation of SOM, microorganisms and extracellular enzyme activity possibly related to the heterogeneity of C input. As a result of the different processes, stabilized SOM in subsoils is horizontally stratified. In order to better understand deep SOM dynamics and to include them into soil C models, quantitative information about C fluxes resulting from C input, stabilization and destabilization processes at the field scale are necessary. © 2010 Springer Science+Business Media B.V.


Egloff S.,Toulouse 1 University Capitole | Egloff S.,French National Center for Scientific Research | Dienstbier M.,University of Oxford | Murphy S.,University of Oxford
Trends in Genetics | Year: 2012

The carboxyl-terminal domain (CTD) of RNA polymerase (pol) II comprises multiple tandem repeats with the consensus sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7 that can be extensively and reversibly modified in vivo. CTD modifications orchestrate the interplay between transcription and processing of mRNA. Although phosphorylation of Ser2 (Ser2P) and Ser5 (Ser5P) residues has been described as being essential for the expression of most pol II-transcribed genes, recent findings highlight gene-specific effects of newly discovered CTD modifications. Here, we incorporate these latest findings in an updated review of the currently known elements that contribute to the CTD code and how it is recognized by proteins involved in transcription and RNA maturation. As modification of the CTD has a major impact on gene expression, a better understanding of the CTD code is integral to the understanding of how gene expression is regulated. © 2012 Elsevier Ltd.


Natoli G.,Italian National Cancer Institute | Andrau J.-C.,Aix - Marseille University | Andrau J.-C.,French Institute of Health and Medical Research | Andrau J.-C.,French National Center for Scientific Research
Annual Review of Genetics | Year: 2012

Mammalian genomes are extensively transcribed outside the borders of protein-coding genes. Genome-wide studies recently demonstrated that cis-regulatory genomic elements implicated in transcriptional control, such as enhancers and locus-control regions, represent major sites of extragenic noncoding transcription. Enhancer-templated transcripts provide a quantitatively small contribution to the total amount of cellular nonribosomal RNA; nevertheless, the possibility that enhancer transcription and the resulting enhancer RNAs may, in some cases, have functional roles, rather than represent mere transcriptional noise at accessible genomic regions, is supported by an increasing amount of experimental data. In this article we review the current knowledge on enhancer transcription and its functional implications. © 2012 by Annual Reviews.


Kolakofsky D.,University of Geneva | Kowalinski E.,Max Planck Institute of Biochemistry | Cusack S.,French National Center for Scientific Research
RNA | Year: 2012

A series of high-resolution crystal structures of RIG-I and RIG-I:dsRNA cocrystals has recently been reported. Comparison of these structures provides considerable insight into how this innate immune pattern recognition receptor is activated upon detecting and binding a certain class of viral RNAs. Copyright © 2012 RNA Society.


Nassoy P.,University Pierre and Marie Curie | Lamaze C.,French National Center for Scientific Research | Lamaze C.,University Pierre and Marie Curie
Trends in Cell Biology | Year: 2012

It has been almost 60 years since caveolae were first visualized by Eichi Yamada and George Palade. Nevertheless, these specialized invaginations of the plasma membrane remain without clear and recognized physiological function. The recent identification of new caveolar components and the ability to probe cell mechanics with sophisticated opticophysical devices have shed new light on this fascinating organelle. Early studies from the 1970s suggested that caveolae could participate in the regulation of membrane dynamics. Recent data have established caveolae as mechanosensors that respond immediately to mechanical stress by flattening into the plasma membrane. Here, we focus on the molecular consequences that result from the caveolar disassembly/reassembly cycle induced by membrane tension variations at the surface of the cell under physiological and pathological conditions. © 2012 Elsevier Ltd.


Jaillais Y.,CNRS Laboratory of Plant Reproduction and Development | Vert G.,French National Center for Scientific Research | Vert G.,Salk Institute for Biological Studies
Nature Cell Biology | Year: 2012

The steroid hormones found in plants, the brassinosteroids, were originally genetically identified about 15 years ago as critical regulators of seedling photomorphogenesis. Two studies now shed light on the molecular mechanisms behind this observation. Brassinosteroids control seedling morphogenesis through direct interaction with master transcriptional regulators downstream of growth-promoting hormones and light signalling. © 2012 Macmillan Publishers Limited. All rights reserved.


Narison S.,French National Center for Scientific Research
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2013

Using recent values of the QCD (non-)perturbative parameters given in Table 1 and an estimate of the N3LO QCD perturbative contributions based on the geometric growth of the PT series, we re-use QCD spectral sum rules (QSSR) known to N2LO PT series and including all dimension-six NP condensate contributions in the full QCD theory, for improving the existing estimates of m̄c,b and fD(s),B(s) from the open charm and beauty systems. We especially study the effects of the subtraction point on "different QSSR data" and use (for the first time) the Renormalization Group Invariant (RGI) scale-independent quark masses in the analysis. The estimates [rigourous model-independent upper bounds within the SVZ framework] reported in Table 8: fD/fπ=1.56(5) [≤1.68(1)], fB/fπ=1.58(5) [≤1.80(3)] and fDs/fK=1.58(4) [≤1.63(1)], fBs/fK=1.50(3) [≤1.61(3.5)], which improve previous QSSR estimates, are in perfect agreement (in values and precisions) with some of the experimental data on fD, Ds and on recent lattice simulations within dynamical quarks. These remarkable agreements confirm both the success of the QSSR semi-approximate approach based on the OPE in terms of the quark and gluon condensates and of the Minimal Duality Ansatz (MDA) for parametrizing the hadronic spectral function which we have tested from the complete data of the J/ψ and Υ systems. The values of the running quark masses m̄c(mc)=1286(66) MeV and m̄b(mb)=4236(69) MeV from MD,B are in good agreement though less accurate than the ones from recent J/ψ and Υ sum rules. © 2012 Elsevier B.V.


Bourgeron T.,Institute Pasteur Paris | Bourgeron T.,French National Center for Scientific Research | Bourgeron T.,University Paris Diderot
Nature Reviews Neuroscience | Year: 2015

Genetics studies of autism spectrum disorder (ASD) have identified several risk genes that are key regulators of synaptic plasticity. Indeed, many of the risk genes that have been linked to these disorders encode synaptic scaffolding proteins, receptors, cell adhesion molecules or proteins that are involved in chromatin remodelling, transcription, protein synthesis or degradation, or actin cytoskeleton dynamics. Changes in any of these proteins can increase or decrease synaptic strength or number and, ultimately, neuronal connectivity in the brain. In addition, when deleterious mutations occur, inefficient genetic buffering and impaired synaptic homeostasis may increase an individual's risk for ASD. © 2015 Macmillan Publishers Limited. All rights reserved.


Suetsugu S.,University of Tokyo | Gautreau A.,French National Center for Scientific Research
Trends in Cell Biology | Year: 2012

Cell and organelle shape can profoundly influence proper cellular function. In recent years, two machineries have emerged as major regulators of membrane shape: Bin-Amphiphysin-Rvs161/167 (BAR) domain-containing proteins, which induce membrane invaginations or protrusions, and nucleation promoting factors (NPFs), which activate the Arp2/3 complex and are thus responsible for the generation of branched actin networks that push on membranes. Several BAR-NPF interactions have been shown to induce various types of protrusions, such as lamellipodia or filopodia, or invaginations, including trafficking organelles such as caveolae, endosomes and clathrin-coated pits (CCPs). This review focuses on how collaboration between these two interacting machineries, which emerges as a unified mechanism of membrane remodeling, accounts for such a variety of membrane shapes. © 2012 Elsevier Ltd.


Receveur-Brechot V.,French National Center for Scientific Research | Durand D.,University Paris - Sud
Current Protein and Peptide Science | Year: 2012

While the crucial role of intrinsically disordered proteins (IDPs) in the cell cycle is now recognized, deciphering their molecular mode of action at the structural level still remains highly challenging and requires a combination of many biophysical approaches. Among them, small angle X-ray scattering (SAXS) has been extremely successful in the last decade and has become an indispensable technique for addressing many of the fundamental questions regarding the activities of IDPs. After introducing some experimental issues specific to IDPs and in relation to the latest technical developments, this article presents the interest of the theory of polymer physics to evaluate the flexibility of fully disordered proteins. The different strategies to obtain 3-dimensional models of IDPs, free in solution and associated in a complex, are then reviewed. Indeed, recent computational advances have made it possible to readily extract maximum information from the scattering curve with a special emphasis on highly flexible systems, such as multidomain proteins and IDPs. Furthermore, integrated computational approaches now enable the generation of ensembles of conformers to translate the unique flexible characteristics of IDPs by taking into consideration the constraints of more and more various complementary experiment. In particular, a combination of SAXS with high-resolution techniques, such as x-ray crystallography and NMR, allows us to provide reliable models and to gain unique structural insights about the protein over multiple structural scales. The latest neutron scattering experiments also promise new advances in the study of the conformational changes of macromolecules involving more complex systems. © 2012 Bentham Science Publishers.


Constantinou A.,French National Center for Scientific Research
Chromosoma | Year: 2012

Chromosomal aberrations are often associated with incomplete genome duplication, for instance at common fragile sites, or as a consequence of chemical alterations in the DNA template that block replication forks. Studies of the cancer-prone disease Fanconi anaemia (FA) have provided important insights into the resolution of replication problems. The repair of interstrand DNA crosslinks induced by chemotherapy drugs is coupled with DNA replication and controlled by FA proteins. We discuss here the recent discovery of new FA-associated proteins and the development of new tractable repair systems that have dramatically improved our understanding of crosslink repair. We focus also on how FA proteins protect against replication failure in the context of fragile sites and on the identification of reactive metabolites that account for the development of Fanconi anaemia symptoms. © The Author(s) 2011.


Kerviel A.,French National Center for Scientific Research
Virus research | Year: 2013

Viral assembly is a key step in the virus life cycle. In this review, we focus mainly on the ability of retroviruses, especially HIV-1, to assemble at the plasma membrane of their host cells. The assembly process of RNA enveloped viruses necessitates a fine orchestration between the different viral components and specific interactions between viral proteins and lipids of the host cell membrane. Searching for a comparison with another RNA enveloped virus, we refer to influenza virus to show how it could share (or not) some common features with HIV-1 assembly since both viruses are believed to assemble mainly in raft microdomains. We also discuss the role of RNA and the cellular actin cytoskeleton in enhancing these viral assembly processes. Finally, based on the literature and on new results we have obtained by molecular docking, we propose another mechanism for HIV-1 assembly in membrane domains. This mechanism involves the trapping of acidic lipids by the viral Gag protein by means of ionic protein-lipid interactions, inducing thereby formation of acidic lipid-enriched microdomains (ALEM). Copyright © 2012 Elsevier B.V. All rights reserved.


Johannes L.,University Pierre and Marie Curie | Parton R.G.,University of Queensland | Bassereau P.,French National Center for Scientific Research | Mayor S.,Institute for Stem Cell Biology and Regenerative Medicine
Nature Reviews Molecular Cell Biology | Year: 2015

How endocytic pits are built in clathrin- and caveolin-independent endocytosis still remains poorly understood. Recent insight suggests that different forms of clathrin-independent endocytosis might involve the actin-driven focusing of membrane constituents, the lectin-glycosphingolipid-dependent construction of endocytic nanoenvironments, and Bin-Amphiphysin-Rvs (BAR) domain proteins serving as scaffolding modules. We discuss the need for different types of internalization processes in the context of diverse cellular functions, the existence of clathrin-independent mechanisms of cargo recruitment and membrane bending from a biological and physical perspective, and finally propose a generic scheme for the formation of clathrin-independent endocytic pits. © 2015 Macmillan Publishers Limited. All rights reserved.


Di Nunzio F.,French National Center for Scientific Research
Virus Research | Year: 2013

Human Immunodeficiency virus type 1 (HIV-1), as well as many other viruses that depend on nuclear entry for replication, has developed an evolutionary strategy to dock and translocate through the nuclear pore complex (NPC). In particular, the nuclear pore is not a static window but it is a dynamic structure involved in many vital cellular functions, as nuclear import/export, gene regulation, chromatin organization and genome stability. This review aims to shed light on viral mechanisms developed by HIV-1 to usurp cellular machinery to favor viral gene expression and their replication. In particular, it will be reviewed both what is known and what is speculated about the link between HIV translocation through the nuclear pore and the proviral integration in the host chromatin. © 2013 Elsevier B.V.


Louisnard O.,French National Center for Scientific Research
Ultrasonics Sonochemistry | Year: 2012

In a companion paper, a reduced model for propagation of acoustic waves in a cloud of inertial cavitation bubbles was proposed. The wave attenuation was calculated directly from the energy dissipated by a single bubble, the latter being estimated directly from the fully nonlinear radial dynamics. The use of this model in a mono-dimensional configuration has shown that the attenuation near the vibrating emitter was much higher than predictions obtained from linear theory, and that this strong attenuation creates a large traveling wave contribution, even for closed domain where standing waves are normally expected. In this paper, we show that, owing to the appearance of traveling waves, the primary Bjerknes force near the emitter becomes very large and tends to expel the bubbles up to a stagnation point. Two-dimensional axi-symmetric computations of the acoustic field created by a large area immersed sonotrode are also performed, and the paths of the bubbles in the resulting Bjerknes force field are sketched. Cone bubble structures are recovered and compare reasonably well to reported experimental results. The underlying mechanisms yielding such structures is examined, and it is found that the conical structure is generic and results from the appearance a sound velocity gradient along the transducer area. Finally, a more complex system, similar to an ultrasonic bath, in which the sound field results from the flexural vibrations of a thin plate, is also simulated. The calculated bubble paths reveal the appearance of other commonly observed structures in such configurations, such as streamers and flare structures. © 2011 Elsevier B.V. All rights reserved.


Oulaidi F.,French National Center for Scientific Research
ChemMedChem | Year: 2011

A series of O-alkyl iminoxylitol derivatives was synthesized and evaluated as β-glucocerebrosidase (GCase) inhibitors. This structure-activity study shows a dramatic influence of the position of the alkyl chain (α-C1, O2, O3, or O4) on human GCase inhibition. Remarkably, 1,2-shift of the alkyl chain from C1 to O2 was found to maintain high inhibitory potency toward GCase as well as chaperone activity at sub-inhibitory concentration (10 nM). Removal of the stereogenic center at the pseudo-anomeric position led to shorter and more practical synthetic sequences. 2-O-Alkyl iminoxylitol derivatives constitute a new promising class of leads for the treatment of Gaucher disease by means of pharmacological chaperone therapy. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Buscaill P.,French National Institute for Agricultural Research | Rivas S.,French National Center for Scientific Research
Current Opinion in Plant Biology | Year: 2014

Mounting of efficient plant defence responses depends on the ability to trigger a rapid defence reaction after recognition of the invading microbe. Activation of plant resistance is achieved by modulation of the activity of multiple transcriptional regulators, both DNA-binding transcription factors and their regulatory proteins, that are able to reprogram transcription in the plant cell towards the activation of defence signalling. Here we provide an overview of recent developments on the transcriptional control of plant defence responses and discuss defence-related hormone signalling, the role of WRKY transcription factors during the regulation of plant responses to pathogens, nuclear functions of plant immune receptor proteins, as well as varied ways by which microbial effectors subvert plant transcriptional reprogramming to promote disease. © 2014 Elsevier Ltd.


Faure V.,French National Center for Scientific Research
Molecular cell | Year: 2010

Lagging-strand and leading-strand synthesis of chromosomes generates two structurally distinct ends at the telomeres. Based on sequence bias of yeast telomeres that contain a 250-300 bp array of C(1-3)A/ TG(1-3) repeats, we developed a method allowing us to distinguish which of the two daughter telomeres chromosome end-binding proteins bind to at the end of S phase. The single-stranded DNA-binding protein Cdc13 and the telomerase subunits Est1 and Est2 can bind to the two daughter telomeres, but only their binding to the leading-strand telomere depends on the Mre11/Rad50/Xrs2 (MRX) complex involved in both telomeric 5' nucleolytic resection and telomerase recruitment at short telomeres. Consistently, the MRX complex is mainly found to bind to the leading-strand telomere. Our results indicate that Cdc13 can bind to the telomeric template for lagging-strand replication. Since mre11-deficient strains have markedly short telomeres, telomere elongation by telomerase is likely to occur mainly at the leading-strand telomere. Copyright (c) 2010 Elsevier Inc. All rights reserved.


Descamps P.,French National Center for Scientific Research
Icarus | Year: 2015

In this work, we investigate the equilibrium figures of a dumb-bell-shaped sequence with which we are still not well acquainted. Studies have shown that these elongated and nonconvex figures may realistically replace the classic "Roche binary approximation" for modeling putative peanut-shaped or contact binary asteroids. The best-fit dumb-bell shapes, combined with the known rotational period of the objects, provide estimates of the bulk density of these objects. This new class of mathematical figures has been successfully tested on the observed light curves of three noteworthy small bodies: main-belt Asteroid 216 Kleopatra, Trojan Asteroid 624 Hektor and Edgeworth-Kuiper-belt object 2001 QG298. Using the direct observations of Kleopatra and Hektor obtained with high spatial resolution techniques and fitting the size of the dumb-bell-shaped solutions, we derived new physical characteristics in terms of equivalent radius, 62.5±5km and 92±5km, respectively, and bulk density, 4.4±0.4gcm-3 and 2.43±0.35gcm-3, respectively. In particular, the growing inadequacy of the radar shape model for interpreting any type of observations of Kleopatra (light curves, AO images, stellar occultations) in a satisfactory manner suggests that Kleopatra is more likely to be a dumb-bell-shaped object than a "dog-bone.". © 2014 Elsevier Inc.


Barboiu M.,French National Center for Scientific Research
Angewandte Chemie - International Edition | Year: 2012

Going through the channels: Synthetic scaffolds mimicking natural protein functions have been developed that allow water/proton or only water translocation pathways in bilayer membranes (see picture). The ion-exclusion behaviors of the synthetic systems are based on hydrophobic or dimensional steric effects, while hydrodynamic effects appear to be less important. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Brault P.,French National Center for Scientific Research
Surface and Coatings Technology | Year: 2011

Plasma deposition of catalytic thin films is reviewed in view of highlighting some interesting features. Plasma sputtering, plasma enhanced chemical vapor deposition and plasma enhanced metalorganic chemical vapor deposition and their preferential use in various kinds of catalytic films are described. Fuel cell electrodes, gas sensors and photocatalytic films are emphasized as significant applications. As example, magnetron sputtering deposition is successfully used for growing fuel cell electrodes with high performances. Doping doped TiO2 photocatalysts are deposited using various kinds of plasma depending on the expected film morphology. Gas sensors are well designed when using plasma deposition. Plasma treatment of catalysts offers a suitable alternative to thermal treatments. Finally, associated simulations, especially recent progress in molecular dynamic simulations of catalytic film growth are surveyed. This is a suitable way to understand basic mechanisms of catalytic film growth. © 2011 Elsevier B.V.


Herzig A.,French National Center for Scientific Research
Autonomous Agents and Multi-Agent Systems | Year: 2015

We overview the most prominent logics of knowledge and action that were proposed and studied in the multiagent systems literature. We classify them according to these two dimensions, knowledge and action, and moreover introduce a distinction between individual knowledge and group knowledge, and between a nonstrategic an a strategic interpretation of action operators. For each of the logics in our classification we highlight problematic properties. They indicate weaknesses in the design of these logics and call into question their suitability to represent knowledge and reason about it. This leads to a list of research challenges. © 2014, The Author(s).


Masson J.-B.,Institute Pasteur Paris | Masson J.-B.,French National Center for Scientific Research
Proceedings of the National Academy of Sciences of the United States of America | Year: 2013

Various insects and small animals can navigate in turbulent streams to find their mates (or food) from sparse pheromone (odor) detections. Their access to internal space perception and use of cognitive maps still are heavily debated, but for some of them, limited space perception seems to be the rule. However, this poor space perception does not prevent them from impressive search capacities. Here, as an attempt to model these behaviors, we propose a scheme that can perform, even without a detailed internal space map, searches in turbulent streams. The algorithm is based on a standardized projection of the probability of the source position to remove space perception and on the evaluation of a free energy, whose minimization along the path gives direction to the searcher. An internal "temperature" allows active control of the exploration/exploitation balance during the search. We demonstrate the efficiency of the scheme numerically, with a computational model of odor plume propagation, and experimentally, with robotic searches of thermal sources in turbulent streams. In addition to being a model to describe animals' searches, this scheme may be applied to robotic searches in complex varying media without odometry error corrections and in problems in which active control of the exploration/exploitation balance is profitable.


Piou T.,Ecole Polytechnique Federale de Lausanne | Neuville L.,French National Center for Scientific Research | Zhu J.,Ecole Polytechnique Federale de Lausanne
Angewandte Chemie - International Edition | Year: 2012

Heck shortens the distance: A method for the palladium-catalyzed activation of a C(sp 3)-H bond by a σ-alkyl Pd II complex generated in-situ from a remote arylhalide function has been developed. This approach allows a novel domino carbopalladation/C(sp 3)-C(sp 3) bond-forming process to provide rapid access to biologically relevant spirooxindoles. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Comparat D.,French National Center for Scientific Research
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2014

We present a study of Sisyphus cooling of molecules: The scattering of a single photon removes a substantial amount of the molecular kinetic energy and an optical pumping step allows one to repeat the process. A review of the produced cold molecules so far indicates that the method can be implemented for most of them, making it a promising method able to produce a large sample of molecules at sub-mK temperatures. Considerations of the required experimental parameters, for instance the laser power and linewidth or the trap anisotropy and dimensionality, are given. Rate equations, as well as scattering and dipolar forces, are solved using kinetic Monte Carlo methods for several lasers and several levels. For NH molecules, such detailed simulation predicts a 1000-fold temperature reduction and an increase of the phase-space density by a factor of 107. Even in the case of molecules with both low Franck-Condon coefficients and a nonclosed pumping scheme, 60% of trapped molecules can be cooled from 100 mK to sub-mK temperatures in a few seconds. Additionally, these methods can be applied to continuously decelerate and cool a molecular beam. © 2014 American Physical Society.


Chavanis P.-H.,French National Center for Scientific Research
European Physical Journal Plus | Year: 2014

We construct models of universe with a generalized equation of state (Formula presented.) having a linear component and a polytropic component. Concerning the linear equation of state (Formula presented.) , we assume (Formula presented.). This equation of state describes radiation ((Formula presented.) or pressureless matter ((Formula presented.). Concerning the polytropic equation of state (Formula presented.) , we remain very general allowing the polytropic constant k and the polytropic index n to have arbitrary values. In this paper, we consider positive indices n > 0. In that case, the polytropic component dominates the linear component in the early universe where the density is high. For (Formula presented.) , n = 1 and (Formula presented.) , where (Formula presented.) g/m3 is the Planck density, we obtain a model of early universe describing the transition from the vacuum energy era to the radiation era. The universe exists at any time in the past and there is no primordial singularity. However, for t < 0 , its size is less than the Planck length (Formula presented.) m. In this model, the universe undergoes an inflationary expansion with the Planck density (Formula presented.) g/m3 (vacuum energy) that brings it from the Planck size (Formula presented.) m at t = 0 to a size (Formula presented.) m at (Formula presented.) s (corresponding to about 23.3 Planck times (Formula presented.) s). For (Formula presented.) , n = 1 and (Formula presented.) , we obtain a model of early universe with a new form of primordial singularity: The universe starts at t = 0 with an infinite density and a finite radius a = a1. Actually, this universe becomes physical at a time (Formula presented.) s from which the velocity of sound is less than the speed of light. When (Formula presented.) , the universe enters in the radiation era and evolves like in the standard model. We describe the transition from the vacuum energy era to the radiation era by analogy with a second-order phase transition where the Planck constant ℏ plays the role of finite-size effects (the standard Big Bang theory is recovered for ℏ = 0. © 2014, Società Italiana di Fisica and Springer-Verlag Berlin Heidelberg.


