New analysis for consistency among markers in the study of genetic diversity: development and application to the description of bacterial diversity

<p>Abstract</p> <p>Background</p> <p>The development of post-genomic methods has dramatically increased the amount of qualitative and quantitative data available to understand how ecological complexity is shaped. Yet, new statistical tools are needed to use these data efficiently. In support of sequence analysis, diversity indices were developed to take into account both the relative frequencies of alleles and their genetic divergence. Furthermore, a method for describing inter-population nucleotide diversity has recently been proposed and named the double principal coordinate analysis (DPCoA), but this procedure can only be used with one locus. In order to tackle the problem of measuring and describing nucleotide diversity with more than one locus, we developed three versions of multiple DPCoA by using three ordination methods: multiple co-inertia analysis, STATIS, and multiple factorial analysis.</p> <p>Results</p> <p>This combination of methods allows i) testing and describing differences in patterns of inter-population diversity among loci, and ii) defining the best compromise among loci. These methods are illustrated by the analysis of both simulated data sets, which include ten loci evolving under a stepping stone model and a locus evolving under an alternative population structure, and a real data set focusing on the genetic structure of two nitrogen fixing bacteria, which is influenced by geographical isolation and host specialization. All programs needed to perform multiple DPCoA are freely available.</p> <p>Conclusion</p> <p>Multiple DPCoA allows the evaluation of the impact of various loci in the measurement and description of diversity. This method is general enough to handle a large variety of data sets. It complements existing methods such as the analysis of molecular variance or other analyses based on linkage disequilibrium measures, and is very useful to study the impact of various loci on the measurement of diversity.</p

A perceptual hash function to store and retrieve large scale DNA sequences

This paper proposes a novel approach for storing and retrieving massive DNA sequences.. The method is based on a perceptual hash function, commonly used to determine the similarity between digital images, that we adapted for DNA sequences. Perceptual hash function presented here is based on a Discrete Cosine Transform Sign Only (DCT-SO). Each nucleotide is encoded as a fixed gray level intensity pixel and the hash is calculated from its significant frequency characteristics. This results to a drastic data reduction between the sequence and the perceptual hash. Unlike cryptographic hash functions, perceptual hashes are not affected by "avalanche effect" and thus can be compared. The similarity distance between two hashes is estimated with the Hamming Distance, which is used to retrieve DNA sequences. Experiments that we conducted show that our approach is relevant for storing massive DNA sequences, and retrieving them

Unsupervised spectral learning of WCFG as low-rank matrix completion

We derive a spectral method for unsupervised learning ofWeighted Context Free Grammars. We frame WCFG induction as finding a Hankel matrix that has low rank and is linearly constrained to represent a function computed by inside-outside recursions. The proposed algorithm picks the grammar that agrees with a sample and is the simplest with respect to the nuclear norm of the Hankel matrix.Peer ReviewedPreprin

Are copepods secondary hosts of Cycliophora?

Ever since the first observations in the late 1960s, Cycliophora were found exclusively living epizoically on lobsters belonging to the family Nephropidae. The complex cycliophoran life cycle, with alternation of asexual and sexual generations, takes place only in the microhabitat provided by the host mouthparts. Herein, we report the first evidence of a symbiotic relationship between cycliophorans and organisms other than nephropid lobsters, namely, the harpacticoid copepods. Two specimens of copepods associated with cycliophoran life cycle stages were collected from the segmental mouthparts of a European lobster, Homarus gammarus. One of the copepods carried two feeding stages with long stalks, which probably belong to an undescribed Symbion sp., while the other copepod was found bearing an undetermined settled stage. We discuss the implications of these novel observations for the understanding of the Cycliophora life cycle and their dispersion abilities

