Éditeur(s) : HAL CCSD National Academy of Sciences
Résumé : International audience
The complexity and depth of the relationships between the three domains of life challenge the reliability of phylogenetic methods, encouraging the use of alternative analytical tools. We reconstructed a gene similarity network comprising the proteomes of 14 eukaryotes, 104 prokaryotes, 2,389 viruses and 1,044 plasmids. This network contains multiple signatures of the chimerical origin of Eukaryotes as a fusion of an archaebacterium and a eubacterium that could not have been observed using phylogenetic trees. A number of connected components (gene sets with stronger similarities than expected by chance) contain pairs of eukaryotic sequences exhibiting no direct detectable similarity. Instead, many eukaryotic sequences were indirectly connected through a ``eukaryote-archaebacterium-eubacterium-eukaryote'' similarity path. Furthermore, eukaryotic genes highly connected to prokaryotic genes from one domain tend not to be connected to genes from the other prokaryotic domain. Genes of archaebacterial and eubacterial ancestry tend to perform different functions and to act at different subcellular compartments, but in such an intertwined way that suggests an early rather than late integration of both gene repertoires. The archaebacterial repertoire has a similar size in all eukaryotic genomes whereas the number of eubacterium-derived genes is much more variable, suggesting a higher plasticity of this gene repertoire. Consequently, highly reduced eukaryotic genomes contain more genes of archaebacterial than eubacterial affinity. Connected componentswith prokaryotic and eukaryotic genes tend to include viral and plasmid genes, compatible with a role of gene mobility in the origin of Eukaryotes. Our analyses highlight the power of network approaches to study deep evolutionary events.
ISSN: 0027-8424

hal-01544798
https://hal.archives-ouvertes.fr/hal-01544798
DOI : 10.1073/pnas.1211371110

Éditeur(s) : HAL CCSD
Résumé : International audience
During the last decade, GIS have suffered of the lack of structured information and semantic definition of the data. The numerous origins of the data and the spatial localization of the object inferred many inconsistencies among them. Indeed, the way to collect data and the level of sampling of the boundary differ from one application to another and from one expert to another. This leads to different representations of the same reality and different models of semantically identical objects or boundaries. To allow the matching of the objects, or parts of the objects, when combining different information layers we introduced a conceptual layer which described a scene with concepts and spatial relationships based on the definition of an ontology. This layer allows detecting and solving conflicts between the common boundaries of two objects. We present in this paper the specification and the way to build and use the ontology.
Geoprocessing proceedings
Gosier, Guadeloupe

hal-00602257
https://hal.archives-ouvertes.fr/hal-00602257

Éditeur(s) : HAL CCSD American Chemical Society
Résumé : International audience
Four bicyclic and three pentacyclic guanidine alkaloids (1–7) were isolated from a French Polynesian Monanchora n. sp. sponge, along with the known alkaloids monalidine A (8), enantiomers 9–11 of known natural product crambescins, and the known crambescidins 12–15. Structures were assigned by spectroscopic data interpretation. The relative and absolute configurations of the alkaloids were established by analysis of 1H NMR and NOESY spectra and by circular dichroism analysis. The new norcrambescidic acid (7) corresponds to interesting biosynthetic variation within the pentacyclic core. All compounds exhibited antiproliferative and cytotoxic efficacy against KB, HCT116, HL60, MRC5, and B16F10 cancer cells, with IC50 values ranging from 4 nM to 10 μM.
ISSN: 0163-3864

hal-01584556
https://hal.archives-ouvertes.fr/hal-01584556
DOI : 10.1021/acs.jnatprod.6b00168

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
The extinct Odontopterygiformes are the sole birds known to possess strong and sharp bony pseudoteeth, the shape and location of which are closely mimetic of real teeth. The structure of the pseudoteeth is investigated here in a late Pliocene/early Pleistocene species, Pelagornis mauretanicus, using X-ray microtomography and thin sections. The results are interpreted with regard to the pseudotooth mode of growth, and have implications concerning aspects of Pelagornis ecology. The larger pseudoteeth are hollow and approximately cone-shaped, and the smaller ones are rostro-caudally constricted. The walls of pseudoteeth are composed of bone tissue of the fibro-lamellar type, which is intensively remodeled by Haversian substitution. The jaw bones display the same structure as the pseudoteeth, but their vascular canals are oriented parallel to the long axis of the bones, whereas they are perpendicular to this direction in the pseudoteeth. There is no hiatus or evidence of a fusion between the pseudoteeth and the jaw bones. Two possible models for pseudotooth growth are derived from the histological data. The most plausible model is that pseudotooth growth began after the completion of jaw bone growth, as a simple local protraction of periosteal osteogenic activity. Pseudotooth development thus occurred relatively late during ontogeny. The highly vascularized structure and the relative abundance of parallel-fibered bone tissue in the pseudoteeth suggest poor mechanical capabilities. The pseudoteeth were most likely covered and protected by the hardened, keratinized rhamphotheca in the adult during life. The late development of the pseudoteeth would involve a similarly late and/or partial hardening of the rhamphotheca, as displayed by extant Anseriformes, Apterygiformes and some Charadriiformes. This would add support to the hypothesis of a close phylogenetic relationship between Odontopterygiformes and Anseriformes. The late maturation of the Pelagornis feeding apparatus, and hence the delayed capability for efficient prey catching, suggests that Pelagornis was altricial.
ISSN: 1932-6203

hal-01545486
https://hal.archives-ouvertes.fr/hal-01545486
DOI : 10.1371/journal.pone.0080372