Valageas P.,CEA Saclay Nuclear Research Center | Valageas P.,French National Center for Scientific Research
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2014

The cosmological dynamics of gravitational clustering satisfies an approximate invariance with respect to the cosmological parameters that is often used to simplify analytical computations. We describe how this approximate symmetry gives rise to angular-averaged consistency relations for the matter density correlations. This allows one to write the (?+n) density correlation, with ? large-scale linear wave numbers that are integrated over angles, and n fixed small-scale nonlinear wave numbers, in terms of the small-scale n-point density correlation and ? prefactors that involve the linear power spectra at the large-scale wave numbers. These relations, which do not vanish for equal-time statistics, go beyond the already known kinematic consistency relations. They could be used to detect primordial non-Gaussianities, modifications of gravity, limitations of galaxy biasing schemes, or to help design analytical models of gravitational clustering. © 2014 American Physical Society.


Martinez O.R.,French National Center for Scientific Research
Nature Materials | Year: 2015

Designing structures that dilate rapidly in both tension and compression would benefit devices such as smart filters, actuators or fasteners. This property however requires an unusual Poisson ratio, or Poisson function at finite strains, which has to vary with applied strain and exceed the familiar bounds: less than 0 in tension and above 1/2 in compression. Here, by combining mechanical tests and discrete element simulations, we show that a simple three-dimensional architected material, made of a self-entangled single long coiled wire, behaves in between discrete and continuum media, with a large and reversible dilatancy in both tension and compression. This unusual behaviour arises from an interplay between the elongation of the coiled wire and rearrangements due to steric effects, which, unlike in traditional discrete media, are hysteretically reversible when the architecture is made of an elastic fibre. © 2015 Nature Publishing Group


Changeux J.-P.,French National Center for Scientific Research
Nature Reviews Molecular Cell Biology | Year: 2013

The concept of indirect or 'allosteric' interaction between topographically distinct sites, and the subsequent 1965 Monod-Wyman-Changeux (MWC) model for the conformational change mediating them, arose around 50 years ago. Many classic regulatory proteins (including haemoglobin, Asp transcarbamylase and nicotinic acetylcholine receptor) follow the central paradigm of the MWC model, which has been expanded and challenged as a result of novel technologies. Importantly, the concept of allosteric interaction has aided our understanding of human diseases and drug design. © 2013 Macmillan Publishers Limited. All rights reserved.


Curien N.,French National Center for Scientific Research
Communications in Mathematical Physics | Year: 2015

We present a way to study the conformal structure of random planar maps. The main idea is to explore the map along an SLE (Schramm–Loewner evolution) process of parameter (Formula presented.) and to combine the locality property of the SLE6 together with the spatial Markov property of the underlying lattice in order to get a non-trivial geometric information. We follow this path in the case of the conformal structure of random triangulations with a boundary.Under a reasonable assumption called (*) that we have unfortunately not been able to verify, we prove that the limit of uniformized random planar triangulations has a fractal boundary measure of Hausdorff dimension (Formula presented.) almost surely. This agrees with the physics KPZ predictions and represents a first step towards a rigorous understanding of the links between random planar maps and the Gaussian free field (GFF). © 2014, Springer-Verlag Berlin Heidelberg.


Nitschke W.,French National Center for Scientific Research | Russell M.J.,Jet Propulsion Laboratory
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2013

Attempts to draft plausible scenarios for the origin of life have in the past mainly built upon palaeogeochemical boundary conditions while, as detailed in a companion article in this issue, frequently neglecting to comply with fundamental thermodynamic laws. Even if demands from both palaeogeochemistry and thermodynamics are respected, then a plethora of strongly differing models are still conceivable. Although we have no guarantee that life at its origin necessarily resembled biology in extant organisms, we consider that the only empirical way to deduce how life may have emerged is by taking the stance of assuming continuity of biology from its inception to the present day. Building upon this conviction, we have assessed extant types of energy and carbon metabolism for their appropriateness to conditions probably pertaining in those settings of the Hadean planet that fulfil the thermodynamic requirements for life to come into being. Wood-Ljungdahl (WL) pathways leading to acetyl CoA formation are excellent candidates for such primordial metabolism. Based on a review of our present understanding of the biochemistry and biophysics of acetogenic, methanogenic and methanotrophic pathways and on a phylogenetic analysis of involved enzymes, we propose that a variant of modern methanotrophy is more likely than traditional WL systems to date back to the origin of life. The proposed model furthermore better fits basic thermodynamic demands and palaeogeochemical conditions suggested by recent results from extant alkaline hydrothermal seeps. © 2013 The Author(s) Published by the Royal Society. All rights reserved.


Nitschke W.,French National Center for Scientific Research
Philosophical transactions of the Royal Society of London. Series B, Biological sciences | Year: 2013

Attempts to draft plausible scenarios for the origin of life have in the past mainly built upon palaeogeochemical boundary conditions while, as detailed in a companion article in this issue, frequently neglecting to comply with fundamental thermodynamic laws. Even if demands from both palaeogeochemistry and thermodynamics are respected, then a plethora of strongly differing models are still conceivable. Although we have no guarantee that life at its origin necessarily resembled biology in extant organisms, we consider that the only empirical way to deduce how life may have emerged is by taking the stance of assuming continuity of biology from its inception to the present day. Building upon this conviction, we have assessed extant types of energy and carbon metabolism for their appropriateness to conditions probably pertaining in those settings of the Hadean planet that fulfil the thermodynamic requirements for life to come into being. Wood-Ljungdahl (WL) pathways leading to acetyl CoA formation are excellent candidates for such primordial metabolism. Based on a review of our present understanding of the biochemistry and biophysics of acetogenic, methanogenic and methanotrophic pathways and on a phylogenetic analysis of involved enzymes, we propose that a variant of modern methanotrophy is more likely than traditional WL systems to date back to the origin of life. The proposed model furthermore better fits basic thermodynamic demands and palaeogeochemical conditions suggested by recent results from extant alkaline hydrothermal seeps.


Carrozza S.,French National Center for Scientific Research
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2015

Building on an analogy with ordinary scalar field theories, an -expansion for rank-3 tensorial group field theories with gauge invariance condition is introduced. This allows us to continuously interpolate between the dimension four group SU(2)×U(1) and the dimension three SU(2). In the first situation, there is a unique marginal φ4 coupling constant, but in contrast to ordinary scalar field theory this model is asymptotically free. In the SU(2) case, the presence of two marginally relevant φ6 coupling constants and one φ4 super-renormalizable interaction spoils this interesting property. However, the existence of a nontrivial fixed point is established in dimension 4-, hence suggesting that the SU(2) theory might be asymptotically safe. To pave the way to future nonperturbative calculations, the present perturbative results are discussed in the framework of the effective average action. © 2015 American Physical Society.


Kroymann J.,French National Center for Scientific Research
Current Opinion in Plant Biology | Year: 2011

Technological advances in metabolomics, transcriptomics and genomics have facilitated the detection of genes that contribute to diversification in plant secondary metabolism. Statistical tools from molecular population genetics may help in evaluating whether the corresponding genes or genomic regions carry a signature of selection and answering the question of whether novel compounds are 'adaptive'. Gene duplication fuels diversification in plant secondary metabolism and the evolutionary mechanism for adaptation may follow a path of neofunctionalization subsequent to gene duplication, or gene duplication may occur subsequent to - and resolve - an adaptive conflict present in a single ancestral gene sequence. © 2011 Elsevier Ltd.


Galam S.,French National Center for Scientific Research
Scientometrics | Year: 2011

A quantitative modification to keep the number of published papers invariant under multiple authorship is suggested. In those cases, fractional allocations are attributed to each co-author with a summation equal to one. These allocations are tailored on the basis of each author contribution. It is denoted "Tailor Based Allocations (TBA)" for multiple authorship. Several protocols to TBA are suggested. The choice of a specific TBA may vary from one discipline to another. In addition, TBA is applied to the number of citations of a multiple author paper to have also this number conserved. Each author gets only a specific fraction of the total number of citations according to its fractional paper allocation. The equivalent of the h-index obtained by using TBA is denoted the gh-index. It yields values which differ drastically from those given by the h-index. The gh-index departs also from h̄ recently proposed by Hirsh to account for multiple authorship. Contrary to the h-index, the gh-index is a function of the total number of citations of each paper. A highly cited paper allows a better allocation for all co-authors while a less cited paper contributes essentially to one or two of the co-authors. The scheme produces a substantial redistribution of the ranking of scientists in terms of quantitative records. A few illustrations are provided. © 2011 Akadémiai Kiadó, Budapest, Hungary.


Eberl G.,Institute Pasteur Paris | Eberl G.,French National Center for Scientific Research
Mucosal Immunology | Year: 2010

The immune system is commonly perceived as an army of organs, tissues, cells, and molecules that protect from disease by eliminating pathogens. However, as in human society, a clear definition of good and evil might be sometimes difficult to achieve. Not only do we live in contact with a multitude of microbes, but we also live with billions of symbionts that span all the shades from mutualists to potential killers. Together, we compose a superorganism that is capable of optimal living. In that context, the immune system is not a killer, but rather a force that shapes homeostasis within the superorganism.


Avargues-Weber A.,Toulouse 1 University Capitole | Avargues-Weber A.,French National Center for Scientific Research
Proceedings. Biological sciences / The Royal Society | Year: 2013

Concepts act as a cornerstone of human cognition. Humans and non-human primates learn conceptual relationships such as 'same', 'different', 'larger than', 'better than', among others. In all cases, the relationships have to be encoded by the brain independently of the physical nature of objects linked by the relation. Consequently, concepts are associated with high levels of cognitive sophistication and are not expected in an insect brain. Yet, various works have shown that the miniature brain of honeybees rapidly learns conceptual relationships involving visual stimuli. Concepts such as 'same', 'different', 'above/below of' or 'left/right are well mastered by bees. We review here evidence about concept learning in honeybees and discuss both its potential adaptive advantage and its possible neural substrates. The results reviewed here challenge the traditional view attributing supremacy to larger brains when it comes to the elaboration of concepts and have wide implications for understanding how brains can form conceptual relations.


Bleicher (2013) discussed interpretations proposed by Magny (2004) that Holocene lake-level fluctuations in west-central Europe suggest possible solar forcing of climate. He pointed out that the method used by Magny (2004) is a variant of a cumulative probability function (CPF) and cannot prove solar forcing of central European lake-level changes. He concluded that only few episodes of lake-level changes are climatically driven and that non-climatic factors were dominating. While Bleicher's paper offers a stimulating contribution to the general debate on CPFs, the present comment is based on an approach which, in contrast to CPFs, excludes any consideration of variations in the probabilities over the time intervals given by calibration of 14C dates, as well as any distinction between types of dates (radiocarbon versus tree ring). It produces a revised pattern of the mid-European high lake-level events for the whole Holocene, supporting the hypothesis proposed in Magny (2004). Comparisons with other regional and North Atlantic palaeoclimatic records suggest that, without excluding other forcing factors, the successive high lake-level events recognised in west-central Europe reflect a combination of three main forcing factors acting on millennial and centennial scales, i.e. orbitally driven changes in insolation, impacts of deglacial outbursts and, possibly, variations in solar activity. Finally, it is clear that further investigations are still needed in order to improve the chronological data set for mid-European lake-level fluctuations, with particular attention to better defining the beginning and end of events. © The Author(s) 2013.


Fillatre L.,French National Center for Scientific Research
IEEE Transactions on Information Theory | Year: 2011

A constrained epsilon-minimax test is proposed to detect and classify nonorthogonal vectors in Gaussian noise, with a general covariance matrix, and in presence of linear interferences. This test is epsilon-minimax in the sense that it has a small loss of optimality with respect to the purely theoretical and incalculable constrained minimax test which minimizes the maximum classification error probability subject to a constraint on the false alarm probability. This loss is even more negligible as the signal-to-noise ratio is large. Furthermore, it is also an epsilon-equalizer test since its classification error probabilities are equalized up to a negligible difference. When the signal-to-noise ratio is sufficiently large, an asymptotically equivalent test with a very simple form is proposed. This equivalent test coincides with the generalized likelihood ratio test when the vectors to classify are strongly separated in term of Euclidean distance. Numerical experiments on active user identification in a multiuser system confirm the theoretical findings. © 2006 IEEE.


Bacaud R.,French National Center for Scientific Research
Fuel | Year: 2014

Bergius process for coal liquefaction was patented one century ago. It constituted the first application of dispersed phase catalysts in slurry reactors, considered as once-through disposable solids. Starting from waste materials as additive, the role of catalysts in the conversion of heavy carbonaceous feeds like coal of petroleum residues was progressively identified. Cracking activity was initially considered as necessary, but it was later recognized that hydrogenation activity is essential. The desired properties were established: small particle size, resistance to agglomeration and low cost. Synthesis methods for the production of dispersed phase catalysts are reviewed. Based on historical developments, prospective ways are proposed for improving efficiency of existing conversion processes. © 2013 Elsevier Ltd. All rights reserved.


Andre J.-B.,French National Center for Scientific Research
American Naturalist | Year: 2015

Reciprocity is characterized by individuals actively making it beneficial for others to cooperate by responding to them. This makes it a particularly powerful generator of mutual interest, because the benefits accrued by an individual can be redistributed to another. However, reciprocity is a composite biological function, entailing at least two subfunctions: (i) a behavioral ability to provide fitness benefits to others and (ii) a cognitive ability to evaluate the benefits received from others. For reciprocity to evolve, these two subfunctions must appear together, which raises an evolutionary problem of bootstrapping. In this article, I develop mathematical models to study the necessary conditions for the gradual emergence of reciprocity in spite of this bootstrapping problem. I show that the evolution of reciprocity is based on three conditions. First, there must be some variability in behavior. Second, cooperation must pre-evolve for reasons independent of reciprocity. Third, and most significantly, selection favors conditional cooperation only if the cooperation expressed by others is already conditional, that is, if some reciprocity is already present in the first place. In the discussion, I show that these three conditions help explain the specific features of the instances in which reciprocity does occur in the wild. For instance, it accounts for the role of spatial symmetry (as in ungulate allogrooming), the importance of synergistic benefits (as in nuptial gifts), the facilitating role of collective actions (as in many instances of human cooperation), and the potential role of kinship (as in primate grooming). © 2015 by The University of Chicago.


Thierry B.,French National Center for Scientific Research
Philosophical transactions of the Royal Society of London. Series B, Biological sciences | Year: 2013

The evolutionary study of social systems in non-human primates has long been focused on ecological determinants. The predictive value of socio-ecological models remains quite low, however, in particular because such equilibrium models cannot integrate the course of history. The use of phylogenetic methods indicates that many patterns of primate societies have been conserved throughout evolutionary history. For example, the study of social relations in macaques revealed that their social systems are made of sets of correlated behavioural traits. Some macaque species are portrayed by marked social intolerance, a steep dominance gradient and strong nepotism, whereas others display a higher level of social tolerance, relaxed dominance and a weaker influence of kinship. Linkages between behavioural traits occur at different levels of organization, and act as constraints that limit evolutionary responses to external pressures. Whereas these constraints can exert strong stabilizing selection that opposes the potential changes required by the ecological environment, selective mechanisms may have the potential to switch the whole social system from one state to another by acting primarily on some key behavioural traits that could work as pacemakers.


Manceau A.,French National Center for Scientific Research
American Mineralogist | Year: 2011

The defect-free akdalaite model (fhyd6) for six-line ferrihydrite (6Fh) derived from a pair distribution function (PDF) analysis of high-energy X-ray scattering (HEXS) data was revised (model ferrifh) by Michel et al (2010) using data from a sample produced by heating two-line ferrihydrite (2Fh) at 175 °C for 8 h in the presence of citrate. We show here that the scattering pattern for this sample is similar if not the same as that for hydromaghemite, which in turn is a mixture of maghemite (γ-Fe 2O 3), hematite and 6Fh. As in the case of fhyd6, the PDF of ferrifh was regressed using the structure of the weakly hydrated phase akdalaite [Al 10O 14(OH) 2] after substituting Fe for Al as a starting model. We show that the ferrifh model is implausible for the following reasons. (1) It is derived from a sample, ferrifh, that appears to be hydromaghemite, not pure 6Fh. (2) It has 20% tetrahedral Fe, a coordination that had been eliminated previously using XANES, Mössbauer, and EELS spectroscopies. (3) 75% of the Fe octahedra have shared edge lengths considerably longer than the shortest unshared edges in violation of Pauling's distortion rule. (4) Three tetrahedral Fe-O bonds are longer than three octahedral Fe-O bonds, inducing significant polyhedral distortions. And (5) the calculated composition [Fe 10O 14(OH) 21.2H 2O] disagrees with literature data on weight loss from dehydration for 6Fh. We present an alternative interpretation of the histogram of Fe-Fe distances up to 3.7 Å obtained from the PDF of the fhyd6 ferrihydrite as a mixture of local structures of goethite/akaganeite (α/β-FeOOH) and feroxyhite/hematite (δ-FeOOH/α-Fe 2O 3). Within this interpretation Fe only occupies octahedra that are bonded to each other by faces, edges, or double-corners. This polyhedral connectivity is confirmed experimentally by analysis of the EXAFS spectra of six-line ferrihydrites measured at room and liquid helium temperature. The Fe-Fe pairs from EXAFS data are described reasonably well by a mixture of approximately 70% feroxyhite (containing some nanohematite) and 30% akaganeite, without resorting to other phases. This set of evidence indicates that HEXS data are consistent with the Drits model for ferrihydrite (Drits et al. 1993a).


Wurger A.,French National Center for Scientific Research
Physical Review Letters | Year: 2015

We theoretically study the self-propulsion of a laser-heated Janus particle in a near-critical water-lutidine mixture, and we relate its velocity vp and squirmer parameter β to the wetting properties of its two hemispheres. For nonionic surface forces, the particle moves the active cap at the front, whereas a charged hydrophilic cap leads to backward motion, in agreement with the experiment. Both vp and β show nonmonotonic dependencies on the heating power, and they may even change sign. The variation of β is expected to strongly affect the collective behavior of dense squirmer systems. © 2015 American Physical Society. © 2015 American Physical Society.


Tomassetti N.,French National Center for Scientific Research
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2015

We report calculations of cosmic-ray proton, nuclei, antiproton, electron and positron energy spectra within a "two-halo model" of diffusive transport. The two halos represent a simple, physically consistent generalization of the standard diffusion models, which assume a unique type of diffusion for cosmic rays in the whole galactic halo. We believe instead that cosmic rays may experience a smaller energy dependence of diffusion when they are in proximity of the galactic disk. Our scenario is supported by recent observations of cosmic ray protons, nuclei, anisotropy, and gamma-rays. We predict remarkably hard antiparticle spectra at high energy. In particular, at E10GeV, the antiproton/proton ratio is expected to flatten, while the positron fraction is found to increase with energy. We discuss the implications for cosmic-ray physics and dark matter searches via antimatter. © 2015 American Physical Society.


Tomassetti N.,French National Center for Scientific Research
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2015

The observed spectrum of Galactic cosmic rays has several exciting features such as the rise in the positron fraction above ∼10GeV of energy and the spectral hardening of protons and helium at 300GeV/nucleon of energy. The ATIC-2 experiment has recently reported an unexpected spectral upturn in the elemental ratios involving iron, such as the C/Fe or O/Fe ratios, at energy 50GeV per nucleon. It is recognized that the observed positron excess can be explained by pion production processes during diffusive shock acceleration of cosmic-ray hadrons in nearby sources. Recently, it was suggested that a scenario with nearby source dominating the GeV-TeV spectrum may be connected with the change of slope observed in protons and nuclei, which would be interpreted as a flux transition between the local component and the large-scale distribution of Galactic sources. Here I show that, under a two-component scenario with nearby source, the shape of the spectral transition is expected to be slightly different for heavy nuclei, such as iron, because their propagation range is spatially limited by inelastic collisions with the interstellar matter. This enables a prediction for the primary/primary ratios between light and heavy nuclei. From this effect, a spectral upturn is predicted in the C/Fe and O/Fe ratios in good accordance with the ATIC-2 data. © 2015 American Physical Society.


Leonard A.C.,Florida Institute of Technology | Mechali M.,French National Center for Scientific Research
Cold Spring Harbor Perspectives in Medicine | Year: 2013

The onset of genomic DNA synthesis requires precise interactions of specialized initiator proteins with DNA at sites where the replication machinery can be loaded. These sites, defined as replication origins, are found at a few unique locations in all of the prokaryotic chromosomes examined so far. However, replication origins are dispersed among tens of thousands of loci in metazoan chromosomes, thereby raising questions regarding the role of specific nucleotide sequences and chromatin environment in origin selection and the mechanisms used by in itiatorsto recognize replication origins. Close examination of bacterial and archaeal replication origins reveals an array of DNA sequence motifs that position individual initiator protein molecules and promote initiator oligomerization on origin DNA. Conversely, the need for specific recognition sequences in eukaryotic replication origins is relaxed. In fact, the primary rule for origin selection appears to be flexibility, a feature that is modulated either by structural elements or by epigenetic mechanisms at least partly linked to the organization of the genome for gene expression. © 2013 Cold Spring Harbor Laboratory Press; all rights reserved.


Pic E.,French National Center for Scientific Research
Molecular imaging and biology : MIB : the official publication of the Academy of Molecular Imaging | Year: 2010

PURPOSE: This study compares fluorescence imaging to mass spectroscopy (inductively coupled plasma-mass spectroscopy, ICP-MS) for detection of quantum dots (QDs) in sentinel lymph node (LN) mapping of breast cancer. PROCEDURES: We study the accumulation of near-infrared-emitting QDs into regional LNs and their whole-body biodistribution in mice after subcutaneous injection, using in vivo fluorescence imaging and ex vivo elemental analysis by ICP-MS. RESULTS: We show that the QD accumulation in regional LNs is detectable by fluorescence imaging as early as 5 min post-delivery. Their concentration reaches a maximum at 4 h then decreases over a 10-day observation period. These data are confirmed by ICP-MS. The QD uptake in other organs, assessed by ICP-MS, increases steadily over time; however, its overall level remains rather low. CONCLUSIONS: Fluorescence imaging can be used as a non-invasive alternative to ICP-MS to follow the QD accumulation kinetics into regional LNs.


Gavard J.,French National Center for Scientific Research
BMC cell biology | Year: 2014

BACKGROUND: The interleukin-8 chemokine (IL-8) G-protein coupled receptor CXCR2 governs pro-inflammatory and pro-angiogenic responses in leukocytes and endothelial cells. At a molecular standpoint, CXCR2 is widely reported to operate through calcium flux, phosphoinoisitide 3 kinase (PI3K) and mitogen-activated protein kinase (MAPK). While CXCR2 trafficking is suspected to be intertwined with its signaling, the exact mechanism is not fully elucidated.RESULTS: Here, we identified the lysine 327 within the CXCR2 C-terminal tail as a key residue for ubiquitination, internalization, and signaling. First, the substitution to an arginine of K327 mutation was associated with a reduction in CXCR2 poly-ubiquitination. While WT CXCR2 was rapidly internalized following IL-8 administration, K327R mutant remained at the plasma membrane. Finally, K327R mutant failed to promote the recruitment of β-arrestin2, as estimated by imagery and bioluminescence resonance transfer. As a consequence, the activation of intracellular signaling, including both early events such as ERK phosphorylation and the increase in calcium flux, and the latter activation of the AP1 and NF-κB transcription factors, was blunted.CONCLUSIONS: Overall, our results demonstrate that CXCR2 ubiquitination on K327 residue modulates agonist-activated CXCR2 cell sorting and intracellular signaling. Thus, the inhibition of K327 ubiquitination might emerge as an effective mean to curb exacerbated CXCR2 signaling in several pathological conditions, such as inflammatory diseases and cancer.