Direct noise computation of adaptive control applied to a cavity flow

The Large Eddy Simulation of closed-loop active flow control applied to a 3D cavity excited by a compressible airflow with a Mach number of 0.6 is presented. The control actuator is an idealized synthetic jet located at the upstream cavity edge, and the control function is supplied by a feedback LMS-type algorithm whose input is a pressure signal measured inside the cavity. The radiated sound, provided directly by the LES simulation, was shown to decrease substantially when active control was applied. A simultaneous reduction of the vertical velocity fluctuations in the shear layer was observed. The intensity of vortical structures inside the cavity was also reduced, although the general aspect of the recirculation zone was not modified. The direct noise computation technique, which supplies the pressure field by solving the fluid mechanics equations, is shown to constitute a powerful tool for studying active aeroacoustic noise control. To cite this article: O. Marsden et al., C. R. Mecanique 331 (2003). 2003 Académie des sciences. Published by Éditions scientifiques et médicales Elsevier SAS. All rights reserved

Résistance du mortier en flexion dynamique approche non parfaitement fragile

La rupture des géo-matériaux, tel le mortier, est souvent considérée comme fragile et sensible à la vitesse de déformation. Pour caractériser cette rupture en traction, des essais de flexion trois points à différentes vitesses de déformation sont réalisés. Nous nous intéressons particulièrement à une gamme de vitesse peu documentée (entre 5 et 15 s−1). Différentes approches sont mises en oeuvre pour dépouiller les essais afin de déterminer la contrainte de rupture ainsi que son évolution en fonction de la vitesse de déformation. La prise en compte d'un comportement avec endommagement permet une nouvelle estimation de la contrainte en rupture

The phylogenetic position of Acoela as revealed by the complete mitochondrial genome of Symsagittifera roscoffensis

<p>Abstract</p> <p>Background</p> <p>Acoels are simply organized unsegmented worms, lacking hindgut and anus. Several publications over recent years challenge the long-held view that acoels are early offshoots of the flatworms. Instead a basal position as sister group to all other bilaterian animals was suggested, mainly based on molecular evidence. This led to the view that features of acoels might reflect those of the last common ancestor of Bilateria, and resulted in several evo-devo studies trying to interpret bilaterian evolution using acoels as a proxy model for the "Urbilateria".</p> <p>Results</p> <p>We describe the first complete mitochondrial genome sequence of a member of the Acoela, <it>Symsagittifera roscoffensis</it>. Gene content and circular organization of the mitochondrial genome does not significantly differ from other bilaterian animals. However, gene order shows no similarity to any other mitochondrial genome within the Metazoa. Phylogenetic analyses of concatenated alignments of amino acid sequences from protein coding genes support a position of Acoela and Nemertodermatida as the sister group to all other Bilateria. Our data provided no support for a sister group relationship between Xenoturbellida and Acoela or Acoelomorpha. The phylogenetic position of <it>Xenoturbella bocki </it>as sister group to or part of the deuterostomes was also unstable.</p> <p>Conclusions</p> <p>Our phylogenetic analysis supports the view that acoels and nemertodermatids are the earliest divergent extant lineage of Bilateria. As such they remain a valid source for seeking primitive characters present in the last common ancestor of Bilateria. Gene order of mitochondrial genomes seems to be very variable among Acoela and Nemertodermatida and the groundplan for the metazoan mitochondrial genome remains elusive. More data are needed to interpret mitochondrial genome evolution at the base of Bilateria.</p

A complete three-dimensional reconstruction of the myoanatomy of Loricifera:comparative morphology of an adult and a Higgins larva stage