Éditeur(s) : HAL CCSD
Résumé : La présente invention concerne un vecteur recombinant pour l'expression et la sécrétion, par une bactérie propionique, d'une ou plusieurs séquences d'acides aminés d'intérêt, ledit vecteur comprenant au moins : - sous le contrôle d'au moins un promoteur approprié, - au moins une séquence nucléotidique codant un peptide signal de bactérie propionique et, en fusion traductionnelle avec celle-ci, - une ou plusieurs séquences nucléotidiques codant la ou lesdites séquences d'acides aminés d'intérêt. L'invention s'intéresse également aux utilisations d'un tel vecteur dans le domaine pharmaceutique ou pour la production à grande échelle de peptides ou protéines d'intérêt.
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01122525

Patent N° : FR 2960001 (A1), WO 2011141558 (A1)
hal-01122525
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01122525

Éditeur(s) : HAL CCSD Elsevier
Résumé : Water molecules play a fundamental role in the physics of slow crack propagation in glasses. It is commonly understood that, during stress-corrosion, water molecules that move in the crack cavity effectively reduce the bond strength at the strained crack tip and, thus, support crack propagation. Yet the details of the environmental condition at the crack tip in moist air are not well determined. In a previous work, we reported direct evidence of the presence of a 100 nm long liquid condensate at the crack tip in fused silica glass during very slow crack propagation (10(-9)-10(-10) m/s). These observations are based on in situ AFM phase imaging techniques applied on DCDC glass specimens in controlled atmosphere. Here, we discuss the physical origin of the AFM phase contrast between the liquid condensate and the glass surface in relation to tip-sample adhesion induced by capillary bridges. We then report new experimental data on the water condensation length increase with relative humidity in the atmosphere. The measured condensation lengths were much larger than what predicted using the Kelvin equation and expected geometry of the crack tip.
ISSN: 0022-3093

hal-00412153
https://hal.archives-ouvertes.fr/hal-00412153
DOI : 10.1016/j.jnoncrysol.2007.06.090

Éditeur(s) : HAL CCSD Société géologique de France
Résumé : International audience
– The 300 km long allochthonous sheet of oceanic mantle forming the New Caledonia ophiolite displays three specific characters: 1) the ophiolite pile lacks concordant sheeted dykes and pillow basalt layers; 2) the ophiolite, refered to as the Peridotite nappe, is thrusted over the basaltic formations of the Poya terrane which are classicaly thought to originate from a different oceanic environment; 3) The basal contact of the ultramafic sheet is remarkably flat all along New-Caledonia and the Peridotite nappe has not been thickened during obduction, rather it experienced significant extension. This suggests that the peridotites have not been emplaced by a tectonic force applied to the rear. New petrological and geochemical results obtained from mantle rocks finally show that the Poya terrane may originate from the same oceanic basin as the peridotites. In this article, we consider such possible cogenetic links and we propose a simple model for the obduction of the New Caledonia ophiolite in which the Poya basalts represent the original cover of the Peridotite nappe. We infer that continuous uplift of the subducted units buried beneath the oceanic lithosphere in the northern part of New Caledonia drove passive uplift of the ophiolite and led to erosion and to initiation of sliding of the basaltic layer. During the Priabonian (latest Eocene), products of the erosion of the basaltic layer were deposited together with sediments derived from the Norfolk passive oceanic margin. These sediments are involved as tectonic slices into an accretionary wedge formed in response to plate convergence. The volcaniclastic sedimentation ends up with the emplacement of large slided blocks of basalts and rafted mafic units that progressively filled up the basin. Obduction process ended with the gravity sliding of the oceanic mantle sheet, previously scalped from its mafic cover. This process is contemporaneous with the exhumation of the HP-LT units of Pouebo and Diahot. Gravity sliding was facilitated by the occurrence of a continuous serpentine sole resulting from metasomatic hydratation of mantle rocks, which developed during the uplift of the Norfolk basement and overlying Diahot and Pouébo units. Progressive emersion of the obducted lithosphere allowed subsequent weathering under subaerial, tropical conditions. Obduction passive et mise en place gravitaire des grandes nappes ophiolitiques : les ophiolites de Nouvelle-Calédonie (SW Pacifique) sont-elles un cas d'école ? Résumé. – La nappe de manteau de Nouvelle-Calédonie, s'étendant sur 300 km de long montre trois caractéristiques im-portantes: 1) La succession ophiolitique ne contient ni dykes, ni basaltes en coussin, 2) l'ophiolite est charriée sur des formations basaltiques (nappe de Poya) que l'on considère classiquement comme originaires d'un bassin océanique dif-férent de celui d'où est issu le manteau, et 3) le contact basal de la nappe ultrabasique est remarquablement plat tout le long de l'île et celle-ci n'a pas été épaissie durant l'obduction. Cela suggère que les péridotites n'ont pas été mises en place en réponse à une poussée tectonique arrière. De nouveaux résultats pétrologiques et géochimiques obtenus sur l'ophiolite montrent en réalité que les basaltes de Poya peuvent être extraits de la fusion du manteau de l'ophiolite. Nous proposons donc un nouveau modèle pour l'obduction, dans lequel les basaltes de Poya forment la couver-ture initiale primitive du manteau de la nappe des péridotites. La surrection progressive des unités profondes enfouies lors de la subduction de la lithosphère du bassin sud-Loyauté à l'Eocène, a permis le soulèvement passif de l'ophiolite et l'érosion puis le glissement des unités basaltiques. Durant le Priabonien, l'accumulation des produits de l'érosion de la couche des basaltes et de la marge passive de Norfolk ont formé les séquences de flysch comprenant localement des débris basaltiques grossiers. Ces sédiments font partie d'un prisme d'accrétion tectonique construit en réponse à la convergence au front de la subduction. La sédimentation détritique se termine par la mise en place de grandes unités ba-saltiques glissées qui comblent le bassin. Le processus de l'obduction se termine par le glissement gravitaire de l'écaille de manteau océanique sur les basaltes. Cet événement est contemporain de l'exhumation des unités HP-BT de Pouébo et du Diahot. Le glissement gravitaire a été facilité par la présence sous l'ophiolite, d'une semelle continue de serpentines résultant de l'interaction du manteau avec des fluides métasomatiques remontant durant l'exhumation des unités en-fouies pendant la subduction continentale. L'émersion progressive de la lithosphère obduite a placé le manteau dans des conditions d'altération supergène tropicale.
EISSN: 1777-5817