Barboiu M.,French National Center for Scientific Research
Topics in Current Chemistry | Year: 2012

Molecular architectures and materials can be constitutionally self-sorted in the presence of different biomolecular targets or external physical stimuli or chemical effectors, thus responding to an external selection pressure. The high selectivity and specificity of different bioreceptors or self-correlated internal interactions may be used to describe the complex constitutional behaviors through multistate component selection from a dynamic library. The self-selection may result in the dynamic amplification of self-optimized architectures during the phase change process. The sol-gel resolution of dynamic molecular/supramolecular libraries leads to higher self-organized constitutional hybrid materials, in which organic (supramolecular)/inorganic domains are reversibily connected. © 2011 Springer-Verlag Berlin Heidelberg.


Abergel C.,French National Center for Scientific Research
Acta Crystallographica Section D: Biological Crystallography | Year: 2013

Molecular replacement is the method of choice for X-ray crystallographic structure determination provided that suitable structural homologues are available in the PDB. Presently, there are ∼80000 structures in the PDB (8074 were deposited in the year 2012 alone), of which ∼70% have been solved by molecular replacement. For successful molecular replacement the model must cover at least 50% of the total structure and the Cα r.m.s.d. between the core model and the structure to be solved must be less than 2Å. Here, an approach originally implemented in the CaspR server (http://www.igs.cnrs-mrs.fr/ Caspr2/index.cgi) based on homology modelling to search for a molecular-replacement solution is discussed. How the use of as much information as possible from different sources can improve the model(s) is briefly described. The combination of structural information with distantly related sequences is crucial to optimize the multiple alignment that will define the boundaries of the core domains. PDB clusters (sequences with ≥30% identical residues) can also provide information on the eventual changes in conformation and will help to explore the relative orientations assumed by protein subdomains. Normal-mode analysis can also help in generating series of conformational models in the search for a molecular-replacement solution. Of course, finding a correct solution is only the first step and the accuracy of the identified solution is as important as the data quality to proceed through refinement. Here, some possible reasons for failure are discussed and solutions are proposed using a set of successful examples.


Taddei A.,French National Center for Scientific Research
Cold Spring Harbor perspectives in biology | Year: 2010

The budding yeast nucleus, like those of other eukaryotic species, is highly organized with respect to both chromosomal sequences and enzymatic activities. At the nuclear periphery interactions of nuclear pores with chromatin, mRNA, and transport factors promote efficient gene expression, whereas centromeres, telomeres, and silent chromatin are clustered and anchored away from pores. Internal nuclear organization appears to be function-dependent, reflecting localized sites for tRNA transcription, rDNA transcription, ribosome assembly, and DNA repair. Recent advances have identified new proteins involved in the positioning of chromatin and have allowed testing of the functional role of higher-order chromatin organization. The unequal distribution of silent information regulatory factors and histone modifying enzymes, which arises in part from the juxtaposition of telomeric repeats, has been shown to influence chromatin-mediated transcriptional repression. Other localization events suppress unwanted recombination. These findings highlight the contribution budding yeast genetics and cytology have made to dissecting the functional role of nuclear structure.


Yan L.,French National Center for Scientific Research
Physical Review C - Nuclear Physics | Year: 2015

I propose event-plane correlations as a test of collectivity in small colliding systems: In d-Au and He3-Au collisions, I predict a strong anticorrelation between elliptic and triangular flow, generated by the geometry of the light projectile. A significant anticorrelation is also predicted in central p-Pb collisions at the CERN Large Hadron Collider, which is solely generated by fluctuations. Similar, but stronger correlation patterns are predicted in correlations involving dipolar flow. © 2015 American Physical Society.


Kostov I.,French National Center for Scientific Research
Nuclear Physics B | Year: 2010

We show how the formulation of the matrix models as conformal field theories on a Riemann surfaces can be used to compute the genus expansion of the observables. Here we consider the simplest example of the Hermitian matrix model, where the classical solution is described by a hyperelliptic Riemann surface. To each branch point of the Riemann surface we associate an operator which represents a twist field dressed by the modes of the twisted boson. The partition function of the matrix model is computed as a correlation function of such dressed twist fields. The perturbative construction of the dressing operators yields a set of Feynman rules for the genus expansion, which involve vertices, propagators and tadpoles. The vertices are universal, the propagators and the tadpoles depend on the Riemann surface. As a demonstration we evaluate the genus-two free energy using the Feynman rules. © 2010 Elsevier B.V.


Narison S.,French National Center for Scientific Research
International Journal of Modern Physics A | Year: 2015

Anticipating future precise measurements of the D- and B-like (semi)leptonic and hadronic decays for alternative determinations of the CKM mixing angles, we pursue our program on the D- and B-like mesons by improving the estimates of fD(s) and fB(s) (analogue to fπ) by using the well-established (inverse) Laplace sum rules (LSR) and/or their suitable ratios less affected by the systematics, which are known to N2LO pQCD and where the complete d = 6 nonperturbative condensate contributions are included. The convergence of the PT series is analyzed by an estimate of the N3LO terms based on geometric growth of the coefficients. In addition to the standard LSR variable τ and the QCD continuum threshold tc stability criteria, we extract our optimal results by also requiring stability on the variation of the arbitrary QCD subtraction point μ which reduces the errors in the analysis. We complete the study of the open bottom states by an estimate of fBc . Our results summarized in Tables 3 and 4 are compared with some other recent sum rules and lattice estimates. © World Scientific Publishing Company.


Narison S.,French National Center for Scientific Research
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2010

We extract (for the first time) the ratio of the gluon condensate 〈g 3f abcG 3〉/〈α sG 2〉 expressed in terms of the liquid instanton radius ρc from charmonium moments sum rules by examining the effects of 〈α sG 2〉 in the determinations of both ρc and the running MS mass m c(m c). Using a global analysis of selected ratios of moments at different Q 2=0, 4m c 2 and 8m c 2 and keeping 〈α sG 2〉 from 0.06 GeV 4, where the estimate of ρ c is almost independent of 〈α sG 2〉, we deduce: ρ c=0.98(21) GeV -1 corresponding to 〈g 3f abcG 3〉=(31±13) GeV 2〈α sG 2〉. The value of m c(m c) is less affected (within the errors) by the variation of 〈g 3f abcG 3〉, where a common solution from different moments are reached for 〈α sG 2〉≥0.02 GeV 4. Using the values of 〈α sG 2〉=0.06(2) GeV 4 from some other channels and the previous value of 〈g 3f abcG 3〉, we deduce: m̄c(mc)=1261(18) MeV and m b(m b)=4232(10) MeV, where an estimate of the 4-loops (O(α s 3)) contribution has been included. Our analysis indicates that the errors in the determinations of the charm quark mass and of αs without taking into account the ones of the gluon condensates have been underestimated. To that accuracy, one can deduce the running light and heavy quark masses and their ratios evaluated at M Z, where it is remarkable to notice the approximate equalities: m s/m u≈m b/m s≈m t/m b≈51(9), which might reveal some eventual underlying novel symmetry of the quark mass matrix in some Grand Unified Theories. © 2010 Elsevier B.V.


Chami L.,French National Center for Scientific Research
Molecular neurodegeneration | Year: 2012

Alzheimer's disease (AD) is a complex age-related pathology, the etiology of which has not been firmly delineated. Among various histological stigmata, AD-affected brains display several cellular dysfunctions reflecting enhanced oxidative stress, inflammation process and calcium homeostasis disturbance. Most of these alterations are directly or indirectly linked to amyloid β-peptides (Aβ), the production, molecular nature and biophysical properties of which likely conditions the degenerative process. It is particularly noticeable that, in a reverse control process, the above-described cellular dysfunctions alter Aβ peptides levels. β-secretase βAPP-cleaving enzyme 1 (BACE1) is a key molecular contributor of this cross-talk. This enzyme is responsible for the primary cleavage generating the N-terminus of "full length" Aβ peptides and is also transcriptionally induced by several cellular stresses. This review summarizes data linking brain insults to AD-like pathology and documents the key role of BACE1 at the cross-road of a vicious cycle contributing to Aβ production.


Le Doussal P.,French National Center for Scientific Research
Annals of Physics | Year: 2010

Some aspects of the functional RG (FRG) approach to pinned elastic manifolds (of internal dimension d) at finite temperature T > 0 are reviewed and reexamined in this much expanded version of Le Doussal (2006) [67]. The particle limit d = 0 provides a test for the theory: there the FRG is equivalent to the decaying Burgers equation, with viscosity ν ∼ T-both being formally irrelevant. An outstanding question in FRG, i.e. how temperature regularizes the otherwise singular flow of T = 0 FRG, maps to the viscous layer regularization of inertial range Burgers turbulence (i.e. to the construction of the inviscid limit). Analogy between Kolmogorov scaling and FRG cumulant scaling is discussed. First, multi-loop FRG corrections are examined and the direct loop expansion at T > 0 is shown to fail already in d = 0, a hierarchy of ERG equations being then required (introduced in Balents and Le Doussal (2005) [36]). Next we prove that the FRG function R(u) and higher cumulants defined from the field theory can be obtained for any d from moments of a renormalized potential defined in an sliding harmonic well. This allows to measure the fixed point function R(u) in numerics and experiments. In d = 0 the beta function (of the inviscid limit) is obtained from first principles to four loop. For Sinai model (uncorrelated Burgers initial velocities) the ERG hierarchy can be solved and the exact function R(u) is obtained. Connections to exact solutions for the statistics of shocks in Burgers and to ballistic aggregation are detailed. A relation is established between the size distribution of shocks and the one for droplets. A droplet solution to the ERG functional hierarchy is found for any d, and the form of R(u) in the thermal boundary layer is related to droplet probabilities. These being known for the d = 0 Sinai model the function R(u) is obtained there at any T. Consistency of the ε{lunate} = 4 - d expansion in one and two loop FRG is studied from first principles, and connected to shock and droplet relations which could be tested in numerics. © 2009 Elsevier Inc. All rights reserved.


Tomassetti N.,French National Center for Scientific Research
Nuclear and Particle Physics Proceedings | Year: 2015

The Alpha Magnetic Spectrometer (AMS-02) is a state of the art particle detector measuring cosmic rays (CRs) on the International Space Station (ISS) since May 19th 2011. AMS-02 identifies CR leptons and nuclei in the energy range from hundreds MeV to few TeV per nucleon. Several sub-detector systems allow for redundant particle identification with unprecedented precision, a powerful lepton-hadron separation, and a high purity of the antimatter signal. The new AMS-02 leptonic data from 1 to 500 GeV are presented and discussed. These new data indicate that new sources of CR leptons need to be included to describe the observed spectra at high energies. Explanations of this anomaly may be found either in dark-matter particles annihilation or in the existence of nearby astrophysical sources of e±. Future data at higher energies and forthcoming measurements on the antiproton spectrum and the boron-to-carbon ratio will be crucial in providing the discrimination among the different scenario. © 2015 Elsevier B.V.


Wurger A.,French National Center for Scientific Research
Physical Review Letters | Year: 2011

We show that thermal creep is at the origin of the recently discovered Leidenfrost ratchet, where liquid droplets float on a vapor layer along a heated sawtooth surface and accelerate to velocities of up to 40cm/s. As the active element, the asymmetric temperature profile at each ratchet summit rectifies the vapor flow in the boundary layer. This mechanism works at low Reynolds number and provides a novel tool for controlling gas flow at nanostructured surfaces. © 2011 American Physical Society.


Roze D.,French National Center for Scientific Research | Roze D.,University Pierre and Marie Curie
PLoS Biology | Year: 2012

Understanding the evolutionary advantage of sexual reproduction remains one of the most fundamental questions in evolutionary biology. Most of the current hypotheses rely on the fact that sex increases genetic variation, thereby enhancing the efficiency of natural selection; an important body of theoretical work has defined the conditions under which sex can be favoured through this effect. Over the last decade, experimental evolution in model organisms has provided evidence that sex indeed allows faster rates of adaptation. A new study on facultatively sexual rotifers shows that increased rates of sex can be favoured during adaptation to new environmental conditions and explores the cause of this effect. The results provide support for the idea that the benefits of increasing genetic variation may compensate for the short-term costs of sexual reproduction. © 2012 Denis Roze.


Perrot-Rechenmann C.,French National Center for Scientific Research
Cold Spring Harbor perspectives in biology | Year: 2010

The phytohormone auxin is a major regulator of plant growth and development. Many aspects of these processes depend on the multiple controls exerted by auxin on cell division and cell expansion. The detailed mechanisms by which auxin controls these essential cellular responses are still poorly understood, despite recent progress in the identification of auxin receptors and components of auxin signaling pathways. The purpose of this review is to provide an overview of the present knowledge of the molecular mechanisms involved in the auxin control of cell division and cell expansion. In both cases, the involvement of at least two signaling pathways and of multiple targets of auxin action reflects the complexity of the subtle regulation of auxin-mediated cellular responses. In addition, it offers the necessary flexibility for generating differential responses within a given cell depending on its developmental context.


Briscoe J.,UK National Institute for Medical Research | Therond P.P.,French National Center for Scientific Research | Therond P.P.,University of Nice Sophia Antipolis
Nature Reviews Molecular Cell Biology | Year: 2013

The cloning of the founding member of the Hedgehog (HH) family of secreted proteins two decades ago inaugurated a field that has diversified to encompass embryonic development, stem cell biology and tissue homeostasis. Interest in HH signalling increased when the pathway was implicated in several cancers and congenital syndromes. The mechanism of HH signalling is complex and remains incompletely understood. Nevertheless, studies have revealed novel biological insights into this system, including the function of HH lipidation in the secretion and transport of this ligand and details of the signal transduction pathway, which involves Patched 1, Smoothened and GLI proteins (Cubitus interruptus in Drosophila melanogaster), as well as, in vertebrates, primary cilia. © 2013 Macmillan Publishers Limited. All rights reserved.


Seaman M.N.J.,Cambridge Institute for Medical Research | Gautreau A.,French National Center for Scientific Research
Trends in Cell Biology | Year: 2013

Endosomal protein sorting governs the fate of many physiologically important proteins involved in a panoply of cellular functions. Recent discoveries have revealed a vital role for endosomally localised branched actin patches in facilitating protein sorting. The formation of the actin patches has been shown to require the function of the WASH complex - the major endosomal actin polymerisation-promoting complex - which stimulates the activity of the ubiquitously expressed Arp2/3 complex. Another key component of the endosomal protein-sorting machinery is the retromer complex. Studies now show that retromer mediates the recruitment of the WASH complex and its regulators to endosomes. In this review, recent progress in understanding the role of the WASH complex along with retromer in endosomal protein sorting is discussed. © 2013 Elsevier Ltd.


Rostain S.,French National Center for Scientific Research
Quaternary International | Year: 2012

Numerous pre-Columbian sites with artificial earth mounds have been found in the Upano valley, at the foot of the Andes, in the Ecuadorian Amazon. Large-scale excavations conducted during a Franco-Ecuadorian project helped to reveal techniques in building, mound functions, chronology of occupation, and house plan and associated activities. Groups of the Upano culture built these mound complexes from 500 BC and left the valley ca. 400-600 AD. These groups transformed the natural landscape, building hundreds of earth mound complexes along terraces. Located at a key-area, the Upano people had strong relationships with the Andean highlands, where they traded their pottery. The most striking aspect is the existence of a spatial pattern organizing the mounds. The delimitation of a square or rectangular, low, and flat plaza is the basis of the spatial pattern in the Upano valley. It is closed on four sides by mounds, modified slopes, banks or dug pathways. Variations occur, but the basic pattern is generally the same. In several complexes, a central mound is built in the center of the plaza with four or six peripheral elevations. © 2011 Elsevier Ltd and INQUA.


Manceau A.,French National Center for Scientific Research
American Mineralogist | Year: 2012

The XRD pattern of hydromaghemite, previously interpreted as a mixture of hydroxylated maghemite, ferrihydrite, and hematite (Barrón et al. 2003; Liu 2008), has been reinterpreted as being from a new form of ferrihydrite called "ferrimagnetic ferrihydrite" (ferrifh, Michel et al. 2010; Barrón et al. 2012). Although ferrihydrite sensu stricto and ferrifh have distinct XRD patterns, their profiles have been fit with the same akdalaite-type model using atomic pair distribution (PDF) analysis (Michel et al. 2007, 2010). This ambivalence shows that the crystal structure problem is ill-conditioned, as often the case for the study of nanostructured materials by PDF (Billinge and Levin 2007).


Mazeau K.,French National Center for Scientific Research
Carbohydrate Polymers | Year: 2011

This study is based on the working hypothesis that the external morphology of the cellulose microfibrils is correctly represented by a combination of eight surfaces issued from four lateral cleavage planes of the I-α and I-β allomorphs. Models of these surfaces have been generated and investigated before and after relaxation, thus allowing one to predict, for each of these, their roughness, the accessibility of the hydrophilic and hydrophobic groups as well as their surface and attachment energies. Results showed that the ensemble of eight surfaces could be divided into three families. The first family contains four hydrophilic and moderately rough surfaces, which dominate the external morphology of the microfibrils and are thus responsible for their macroscopic properties. Surfaces of the two other families are of minor importance in the external morphology as they are located at the corners of the cellulosic macrocrystals. They are either flat and hydrophobic or rough and hydrophilic. The flat surfaces are of high biological and technical significance as they are specifically recognized by hydrophobic substances, including the cellulose binding modules of cellulases. Relaxation resulted in a significant disorganization of the rough surfaces whereas the other surfaces remain close to their original organisation. The interpretation of the surface and attachment energies of the surfaces, evidences the major influence of the biosynthetic process in the design of the external morphology of the cellulose microfibrils, as opposed to the classical kinetic and thermodynamic crystal growth mechanism. © 2010 Elsevier Ltd. All rights reserved.


Willcox G.,French National Center for Scientific Research
Vegetation History and Archaeobotany | Year: 2012

This short note adds to earlier attempts at identifying arable weeds on late Pleistocene/early Holocene sites in the Near East. Nineteen potential arable weed taxa that have no known use were selected. The occurrence of these taxa at sites with morphologically wild cereals was compared to sites with morphologically domestic cereals. The presumed arable weed taxa were as common on three PPNA (Pre Pottery Neolithic A) sites without domestication as they were on Middle PPNB (Pre Pottery Neolithic B) sites with domestication, which lends support to arguments for pre-domestic cultivation at the former sites. Arable weed taxa were less common at Natufian sites but their presence raises the question of whether they originated in cultivated fields or were the ancestors of weeds gathered accidentally alongside wild cereals in their natural habitat. © 2011 Springer-Verlag.


Parrot M.,French National Center for Scientific Research
Annals of Geophysics | Year: 2012

Many examples of ionospheric perturbations observed during large seismic events were recorded by the low-altitude satellite DEMETER. However, there are also ionospheric variations without seismic activity. The present study is devoted to a statistical analysis of the night-time ion density variations. Software was implemented to detect variations in the data before earthquakes world-wide. Earthquakes with magnitudes >4.8 were selected and classified according to their magnitudes, depths and locations (land, close to the coast, or below the sea). For each earthquake, an automatic search for ion density variations was conducted from 15 days before the earthquake, when the track of the satellite orbit was at less than 1,500 km from the earthquake epicenter. The result of this first step provided the variations relative to the background in the vicinity of the epicenter for each 15 days before each earthquake. In the second step, comparisons were carried out between the largest variations over the 15 days and the earthquake magnitudes. The statistical analysis is based on calculation of the median values as a function of the various seismic parameters (magnitude, depth, location). A comparison was also carried out with two other databases, where on the one hand, the locations of the epicenters were randomly modified, and on the other hand, the longitudes of the epicenters were shifted. The results show that the intensities of the ionospheric perturbations are larger prior to the earthquakes than prior to random events, and that the perturbations increase with the earthquake magnitudes. © 2012 by the Istituto Nazionale di Geofisica e Vulcanologia. All rights reserved.


Luzum M.,CEA Saclay Nuclear Research Center | Ollitrault J.-Y.,French National Center for Scientific Research
Physical Review Letters | Year: 2011

It was recently shown that fluctuations in the initial geometry of a heavy-ion collision generally result in a dipole asymmetry of the distribution of outgoing particles. This asymmetry, unlike the usual directed flow, is expected to be present at a wide range of rapidity-including midrapidity. The first evidence of this phenomenon can be seen in recent two-particle correlation data by the STAR Collaboration, providing the last element necessary to quantitatively describe long-range dihadron correlations. We extract differential directed flow from these data and propose a new direct measurement. © 2011 American Physical Society.


Suzanne M.,Toulouse 1 University Capitole | Suzanne M.,French National Center for Scientific Research | Steller H.,Howard Hughes Medical Institute
Cell Death and Differentiation | Year: 2013

Programmed cell death is an important process during development that serves to remove superfluous cells and tissues, such as larval organs during metamorphosis, supernumerary cells during nervous system development, muscle patterning and cardiac morphogenesis. Different kinds of cell death have been observed and were originally classified based on distinct morphological features: (1) type I programmed cell death (PCD) or apoptosis is recognized by cell rounding, DNA fragmentation, externalization of phosphatidyl serine, caspase activation and the absence of inflammatory reaction, (2) type II PCD or autophagy is characterized by the presence of large vacuoles and the fact that cells can recover until very late in the process and (3) necrosis is associated with an uncontrolled release of the intracellular content after cell swelling and rupture of the membrane, which commonly induces an inflammatory response. In this review, we will focus exclusively on developmental cell death by apoptosis and its role in tissue remodeling. © 2013 Macmillan Publishers Limited All rights reserved.


Borde V.,Institute Pasteur Paris | de Massy B.,French National Center for Scientific Research
Current Opinion in Genetics and Development | Year: 2013

During the first meiotic prophase, hundreds of DNA double strand breaks (DSBs) are deliberately self-inflicted along chromosomes in order to promote homologous recombination between homologs. These DSBs, catalyzed by the evolutionary conserved Spo11 protein, are highly regulated. Recent studies in yeast and mammals have identified key components involved in meiotic DSB formation. In mammals, the DNA binding specificity of PRDM9 determines where DSB occur, whereas in yeast, Spo11 acts in regions which one important feature is chromatin accessibility. However, DSB formation requires additional proteins located on chromosome axes, and the Saccharomyces cerevisiae protein, Spp1 has been recently identified to make the link between axes and DSB sites. These recent findings open exciting routes to understanding how the requirement to regulate DSBs along and between homologs is achieved. © 2012 Elsevier Ltd.


