Multivariate approach for brain decomposable connectivity networks

International audienceThis paper deals with the analysis of brain functional network using fMRI data. It recapitulates the concept of decomposable connectivity graph. Graphs are a usual tool to represent complex systems behavior, although edge strength estimation issues have not yet received a universally adopted solution. In the framework of linear Gaussian instantaneous exchanges, the well known partial correlation is usually introduced. However its estimation remains a challenge for highly connected or dense systems. Here, we propose to combine a wavelet decomposition and a graphical Gaussian model approach relying on decomposable graphs. This is shown to improve the estimations of brain function networks in the presence of long range dependence; the results are compared to those obtained with classical partial correlation estimators

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

<p>Abstract</p> <p>Background</p> <p>To understand the evolutionary role of Lateral Gene Transfer (LGT), accurate methods are needed to identify transferred genes and infer their timing of acquisition. Phylogenetic methods are particularly promising for this purpose, but the reconciliation of a gene tree with a reference (species) tree is computationally hard. In addition, the application of these methods to real data raises the problem of sorting out real and artifactual phylogenetic conflict.</p> <p>Results</p> <p>We present Prunier, a new method for phylogenetic detection of LGT based on the search for a maximum statistical agreement forest (MSAF) between a gene tree and a reference tree. The program is flexible as it can use any definition of "agreement" among trees. We evaluate the performance of Prunier and two other programs (EEEP and RIATA-HGT) for their ability to detect transferred genes in realistic simulations where gene trees are reconstructed from sequences. Prunier proposes a single scenario that compares to the other methods in terms of sensitivity, but shows higher specificity. We show that LGT scenarios carry a strong signal about the position of the root of the species tree and could be used to identify the direction of evolutionary time on the species tree. We use Prunier on a biological dataset of 23 universal proteins and discuss their suitability for inferring the tree of life.</p> <p>Conclusions</p> <p>The ability of Prunier to take into account branch support in the process of reconciliation allows a gain in complexity, in comparison to EEEP, and in accuracy in comparison to RIATA-HGT. Prunier's greedy algorithm proposes a single scenario of LGT for a gene family, but its quality always compares to the best solutions provided by the other algorithms. When the root position is uncertain in the species tree, Prunier is able to infer a scenario per root at a limited additional computational cost and can easily run on large datasets.</p> <p>Prunier is implemented in C++, using the Bio++ library and the phylogeny program Treefinder. It is available at: <url>http://pbil.univ-lyon1.fr/software/prunier</url></p

Graphe de connectivité cérébrale et longue dépendance

National audienceIn this communication, a decomposable graph based partial correlation matrix estimator is proposed for the analysis of time series exhibiting long memory properties. The estimator is derived from the set of wavelet coefficients computed at a given scale; the obtained coefficient are asymptotically uncorrelated, thus avoiding to introduce bias in the estimation. Decomposability of the graph leads to derive an explicit formulation of the maximum likelihood estimation of the partial correlation matrix; however, some spurious links must be introduced in order to insure graph decomposability. Surrogate data that mimik fMRI records are used to illustrate the pertinence and accuracy of the proposed approach. The simulations show that even for small size samples, the proposed methods outperforms the classical approaches. Furthermore, the added links do not affect the quality of the estimation. An appealing feature of decomposabilty resides in the possibility to account for conditional dependences through a clique based approach

Databases of homologous gene families for comparative genomics

International audienceBackground: Comparative genomics is a central step in many sequence analysis studies, from gene annotation and the identification of new functional regions in genomes, to the study of evolutionary processes at the molecular level (speciation, single gene or whole genome duplications, etc.) and phylogenetics. In that context, databases providing users high quality homologous families and sequence alignments as well as phylogenetic trees based on state of the art algorithms are becoming indispensable. Methods: We developed an automated procedure allowing massive all-against-all similarity searches, gene clustering, multiple alignments computation, and phylogenetic trees construction and reconciliation. The application of this procedure to a very large set of sequences is possible through parallel computing on a large computer cluster. Results: Three databases were developed using this procedure: HOVERGEN, HOGENOM and HOMOLENS. These databases share the same architecture but differ in their content. HOVERGEN contains sequences from vertebrates, HOGENOM is mainly devoted to completely sequenced microbial organisms, and HOMOLENS is devoted to metazoan genomes from Ensembl. Access to the databases is provided through Web query forms, a general retrieval system and a client-server graphical interface. The later can be used to perform tree-pattern based searches allowing, among other uses, to retrieve sets of orthologous genes. The three databases, as well as the software required to build and query them, can be used or downloaded from the PBIL (Pôle Bioinformatique Lyonnais) site at http://pbil.univ-lyon1.fr/

Effect of cooling rate and aluminium addition on graphite growth during solidification and graphitization