hal-01257702
https://hal.archives-ouvertes.fr/hal-01257702
https://hal.archives-ouvertes.fr/hal-01257702/document
https://hal.archives-ouvertes.fr/hal-01257702/file/Lagabrielleetal-BSGF-2012-revised-light.pdf
DOI : 10.2113/gssgfbull.184.6.545

Éditeur(s) : HAL CCSD
Résumé : International audience
In this paper, we use a multifractal approach based on the computation of two spectrums for image analysis and texture segmentation problems. The two spectrums are the Legendre Spectrum, determined by classical methods, and the Large Deviation Spectrum, determined by kernel density estimation. We propose a way for the fusion of these two spectrums to improve textured image segmentation results. An unsupervised k-means is used as clustering approach for the texture classification. The algorithm is applied on mosaic image built using IKONOS images and various natural textures from the Brodatz album. The segmentation obtained with our approach gives better results than the application of each spectrum separately.
CIARP Proceedings
Cancun, Mexico

hal-00602268
https://hal.archives-ouvertes.fr/hal-00602268

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Ecological signs of Earth's biosphere forewarn an alarming trajectory towards a global mass-extinction. Assessing species performance and susceptibilities to decline is essential to comprehend and reverse this trend. Yet it is challenging, given difficulties associated with quantifying individual and population processes that are variable across time, space, and life-stages. We describe a new approach to estimating and comparing species performances that combines empirical data, a novel theoretical consideration of population dynamics, and modern statistics. Our approach allows for a more realistic continuous representation of individual performances along development stages while taking into account non-linearity, and natural variability as captured by spatio-temporally replicated observations. We illustrate its application in a coral meta-assemblage composed of populations of the three major reef-building taxa Acropora, Pocillopora, Porites. Using a unique set of highly replicated observations of individual coral dynamics under various environmental conditions, we show how taxa differ in their investment in recruitment and size-specific aptitude for growth and survival, notably through different use of clonal shrinkage, fragmentation, fission, and fusion processes. Our results reveal contrasting life-history trade-offs among taxa which, along with differing patterns of density-dependent recruitment, modulate species responses to decline. These differences in coral life history traits reflect opposing life-strategies, imply regulation at differing life-stages, and explain divergence in species trajectories. Our findings indicate a high potential for resilience in Pocillopora and Porites populations, thanks respectively to a sustained recruitment that promotes demographic elasticity through replacement of individuals, and a steady resistance to mortality which confers persistence through lingering of individuals. Resilience in Acropora appears more arbitrary, given high susceptibility to perturbations and dependency of recruitment on presence of established local populations. We identify management actions that can complement Acropora's life history and benefit recovery of its populations following mortality events. Our regression-modelling approach to quantifying and comparing species performances in different population processes is applicable to all taxa, as illustrated even those with complex clonal life histories, and can be implemented at wide spatio-temporal and taxonomic coverage. It can promote more accurate representation of species dynamics in both descriptive and predictive modelling approaches. The semi-parametric contrast curve method we develop facilitates comparing response variables along continuous explicative metrics while accounting for multiple sources of complexity in empirical data. It should widely benefit investigations in ecology and quantitative science.
ISSN: 1476-945X

hal-01212337
https://hal-univ-perp.archives-ouvertes.fr/hal-01212337
DOI : 10.1016/j.ecocom.2015.07.003