De Massy B.,French National Center for Scientific Research
Annual Review of Genetics | Year: 2013

Meiotic recombination is essential for fertility in most sexually reproducing species. This process also creates new combinations of alleles and has important consequences for genome evolution. Meiotic recombination is initiated by the formation of DNA double-strand breaks (DSBs), which are repaired by homologous recombination. DSBs are catalyzed by the evolutionarily conserved SPO11 protein, assisted by several other factors. Some of them are absolutely required, whereas others are needed only for full levels of DSB formation and may participate in the regulation of DSB timing and frequency as well as the coordination between DSB formation and repair. The sites where DSBs occur are not randomly distributed in the genome, and remarkably distinct strategies have emerged to control their localization in different species. Here, I review the recent advances in the components required for DSB formation and localization in the various model organisms in which these studies have been performed. © 2013 by Annual Reviews. All rights reserved.


de Vignemont F.,French National Center for Scientific Research | Iannetti G.D.,University College London
Neuropsychologia | Year: 2015

Several studies in humans and non-human primates have explored and characterised the features of the cortical representation of the portion of space immediately surrounding the body - the peripersonal space. In this paper we ask the following question: is it legitimate to assume that there is a single representation of peripersonal space? This issue has rarely been addressed in the literature, leading to much confusion, especially when one compares results reported in social psychology and in cognitive neuroscience. Indeed, studies in both fields explore and refer to more or less the same portion of space, but the terminology used to describe it differs greatly. Therefore, the definition of this portion of space immediately surrounding the body has remained quite vague, allowing for many variations. Here, we propose a dual model of peripersonal space, based on a clear functional distinction between bodily protection and goal-directed action. We argue that the two functions of peripersonal space require distinct sensory and motor processes that obey different principles. Furthermore, we highlight that the effects of anxiety and tool use on peripersonal space provide empirical support to our distinction. © 2014 Elsevier Ltd.


Louisnard O.,French National Center for Scientific Research
Ultrasonics Sonochemistry | Year: 2012

The bubbles involved in sonochemistry and other applications of cavitation oscillate inertially. A correct estimation of the wave attenuation in such bubbly media requires a realistic estimation of the power dissipated by the oscillation of each bubble, by thermal diffusion in the gas and viscous friction in the liquid. Both quantities and calculated numerically for a single inertial bubble driven at 20 kHz, and are found to be several orders of magnitude larger than the linear prediction. Viscous dissipation is found to be the predominant cause of energy loss for bubbles small enough. Then, the classical nonlinear Caflish equations describing the propagation of acoustic waves in a bubbly liquid are recast and simplified conveniently. The main harmonic part of the sound field is found to fulfill a nonlinear Helmholtz equation, where the imaginary part of the squared wave number is directly correlated with the energy lost by a single bubble. For low acoustic driving, linear theory is recovered, but for larger drivings, namely above the Blake threshold, the attenuation coefficient is found to be more than 3 orders of magnitude larger then the linear prediction. A huge attenuation of the wave is thus expected in regions where inertial bubbles are present, which is confirmed by numerical simulations of the nonlinear Helmholtz equation in a 1D standing wave configuration. The expected strong attenuation is not only observed but furthermore, the examination of the phase between the pressure field and its gradient clearly demonstrates that a traveling wave appears in the medium. © 2011 Elsevier B.V. All rights reserved.


David J.F.,French National Center for Scientific Research
Soil Biology and Biochemistry | Year: 2014

Saprophagous macroarthropods are usually described as litter transformers that have low assimilation efficiencies and little direct effect on carbon mineralization. They are considered to enhance decomposition indirectly, by fragmenting leaf litter and increasing the surface area available for microbial colonization, thus stimulating microbial activity in their faeces. A review of experimental studies on the direct and indirect effects of macroarthropods on leaf litter decomposition does not confirm these views. (1) Laboratory estimates of assimilation efficiency are highly variable across studies, ranging from less than 5% to over 50%; this suggests that under field conditions that offer a variety of food choices, direct impacts of macroarthropods on carbon mineralization may be stronger than generally assumed. (2) Macroarthropod faeces are poor in easily assimilable organic compounds and rich in lignin; microbial respiration is only transiently stimulated in this material and, in the long term, there is no evidence of increased mass loss in faeces compared with intact leaf litter; faecal pellets are more akin to partially stabilized organic matter than to hotspots of microbial activity. (3) The overall impact of macroarthropods on microbial respiration in litter or soil-litter microcosms can be positive or negative; the results vary depending on animal abundance and litter type, but macroarthropod-microorganism interactions in unconsumed leaf litter may also be involved; recent studies have shown that macroarthropods grazing on fungi have complex, species-specific effects on fungal-mediated decomposition, which may partly explain the variability of microbial responses in microcosm experiments. (4) The most consistent effect of macroarthropods in decomposing leaf litter is an increased rate of nitrogen mineralization, which results predominantly from interactions with microorganisms and not from excretion; fresh macroarthropod faeces probably stimulate microfaunal activity, thereby increasing nitrogen release, although the actual mechanism remains unclear. It is concluded that soil macroarthropods play important roles in nutrient cycling, while their impact on carbon mineralization is much less clear. Significant alterations of carbon and nutrient dynamics may result from their interactions with fungi and more research is required in this area. © 2014 Elsevier Ltd.


Besteiro S.,French National Center for Scientific Research
Molecular and Biochemical Parasitology | Year: 2012

Autophagy is a life-sustaining process by which cytoplasmic components are sequestered in double-membrane vesicles called autophagosomes, and degraded after fusion with a lytic compartment. This process can be triggered under cellular stress conditions in order to recycle damaged organelles or provide nutrients to the cell, but may also be involved in cell remodelling during normal development. This catabolic process is conserved among most eukaryotes and characterisation of its molecular machinery has benefited greatly from functional genetic studies in yeast and mammalian models. Until recently, not much was known about the functions of autophagy in Apicomplexa, but recent data obtained in Toxoplasma have shed light on a very important role for this machinery, potentially at the crossroads between life and death decisions for the parasite. The possible roles for autophagy during the life cycles of other medically important apicomplexan parasites and the perspectives for discovering new drug targets in this pathway for combating these parasites are discussed in this review. © 2012 Elsevier B.V.


Narison S.,French National Center for Scientific Research
Nuclear and Particle Physics Proceedings | Year: 2016

We summarize our recently improved results for the pseudoscalar [S. Narison, Phys.Lett. B718 (2013) 132; S. Narison, Nucl. Phys. Proc. Suppl. 234 (2013) 187; S. Narison, Phys.Lett. B721 (2013) 269], vector and Bc [S. Narison, Int. J. Mod. Phys. A30 (2015) 20, 1550116] meson decay constants from QCD spectral sum rules where N2LO⊕ estimate of the N3LO PT⊕d≤6 condensates have been included in the SVZ expansion. The "optimal results" based on stability criteria with respect to the variations of the Laplace/Moments sum rule variables, QCD continuum threshold and subtraction constant μ are compared with recent sum rules and lattice calculations. To understand the "apparent tension" between some recent results, we present in Section 8 a novel extraction of for fB*/fB from heavy quark effective theory (HQET) sum rules by including the normalization factor (Mb/MB)2 relating the pseudoscalar to the universal HQET correlators for finite b-quark and B-meson masses. We obtain fB*/fB=1.025(16) in good agreement with 1.016(16) from spectral sum rules (SR) in full QCD [3]. We complete the paper by including new improved estimates of the scalar, axial and Bc* meson decay constants (Sections 11-13). For further phenomenological uses, we attempt to extract a Global Average of the sum rules and lattice determinations which are summarized in Tables 2-6. We do not found any deviation of these SM results from the present data. © 2016 Elsevier B.V.


Collins T.,French National Center for Scientific Research
Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | Year: 2012

In this paper we present the first solution to 3D reconstruction in monocular laparoscopy using methods based on Photometric Stereo (PS). Our main contributions are to provide the new theory and practical solutions to successfully apply PS in close-range imaging conditions. We are specifically motivated by a solution with minimal hardware modification to existing laparoscopes. In fact the only physical modification we make is to adjust the colour of the laparoscope's illumination via three colour filters placed at its tip. Once calibrated, our approach can compute 3D from a single image, does not require correspondence estimation, and computes absolute depth densely. We demonstrate the potential of our approach with ground truth ex-vivo and in-vivo experimentation.


Dechanet-Merville J.,French National Center for Scientific Research
Clinical Cancer Research | Year: 2014

Gamma delta T-cell response to cellular stress signals expressed by tumor cells makes them promising candidates for cancer immunotherapy. The proof of concept for clinical scale propagation of polyclonal γδ T-cell lines with efficient in vitro and in vivo response against cancer is an important step in this direction. ©2014 AACR.


Chavanis P.-H.,French National Center for Scientific Research
Physica A: Statistical Mechanics and its Applications | Year: 2012

Starting from the Liouville equation and using a BBGKY-like hierarchy, we derive a kinetic equation for the point vortex gas in two-dimensional (2D) hydrodynamics, taking two-body correlations and collective effects into account. This equation is valid at the order 1N where N≫1 is the number of point vortices in the system (we assume that their individual circulation scales like γ∼1N). It gives the first correction, due to graininess and correlation effects, to the 2D Euler equation that is obtained for N→+∞. For axisymmetric distributions, this kinetic equation does not relax towards the Boltzmann distribution of statistical equilibrium. This implies either that (i) the "collisional" (correlational) relaxation time is larger than N tD, where tD is the dynamical time, so that three-body, four-body⋯ correlations must be taken into account in the kinetic theory, or (ii) that the point vortex gas is non-ergodic (or does not mix well) and will never attain statistical equilibrium. Non-axisymmetric distributions may relax towards the Boltzmann distribution on a timescale of the order N tD due to the existence of additional resonances, but this is hard to prove from the kinetic theory. On the other hand, 2D Euler unstable vortex distributions can experience a process of "collisionless" (correlationless) violent relaxation towards a non-Boltzmannian quasistationary state (QSS) on a very short timescale of the order of a few dynamical times. This QSS is possibly described by the Miller-Robert-Sommeria (MRS) statistical theory which is the counterpart, in the context of two-dimensional hydrodynamics, of the Lynden-Bell statistical theory of violent relaxation in stellar dynamics. © 2012 Elsevier B.V. All rights reserved.


Chavanis P.-H.,French National Center for Scientific Research
Physica A: Statistical Mechanics and its Applications | Year: 2012

We develop a kinetic theory of systems with long-range interactions taking collective effects and spatial inhomogeneity into account. Starting from the Klimontovich equation and using a quasilinear approximation, we derive a Lenard-Balescu-type kinetic equation written in angle-action variables. We confirm the result obtained by Heyvaerts [Heyvaerts, Mon. Not. R. Astron. Soc. 407, 355 (2010)] who started from the Liouville equation and used the BBGKY hierarchy truncated at the level of the two-body distribution function (i.e., neglecting three-body correlations). When collective effects are ignored, we recover the Landau-type kinetic equation obtained in our previous papers [P.H. Chavanis, Physica A 377, 469 (2007); J. Stat. Mech., P05019 (2010)]. We also consider the relaxation of a test particle in a bath of field particles. Its stochastic motion is described by a Fokker-Planck equation written in angle-action variables. We determine the diffusion tensor and the friction force by explicitly calculating the first and second order moments of the increment of action of the test particle from its equations of motion, taking collective effects into account. This generalizes the expressions obtained in our previous works. We discuss the scaling with N of the relaxation time for the system as a whole and for a test particle in a bath. © 2012 Elsevier B.V. All rights reserved.


Gillet D.,French National Center for Scientific Research
Astronomy and Astrophysics | Year: 2013

Context. Discovered in 1907, the Blazhko effect is a modulation of the light variations of about half of the RR Lyr stars. It has remained unexplained for over 100 years, despite more than a dozen proposed explanations. Today it represents an ongoing challenge in variable-star research. Aims. We propose a new explanation. It is based on the observation that Blazhko stars seem to be located in the region of the instability strip where fundamental and first overtone modes are excited at the same time. Methods. An analysis of nonlinear and nonadiabatic pulsation models of RR Lyrae stars shows that a specific shock (called first overtone shock) may be generated by the perturbation of the fundamental mode by the transient first overtone. Results. The first overtone shock induces a sharp slowdown of the atmospheric layers during their infalling motion. This slowdown in turn affects the compression rate on the deep photospheric layers and the intensity of the κ-mechanism. After an amplification phase, the intensity of the main shock wave before the Blazhko maximum becomes high enough to provoke large radiative losses. These can be at least equal to 70% of the total energy flux of the shock, which induces a small decrease of the effective temperature at each pulsation cycle. In these conditions, when the intensity of the main shock reaches its highest critical value at the Blazhko maximum, it completely desynchronizes the motion of the phostospheric layers. At this point, the atmosphere relaxes and reaches a new synchronous state that occurs at the Blazhko minimum. Conclusions. The combined effects of these two shocks on the atmosphere cause the Blazhko effect. This effect can only exist if the first overtone mode is excited together with the fundamental mode. Because the involved physical mechanisms are essentially nonlinear (shocks, atmospheric dynamics, radiative losses, mode excitations), the Blazhko process is expected to be unstable and irregular. Consequently, the Blazhko process has a specific random nature that is in contrast with the pulsation of non-Blazhko stars. © ESO 2013.


From MIS 5 to 3, Western Europe has seen important climate changes that shaped the environments inhabited by past human societies. As a consequence, climate is often considered as a key factor in explaining the cultural and biological events of the Middle and Early Upper Paleolithic (e.g. changes in lithic technology and mobility strategies during the Mousterian, Neanderthal extinction, emergence of "modern" behavior, onset of the Upper Paleolithic). However, the exact impact of Upper Pleistocene global climatic changes on terrestrial ecosystems is still poorly documented. Remarkably, large predators can be affected by changes in herbivore communities because they result in fluctuations of the ecosystem's carrying capacity. Paleoenvironmental reconstructions that include data on faunal dynamics are still rare, so that questions concerning human-environment interactions cannot be properly discussed.Building on a review of modern analogs for ungulate biomass, this paper tries to reconstruct changes in carrying capacity of terrestrial ecosystems in southwestern France. In order to assess the importance of these biomass fluctuations for large predators, cave hyena paleodemographic shifts are estimated through Bayesian analyses of the chronological distribution of hyena den assemblages. Comparison between these two proxies (ungulate biomass modern analogs and cave hyena paleodemography) allows for an adequate discussion of the impact of ungulate biomass fluctuations on large predators.Results show that fluctuations in ungulate biomass are noticeable, with an increase at the end of the Mousterian and a significant drop at the beginning of the Aurignacian. These changes likely had a pronounced impact on large predator populations, as interesting parallels can be identified between the demographic history of hyenas and reconstructed fluctuations in carrying capacity. These results bring new insights on the role played by MIS 3 environmental changes in the demise of the last Neanderthals and the emergence of the Upper Paleolithic in southwestern France. © 2013 Elsevier Ltd and INQUA.


Brugere A.,French National Center for Scientific Research
Quaternary International | Year: 2014

In southern Moravia (Czech Republic), the Gravettian groups based part of their economic system on mammoth exploitation between 29 and 24,000 uncal. BP. The origin of mammoth bone accumulations at several sites of this area has been debated since the discovery of Předmosti in the middle of the 19th century. Study of the Milovice faunal remains demonstrated that hunting was the main, if not the only, procurement pattern. Considering the published data from Pavlov I (Moravia) and the reconstructed age profiles based on mammoth teeth, we suggest the proboscidean was hunted at that site. More unexpectedly, two hunting strategies have been identified in the Pavlov Hills area: one affecting subadults and adults, and the second one affecting young and subadult individuals. Chronology and the physical condition of the mammoth population are not convincing arguments to explain such a difference. Human behaviour was involved, and we suggest economic goals related to mammoth resources were the reasons for such a hunting selection. Nevertheless, it is unclear whether season or human group identity could have produced this behaviour. © 2014 Elsevier Ltd and INQUA.


Schneider K.,French National Center for Scientific Research | Schneider K.,Aix - Marseille University | Vasilyev O.V.,University of Colorado at Boulder
Annual Review of Fluid Mechanics | Year: 2010

This article reviews state-of-the-art adaptive, multiresolution wavelet methodologies for modeling and simulation of turbulent flows with various examples. Different numerical methods for solving the Navier-Stokes equations in adaptive wavelet bases are described. We summarize coherent vortex extraction methodologies, which utilize the efficient wavelet decomposition of turbulent flows into space-scale contributions, and present a hierarchy of wavelet-based turbulence models. Perspectives for modeling and computing industrially relevant flows are also given. Copyright © 2010 by Annual Reviews. All rights reserved.


Bronner C.,French National Center for Scientific Research
Science Signaling | Year: 2011

Inheritance of DNA methylation patterns is a key mechanism involved in epigenetic cell memory transmission from mother cell to daughter cell. This occurs due to cooperation between the DNA methyltransferase DNMT1 and the ubiquitin ligase UHRF1 (ubiquitin-like, containing plant homeo domain and RING finger 1) in a macromolecular complex. Newly identified members of this complex are the acetyltransferase Tip60 (Tat-interactive protein) and the deubiquitinase HAUSP (herpes virus-associated ubiquitin specific protease), which exert tight regulation of DNMT1 abundance through a ubiquitylation-dependent process. It is important to determine how all of these actors communicate with each other and what signals coordinate their communication. In the case of DNMT1, the balance of UHRF1 and HAUSP activities might be influenced by the local environment, such as histone code, cell-cycle status, and local DNA methylation status.


Vert G.,French National Center for Scientific Research
Developmental cell | Year: 2011

During the past two decades, molecular biologists and geneticists have deconstructed intracellular signaling pathways in individual cells, revealing a great deal of crosstalk among key signaling pathways in the animal kingdom. Fewer examples have been reported in plants, which appear to integrate multiple signals on the promoters of target genes or to use gene family members to convey signal-specific output. For both plants and animals, the question now is whether the "crosstalk" is biologically relevant or simply noise in the experimental system. To minimize such noise, we suggest studying signaling pathways in the context of intact organisms with minimal perturbation from the experimenter. Copyright © 2011 Elsevier Inc. All rights reserved.


Betancur C.,University Pierre and Marie Curie | Betancur C.,French National Center for Scientific Research
Brain Research | Year: 2011

There is increasing evidence that autism spectrum disorders (ASDs) can arise from rare highly penetrant mutations and genomic imbalances. The rare nature of these variants, and the often differing orbits of clinical and research geneticists, can make it difficult to fully appreciate the extent to which we have made progress in understanding the genetic etiology of autism. In fact, there is a persistent view in the autism research community that there are only a modest number of autism loci known. We carried out an exhaustive review of the clinical genetics and research genetics literature in an attempt to collate all genes and recurrent genomic imbalances that have been implicated in the etiology of ASD. We provide data on 103 disease genes and 44 genomic loci reported in subjects with ASD or autistic behavior. These genes and loci have all been causally implicated in intellectual disability, indicating that these two neurodevelopmental disorders share common genetic bases. A genetic overlap between ASD and epilepsy is also apparent in many cases. Taken together, these findings clearly show that autism is not a single clinical entity but a behavioral manifestation of tens or perhaps hundreds of genetic and genomic disorders. Increased recognition of the etiological heterogeneity of ASD will greatly expand the number of target genes for neurobiological investigations and thereby provide additional avenues for the development of pathway-based pharmacotherapy. Finally, the data provide strong support for high-resolution DNA microarrays as well as whole-exome and whole-genome sequencing as critical approaches for identifying the genetic causes of ASDs. © 2010 Elsevier B.V. All rights reserved.


Bruneau C.,French National Center for Scientific Research
Topics in Organometallic Chemistry | Year: 2013

The formation of carbon-oxygen bond upon addition of O-nucleophiles to unsaturated molecules is very attractive as it represents an atom economical strategy to prepare a variety of saturated compounds from olefins and vinylic derivatives from alkynes. Group 8 metals, especially ruthenium have provided an important contribution in this field. We report here on iron- and ruthenium-catalyzed addition of nucleophiles to unsaturated systems. As additions to alkenes are still scarce with these metals and the use of iron catalysts is limited, the main part of the chapter is dedicated to addition of carbamates, carboxylic acids, alcohols and water to triple bonds with ruthenium catalysts. © 2013 Springer-Verlag Berlin Heidelberg.


Manceau A.,French National Center for Scientific Research
Clay Minerals | Year: 2010

The risk of overfitting pair distribution function (PDF) data for highly defective material (Farrow et al., 2007) is illuminated with the example of the nanocrystalline hydrous ferric oxyhydroxide, ferrihydrite. Two structural models have been published by Michel et al. (2007, 2010) using this method, both of which contradict the standard 'ferrihydrits' model established by X-ray diffraction (Drits et al., 1993), and confirmed by single-crystal electron nanodiffraction (Janney et al., 2001) and neutron diffraction (Jansen et al., 2002). Although PDF data are reproduced equally well with the two regression models, neither model is realistic: the first (fhyd6) violates Pauling's 2 nd rule, and the second (ferrifh), Pauling's 3rd rule. © 2010 Mineralogical Society.


Mucchielli L.,French National Center for Scientific Research
British Journal of Criminology | Year: 2010

This text suggests a general sociological model to interpret the development of violent behaviours in interpersonal relationships, based on the French case. An original synthesis of various types of data is used: police and judicial statistics, victimization and self-reported surveys, demographic and socio-economic data. The model links together five processes at work in French society: a societal process of pacification, a political and legal process of criminalization, a process of judiciarization of everyday life conflicts, a socio-economic process of competition for consumer goods, and a process of economic, social and spatial segregation. This model also attempts to link many theoretical contributions that have shaped the history of sociology and criminology. copyright The Author 2010. Published by Oxford University Press on behalf of the Centre for Crime and Justice Studies (ISTD). All rights reserved.2010 © The Author 2010. Published by Oxford University Press on behalf of the Centre for Crime and Justice Studies (ISTD). All rights reserved.


Tan X.,Nanjing University of Aeronautics and Astronautics | Triggs B.,French National Center for Scientific Research
IEEE Transactions on Image Processing | Year: 2010

Making recognition more reliable under uncontrolled lighting conditions is one of the most important challenges for practical face recognition systems. We tackle this by combining the strengths of robust illumination normalization, local texture-based face representations, distance transform based matching, kernel-based feature extraction and multiple feature fusion. Specifically, we make three main contributions: 1) We present a simple and efficient preprocessing chain that eliminates most of the effects of changing illumination while still preserving the essential appearance details that are needed for recognition; 2) We introduce local ternary patterns (LTP), a generalization of the local binary pattern (LBP) local texture descriptor that is more discriminant and less sensitive to noise in uniform regions, and we show that replacing comparisons based on local spatial histograms with a distance transform based similarity metric further improves the performance of LBP/LTP based face recognition; and 3) We further improve robustness by adding Kernel principal component analysis (PCA) feature extraction and incorporating rich local appearance cues from two complementary sourcesGabor wavelets and LBPshowing that the combination is considerably more accurate than either feature set alone. The resulting method provides state-of-the-art performance on three data sets that are widely used for testing recognition under difficult illumination conditions: Extended Yale-B, CAS-PEAL-R1, and Face Recognition Grand Challenge version 2 experiment 4 (FRGC-204). For example, on the challenging FRGC-204 data set it halves the error rate relative to previously published methods, achieving a face verification rate of 88.1% at 0.1% false accept rate. Further experiments show that our preprocessing method outperforms several existing preprocessors for a range of feature sets, data sets and lighting conditions. © 2010 IEEE.