INTRODUCTION: Loricifera is a group of small, marine animals, with undetermined phylogenetic relationships within Ecdysozoa (molting protostome animals). Despite their well-known external morphology, data on the internal anatomy of loriciferans are still incomplete. Aiming to increase the knowledge of this enigmatic phylum, we reconstruct for the first time the three-dimensional myoanatomy of loriciferans. Adult Nanaloricus sp. and the Higgins larva of Armorloricus elegans were investigated with cytochemical labeling techniques and CLSM. We discuss our findings with reference to other loriciferan species and recently established phylogenies. RESULTS: The somatic musculature of both adult and larval stages is very complex and includes several muscles arranged in three orientations: circular, transverse and longitudinal. In adult Nanaloricus sp., the introvert is characterized by a net-like muscular arrangement, which is composed of five thin circular fibers crossed by several (up to 30) thin longitudinal fibers with bifurcated anterior ends. Two sets of muscles surround the pre-pharyngeal armature: 6 buccal tube retractors arranged 3 × 2 in a conical shaped structure, and 8 mouth cone retractors. Additionally, a thick, circular muscle marks the neck region and a putative anal sphincter is the posteriormost myoanatomical feature. In the Higgins larva of A. elegans, two circular muscles are distinguished anteriorly in the introvert: a dorsal semicircular fiber and a thin ring muscle. The posteriormost region of the body is characterized by an anal sphincter and a triangular muscle. CONCLUSIONS: Based on the currently available knowledge, the myoanatomical bodyplan of adult loriciferans includes: (i) 8 mouth cone retractors, (ii) a pharynx bulb composed of transversal fibers arranged radially, (iii) circular muscles of the head and neck, (iv) internal muscles of the spinoscalids, (v) longitudinal muscles spanning all body regions, and (vi) transverse (circular) muscles in the abdomen. Concerning the Higgins larva, the muscle subsets assigned to its myoanatomical ground pattern are the (i) longitudinal retractors of the mouth cone, introvert, and abdomen, (ii) abdominal transverse muscles, and (iii) a pharynx bulb composed of transverse, radial fibers. In a comparison with phyla traditionally regarded as phylogenetically close, our data show that the overall myoanatomy of Loricifera is more similar to Kinorhyncha and Nematomorpha than to Priapulida. However, the head musculature of all these groups is very similar, which supports homology of their introverts and head morphology

Perles supposées en variscite du sud-est de la France (Arles-Fontvieille, IVe mill. av. J.-C.) : premiers résultats d’une recherche en devenir

International audiencePutative variscite beads, discovered in megalithic monuments of Arles Fontvieille (Bouches-du- Rhône, France) used at the end of the Neolithic period (3400 to 2200 BC) are a relatively unknown and still unpublished corpus. It includes 116 beads. Since its discovery in the nineteenth century, in fact, this corpus has not been thoroughly analysed, neither from the geographical origin of the raw material used, nor from the technolgical point of view of their very method of production. This paper provides the first results of an ongoing research project. Thus, macroscopic observations at the stereo microscope, suggests that the body is not entirely composed of variscite, but that other rocks have been potentially used (sericite? muscovite?). On the mean time, a link is to be done between the raw material used and the beads’ morphology. These observations, which will be soon verified by PIXE analysis already raise several questions : what are the different origins of the beads, what is their manufacture process, what is the timeline of their production, etc. ? This article presents for the first time the new research agenda that emerges from the detailed analysis of the corpus.Les perles supposées en variscite découvertes au sein des monuments mégalithiques d’Arles-Fontvieille (Bouches-du-Rhône, France) utilisés à la fin du Néolithique (3400-2200 av. J.-C.) constituent un corpus relativement méconnu et encore inédit. Il comprend 116 perles au total. Depuis sa découverte au XIXe s., en effet, ce corpus n’a fait l’objet d’aucune analyse approfondie, qu’il s’agisse d’étudier la matière première, d’en identifier l’origine, de caractériser les types d’objets et leurs modes de production, notamment. Ce travail, actuellement en cours, livre de premiers résultats. Ainsi, l’observation macroscopique des perles à la loupe binoculaire, en particulier, suggère-t-elle que le corpus n’est pas intégralement composé de variscite, d’autres roches ont potentiellement été utilisées (séricite ? muscovite ?). De même, un lien semble pouvoir être établi entre la matière et la morphologie des pièces. Ces observations, qui seront vérifiées prochainement par des analyses PIXE, soulèvent déjà plusieurs interrogations : quelles sont les différentes origines des perles ? De quels processus opératoires procèdentelles ? Quelle chronologie s’attache à ces productions ? etc. Cet article expose pour la première fois ces nouvelles problématiques de recherche qui émergent à partir de l’analyse approfondie de ces corpus