Even using high inoculation levels, mottled structures are often obtained when casting Mg-treated cast irons in thin wall parts. For full graphitization of the cast components, this calls for a subsequent heat-treatment which is generally achieved in the austenite field. The aim of this work was investigating the impact of the process and the cooling rate on the graphite structure for two different casting conditions. The influence of the cooling rate on graphite degeneracy due to the presence of impurity was also investigated considering low-level additions of aluminium. Extensive metallographic investigation has been carried out from which it is concluded that the internal graphite structure is the same for the two studied cooling conditions. Accordingly, the growth mechanism of graphite should be the same when it precipitates from liquid, during eutectic reaction or else solid-state graphitization. Finally, microanalyses suggest magnesium and aluminium do not interact in the same way with graphite during its growth

Immune Subversion and Quorum-Sensing Shape the Variation in Infectious Dose among Bacterial Pathogens

Many studies have been devoted to understand the mechanisms used by pathogenic bacteria to exploit human hosts. These mechanisms are very diverse in the detail, but share commonalities whose quantification should enlighten the evolution of virulence from both a molecular and an ecological perspective. We mined the literature for experimental data on infectious dose of bacterial pathogens in humans (ID50) and also for traits with which ID50 might be associated. These compilations were checked and complemented with genome analyses. We observed that ID50 varies in a continuous way by over 10 orders of magnitude. Low ID50 values are very strongly associated with the capacity of the bacteria to kill professional phagocytes or to survive in the intracellular milieu of these cells. Inversely, high ID50 values are associated with motile and fast-growing bacteria that use quorum-sensing based regulation of virulence factors expression. Infectious dose is not associated with genome size and shows insignificant phylogenetic inertia, in line with frequent virulence shifts associated with the horizontal gene transfer of a small number of virulence factors. Contrary to previous proposals, infectious dose shows little dependence on contact-dependent secretion systems and on the natural route of exposure. When all variables are combined, immune subversion and quorum-sensing are sufficient to explain two thirds of the variance in infectious dose. Our results show the key role of immune subversion in effective human infection by small bacterial populations. They also suggest that cooperative processes might be important for successful infection by bacteria with high ID50. Our results suggest that trade-offs between selection for population growth-related traits and selection for the ability to subvert the immune system shape bacterial infectiousness. Understanding these trade-offs provides guidelines to study the evolution of virulence and in particular the micro-evolutionary paths of emerging pathogens

Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)

55 Pág.In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.This work was supported in part through the Laulima Government Solutions, LLC, prime contract with the U.S. National Institute of Allergy and Infec tious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC, under Contract No. HHSN272201800013C. U.J.B. was supported by the Division of Intramural Resarch, NIAID. This work was also funded in part by Contract No. HSHQDC15-C-00064 awarded by DHS S and T for the management and operation of The National Biodefense Analysis and Countermeasures Centre, a federally funded research and development centre operated by the Battelle National Biodefense Institute (V.W.); and NIH contract HHSN272201000040I/HHSN27200004/D04 and grant R24AI120942 (N.V., R.B.T.). S.S. acknowl edges support from the Mississippi Agricultural and Forestry Experiment Station (MAFES), USDA-ARS project 58-6066-9-033 and the National Institute of Food and Agriculture, U.S. Department of Agriculture, Hatch Project, under Accession Number 1021494. The funders had no role in the design of the study; in the collection, analysis, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the U.S. Department of the Army, the U.S. Department of Defence, the U.S. Department of Health and Human Services, including the Centres for Disease Control and Prevention, the U.S. Department of Homeland Security (DHS) Science and Technology Directorate (S and T), or of the institutions and companies affiliated with the authors. In no event shall any of these entities have any responsibility or liability for any use, misuse, inability to use, or reliance upon the information contained herein. The U.S. departments do not endorse any products or commercial services mentioned in this publication. The U.S. Government retains and the publisher, by accepting the article for publication, acknowledges that the U.S.Government retains a non-exclusive, paid up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for U.S. Government purposes.Peer reviewe

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Mineralogical and geochemical features of the Allan Hills tephra, South Victoria Land: Implications for mid-Pleistocene volcanic activity in Antarctica

International audienceMore than 100 volcanoes have been discovered in Antarctica, however, the sources of many Antarctic tephras are not yet constrained. In this study, four tephra samples recovered from the environment of Site 27 on an area of blue ice at Allan Hills, South Victoria Land, provide information on magma and crustal sources for the tephra erupted in Antarctica. We report data on the chemistry of Antarctic tephra glasses and minerals analysed by electron microscopy, electron probe microanalysis and laser ablation inductively coupled plasma mass spec-trometry. The tephra amphibole chemistry indicates magma residence at ~1 GPa and ~1100 °C. Abundant Ca-Al-Si-rich minerals imply that the magma ascended from a reservoir at 29.4 +/- 2.7 km depth was affected by the assimilation of calc-silicate crust. The high Fe and Ti contents in the magmatic minerals and the trace element patterns of the glasses typical of a hydrothermally altered oceanic crust suggest that the Allan Hills tephra originated from a mantle plume-derived magma. The fragmented morphology of the glasses implies that the magmatic activity was associated with explosive eruptions during the mid-Pleistocene. The chemistry of the glasses and the presence of rh€ onite and Al-rich spinel minerals suggest that the magma might be genetically related to the currently active McMurdo volcanic group