Rebotier J.,French National Center for Scientific Research
Global Environmental Change | Year: 2012

In risk studies, a large scope of approaches has already been defined, from hazard-centered to socially rooted analysis; being social scientists' focus on vulnerability more obvious from the late 1960s on. The present epistemological article locates risk causes in society and states that the production of risks is two fold: these are both material and discursive. The conceptual proposal of the article consists of setting an integrative framework that accounts for material aspects of risk as well as for the performative dimensions of its discourses, representations and conceptions. By performativity we mean that discourses and representations do not only reflect what people see or have in mind, but that they also operate the world and make things exist, having concrete consequences in society and its relations with the environment. The proposed framework is called the territorialization-of-risk framework and requires contextualizing and politicizing risk. We state that such framework lays epistemological and methodological groundwork for such a perspective. Territories are viewed as social constructions that are more than bounded pieces of space where an authority takes place. They are spaces where competing social meanings and identification are ascribed, and their making accounts for both material and ideal social drivers that also do intervene in the production of risk. Drawing on different Latin-American cities' case studies, and mainly on the case of Caracas as former PhD fieldwork, the territorialization-of-risk allows asking critical questions related with power relations, social status, identity and discourses. Actually, risk appears to be the result of a social (both material and ideal) production as it contributes to the shaping of society. It is an outcome and a driver of society at the same time. The territorialization-of-risk framework sheds the light on the importance of non-material aspects in framing risk, as well as on the factual and discursive consequences of its management and policy. © 2011 Elsevier Ltd.


Laurencot P.,French National Center for Scientific Research | Walker C.,Leibniz University of Hanover
Archive for Rational Mechanics and Analysis | Year: 2013

We investigate a free boundary problem describing small deformations in a membrane based model of electrostatically actuated microelectromechanical systems (MEMS). The existence of stationary solutions is established for small voltage values and non-existence is obtained for high voltage values. We give a justification of the widely studied narrow-gap model by showing that steady state solutions of the free boundary problem converge toward stationary solutions of the narrow-gap model when the aspect ratio of the device tends to zero. © 2012 Springer-Verlag.


Labat D.,French National Center for Scientific Research
Journal of Hydrology | Year: 2010

It is now well recognized that large scale atmospheric and oceanic circulations fluctuations have a strong impact on the global hydrological cycle. Because of the complexity of the hydrological processes over continental surfaces, it is often proposed to deduce this variability from insightful analysis of river discharge time series since it integrates a large number of climatological parameters such as precipitation, temperature and evapotranspiration but also land cover evolutions. However, up to now these studies remain restricted to basin or regional scale and no larger scale of these relationships between climate and continental hydrology has yet been proposed. Such relationships are helpful in the global understanding of the non-stationary relationships that exist between ocean and atmosphere mean conditions and freshwater discharge integrated at a continental scale. Based on a recent estimation of annual continental freshwater discharge over the 1876-1994 interval, a cross wavelet analysis (including cross wavelet spectrum and wavelet coherence) together with selected climate indices (North Atlantic Oscillation - NAO, Arctic Oscillation - AO, Southern Oscillation Index - SOI, Pacific Decadal Oscillation - PDO and NINO3.4 - Pacific mean Sea Surface Temperature) is exposed. The relationships are characterised by a high temporal unstationarity but three main bands of variability are identified and analyzed: 2-10-year, 10-20-year and 20-30-year variability. The five continents exhibit a temporal correlation with the five indexes sometimes on the entire interval but more often on restricted intervals. NAO and AO impact the 4-15-year variability of the five continents discharge. SOI impacts the 2-7-year variability of all continent discharge variability except Europe. NINO3.4 impacts the 2-8-year variability of Africa, Asia and South America discharge but also the 10-20-year variability of Africa, Asia, North America and South America discharge variability. Finally, PDO impacts the ∼10-30-year variability of Asia, Europe, North America and South America discharge variability. These results could allow a first order prediction of the future evolutions of continental water resources from a climate change point of view in relationship with climate scenarios of evolution of atmospheric and sea surface temperature conditions. © 2010 Elsevier B.V. All rights reserved.


Chavanis P.-H.,French National Center for Scientific Research | Harko T.,University of Hong Kong
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2012

We analyze the possibility that due to their superfluid properties some compact astrophysical objects may contain a significant part of their matter in the form of a Bose-Einstein condensate. To study the condensate we use the Gross-Pitaevskii equation with arbitrary nonlinearity. By introducing the Madelung representation of the wave function, we formulate the dynamics of the system in terms of the continuity and hydrodynamic Euler equations. The nonrelativistic and Newtonian Bose-Einstein gravitational condensate can be described as a gas, whose density and pressure are related by a barotropic equation of state. In the case of a condensate with quartic nonlinearity, the equation of state is polytropic with index one. In the framework of the Thomas-Fermi approximation the structure of the Newtonian gravitational condensate is described by the Lane-Emden equation, which can be exactly solved. The case of the rotating condensate is briefly discussed. General relativistic configurations with quartic nonlinearity are studied numerically with both nonrelativistic and relativistic equations of state, and the maximum mass of the stable configuration is determined. Condensates with particle masses of the order of two neutron masses (Cooper pair) and scattering length of the order of 10-20fm have maximum masses of the order of 2M, maximum central density of the order of 0.1-0.3×1016g/cm3 and minimum radii in the range of 10-20km. In this way we obtain a large class of stable astrophysical objects, whose basic astrophysical parameters (mass and radius) sensitively depend on the mass of the condensed particle, and on the scattering length. We also propose that the recently observed neutron stars with masses in the range of 2-2.4M are Bose-Einstein condensate stars. We discuss the connection of our results with previous boson star models based on scalar field theory. © 2012 American Physical Society.


Klumperman J.,University Utrecht | Raposo G.,University Pierre and Marie Curie | Raposo G.,French National Center for Scientific Research
Cold Spring Harbor Perspectives in Biology | Year: 2014

Live-cell imaging reveals the endolysosomal system as a complex and highly dynamic network of interacting compartments. Distinct types of endosomes are discerned by kinetic, molecular, and morphological criteria. Although none of these criteria, or combinations thereof, can capture the full complexity of the endolysosomal system, they are extremely useful for experimental purposes. Some membrane domain specializations and specific morphological characteristics can only be seen by ultrastructural analysis after preparation for electron microscopy (EM). Immuno-EM allows a further discrimination of seemingly identical compartments by their molecular makeup. In this review we provide an overview of the ultrastructural characteristics and membrane organization of endosomal compartments, along with their organizing machineries. ©2014 Cold Spring Harbor Laboratory Press; all rights reserved.


Taylor M.J.,Medical Research Council Laboratory of Molecular Biology | Perrais D.,Institut Universitaire de France | Perrais D.,French National Center for Scientific Research | Merrifield C.J.,Medical Research Council Laboratory of Molecular Biology
PLoS Biology | Year: 2011

Dual colour total internal reflection fluorescence microscopy is a powerful tool for decoding the molecular dynamics of clathrin-mediated endocytosis (CME). Typically, the recruitment of a fluorescent protein-tagged endocytic protein was referenced to the disappearance of spot-like clathrin-coated structure (CCS), but the precision of spot-like CCS disappearance as a marker for canonical CME remained unknown. Here we have used an imaging assay based on total internal reflection fluorescence microscopy to detect scission events with a resolution of ~2 s. We found that scission events engulfed comparable amounts of transferrin receptor cargo at CCSs of different sizes and CCS did not always disappear following scission. We measured the recruitment dynamics of 34 types of endocytic protein to scission events: Abp1, ACK1, amphiphysin1, APPL1, Arp3, BIN1, CALM, CIP4, clathrin light chain (Clc), cofilin, coronin1B, cortactin, dynamin1/2, endophilin2, Eps15, Eps8, epsin2, FBP17, FCHo1/2, GAK, Hip1R, lifeAct, mu2 subunit of the AP2 complex, myosin1E, myosin6, NECAP, N-WASP, OCRL1, Rab5, SNX9, synaptojanin2β1, and syndapin2. For each protein we aligned ~1,000 recruitment profiles to their respective scission events and constructed characteristic "recruitment signatures" that were grouped, as for yeast, to reveal the modular organization of mammalian CME. A detailed analysis revealed the unanticipated recruitment dynamics of SNX9, FBP17, and CIP4 and showed that the same set of proteins was recruited, in the same order, to scission events at CCSs of different sizes and lifetimes. Collectively these data reveal the fine-grained temporal structure of CME and suggest a simplified canonical model of mammalian CME in which the same core mechanism of CME, involving actin, operates at CCSs of diverse sizes and lifetimes. © 2011 Taylor et al.


Veenstra J.A.,French National Center for Scientific Research
General and Comparative Endocrinology | Year: 2015

Transcriptomes of the crayfish Procambarus clarkii were analyzed for the presence of transcripts encoding neurohormones, neuropeptides and their receptors. A total of 58 different transcripts were found to encode such ligands and another 82 for their receptors. A very large number of the neuropeptide transcripts appeared to be complete and for those that were not only small parts seemed to be lacking. Transcripts for the neuropeptide GPCRs as well as for the putative receptors for insulin, neuroparsin and eclosion hormone were often also complete or almost so. Of particular interest is the presence of three different neuroparsin genes and two putative neuroparsin receptors. There are also three pigment dispersing hormones as well three likely receptors for these neuropeptides. CNMamide, calcitonin, CCRFamide, natalisin, trissin and relaxin appear to be new crustacean neuropeptides. The recently identified crustacean female sex hormone was also found and in the crayfish appears to be not only expressed in the eyestalk, but in the ovary as well (though not in the testis). Interestingly, there are two other proteins in the crayfish with a structure similar to crustacean female sex hormone, that could be precursors of neurohormones, but these are not expressed by the ovary. The ovary also appears to contain significant numbers of transcripts encoding pigment dispersing hormones, CNMamide as well as glycoprotein B5, but not glycoprotein A2. © 2015 Elsevier Inc.


Drane P.,French National Center for Scientific Research
Genes and Development | Year: 2010

The histone variant H3.3 marks active chromatin by replacing the conventional histone H3.1. In this study, we investigate the detailed mechanism of H3.3 replication-independent deposition. We found that the death domain-associated protein DAXX and the chromatin remodeling factor ATRX (α-thalassemia/mental retardation syndrome protein) are specifically associated with the H3.3 deposition machinery. Bacterially expressed DAXX has a marked binding preference for H3.3 and assists the deposition of (H3.3-H4) 2 tetramers on naked DNA, thus showing that DAXX is a H3.3 histone chaperone. In DAXX-depleted cells, a fraction of H3.3 was found associated with the replication-dependent machinery of deposition, suggesting that cells adapt to the depletion. The reintroduced DAXX in these cells colocalizes with H3.3 into the promyelocytic leukemia protein (PML) bodies. Moreover, DAXX associates with pericentric DNA repeats, and modulates the transcription from these repeats through assembly of H3.3 nucleosomes. These findings establish a new link between the PML bodies and the regulation of pericentric DNA repeat chromatin structure. Taken together, our data demonstrate that DAXX functions as a bona fide histone chaperone involved in the replication-independent deposition of H3.3. © 2010 by Cold Spring Harbor Laboratory Press.


Van Regenmortela M.H.V.,French National Center for Scientific Research
Journal of Molecular Recognition | Year: 2011

In spite of 25 years of intensive research, no effective human immunodeficiency virus type 1 (HIV-1) vaccine has yet been developed. One reason for this is that investigators have concentrated mainly on the structural analysis of HIV-1 antigens because they assumed that it should be possible to deduce vaccine-relevant immunogens from the structure of viral antigens bound to neutralizing monoclonal antibodies. This unwarranted assumptionarises from misconceptions regarding the nature of protein epitopes and from the belief that it is justified to extrapolate from the antigenicity to the immunogenicity of proteins. Although the structure of the major HIV-1 antigenic sites has been elucidated, this knowledge has been of little use for designing an HIV-1 vaccine. Little attention has been given to the fact that protective immune responses tend to be polyclonal and involve antibodies directed to several different epitopes. It is concluded that only trial and error,empirical investigations using numerous immunization protocols may eventually allow us toidentify which mixtures of immunogens are likely to be the best candidates for an HIV-1 vaccine. © 2011 John Wiley & Sons, Ltd.


Lichten M.,U.S. National Cancer Institute | De Massy B.,French National Center for Scientific Research
Cell | Year: 2011

Two high-resolution maps of meiotic recombination initiation sites across the genomes of budding yeast and mice illuminate broad similarities in the control of meiotic recombination in these diverse species but also highlight key differences. These studies offer new insights into the relationships between recombination, chromosome structure, and genome evolution. © 2011 Elsevier Inc.


Clastres C.,French National Center for Scientific Research
Energy Policy | Year: 2011

The deployment of smart grids in electricity systems has given rise to much interdisciplinary research. The new technology is seen as an additional instrument available to States to achieve targets for promoting competition, increasing the safety of electricity systems and combating climate change. But the boom in smart grids also raises many economic questions. Public policies will need to be adapted, firstly to make allowance for the potential gains from smart grids and the associated information flow, and secondly to regulate the new networks and act as an incentive for investors. The new competitive offerings and end-user pricing systems will contribute to improving allocative and productive efficiency, while minimizing the risks of market power. With real-time data on output and consumption, generators and consumers will be able to adapt to market conditions. Lastly smart grids will boost the development of renewable energy sources and new technologies, by assisting their integration and optimal use. © 2011 Elsevier Ltd.


Probst A.V.,French Institute of Health and Medical Research | Almouzni G.,University Pierre and Marie Curie | Almouzni G.,French National Center for Scientific Research
Trends in Genetics | Year: 2011

Heterochromatin at pericentric satellites, characterized by a specific chromatin signature and chromocenter organization, is of paramount importance for genome function. Re-establishment of this organization after fertilization takes place in the context of genome-wide epigenetic reprogramming. We review how the asymmetry in histone variants and post-translational modifications between paternal and maternal genomes and their respective pericentric heterochromatin domains evolve during early cleavage stages in mouse. We draw a parallel between these data and the burst of pericentric satellite transcription that occurs concomitantly with the dynamic reorganization of the pericentric domains into chromocenters in two-cell stage embryos. Based on this new angle, we propose that a crucial developmental transition at the two-cell stage allows chromocenter formation by involving non-coding satellite transcripts to trigger specific chromatin changes. © 2011 Elsevier Ltd.


Vert G.,French National Center for Scientific Research | Vert G.,Salk Institute for Biological Studies | Chory J.,Salk Institute for Biological Studies
Developmental Cell | Year: 2011

During the past two decades, molecular biologists and geneticists have deconstructed intracellular signaling pathways in individual cells, revealing a great deal of crosstalk among key signaling pathways in the animal kingdom. Fewer examples have been reported in plants, which appear to integrate multiple signals on the promoters of target genes or to use gene family members to convey signal-specific output. For both plants and animals, the question now is whether the " crosstalk" is biologically relevant or simply noise in the experimental system. To minimize such noise, we suggest studying signaling pathways in the context of intact organisms with minimal perturbation from the experimenter. © 2011 Elsevier Inc.


Soria G.,Chromatin | Almouzni G.,French National Center for Scientific Research
Cell Cycle | Year: 2013

Heterochromatin protein 1 paralogs (HP 1α, β and γ in mammals) are not only central in heterochromatin organization, but have also been linked to transcriptional activation at euchromatic regions, maintenance of telomere stability and, most recently, to the DNA damage response (DDR). However, how HP 1 proteins contribute to the DDR at a molecular level, and whether HP 1 paralogs within the same organism, as well as their respective orthologs, have overlapping or unique roles in the DDR, remain to be elucidated. Herein, we have combined the analysis of the efficiency and kinetics of recruitment of key repair proteins to sites of DNA damage with specific DNA repair assays to demonstrate that human HP1 paralogs differentially modulate homology-directed repair (HDR) pathways, including homologous recombination (HR) and single-strand annealing (SSA). We find that while HP 1α and β stimulate HR and SSA , HP1γ has an inhibitory role. In addition, we show that the stimulatory role of HP 1α and β in HDR is linked to the DNA-end resection step of DNA breaks, through the promotion of RPA loading and phosphorylation at damage sites. Altogether, our findings provide mechanistic insight into how human HP 1 proteins participate in the recombination process, emerging as important chromatin regulators during HDR. © 2013 Landes Bioscience.


Blum M.G.B.,French National Center for Scientific Research | Francois O.,Ecole Polytechnique - Palaiseau
Statistics and Computing | Year: 2010

Approximate Bayesian inference on the basis of summary statistics is well-suited to complex problems for which the likelihood is either mathematically or computationally intractable. However the methods that use rejection suffer from the curse of dimensionality when the number of summary statistics is increased. Here we propose a machine-learning approach to the estimation of the posterior density by introducing two innovations. The new method fits a nonlinear conditional heteroscedastic regression of the parameter on the summary statistics, and then adaptively improves estimation using importance sampling. The new algorithm is compared to the state-of-the-art approximate Bayesian methods, and achieves considerable reduction of the computational burden in two examples of inference in statistical genetics and in a queueing model. © Springer Science+Business Media, LLC 2009.


Poilblanc D.,French National Center for Scientific Research
Physical Review B - Condensed Matter and Materials Physics | Year: 2011

Thermalization plays a central role in out-of-equilibrium physics of ultracold atoms or electronic transport phenomena. On the other hand, entanglement concepts have proven to be extremely useful to investigate quantum phases of matter. Here, it is argued that bipartite entanglement measures provide key information on out-of-equilibrium states and might therefore offer stringent thermalization criteria. This is illustrated by considering a global quench in an (extended) XXZ spin-1/2 chain across its (zero-temperature) quantum critical point. A nonlocal bipartition of the chain preserving translation symmetry is proposed. The time evolution after the quench of the reduced density matrix of the half-system is computed and its associated (time-dependent) entanglement spectrum is analyzed. Generically, the corresponding entanglement entropy quickly reaches a "plateau" after a short transient regime. However, in the case of the integrable XXZ chain, the low-energy entanglement spectrum still reveals strong time fluctuations. In addition, its infinite-time average shows strong deviations from the spectrum of a Boltzmann thermal density matrix. In contrast, when the integrability of the model is broken (by small next-nearest-neighbor couplings), the entanglement spectra of the time average and thermal density matrices become remarkably similar. © 2011 American Physical Society.


Mouquet H.,Institute Pasteur Paris | Mouquet H.,French National Center for Scientific Research
Trends in Immunology | Year: 2014

In rare cases, B cells can supply HIV-1-infected individuals with unconventional antibodies equipped to neutralize the wide diversity of viral variants. Innovations in single-cell cloning, high-throughput sequencing, and structural biology methods have enabled the capture and thorough characterization of these exceptionally potent broadly neutralizing antibodies (bNAbs). Here, I review the recent findings in humoral responses to HIV-1, focusing on the interplay between naturally occurring bNAbs and the virus both at systemic and mucosal levels. In this context, I discuss how an improved understanding of bNAb generation may provide invaluable insight into the fundamental mechanisms governing adaptive B cell responses to viruses, and how this knowledge is currently contributing to the development of vaccine and therapeutic strategies against HIV-1. © 2014 Elsevier Ltd.


Jensen M.R.,CNRS Institute of Pharmacology and Structural Biology | Ruigrok R.W.H.,French National Center for Scientific Research | Blackledge M.,CNRS Institute of Pharmacology and Structural Biology
Current Opinion in Structural Biology | Year: 2013

There is growing interest in the development of physical methods to study the conformational behaviour and biological activity of intrinsically disordered proteins (IDPs). In this review recent advances in the elucidation of quantitative descriptions of disordered proteins from nuclear magnetic resonance spectroscopy are presented. Ensemble approaches are particularly well adapted to map the conformational energy landscape sampled by the protein at atomic resolution. Significant advances in development of calibrated approaches to the statistical representation of the conformational behaviour of IDPs are presented, as well as applications to some biologically important systems where disorder plays a crucial role. © 2013 Elsevier Ltd.


Marks M.S.,University of Pennsylvania | Heijnen H.F.G.,Laboratory of Clinical Chemistry and Haematology | Raposo G.,University Pierre and Marie Curie | Raposo G.,French National Center for Scientific Research
Current Opinion in Cell Biology | Year: 2013

Lysosome-related organelles (LROs) comprise a group of cell type-specific subcellular compartments with unique composition, morphology and structure that share some features with endosomes and lysosomes and that function in varied processes such as pigmentation, hemostasis, lung plasticity and immunity. In recent years, studies of genetic diseases in which LRO functions are compromised have provided new insights into the mechanisms of LRO biogenesis and the regulated secretion of LRO contents. These insights have revealed previously unappreciated specialized endosomal sorting processes in all cell types, and are expanding our views of the plasticity of the endosomal and secretory systems in adapting to cell type-specific needs. © 2013 Elsevier Ltd.


Giege R.,French National Center for Scientific Research
FEBS Journal | Year: 2013

Protein crystallization has been known since 1840 and can prove to be straightforward but, in most cases, it constitutes a real bottleneck. This stimulated the birth of the biocrystallogenesis field with both 'practical' and 'basic' science aims. In the early years of biochemistry, crystallization was a tool for the preparation of biological substances. Today, biocrystallogenesis aims to provide efficient methods for crystal fabrication and a means to optimize crystal quality for X-ray crystallography. The historical development of crystallization methods for structural biology occurred first in conjunction with that of biochemical and genetic methods for macromolecule production, then with the development of structure determination methodologies and, recently, with routine access to synchrotron X-ray sources. Previously, the identification of conditions that sustain crystal growth occurred mostly empirically but, in recent decades, this has moved progressively towards more rationality as a result of a deeper understanding of the physical chemistry of protein crystal growth and the use of idea-driven screening and high-throughput procedures. Protein and nucleic acid engineering procedures to facilitate crystallization, as well as crystallization methods in gelled-media or by counter-diffusion, represent recent important achievements, although the underlying concepts are old. The new nanotechnologies have brought a significant improvement in the practice of protein crystallization. Today, the increasing number of crystal structures deposited in the Protein Data Bank could mean that crystallization is no longer a bottleneck. This is not the case, however, because structural biology projects always become more challenging and thereby require adapted methods to enable the growth of the appropriate crystals, notably macromolecular assemblages. In the early time of biochemistry, crystallization was a tool for protein purification. It became a bottleneck when crystals were needed for X-ray crystallography. This stimulated the birth of biocrystallogenesis as a science. The review outlines the history of the field, discusses how it developed together with structural biology and reviews its advances in the present era of structural genomics. © 2013 FEBS.


Schapira A.H.V.,University College London | Olanow C.W.,Mount Sinai School of Medicine | Greenamyre J.T.,University of Pittsburgh | Bezard E.,Institut Universitaire de France | Bezard E.,French National Center for Scientific Research
The Lancet | Year: 2014

Summary Several important advances have been made in our understanding of the pathways that lead to cell dysfunction and death in Parkinson's disease and Huntington's disease. These advances have been informed by both direct analysis of the post-mortem brain and by study of the biological consequences of the genetic causes of these diseases. Some of the pathways that have been implicated so far include mitochondrial dysfunction, oxidative stress, kinase pathways, calcium dysregulation, inflammation, protein handling, and prion-like processes. Intriguingly, these pathways seem to be important in the pathogenesis of both diseases and have led to the identification of molecular targets for candidate interventions designed to slow or reverse their course. We review some recent advances that underlie putative therapies for neuroprotection in Parkinson's disease and Huntington's disease, and potential targets that might be exploited in the future. Although we will need to overcome important hurdles, especially in terms of clinical trial design, we propose several target pathways that merit further study. In Parkinson's disease, these targets include agents that might improve mitochondrial function or increase degradation of defective mitochondria, kinase inhibitors, calcium channel blockers, and approaches that interfere with the misfolding, templating, and transmission of α-synuclein. In Huntington's disease, strategies might also be directed at mitochondrial bioenergetics and turnover, the prevention of protein dysregulation, disruption of the interaction between huntingtin and p53 or huntingtin-interacting protein 1 to reduce apoptosis, and interference with expression of mutant huntingtin at both the nucleic acid and protein levels. © 2014 Elsevier Ltd.


To respond to the changing needs of the chemical and related industries in order both to meet today's economy demands and to remain competitive in global trade, a modern chemical engineering is vital to satisfy both the market requirements for specific nano and microscale end-use properties of products, and the social and environmental constraints of industrial meso and macroscale processes. Thus an integrated system approach of complex multidisciplinary, non-linear, non-equilibrium processes and phenomena occurring on different length and time scales of the supply chain is required. That is, a good understanding of how phenomena at a smaller length-scale relates to properties and behaviour at a longer length-scale is necessary (from the molecular-scale to the production-scales). This has been defined as the triplet "molecular Processes-Product-Process (3PE)" integrated multiscale approach of chemical engineering. Indeed a modern chemical engineering can be summarized by four main objectives: (1) Increase productivity and selectivity through intensification of intelligent operations and a multiscale approach to processes control: nano and micro-tailoring of materials with controlled structure. (2) Design novel equipment based on scientific principles and new production methods: process intensification using multifunctional reactors and micro-engineering for micro structured equipment. (3) Manufacturing end-use properties to synthesize structured products, combining several functions required by the customer with a special emphasis on complex fluids and solid technology, necessating molecular modeling, polymorph prediction and sensor development. (4) Implement multiscale application of computational chemical engineering modeling and simulation to real-life situations from the molecular-scale to the production-scale, e.g., in order to understand how phenomena at a smaller length-scale relate to properties and behaviour at a longer length-scale. The presentation will emphasize the 3PE multiscale approach of chemical engineering for investigations in the previous objectives and on its success due to the today's considerable progress in the use of scientific instrumentation, in modeling, simulation and computer-aided tools, and in the systematic design methods. © 2009 The Institution of Chemical Engineers.


Hapiot P.,French National Center for Scientific Research
Journal of the American Chemical Society | Year: 2010

A global strategy to prepare a versatile and robust reactive platform for immobilizing molecules on carbon substrates with controlled morphology and high selectivity is presented. The procedure is based on the electroreduction of a selected triisopropylsilyl (TIPS)-protected ethynyl aryldiazonium salt. It avoids the formation of multilayers and efficiently protects the functional group during the electrografting step. After TIPS deprotection, a dense reactive ethynyl aryl monolayer is obtained which presents a very low barrier to charge transfer between molecules in solution and the surface. As a test functionalization, azidomethylferrocene was coupled by "click" chemistry with the modified surface. Analysis of the redox activity highlights a surface concentration close to the maximum possible attachment considering the steric hindrance of a ferrocenyl group. © 2010 American Chemical Society.


Ugolini G.,French National Center for Scientific Research
Advances in Virus Research | Year: 2011

Powerful transneuronal tracing technologies exploit the ability of some neurotropic viruses to travel across neuronal pathways and to function as self-amplifying markers. Rabies virus is the only viral tracer that is entirely specific, as it propagates exclusively between connected neurons by strictly unidirectional (retrograde) transneuronal transfer, allowing for the stepwise identification of neuronal connections of progressively higher order. Transneuronal tracing studies in primates and rodent models prior to the development of clinical disease have provided valuable information on rabies pathogenesis. We have shown that rabies virus propagation occurs at chemical synapses but not via gap junctions or cell-to-cell spread. Infected neurons remain viable, as they can express their neurotransmitters and cotransport other tracers. Axonal transport occurs at high speed, and all populations of the same synaptic order are infected simultaneously regardless of their neurotransmitters, synaptic strength, and distance, showing that rabies virus receptors are ubiquitously distributed within the CNS. Conversely, in the peripheral nervous system, rabies virus receptors are present only on motor endplates and motor axons, since uptake and transneuronal transmission to the CNS occur exclusively via the motor route, while sensory and autonomic endings are not infected. Infection of sensory and autonomic ganglia requires longer incubation times, as it reflects centrifugal propagation from the CNS to the periphery, via polysynaptic connections from sensory and autonomic neurons to the initially infected motoneurons. Virus is recovered from end organs only after the development of rabies because anterograde spread to end organs is likely mediated by passive diffusion, rather than active transport mechanisms. © 2011 Elsevier Inc.


Saint-Dizier P.,French National Center for Scientific Research
Argument and Computation | Year: 2012

In this article, we first present theplatform and the Dislog language, designed for discourse analysis with a logic and linguistic perspective. The platform has now reached a certain level of maturity which allows the recognition of a large diversity of discourse structures including general-purpose rhetorical structures as well as domain-specific discourse structures. The Dislog language is based on linguistic considerations and includes knowledge access and inference capabilities. Functionalities of the language are presented together with a method for writing discourse analysis rules. Efficiency and portability of the system over domains and languages are investigated to conclude this first part. In a second part, we analyse the different types of arguments found in several document genres, most notably: procedures, didactic texts and requirements. Arguments form a large class of discourse relations. A generic and frequently encountered form emerges from our analysis: reasons for conclusion which constitutes a homogeneous family of arguments from a language, functional and conceptual point of view. This family can be viewed as a kind of proto-argument. We then elaborate its linguistic structure and show how it is implemented in. We then investigate the cooperation between explanation and arguments, in particular in didactic texts where they are particularly rich and elaborated. This article ends with a prospective section that develops current and potential uses of this work and how it can be extended to the recognition of other forms of arguments. © 2012 Copyright Taylor and Francis Group, LLC.


Muselli M.,French National Center for Scientific Research
Energy and Buildings | Year: 2010

Passive cooling is considered as an alternative technology to avoid unwanted heat gains, to reduce urban heat islands and to generate cooling potential for buildings (limiting air-conditioning energy). According to materials and surface treatments, the roof can represent to be a major heat gain source from opaque elements of the building fabric, heating up the outer surface and increasing heat flow by conduction. This paper presents low-cost new radiative materials (1 ∉/m2) allowing to limit heat gains during diurnal cycle for hot seasons. To evaluate the relevance of these new substrates, their reflective UV-VIS-IR behavior are studied and compared to classical roofed materials available in industrial and developing countries. A 48 m2 experimental roof having different surfaces (plate steel sheets, fiber cement, terra cotta tiles and corrugated sheets) allows to determine the temperature ratio δ between uncoated and coated materials. Up to 34% surface temperature gains are obtained for white coated CS, 25% for FC and ∼18% for TCT and PSS. According to uncoated materials for a surface temperature T0 = 60 °C, simulations showed that the low-cost white opaque reflective roofs (50 m2) presented in this study would reduce cooling energy consumption by 26-49%. © 2010 Elsevier B.V. All rights reserved.


Absil P.-A.,Catholic University of Louvain | Malick J.,French National Center for Scientific Research
SIAM Journal on Optimization | Year: 2012

This paper deals with constructing retractions, a key step when applying optimization algorithms on matrix manifolds. For submanifolds of Euclidean spaces, we show that the operation consisting of taking a tangent step in the embedding Euclidean space followed by a projection onto the submanifold is a retraction. We also show that the operation remains a retraction if the projection is generalized to a projection-like procedure that consists of coming back to the submanifold along "admissible" directions, and we give a sufficient condition on the admissible directions for the generated retraction to be second order. This theory offers a framework in which previously proposed retractions can be analyzed, as well as a toolbox for constructing new ones. Illustrations are given for projection-like procedures on some specific manifolds for which we have an explicit, easy-to-compute expression. © 2012 Society for Industrial and Applied Mathematics.


Garanger E.,CNRS Organic Polymer Chemistry Laboratory | Lecommandoux S.,French National Center for Scientific Research
Angewandte Chemie - International Edition | Year: 2012

Interdisciplinary: The application of protein-engineering techniques to polymer materials can lead to the design and preparation of biocompatible, biodegradable, stimuli-sensitive copolymers bearing biologically responsive peptide motifs (see picture). Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Klumpp K.,Novira Therapeutics, Inc. | Crepin T.,French National Center for Scientific Research
Current Opinion in Virology | Year: 2014

Viral proteins have enabled the design of selective and efficacious treatments for viral diseases. While focus in this area has been on viral enzymes, it appears that multifunctional viral proteins may be even more susceptible to small molecule interference. As exemplified by HIV capsid, small molecule inhibitors can bind to multiple binding sites on the capsid protein and induce or prevent protein interactions and conformational changes. Resistance selection is complicated by the fact that the capsid proteins have to engage in different protein interactions at different times of the life cycle. Viral capsid assembly and disassembly have therefore emerged as highly sensitive processes that could deliver a new generation of antiviral agents across viral diseases. © 2014 Elsevier B.V.


Davison A.,French National Center for Scientific Research
Computing in Science and Engineering | Year: 2012

Published scientific research that relies on numerical computations is too often not reproducible. For computational research to become consistently and reliably reproducible, the process must become easier to achieve, as part of day-to-day research. A combination of best practices and automated tools can make it easier to create reproducible research. © 2012 IEEE.


Benmerah A.,French Institute of Health and Medical Research | Benmerah A.,French National Center for Scientific Research | Benmerah A.,University of Paris Descartes
Current Opinion in Cell Biology | Year: 2013

Cilia are fascinating highly conserved organelles shared by very different organisms from unicellular eukaryotes to vertebrates where they are involved in motility and sensory functions. In vertebrates, the function of the primary cilium, a unique nonmotile cilium found at the surface of most cell types during development, remained mysterious during 40 years until its crucial function in the control of key signaling cascades during development and its involvement in complex genetic disorders now called ciliopathies were uncovered. Recent studies have focused on a specific membrane domain found at the base of primary cilia in most cell types which was already mentioned in the first descriptions of these cilia but did not raise much interest during 50 years. This membrane domain, the 'ciliary pocket', also found at the base of some motile cilia, may act as a platform for cilia-associated vesicular trafficking and as an interface with the actin cytoskeleton but also likely in additional important functions which remain to be discovered. © 2012 Elsevier Ltd.


Gandon S.,French National Center for Scientific Research
Philosophical transactions of the Royal Society of London. Series B, Biological sciences | Year: 2013

The ability of a pathogen to cause an epidemic when introduced in a new host population often relies on its ability to adapt to this new environment. Here, we give a brief overview of recent theoretical and empirical studies of such evolutionary emergence of pathogens. We discuss the effects of several ecological and genetic factors that may affect the likelihood of emergence: migration, life history of the infectious agent, host heterogeneity, and the rate and effects of mutations. We contrast different modelling approaches and indicate how details in the way we model each step of a life cycle can have important consequences on the predicted probability of evolutionary emergence. These different theoretical perspectives yield important insights into optimal surveillance and intervention strategies, which should aim for a reduction in the emergence (and re-emergence) of infectious diseases.


Althoff T.,Max Planck Institute For Biophysik | Mills D.J.,Max Planck Institute For Biophysik | Popot J.-L.,French National Center for Scientific Research | Kuhlbrandt W.,Max Planck Institute For Biophysik
EMBO Journal | Year: 2011

The respiratory chain in the inner mitochondrial membrane contains three large multi-enzyme complexes that together establish the proton gradient for ATP synthesis, and assemble into a supercomplex. A 19-à.. 3D map of the 1.7-MDa amphipol-solubilized supercomplex I 1 III 2 IV 1 from bovine heart obtained by single-particle electron cryo-microscopy reveals an amphipol belt replacing the membrane lipid bilayer. A precise fit of the X-ray structures of complex I, the complex III dimer, and monomeric complex IV indicates distances of 13 nm between the ubiquinol-binding sites of complexes I and III, and of 10-11 nm between the cytochrome c binding sites of complexes III and IV. The arrangement of respiratory chain complexes suggests two possible pathways for efficient electron transfer through the supercomplex, of which the shorter branch through the complex III monomer proximal to complex I may be preferred. © 2011 European Molecular Biology Organization | All Rights Reserved.


Larrieu G.,Roche Holding AG | Han X.-L.,French National Center for Scientific Research
Nanoscale | Year: 2013

Nanowire-based field-effect transistors are among the most promising means of overcoming the limits of today's planar silicon electronic devices, in part because of their suitability for gate-all-around architectures, which provide perfect electrostatic control and facilitate further reductions in "ultimate" transistor size while maintaining low leakage currents. However, an architecture combining a scalable and reproducible structure with good electrical performance has yet to be demonstrated. Here, we report a high performance field-effect transistor implemented on massively parallel dense vertical nanowire arrays with silicided source/drain contacts and scaled metallic gate length fabricated using a simple process. The proposed architecture offers several advantages including better immunity to short channel effects, reduction of device-to-device variability, and nanometer gate length patterning without the need for high-resolution lithography. These benefits are important in the large-scale manufacture of low-power transistors and memory devices. © 2013 The Royal Society of Chemistry.


Merrifield C.J.,French National Center for Scientific Research
Nature Cell Biology | Year: 2012

The membrane-curvature-inducing protein Fcho was proposed to be part of a ubiquitous nucleation mechanism for clathrin-coated pits. However, studies in developing zebrafish embryos now indicate a role for Fcho as a receptor-specific adaptor in bone morphogenetic protein (BMP) signalling, rather than a global coated-pit nucleator. © 2012 Macmillan Publishers Limited. All rights reserved.


Loria A.,French National Center for Scientific Research
IEEE Transactions on Circuits and Systems II: Express Briefs | Year: 2010

We solve the problem of masterslave synchronization of fourth-order lü's hyperchaotic systems via feedback control. We use only one control input that enters in the slave system. We show that this simple feedback suffices to synchronize both systems exponentially fast. We provide a proof of stability and convergence (hence, that synchronization takes place) via Lyapunov's second stability method. We provide some numeric simulations that illustrate our findings. © 2010 IEEE.


Bernard P.,French National Center for Scientific Research
Archive for Rational Mechanics and Analysis | Year: 2010

In 1996, Ricardo Ricardo Mañé discovered that Mather measures are in fact the minimizers of a "universal" infinite dimensional linear programming problem. This fundamental result has many applications, of which one of the most important is to the estimates of the generic number of Mather measures. Mañé obtained the first estimation of that sort by using finite dimensional approximations. Recently, we were able, with Gonzalo Contreras, to use this method of finite dimensional approximation in order to solve a conjecture of John Mather concerning the generic number of Mather measures for families of Lagrangian systems. In the present paper we obtain finer results in that direction by applying directly some classical tools of convex analysis to the infinite dimensional problem. We use a notion of countably rectifiable sets of finite codimension in Banach (and Frechet) spaces which may deserve independent interest. © 2010 Springer-Verlag.


Gertner-Dardenne J.,French National Center for Scientific Research
Blood | Year: 2013

Vγ9Vδ2 cells, the major γδ T-cell subset in human peripheral blood, represent a T-cell subset that displays reactivity against microbial agents and tumors. The biology of Vγ9Vδ2 T cells remains poorly understood. We show herein that the interaction between B- and T-lymphocyte attenuator (BTLA) and herpesvirus entry mediator (HVEM) is a major regulator of Vγ9Vδ2 T-cell proliferation control. BTLA was strongly expressed at the surface of resting Vγ9Vδ2 T cells and inversely correlated with T-cell differentiation. BTLA-HVEM blockade by monoclonal antibodies resulted in the enhancement of Vγ9Vδ2 T-cell receptor-mediated signaling, whereas BTLA-HVEM interaction led to a decrease in phosphoantigen-mediated proliferation by inducing a partial S-phase arrest. Our data also suggested that BTLA-HVEM might participate in the control of γδ T-cell differentiation. In addition, the proliferation of autologous γδ T cells after exposition to lymphoma cells was dramatically reduced through BTLA-HVEM interaction. These data suggest that HVEM interaction with BTLA may play a role in lymphomagenesis by interfering with Vγ9Vδ2 T-cell proliferation. Moreover, BTLA stimulation of Vγ9Vδ2 T cells appears as a new possible mechanism of immune escape by lymphoma cells.


Mercier N.,French National Center for Scientific Research
European Journal of Inorganic Chemistry | Year: 2013

Although the chemistry of viologens in solution has been thoroughly investigated, their intriguing functions in the crystalline state have been the subject of less attention. Recently, many hybrid structures incorporating viologen cations have been published, and a considerable number of them possess interesting properties in the solid state. Elaborate examination of these structures has indicated that peculiar interactions between the viologen dication and anions, including side contacts and face contacts, are very often encountered. This suggests that the viologen dications have a great influence on their surroundings at the atomic level. This remarkable templating effect is well demonstrated by a series of hybrids, in which the rare MX5 (M = BiIII, SbIII; X = Cl, Br, I) inorganic chain of trans-connected octahedra is stabilised by a methylviologen dication; this leads to a new fascinating family of ferroelectrics. In contrast, owing to their unique structural features, viologen dications exhibit prominent photochemistry. Upon irradiation, viologen dications (V2+), with good electron-accepting abilities, are able to accept one electron from an electron donor, either an anion or a molecule, to afford stable separated charge state systems with photochromic properties resulting from the coloured V ·+ radicals. This process takes place in the crystalline solid state and offers great opportunities to understand their structure-property relationships. The relationships discovered in the current system will guide subsequent rational syntheses to optimise the properties of the materials. © 2013 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.


Chavanis P.-H.,French National Center for Scientific Research
Astronomy and Astrophysics | Year: 2013

We review and complete the kinetic theory of spatially inhomogeneous stellar systems when collective effects (dressing of the stars by their polarization cloud) are neglected. We start from the BBGKY hierarchy issued from the Liouville equation and consider an expansion in powers of 1/N in a proper thermodynamic limit. For N → +∞, we obtain the Vlasov equation describing the evolution of collisionless stellar systems like elliptical galaxies. This corresponds to the mean field approximation. At the order 1/N, we obtain a kinetic equation describing the evolution of collisional stellar systems like globular clusters. This corresponds to the weak coupling approximation. This equation coincides with the generalized Landau equation derived from a more abstract projection operator formalism. This equation does not suffer logarithmic divergences at large scales since spatial inhomogeneity is explicitly taken into account. Making a local approximation, and introducing an upper cut-off at the Jeans length, it reduces to the Vlasov-Landau equation which is the standard kinetic equation of stellar systems. Our approach provides a simple and pedagogical derivation of these important equations from the BBGKY hierarchy which is more rigorous for systems with long-range interactions than the two-body encounters theory. Making an adiabatic approximation, we write the generalized Landau equation in angle-action variables and obtain a Landau-type kinetic equation that is valid for fully inhomogeneous stellar systems and is free of divergences at large scales. This equation is less general than the recently derived Lenard-Balescu-type kinetic equation since it neglects collective effects, but it is substantially simpler and could be useful as a first step. We discuss the evolution of the system as a whole and the relaxation of a test star in a bath of field stars. We derive the corresponding Fokker-Planck equation in angle-action variables and provide expressions for the diffusion coefficient and friction force. © 2013 ESO.


Aubret F.,French National Center for Scientific Research
Scientific Reports | Year: 2013

Experimental studies have shown heart rates to decrease from embryo to hatchling stage in turtles, remain steady in skinks, and increase in birds. However, no snake species has been studied in this regard. I recorded heart rate evolution trajectories from embryo to juvenile stage in 78 eggs from two species of European Natricine snakes. Unexpectedly, snakes behaved more like birds than turtles or lizards: heart rates increased after hatching in both N. maura and N. natrix, respectively by 43.92 ± 22.84% and 35.92 ± 24.52%. Heart rate shift was not related to an abrupt elevation of metabolism per se (snakes that increased their heart rates the most sharply grew the least after birth), but rather due to a number of smaller eggs that experienced lower than normal heart rates throughout the incubation and recovered a normal heart rate post-birth. This finding is discussed in the light of hatching synchrony benefits.


Benecke A.G.,French National Center for Scientific Research
Current Topics in Microbiology and Immunology | Year: 2012

Host-pathogen interactions provide a fascinating example of two or more active genomes directly exerting mutual influence upon each other. These encounters can lead to multiple outcomes from symbiotic homeostasis to mutual annihilation, undergo multiple cycles of latency and lysogeny, and lead to coevolution of the interacting genomes. Such systems pose numerous challenges but also some advantages to modeling, especially in terms of functional, mathematical genome representations. The main challenges for the modeling process start with the conceptual definition of a genome for instance in the case of host-integrated viral genomes. Furthermore, hardly understood influences of the activity of either genome on the other(s) via direct and indirect mechanisms amplify the needs for a coherent description of genome activity. Finally, genetic and local environmental heterogeneities in both the host's cellular and the pathogen populations need to be considered in multiscale modeling efforts. We will review here two prominent examples of host-pathogen interactions at the genome level, discuss the current modeling efforts and their shortcomings, and explore novel ideas of representing active genomes which promise being particularly adapted to dealing with the modeling challenges posed by host-pathogen interactions. © 2013 Springer-Verlag Berlin Heidelberg.


Blin J.L.,University of Lorraine | Blin J.L.,French National Center for Scientific Research | Imperor-Clerc M.,University Paris - Sud
Chemical Society Reviews | Year: 2013

In this review, recent progress in the understanding of the formation of various silica mesoporous materials is reported. Owing to time-resolved experiments using Small Angle X-ray or Neutron Scattering (SAXS or SANS), it is possible to follow in situ the formation of a material during its synthesis via the Cooperative Templating Mechanism (CTM). Such experiments directly provide unique information about the structural properties of the material inside the synthesis solution. One of the main findings is that phase transformations often occur in the material prior to the stabilisation of its final structure. Moreover, during the very early stages of the synthesis, it is also possible to detect the first hybrid silica-surfactant micellar aggregates, prior to the precipitation of the material, as reported in the case of the SBA-15 materials. All these experiments allow a better understanding of the formation mechanisms and of the influence of the many synthesis parameters. These results open the way to a better prediction and control of the structure of mesoporous materials. © The Royal Society of Chemistry 2013.


Universities are expected to be important players in the development of knowledge economies; therefore, they are a priority on the policy agenda of the European commission and of member states. To understand the new institutional settings where knowledge production is achieved, we must turn our attention to analyzing the reforms underway. Building on conclusions from the sociology of professions, the sociology of organizations and public policy analysis, this paper argues that the policy instruments developed by public authorities to measure scientific performance and selectively allocate resources rely on peer review processes and reinforce an academic elite. As a result, the internal power distribution within the academic profession as well as within universities has changed. On the one hand, peer review is used as a managerial tool by universities. The decisions made at the university level are largely based on (and legitimated by) evaluations conducted outside the university by an elite sitting in research councils, editorial boards, and evaluation agencies. On the other hand, rather than weakening professional power, the recent reforms have instead led to a reconfiguration of the academic profession. Their influence is twofold. First, they have empowered those individuals who set the norms according to which academic activities are rewarded and funded by public actors. Second, they bolster those who receive positive reviews, since they gain a stronger position to negotiate with the managers of their university. © 2013 Elsevier B.V. All rights reserved.


Thierry B.,French National Center for Scientific Research | Thierry B.,CNRS Hubert Curien Multi-disciplinary Institute
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2013

The evolutionary study of social systems in non-human primates has long been focused on ecological determinants. The predictive value of socioecological models remains quite low, however, in particular because such equilibrium models cannot integrate the course of history. The use of phylogenetic methods indicates that many patterns of primate societies have been conserved throughout evolutionary history. For example, the study of social relations in macaques revealed that their social systems are made of sets of correlated behavioural traits. Some macaque species are portrayed by marked social intolerance, a steep dominance gradient and strong nepotism, whereas others display a higher level of social tolerance, relaxed dominance and a weaker influence of kinship. Linkages between behavioural traits occur at different levels of organization, and act as constraints that limit evolutionary responses to external pressures. Whereas these constraints can exert strong stabilizing selection that opposes the potential changes required by the ecological environment, selective mechanisms may have the potential to switch thewhole social system from one state to another by acting primarily on some key behavioural traits that could work as pacemakers. © 2013 The Author(s) Published by the Royal Society. All rights reserved.


Morris M.C.,French National Center for Scientific Research
Biochimica et Biophysica Acta - Proteins and Proteomics | Year: 2013

One of the challenges of modern biology and medicine is to visualize biomolecules in their natural environment, in real-time and in a non-invasive fashion, so as to gain insight into their physiological behavior and highlight alterations in pathological settings, which will enable to devise appropriate therapeutic strategies. Fluorescent biosensors constitute a class of imaging agents which have provided major insights into the function and regulation of enzymes in their cellular context. GFP-based reporters and genetically-encoded FRET biosensors, have been successfully applied to study protein kinases in living cells with high spatial and temporal resolution. In parallel, combined efforts in fluorescence chemistry and in chemical biology have enabled the design of non-genetic, polypeptide biosensors coupled to small synthetic fluorescent probes, which have been applied to monitor protein kinase activities in vitro and in more complex biological samples, with an equally successful outcome. From a biomedical perspective, fluorescent biosensor technology is well suited to development of diagnostic approaches, for monitoring disease progression and for evaluating response to therapeutics. Moreover it constitutes an attractive technology for drug discovery programs, for high content, high throughput screening assays, to assess the potency of new hits and optimize lead compounds, whilst also serving to characterize drugs developed through rational design. This review describes the utility and versatility of fluorescence biosensor technology to probe protein kinases with a specific focus on CDK/cyclin biosensors we have developed to probe abundance, activity and conformation. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases (2012). © 2013 Elsevier B.V.


Arndt N.,French National Center for Scientific Research
Economic Geology | Year: 2013

The hypothesis that the metals in certain orthomagmatic ore deposits come from a source in the subcontinental lithospheric mantle is evaluated in this paper. According to this hypothesis, parts of the mantle beneath the continents are metasomatically enriched in metals like Ni, Cu, and the platinum group elements (PGE). It is proposed that under some circumstances, these metals are transported into the crust where they become concentrated in orebodies. An examination of the compositions of xenoliths from the lithospheric mantle reveals little evidence, however, of components that could represent the source of metal-enriched magmas. In addition, the mechanism whereby metals are brought from the source to the surface is very unclear. The lithosphere is the coldest part of the mantle and it only melts under special circumstances. The normal product is a lowdegree melt, an alkaline, Si-undersaturated magma of the type that only rarely contains ore deposits. Major magmatic orebodies normally form from high-volume, high-flux magmas that are produced by high-degree melting in deeper, hotter parts of the mantlen the asthenosphere or a mantle plume. For melting to occur in the lithosphere, rather than in the hotter parts of the mantle, the melting point of the source must be drastically reduced by the presence of volatiles. On the other hand, there is ample evidence that the host magmas of ore deposits were abnormally rich in water or CO2 as would have been the case if they came from a volatilerich metasomatized source. Magmas from sublithospheric sources could have interacted with the lithospheric mantle as they ascended toward the surface and they could have picked up some metals through this interaction. This process could have contributed to the formation of some ores, a notable example being the PGE deposits in Bushveld Complex. There is ample geological and geochemical evidence, however, that the majority of magmatic deposits form when magmas from sublithosphere sources assimilate material from the continental crust and that the latter process is instrumental in the formation of the deposits.. © 2013 Society of Economic Geologists, Inc.


Djouadi A.,French National Center for Scientific Research | Djouadi A.,CERN
European Physical Journal C | Year: 2013

Now that the Higgs particle has been observed by the ATLAS and CMS experiments at the LHC, the next endeavor would be to probe its fundamental properties and to measure its couplings to fermions and gauge bosons with the highest possible accuracy. However, the measurements will be limited by significant theoretical uncertainties that affect the production cross section in the main production channels as well as by experimental systematical errors. Following earlier work, we propose in this paper to consider ratios of Higgs production cross sections times decay branching ratios in which most of the theoretical uncertainties and some systematical errors, such as the ones due to the luminosity measurement and the Higgs decay branching fractions, cancel out. The couplings of the Higgs particle could be then probed in a way that will be mostly limited by the statistical accuracy achievable at the LHC and accuracies at the percent level are foreseen for some of the ratios at the end of the LHC run. At the theoretical level, these ratios are also interesting as they do not involve the ambiguities that affect the Higgs total decay width in new physics scenarios. To illustrate how these ratios can be used to determine the Higgs couplings, we perform a rough analysis of the recent ATLAS and CMS data which shows that there is presently no significant deviation from the Standard Model expectation. © 2013 The Author(s).


Jourdain V.,CNRS Charles Coulomb Laboratory | Bichara C.,French National Center for Scientific Research
Carbon | Year: 2013

Due to its higher degree of control and its scalability, catalytic chemical vapour deposition is now the prevailing synthesis method of carbon nanotubes. Catalytic chemical vapour deposition implies the catalytic conversion of a gaseous precursor into a solid material at the surface of reactive particles or of a continuous catalyst film acting as a template for the growing material. Significant progress has been made in the field of nanotube synthesis by this method although nanotube samples still generally suffer from a lack of structural control. This illustrates the fact that numerous aspects of the growth mechanism remain ill-understood. The first part of this review is dedicated to a summary of the general background useful for beginners in the field. This background relates to the carbon precursors, the catalyst nanoparticles, their interaction with carbonaceous compounds and their environment. The second part provides an updated review of the influence of the synthesis parameters on the features of nanotube samples: diameters, chirality, metal/semiconductor ratio, length, defect density and catalyst yield. The third part is devoted to important and still open questions, such as the mechanism of nanotube nucleation and the chiral selectivity, and to the hypotheses currently proposed to answer them. © 2013 Elsevier Ltd. All rights reserved.


Nzihou A.,French National Center for Scientific Research | Stanmore B.,University of Queensland
Journal of Hazardous Materials | Year: 2013

The literature on the presence of heavy metals in contaminated wastes is reviewed. Various categories of materials produced from domestic and industrial activities are included, but municipal solid waste, which is a more complex material, is excluded. This review considers among the most abundant the following materials - wood waste including demolition wood, phytoremediation scavengers and chromated copper arsenate (CCA) timber, sludges including de-inking sludge and sewage sludge, chicken litter and spent pot liner. The partitioning of the metals in the ashes after combustion or gasification follows conventional behaviour, with most metals retained, and higher concentrations in the finer sizes due to vaporisation and recondensation. The alkali metals have been shown to catalyse the biomass conversion, particularly lithium and potassium, although other metals are active to a lesser extent. The most prevalent in biomass is potassium, which is not only inherently active, but volatilises to become finely distributed throughout the char mass. Because the metals are predominantly found in the ash, the effectiveness of their removal depends on the efficiency of the collection of particulates. The potential for disposal into soil depends on the initial concentration in the feed material. © 2013 Elsevier B.V.


Hannedouche J.,University Paris - Sud | Schulz E.,University Paris - Sud | Schulz E.,French National Center for Scientific Research
Chemistry - A European Journal | Year: 2013

Asymmetric hydroamination allows the direct and selective formation of a new C-N bond as a simple procedure towards valuable scalemic synthons. Huge efforts have recently been made to overcome the challenges associated with this transformation. This noncomprehensive Concept article aims at pointing out the most recent and original progresses, offering nearby developments, and addressing the next challenges. © 2013 Wiley-VCH Verlag GmbHandCo.


De Sanctis D.,European Synchrotron Radiation Facility | Nanao M.H.,European Molecular Biology Laboratory | Nanao M.H.,French National Center for Scientific Research
Acta Crystallographica Section D: Biological Crystallography | Year: 2012

Specific radiation damage can be used for the phasing of macromolecular crystal structures. In practice, however, the optimization of the X-ray dose used to burn the crystal to induce specific damage can be difficult. Here, a method is presented in which a single large data set that has not been optimized in any way for radiation-damage-induced phasing (RIP) is segmented into multiple sub-data sets, which can then be used for RIP. The efficacy of this method is demonstrated using two model systems and two test systems. A method to improve the success of this type of phasing experiment by varying the composition of the two sub-data sets with respect to their separation by image number, and hence by absorbed dose, as well as their individual completeness is illustrated. © 2012 International Union of Crystallography Printed in Singapore - all rights reserved.


Clemens S.,University of Bayreuth | Aarts M.G.M.,Wageningen University | Thomine S.,French National Center for Scientific Research | Verbruggen N.,Free University of Colombia
Trends in Plant Science | Year: 2013

Practically all human populations are environmentally exposed to cadmium (Cd), mostly through plant-derived food. A growing body of epidemiological evidence suggests that there is no margin of safety between current Cd exposure levels and the threshold for adverse health effects and, hence, there is an urgent need to lower human Cd intake. Here we review recent studies on rice (Oryza sativa) and Cd-hyperaccumulating plants that have led to important insights into the processes controlling the passage of Cd from the soil to edible plant organs. The emerging molecular understanding of Cd uptake, root retention, root-to-shoot translocation and grain loading will enable the development of low Cd-accumulating crops. © 2012 Elsevier Ltd.


Condon C.,French National Center for Scientific Research
RNA Biology | Year: 2010

The discovery of the paralogous ribonucleases J1 and J2 has been a major advance in the study of RNA maturation and decay in Bacillus subtilis and related organisms. RNase J1 was the first bacterial enzyme shown to possess 5′-to-3′ exoribonuclease activity, reversing a dogma that suggested this type of activity was unique to eukaryotic mRNA decay. RNase J1 and J2 form a complex that also has endonuclease activity and these enzymes have been shown to play a key role in the turnover and maturation of many RNAs in B. subtilis. Here, I describe recent progress in our understanding of the role of these enzymes in RNA metabolism in this organism and argue that the 5′-to-3′ exoribonuclease activity may be the more important of the complex's two modes of action. © 2010 Landes Bioscience.


Veitia R.A.,French National Center for Scientific Research | Veitia R.A.,University Paris Diderot
BioEssays | Year: 2010

Testis determination in most mammals is regulated by a genetic hierarchy initiated by the SRY gene. Early ovarian development has long been thought of as a default pathway switched on passively by the absence of SRY. Recent studies challenge this view and show that the ovary constantly represses male-specific genes, from embryonic stages to adulthood. Notably, the absence of the crucial ovarian transcription factor FOXL2 (alone or in combination with other factors) induces a derepression of male-specific genes during development, postnatally and, even more interestingly, during adulthood. Strikingly, in the adult, targeted ablation of Foxl2 leads to a molecular transdifferentiation of the supporting cells of the ovary, which acquire cytological and transcriptomic characteristics of the supporting cells of the testes. These studies bring many answers to the field of gonadal determination, differentiation and maintenance, but also open many questions. © 2010 WILEY Periodicals, Inc.


Mechali M.,French National Center for Scientific Research
Nature Reviews Molecular Cell Biology | Year: 2010

At each cell division in humans, 30,000-50,000 DNA replication origins are activated, and it remains unclear how they are selected and recognized by replication factors. DNA replication in multicellular organisms must accommodate variations in growth conditions and DNA damage. It must also adapt to changes in chromatin organization associated with cell differentiation and development. The selection of replication origins in metazoans seems to involve multiple choices, with the appropriate answers depending on the identity of the cell or the conditions of growth. This suggests that during evolution, the use of replication origins became more controlled by epigenetic mechanisms affecting chromosome dynamics and expression than by DNA synthesis per se. © 2010 Macmillan Publishers Limited. All rights reserved.


Hickman A.B.,U.S. National Institute of Diabetes and Digestive and Kidney Diseases | Chandler M.,French National Center for Scientific Research | Dyda F.,U.S. National Institute of Diabetes and Digestive and Kidney Diseases
Critical Reviews in Biochemistry and Molecular Biology | Year: 2010

DNA rearrangements are important in genome function and evolution. Genetic material can be rearranged inadvertently during processes such as DNA repair, or can be moved in a controlled manner by enzymes specifically dedicated to the task. DNA transposases comprise one class of such enzymes. These move DNA segments known as transposons to new locations, without the need for sequence homology between transposon and target site. Several biochemically distinct pathways have evolved for DNA transposition, and genetic and biochemical studies have provided valuable insights into many of these. However, structural information on transposases particularly with DNA substrates has proven elusive in most cases. On the other hand, large-scale genome sequencing projects have led to an explosion in the number of annotated prokaryotic and eukaryotic mobile elements. Here, we briefly review biochemical and mechanistic aspects of DNA transposition, and propose that integrating sequence information with structural information using bioinformatics tools such as secondary structure prediction and protein threading can lead not only to an additional level of understanding but possibly also to testable hypotheses regarding transposition mechanisms. Detailed understanding of transposition pathways is a prerequisite for the long-term goal of exploiting DNA transposons as genetic tools and as a basis for genetic medical applications. © 2010 Informa UK Ltd.


Belenguer P.,French National Center for Scientific Research | Pellegrini L.,Laval University
Biochimica et Biophysica Acta - Molecular Cell Research | Year: 2013

The studies addressing the molecular mechanisms governing mitochondrial fusion and fission have brought to light a small group of dynamin-like GTPases (Guanosine-Triphosphate hydrolase) as central regulators of mitochondrial morphology and cristae remodeling, apoptosis, calcium signaling, and metabolism. One of them is the mammalian OPA1 (Optic atrophy 1) protein, which resides inside the mitochondrion anchored to the inner membrane and, in a cleaved form, is associated to oligomeric complexes, in the intermembrane space of the organelle. Here, we review the studies that have made OPA1 emerge as the best understood regulator of mitochondrial inner membrane fusion and cristae remodeling. Further, we re-examine the findings behind the recent claim that OPA1 mediates adrenergic control of lipolysis by functioning as a cytosolic A-kinase anchoring protein (AKAP), on the hemimembrane that envelops the lipid droplet. This article is part of a Special Issue entitled: Mitochondrial dynamics and physiology. © 2012 Elsevier B.V.


Kelly R.G.,French National Center for Scientific Research
Experimental Cell Research | Year: 2010

Branchiomeric craniofacial muscles control feeding, breathing and facial expression. These muscles differ on multiple counts from all other skeletal muscles and originate in a progenitor cell population in pharyngeal mesoderm characterized by a common genetic program with an adjacent population of cardiac progenitor cells, the second heart field, that gives rise to much of the heart. The transcription factors and signaling molecules that trigger the myogenic program at sites of branchiomeric muscle formation are correspondingly distinct from those in somite-derived muscle progenitor cells. Here new insights into the regulatory hierarchies controlling branchiomeric myogenesis are discussed. Differences in embryological origin are reflected in the lineage, transcriptional program and proliferative and differentiation properties of branchiomeric muscle satellite cells. These recent findings have important implications for our understanding of the diverse myogenic strategies operative both in the embryo and adult and are of direct biomedical relevance to deciphering the mechanisms underlying the cause and progression of muscle restricted myopathies. © 2010 Elsevier Inc.


Sahut-Barnola I.,French National Center for Scientific Research
PLoS genetics | Year: 2010

Carney complex (CNC) is an inherited neoplasia syndrome with endocrine overactivity. Its most frequent endocrine manifestation is primary pigmented nodular adrenocortical disease (PPNAD), a bilateral adrenocortical hyperplasia causing pituitary-independent Cushing's syndrome. Inactivating mutations in PRKAR1A, a gene encoding the type 1 alpha-regulatory subunit (R1alpha) of the cAMP-dependent protein kinase (PKA) have been found in 80% of CNC patients with Cushing's syndrome. To demonstrate the implication of R1alpha loss in the initiation and development of PPNAD, we generated mice lacking Prkar1a specifically in the adrenal cortex (AdKO). AdKO mice develop pituitary-independent Cushing's syndrome with increased PKA activity. This leads to autonomous steroidogenic genes expression and deregulated adreno-cortical cells differentiation, increased proliferation and resistance to apoptosis. Unexpectedly, R1alpha loss results in improper maintenance and centrifugal expansion of cortisol-producing fetal adrenocortical cells with concomitant regression of adult cortex. Our data provide the first in vivo evidence that loss of R1alpha is sufficient to induce autonomous adrenal hyper-activity and bilateral hyperplasia, both observed in human PPNAD. Furthermore, this model demonstrates that deregulated PKA activity favors the emergence of a new cell population potentially arising from the fetal adrenal, giving new insight into the mechanisms leading to PPNAD.


Veenstra J.A.,French National Center for Scientific Research | Ida T.,University of Miyazaki
Cell and Tissue Research | Year: 2014

Antisera to orcokinin B, CCHamide 1, and CCHamide 2 recognize enteroendocrine cells in the midgut of the fruitfly Drosophila melanogaster and its larvae. Although the antisera to CCHamide 1 and 2 are mutually cross-reactive, polyclonal mouse antisera raised to the C-terminals of their respective precursors allowed the identification of the two different peptides. In both larva and adult, CCHamide 2 immunoreactive endocrine cells are large and abundant in the anterior midgut and are also present in the anterior part of the posterior midgut. The CCHamide 2 immunoreactive endocrine cells in the posterior midgut are also immunoreactive with antiserum to allatostatin C. CCHamide 1 immunoreactivity is localized in endocrine cells in different regions of the midgut; those in the caudal part of the posterior midgut are identical with the allatostatin A cells. In the larva, CCHamide 1 enteroendocrine cells are also present in the endocrine junction and in the anterior part of the posterior midgut. Like in other insect species, the Drosophila orcokinin gene produces two different transcripts, A and B. Antiserum to the predicted biologically active peptide from the B-transcript recognizes enteroendocrine cells in both larva and adult. These are the same cells as those expressing β-galactosidase in transgenic flies in which the promoter of the orcokinin gene drives expression of this enzyme. In the larva, a variable number of orcokinin-expressing enteroendocrine cells are found at the end of the middle midgut, while in the adult, those cells are most abundant in the middle midgut, while smaller numbers are present in the anterior midgut. In both larva and adult, these cells also express allatostatin C. We also made a specific polyclonal antiserum to the NPF precursor in order to determine more precisely the expression of this peptide in the midgut. Using this antiserum, we find expression in the midgut to be the same as described previously using transgenic flies, while in the adult, midgut expression appears to be concentrated in the middle midgut, thus suggesting that in the anterior midgut only minor quantities of NPF are produced. © 2014 Springer-Verlag Berlin Heidelberg.


Vigil D.,University of North Carolina at Chapel Hill | Cherfils J.,French National Center for Scientific Research | Rossman K.L.,University of North Carolina at Chapel Hill | Der C.J.,University of North Carolina at Chapel Hill
Nature Reviews Cancer | Year: 2010

There is now considerable and increasing evidence for a causal role for aberrant activity of the Ras superfamily of small GTPases in human cancers. These GTPases function as GDPĝ€"GTP-regulated binary switches that control many fundamental cellular processes. A common mechanism of GTPase deregulation in cancer is the deregulated expression and/or activity of their regulatory proteins, guanine nucleotide exchange factors (GEFs) that promote formation of the active GTP-bound state and GTPase-activating proteins (GAPs) that return the GTPase to its GDP-bound inactive state. In this Review, we assess the association of GEFs and GAPs with cancer and their druggability for cancer therapeutics. © 2010 Macmillan Publishers Limited. All rights reserved.


Denoeux T.,French National Center for Scientific Research
Fuzzy Sets and Systems | Year: 2011

A method is proposed for estimating the parameters in a parametric statistical model when the observations are fuzzy and are assumed to be related to underlying crisp realizations of a random sample. This method is based on maximizing the observed-data likelihood defined as the probability of the fuzzy data. It is shown that the EM algorithm may be used for that purpose, which makes it possible to solve a wide range of statistical problems involving fuzzy data. This approach, called the fuzzy EM (FEM) method, is illustrated using three classical problems: normal mean and variance estimation from a fuzzy sample, multiple linear regression with crisp inputs and fuzzy outputs, and univariate finite normal mixture estimation from fuzzy data. © 2011 Elsevier B.V. All rights reserved.


Hart D.J.,French National Center for Scientific Research | Waldo G.S.,Los Alamos National Laboratory
Current Opinion in Structural Biology | Year: 2013

Genetic engineering of constructs to improve solubility or stability is a common approach, but it is often unclear how to obtain improvements. When the domain composition of a target is poorly understood, or if there are insufficient structure data to guide sited directed mutagenesis, long iterative phases of subcloning or mutation and expression often prove unsuccessful despite much effort. Random library approaches can offer a solution to this problem and involve construction of large libraries of construct variants that are analysed via screens or selections for the desired phenotype. Huge improvements in construct behaviour can be achieved rapidly with no requirement for prior knowledge of the target. Here we review the development of these experimental strategies and recent successes. © 2013 Elsevier Ltd.


Khan A.R.,Trinity College Dublin | Menetrey J.,French National Center for Scientific Research
Structure | Year: 2013

Arf and Rab proteins, members of small GTPases superfamily, localize to specific subcellular compartments and regulate intracellular trafficking. To carry out their cellular functions, Arfs/Rabs interact with numerous and structurally diverse effector proteins. Over the years, a number of Arf/Rab:effector complexes have been crystallized and their structures reveal shared binding modes including α-helical packing, β-β complementation, and heterotetrameric assemblies. We review available structural information and provide a framework for in-depth analysis of complexes. The unifying features that we identify are organized into a classification scheme for different modes of Arf/Rab:effector interactions, which includes "all-α-helical," "mixed α-helical," "β-β zipping," and "bivalent" modes of binding. Additionally, we highlight structural determinants that are the basis of effector specificity. We conclude by expanding on functional implications that are emerging from available structural information under our proposed classification scheme. © 2013 Elsevier Ltd. All rights reserved.


Pignol G.,French National Center for Scientific Research
International Journal of Modern Physics A | Year: 2015

There is a deep connection between cosmology - the science of the infinitely large - and particle physics - the science of the infinitely small. This connection is particularly manifest in neutron particle physics. Basic properties of the neutron - its Electric Dipole Moment and its lifetime - are intertwined with baryogenesis and nucleosynthesis in the early Universe. I will cover this topic in the first part, that will also serve as an introduction (or rather a quick recap) of neutron physics and Big Bang cosmology. Then, the rest of the paper will be devoted to a new idea: using neutrons to probe models of Dark Energy. In the second part, I will present the chameleon theory: a light scalar field accounting for the late accelerated expansion of the Universe, which interacts with matter in such a way that it does not mediate a fifth force between macroscopic bodies. However, neutrons can alleviate the chameleon mechanism and reveal the presence of the scalar field with properly designed experiments. In the third part, I will describe a recent experiment performed with a neutron interferometer at the Institut Laue Langevin that sets already interesting constraints on the chameleon theory. Last, the chameleon field can be probed by measuring the quantum states of neutrons bouncing over a mirror. In the fourth part, I will present the status and prospects of the GRANIT experiment at the ILL. © 2015 World Scientific Publishing Company.


Puibasset J.,French National Center for Scientific Research
Journal of Chemical Physics | Year: 2010

A molecular simulation approach has been used to model simple fluid adsorption in heterogeneous tubular pores mimicking mesoporous materials such as MCM-41 or porous silicon, allowing to determine the amount adsorbed ρ as a function of the chemical potential μ. A hysteresis loop is observed in adsorption/desorption cycles, which is closely connected to the appearance of many metastable states. The density of these metastable states is studied in the μ- ρ plane. Experimentally, the accessible metastable states are those that can be attained by the μ -path, i.e., a series of increasing or decreasing μ steps. One could also imagine using a quench from high temperature. Although the total density of metastable states is not directly accessible to experiments, it is of primary theoretical importance to understand the structure of metastable states in the hysteresis as determined experimentally. The disorder associated with the porous material realizations is accurately taken into account, and a systematic system size analysis is also performed in order to study the thermodynamic limit. It is shown that the quenched complexity is the relevant quantity to understand the hysteresis structure in the thermodynamic limit. It clearly exhibits a distinctive behavior depending on the distribution of heterogeneities characterizing the disorder in the pore. Some analogies can be found with the situation where an out-of-equilibrium transition appears, but careful examination of the data suggests another interpretation. © 2010 American Institute of Physics.


Cairon O.,French National Center for Scientific Research
Physical Chemistry Chemical Physics | Year: 2010

Based on experimental infrared spectra of CO adsorbed on both amorphous silica-aluminas (ASA) and ultra stable Y zeolites (USY), an additional A 0 band related to high Brønsted acidic sites is evidenced. This result allows us to refine our previous assignments of the complicated and broad massifs in the ν(OH) and ν(CO) regions. © The Owner Societies 2010.


Foucaud J.,French National Center for Scientific Research
Proceedings. Biological sciences / The Royal Society | Year: 2013

Organisms that face behavioural challenges can use different types of information to guide their decisions. First, they can use the personal information they sample in their environment. Second, they can use the inadvertent social information provided by the behaviour of conspecifics or heterospecifics (i.e. public information). Currently, little is known about the interaction between genetic variation and the use of personal versus public information in natural populations. Here, we investigated whether a natural genetic polymorphism affects the use of personal versus public information in a spatial learning task in Drosophila melanogaster. We found that genetic variation at the foraging locus interacts with social context during spatial learning. While both allelic variants are able to use personal and public information to improve their navigation during 10 training trials, a probe trial revealed that individuals carrying the for(R) (rover) allele rely mainly on personal information, whereas individuals carrying the for(s) (sitter) allele either use or display more public information than rovers. Accordingly, transfer of social information is more important in groups of sitters than in groups of rovers. These results suggest that a positive feedback loop can occur between alleles promoting group living, such as for(s), and the use and/or display of public information, ultimately providing the opportunity for the joint evolution of sociality and cultural traits.


Pouthier V.,French National Center for Scientific Research
Journal of Chemical Physics | Year: 2010

Based on dynamical considerations, a simple and intuitive criterion is established to measure the strength of the vibron-phonon coupling in a lattice of H-bonded peptide units. The main idea is to compare separately the influence of both the vibron-phonon coupling and the dipole-dipole interaction on a specific element of the vibron reduced density matrix. This element, which refers to the coherence between the ground state and a local excited amide-I mode, generalizes the concept of survival amplitude at finite temperature. On the one hand, when the dipole-dipole interaction is neglected, it is shown that dephasing-limited coherent dynamics is induced by the vibron-phonon coupling. On the other hand, when the vibron-phonon coupling is disregarded, decoherence occurs due to dipole-dipole interactions since the local excited state couples with neighboring local excited states. Therefore, our criterion simply states that the strongest interaction is responsible for the fastest decoherence. It yields a critical coupling ≈25 pN at biological temperature. © 2010 American Institute of Physics.


Ricci O.,French National Center for Scientific Research
Energy Policy | Year: 2012

Knowing that carbon capture and storage (CCS) could play an important role in reducing emissions, it is important to have a good understanding of this role and the importance of environmental policies to support carbon capture and geological storage from bioenergies (BECCS). To date CCS technologies are not deployed on a commercial level, and policy instruments should be used to provide incentives to firms to use these technologies to reduce pollution. The aim of this paper is to compare the cost-efficiency of several incentive-based instruments (a fossil fuel tax, an emissions tax, a cap and trade system, and a subsidy on captured emissions) needed to spur the adoption of CCS and BECCS, using a dynamic general equilibrium model. This type of model has become the standard for assessing economy-wide impacts of environmental and technological policies. The study shows that BECCS will be deployed only if a specific subsidy per unit of biomass emissions captured with a CCS technology is available. We show also that the two most cost-efficient instruments for achieving a given emissions reduction target are a specific subsidy that rewards captured emissions and a carbon tax whose revenues are recycled to subsidize BECCS. © 2012 Elsevier Ltd.


Cavalli G.,French National Center for Scientific Research
Science | Year: 2012

A transcriptional repressor switches to an activator function in an aggressive form of prostate cancer.


Eberl G.,Institute Pasteur Paris | Eberl G.,French National Center for Scientific Research
Immunological Reviews | Year: 2012

The nuclear hormone receptor retinoid-related orphan receptor γt (RORγt) induces a pro-inflammatory program in lymphoid cells, culminating in the expression of interleukin-6 (IL-6), IL-17, IL-22, granulocyte-macrophage colony-stimulating factor, and tumor necrosis factor. During ontogeny, the first type of cells expressing RORγt are lymphoid tissue inducer cells, a type of innate lymphoid cell (ILC) generated in mammalian fetuses to induce the development of lymph nodes and Peyer's patches. After birth, RORγt + ILCs and RORγt + T cells are involved in the defense of epithelial surfaces against extracellular microbes and play an important role in the intestinal homeostasis with symbiotic microbiota. The development and evolution of RORγt + cells is intimately associated with the construction of a stable host-microbe interface. © 2011 John Wiley & Sons A/S.


Laperrousaz B.,French National Center for Scientific Research
Blood | Year: 2013

Leukemic stem cells in chronic phase chronic myelogenous leukemia (CP-CML) are responsible for disease persistence and eventual drug resistance, most likely because they survive, expand, and are sustained through interactions with their microenvironment. Bone morphogenetic proteins 2 (BMP2) and 4 (BMP4) regulate the fate and proliferation of normal hematopoietic stem cells, as well as interactions with their niche. We show here that the intrinsic expression of members of the BMP response pathway are deregulated in CML cells with differences exhibited in mature (CD34(-)) and immature (CD34(+)) compartments. These changes are accompanied by altered functional responses of primitive leukemic cells to BMP2 and BMP4 and strong increases in soluble BMP2 and BMP4 in the CML bone marrow. Using primary cells and a cell line mimicking CP-CML, we found that myeloid progenitor expansion is driven by the exposure of immature cells overexpressing BMP receptor Ib to BMP2 and BMP4. In summary, we demonstrate that deregulation of intracellular BMP signaling in primary CP-CML samples corrupts and amplifies their response to exogenous BMP2 and BMP4, which are abnormally abundant within the tumor microenvironment. These results provide new insights with regard to leukemic stem cell biology and suggest possibilities for the development of novel therapeutic tools specifically targeting the CML niche.


The atrioventricular node controls cardiac impulse conduction and generates pacemaker activity in case of failure of the sino-atrial node. Understanding the mechanisms of atrioventricular automaticity is important for managing human pathologies of heart rate and conduction. However, the physiology of atrioventricular automaticity is still poorly understood. We have investigated the role of three key ion channel-mediated pacemaker mechanisms namely, Ca(v)1.3, Ca(v)3.1 and HCN channels in automaticity of atrioventricular node cells (AVNCs). We studied atrioventricular conduction and pacemaking of AVNCs in wild-type mice and mice lacking Ca(v)3.1 (Ca(v)3.1(-/-)), Ca(v)1.3 (Ca(v)1.3(-/-)), channels or both (Ca(v)1.3(-/-)/Ca(v)3.1(-/-)). The role of HCN channels in the modulation of atrioventricular cells pacemaking was studied by conditional expression of dominant-negative HCN4 channels lacking cAMP sensitivity. Inactivation of Ca(v)3.1 channels impaired AVNCs pacemaker activity by favoring sporadic block of automaticity leading to cellular arrhythmia. Furthermore, Ca(v)3.1 channels were critical for AVNCs to reach high pacemaking rates under isoproterenol. Unexpectedly, Ca(v)1.3 channels were required for spontaneous automaticity, because Ca(v)1.3(-/-) and Ca(v)1.3(-/-)/Ca(v)3.1(-/-) AVNCs were completely silent under physiological conditions. Abolition of the cAMP sensitivity of HCN channels reduced automaticity under basal conditions, but maximal rates of AVNCs could be restored to that of control mice by isoproterenol. In conclusion, while Ca(v)1.3 channels are required for automaticity, Ca(v)3.1 channels are important for maximal pacing rates of mouse AVNCs. HCN channels are important for basal AVNCs automaticity but do not appear to be determinant for β-adrenergic regulation.


Brochier A.,French National Center for Scientific Research
Communications in Mathematical Physics | Year: 2012

We compute explicitly the monodromy representations of "cyclotomic" analogs of the Knizhnik-Zamolodchikov differential system. These are representations of the type B braid group B n 1. We show how the representations of the braid group B n obtained using quantum groups and universal R-matrices may be enhanced to representations of B n 1 using dynamical twists. Then, we show how these "algebraic" representations may be identified with the above "analytic" monodromy representations. © 2012 Springer-Verlag.


Joly R.,French National Center for Scientific Research
Nonlinearity | Year: 2012

A coupled cell network is a model for many situations such as food webs in ecosystems, cellular metabolism and economic networks. It consists in a directed graph G, each node (or cell) representing an agent of the network and each directed arrow representing which agent acts on which. It yields a system of differential equations , where the component i of f depends only on the cells x j(t) for which the arrow j → i exists in G. In this paper, we investigate the observation problems in coupled cell networks: can one deduce the behaviour of the whole network (oscillations, stabilization, etc) by observing only one of the cells? We show that the natural observation properties hold for almost all the interactions f. © 2012 IOP Publishing Ltd & London Mathematical Society.


Girand A.,French National Center for Scientific Research
Nonlinearity | Year: 2014

In this paper, we set up a 'dictionary' between discrete Schrödinger operators and holomorphic dynamics on certain affine cubic surfaces, building on previous work by Cantat, Damanik and Gorodetski. To achieve this, we make use of potential theory: a detailed description of the dynamical Green functions is obtained; then basic results concerning the equilibrium measures and the Green functions of compact subsets of C are used to transfer statements from the dynamical context to the Schrödinger one. This provides a new viewpoint on several recent theorems. © 2014 IOP Publishing Ltd.


The paper introduces the concept of the microbial electrochemical snorkel (MES), a simplified design of a "short-circuited" microbial fuel cell (MFC). The MES cannot provide current but it is optimized for wastewater treatment. An electrochemically active biofilm (EAB) was grown on graphite felt under constant polarization in an urban wastewater. Controlling the electrode potential and inoculating the bioreactor with a suspension of an established EAB improved the performance and the reproducibility of the anodes. Anodes, colonized by an EAB were tested for the chemical oxygen demand (COD) removal from urban wastewater using a variety of bio-electrochemical processes (microbial electrolysis, MFC, MES). The MES technology, as well as a short-circuited MFC, led to a COD removal 57% higher than a 1000 Ω-connected MFC, confirming the potential for wastewater treatment.


Basile C.,French National Center for Scientific Research
Tectonophysics | Year: 2015

This paper reviews the geodynamic concepts and models related to transform continental margins, and their implications on the structure of these margins. Simple kinematic models of transform faulting associated with continental rifting and oceanic accretion allow to define three successive stages of evolution, including intra-continental transform faulting, active transform margin, and passive transform margin. Each part of the transform margin experiences these three stages, but the evolution is diachronous along the margin. Both the duration of each stage and the cumulated strike-slip deformation increase from one extremity of the margin (inner corner) to the other (outer corner).Initiation of transform faulting is related to the obliquity between the trend of the lithospheric deformed zone and the relative displacement of the lithospheric plates involved in divergence. In this oblique setting, alternating transform and divergent plate boundaries correspond to spatial partitioning of the deformation. Both obliquity and the timing of partitioning influence the shape of transform margins. Oblique margin can be defined when oblique rifting is followed by oblique oceanic accretion. In this case, no transform margin should exist in the prolongation of the oceanic fracture zones. Vertical displacements along transform margins were mainly studied to explain the formation of marginal ridges. Numerous models were proposed, one of the most used is being based on thermal exchanges between the oceanic and the continental lithospheres across the transform fault. But this model is compatible neither with numerical computation including flexural behavior of the lithosphere nor with timing of vertical displacements and the lack of heating related to the passing of the oceanic accretion axis as recorded by the Côte d'Ivoire-Ghana marginal ridge. Enhanced models are still needed. They should better take into account the erosion on the continental slope, and the level of coupling of the transform continental margin with the adjacent oceanic lithosphere. © 2015 Elsevier B.V.


Mintova S.,University of Caen Lower Normandy | Jaber M.,University Pierre and Marie Curie | Jaber M.,French National Center for Scientific Research | Valtchev V.,University of Caen Lower Normandy
Chemical Society Reviews | Year: 2015

This review highlights recent developments in the synthesis and unconventional applications of nanosized microporous crystals including framework (zeolites) and layered (clays) type materials. Owing to their microporous nature nanosized zeolites and clays exhibit novel properties, different from those of bulk materials. The factors controlling the formation of nanosized microporous crystals are first revised. The most promising approaches from the viewpoint of large-scale production of nanosized zeolites and clays are discussed in depth. The preparation and advanced applications of nanosized zeolites and clays in free (suspension and powder forms) and fixed (films) forms are summarized. Further the review emphasises the non-conventional applications of new porous materials. A comprehensive analysis of the emerging applications of microporous nanosized crystals in the field of semiconductor industry, optical materials, chemical sensors, medicine, cosmetics, and food industry is presented. Finally, the future needs and perspectives of nanosized microporous materials (zeolites and clays) are addressed. © The Royal Society of Chemistry.


Mutihac L.,University of Bucharest | Lee J.H.,Korea University | Kim J.S.,Korea University | Vicens J.,French National Center for Scientific Research
Chemical Society Reviews | Year: 2011

The calixarenic receptors exhibit remarkable host-guest properties towards biologically relevant guests. Aspects of complex formation reactions between both native and derivatized amino acids, di-and tripeptides with calixarenic (chiral or not) receptors are summarized in this critical review. Thus, the discussions emphasize the parameters that affect the molecular binding selectivity and efficiency of functionalized calix[n]arenes towards these substrates. A brief survey on their application in separation of amino acids is also considered (123 references). © 2011 The Royal Society of Chemistry.


Sibarita J.-B.,French National Center for Scientific Research
Histochemistry and Cell Biology | Year: 2014

The organization and dynamics of proteins are fundamental parameters for cellular function. Their study, at the single-molecule level, provides precise information on molecular interactions. Over the last 30 years, the single-particle tracking imaging technique has proven its capability to efficiently quantify such parameters in many biological systems, with nanometric accuracy and millisecond temporal resolutions. Nevertheless, the low concentration of labeling required for single-molecule imaging usually prevents the extraction of large statistics. The advent of high-density single-molecule-based super-resolution techniques has revolutionized the field, allowing monitoring of thousands of biomolecules in the minute timescale and providing unprecedented insight into the molecular organization and dynamics of cellular compounds. In this issue, I will review the main principles of single-particle tracking, a highly interdisciplinary technique at the interface between microscopy, image analysis and labeling strategies. I will point out the advantages brought by high-density single-particle tracking which will be illustrated with a few recent biological results. © 2014 Springer-Verlag.


Tanay A.,Weizmann Institute of Science | Cavalli G.,French National Center for Scientific Research
Current Opinion in Genetics and Development | Year: 2013

We review recent developments in mapping chromosomal contacts and compare emerging insights on chromosomal contact domain organization in Drosophila and mammalian cells. Potential scenarios leading to the observation of Hi-C domains and their association with the epigenomic context of the chromosomal elements involved are discussed. We argue that even though the mechanisms and precise physical structure underlying chromosomal domain demarcation are yet to be fully resolved, the implications to genome regulation and genome evolution are profound. Specifically, we hypothesize that domains are facilitating genomic compartmentalization that support the implementation of complex, modular, and tissue specific transcriptional program in metazoa. © 2013 Elsevier Ltd.


Tibayrenc M.,French National Center for Scientific Research | Ayala F.J.,University of California at Irvine
Proceedings of the National Academy of Sciences of the United States of America | Year: 2015

The three species Neisseria meningitidis, Neisseria gonorrheae, and Neisseria lactamica are often regarded as highly recombining bacteria. N. meningitidis has been considered a paradigmatic case of the "semiclonal model" or of "epidemic clonality," demonstrating occasional bouts of clonal propagation in an otherwise recombining species. In this model, occasional clonality generates linkage disequilibrium in the short term. In the long run, however, the effects of clonality are countered by recombination. We show that many data are at odds with this proposal and that N. meningitidis fits the criteria that we have proposed for predominant clonal evolution (PCE). We point out that (i) the proposed way to distinguish epidemic clonality from PCE may be faulty and (ii) the evidence of deep phylogenies by microarrays and whole-genome sequencing is at odds with the predictions of the semiclonal model. Last, we revisit the species status of N. meningitidis, N. gonorrheae, and N. lactamica in the light of the PCE model. © 2015, National Academy of Sciences. All rights reserved.


Carlet C.,French National Center for Scientific Research
IEEE Transactions on Information Theory | Year: 2011

We show that the first of the two constructions by Q. Wang, J. Peng, H. Kan, and X. Xue, IEEE Transactions on Information Theory, vol. 56, no. 6, pp. 3048-3053, 2010, of Boolean functions satisfying the main criteria for filter functions in stream ciphers, is the same as the construction studied by K. Feng and the author at Asiacrypt 2008, LNCS 5350, pp. 425-440. We observe that the bounds shown on the nonlinearities of the functions in this IEEE paper are similar to those shown in the Asiacrypt paper. We point out that these kinds of functions can be implemented in a more efficient way than usually believed. © 2011 IEEE.


Hammani K.,University of Oregon | Hammani K.,French National Center for Scientific Research | Barkan A.,University of Oregon
Nucleic Acids Research | Year: 2014

The mitochondrial transcription termination factor (mTERF) proteins are nucleic acid binding proteins characterized by degenerate helical repeats of ∼30 amino acids. Metazoan genomes encode a small family of mTERF proteins whose members influence mitochondrial gene expression and DNA replication. The mTERF family in higher plants consists of roughly 30 members, which localize to mitochondria or chloroplasts. Effects of several mTERF proteins on plant development and physiology have been described, but molecular functions of mTERF proteins in plants are unknown. We show that a maize mTERF protein, Zm-mTERF4, promotes the splicing of group II introns in chloroplasts. Zm-mTERF4 coimmunoprecipitates with many chloroplast introns and the splicing of some of these introns is disrupted even in hypomorphic Zm-mterf4 mutants. Furthermore, Zm-mTERF4 is found in high molecular weight complexes that include known chloroplast splicing factors. The splicing of two transfer RNAs (trnI-GAU and trnA-UGC) and one ribosomal protein messenger RNA (rpl2) is particularly sensitive to the loss of Zm-mTERF4, accounting for the loss of plastid ribosomes in Zm-mTERF4 mutants. These findings extend the known functional repertoire of the mTERF family to include group II intron splicing and suggest that a conserved role in chloroplast RNA splicing underlies the physiological defects described for mutations in BSM/Rugosa2, the Zm-mTERF4 ortholog in Arabidopsis. © 2014 © The Author(s) 2014. Published by Oxford University Press.


Sieweke M.H.,Aix - Marseille University | Sieweke M.H.,French Institute of Health and Medical Research | Sieweke M.H.,French National Center for Scientific Research | Allen J.E.,University of Edinburgh
Science | Year: 2013

In many mammalian tissues, mature differentiated cells are replaced by self-renewing stem cells, either continuously during homeostasis or in response to challenge and injury. For example, hematopoietic stem cells generate all mature blood cells, including monocytes, which have long been thought to be the major source of tissue macrophages. Recently, however, major macrophage populations were found to be derived from embryonic progenitors and to renew independently of hematopoietic stem cells. This process may not require progenitors, as mature macrophages can proliferate in response to specific stimuli indefinitely and without transformation or loss of functional differentiation. These findings suggest that macrophages are mature differentiated cells that may have a self-renewal potential similar to that of stem cells.


Giuliani A.,French National Center for Scientific Research | Poves A.,Autonomous University of Madrid
Advances in High Energy Physics | Year: 2012

This paper introduces the neutrinoless double-beta decay (the rarest nuclear weak process) and describes the status of the research for this transition, both from the point of view of theoretical nuclear physics and in terms of the present and future experimental scenarios. Implications of this phenomenon on crucial aspects of particle physics are briefly discussed. The calculations of the nuclear matrix elements in case of mass mechanisms are reviewed, and a range for these quantities is proposed for the most appealing candidates. After introducing general experimental concepts - such as the choice of the best candidates, the different proposed technological approaches, and the sensitivity - we make the point on the experimental situation. Searches running or in preparation are described, providing an organic presentation which picks up similarities and differences. A critical comparison of the adopted technologies and of their physics reach (in terms of sensitivity to the effective Majorana neutrino mass) is performed. As a conclusion, we try to envisage what we expect round the corner and at a longer time scale. © 2012 Andrea Giuliani and Alfredo Poves.


Magny M.,French National Center for Scientific Research
Palaeogeography, Palaeoclimatology, Palaeoecology | Year: 2013

High-resolution sediment analysis at Gerzensee, Swiss Plateau, focused on the reconstruction of lake-level changes during the last glaciation Greenland Stadial 2a (GS-2a) and a large portion of Lateglacial including the Gerzensee oscillation. The chronology is derived from a comparison of the oxygen-isotope stratigraphy established at Gerzensee with that of the NGRIP ice core. On a multi-millennial scale differences between the lake-level and oxygen-isotope records established from cores GEJ-GEK reflect a complex interplay among climate, vegetation and lake level during retreat of the ice sheet. But on a multi-centennial scale both the lake-level and oxygen-isotope records show a general agreement, i.e. cool periods such as Greenland Stadial GS-2a and Greenland Interstadials-1d and -1b, which coincided with more positive water budgets and, conversely, warm periods (Greenland Interstadials-1e and -1c) with more negative water budget. This is in agreement with the regional pattern of palaeohydrological changes reconstructed from previous studies. Despite possible reduced annual precipitation during GS-2a, the maintenance of relatively high lake-level conditions at Gerzensee at this time could have resulted from reduced evaporation and stronger runoff on bare slopes, whereas during the Lateglacial Interstadial the phases of lake-level lowering may have been associated with summer dryness linked to increasing summer insolation. © 2012 Elsevier B.V.


Bacteria degrading quorum sensing (QS) signals have been proposed as biocontrol agents able to quench QS-dependent expression of virulence symptoms caused by Pectobacterium on potato plants. We report here that gamma-caprolactone (GCL) treatment stimulated growth of the native QS-degrading bacterial community in an industrial plant hydroponic system for culturing Solanum tuberosum. Post-GCL treatment, QS-degrading bacteria were mainly identified as Rhodococcus isolates, while Agrobacterium isolates dominated under similar untreated conditions. Most of the assayed Rhodococcus isolates exhibited efficient biocontrol activity for protecting potato tubers. Analytical chemistry approach revealed the rapid degradation of GCL introduced in the plant cultures. Copyright © 2011 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.


Branger F.,CIRED | Quirion P.,French National Center for Scientific Research