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1. Combinatorics of the paths towards synchronization

Author

España, A, Leoncini, X, Ugalde, E, Instituto de Fisica [Mexico] (UASLP), Universidad Autonoma de San Luis Potosi [México] (UASLP), Centre de Physique Théorique - UMR 7332 (CPT), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), CPT - E7 Systèmes dynamiques : théories et applications, and Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], FOS: Mathematics, Dynamical Systems (math.DS), Mathematics - Dynamical Systems, MathematicsofComputing_DISCRETEMATHEMATICS
Abstract

In this paper, we introduce a codification of the paths towards synchronization for synchronizing flows defined over a network. The collection of paths toward synchronization defines a combinatorial structure: the transition diagram. We describe the transition diagram corresponding to the Laplacian flow over the completely connected graph. This applies to the Kuramoto flow over the same graph when initial conditions close to the diagonal are considered. We present as well some results concerning the Laplacian and Kuramoto flows over the complete bipartite graph.

Published
2022
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2. Diameter mean equicontinuity and cellular automata

Author

De Los Santos Baños, Luguis, García-Ramos, Felipe, Instituto de Fisica [Mexico] (UASLP), Universidad Autonoma de San Luis Potosi [México] (UASLP), and de los Santos Baños, Luguis

Subjects
[PHYS]Physics [physics], [INFO]Computer Science [cs], [MATH] Mathematics [math], [INFO] Computer Science [cs], [MATH]Mathematics [math], [PHYS] Physics [physics]
Abstract

International audience; Mean and diam-mean equicontinuity are dynamical properties that have been of use in the study of non-periodic order. We show that the Pacman automaton is not almost diam-mean equicontinuous (it is already known that it is almost mean equicontinuous).

Published
2021

3. Gaussian concentration and uniqueness of equilibrium states in lattice systems

Author

J. Moles, Edgardo Ugalde, J.-R. Chazottes, Frank Redig, Centre de Physique Théorique [Palaiseau] (CPHT), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Instituto de Fisica [Mexico] (UASLP), Universidad Autonoma de San Luis Potosi [México] (UASLP), Delft Institute of Applied Mathematics (DIAM), Delft University of Technology (TU Delft), and Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)

Subjects
Pure mathematics, Kullback–Leibler divergence, Thermodynamic equilibrium, Gaussian, FOS: Physical sciences, 01 natural sciences, large deviations, 010305 fluids & plasmas, symbols.namesake, Hamming distance, [MATH.MATH-MP]Mathematics [math]/Mathematical Physics [math-ph], Lattice (order), 0103 physical sciences, FOS: Mathematics, Blowing-up property, Uniqueness, 010306 general physics, Finite set, Mathematical Physics, Physics, blowing- up property, and phrases: concentration inequalities, relative entropy, Probability (math.PR), equilibrium states, blowingup property, Statistical and Nonlinear Physics, Mathematical Physics (math-ph), [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], concentration inequalities, symbols, Large deviations theory, Configuration space, Mathematics - Probability
Abstract

We consider equilibrium states (that is, shift-invariant Gibbs measures) on the configuration space $S^{\mathbb{Z}^d}$ where $d\geq 1$ and $S$ is a finite set. We prove that if an equilibrium state for a shift-invariant uniformly summable potential satisfies a Gaussian concentration bound, then it is unique. Equivalently, if there exist several equilibrium states for a potential, none of them can satisfy such a bound., Comment: 24 pages. Accepted for publication in J. Stat. Phys. (2020). Some typos have been corrected. Proposition 2.2 has been strengthened: if a Gaussian concentration bound holds then the measure is mixing, not only ergodic

Published
2020
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4. Microbial abundance, activity and population genomic profiling with mOTUs2

Author

Pascal Hingamp, Paul I. Costea, Renato J. Alves, Lucas Paoli, Alessio Milanese, Shinichi Sunagawa, Miguelangel Cuenca, Thomas Schmidt, Hans-Joachim Ruscheweyh, Daniel R. Mende, Georg Zeller, Luis Pedro Coelho, Jaime Huerta-Cepas, Alexandre Almeida, Alex L. Mitchell, Peer Bork, Robert D. Finn, Guillem Salazar, European Molecular Biology Laboratory (EMBL), University of Hawai'i [Honolulu] (UH), Institute of Microbiology and Swiss Institute of Bioinformatics, Instituto de Fisica [Mexico] (UASLP), Universidad Autonoma de San Luis Potosi [México] (UASLP), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Heidelberg University, European Molecular Biology Laboratory [Heidelberg] (EMBL), Leuphana University of Lueneburg, National University of Singapore (NUS), Center for Genomic Regulation (CRG-UPF), CIBER de Epidemiología y Salud Pública (CIBERESP), European Molecular Biology Laboratory, European Molecular Biology Laboratory [Grenoble] (EMBL), and EMBL, ETH Zürich [PHRT-521], the Helmut Horten Foundation, and the Novartis Foundation for Medical-Biological Research [#17B077], the BMBF through the German Network for Bioinformatics Infrastructure (de.NBI) [#031A537B], and the European Molecular Biology Organization [ALTF 721-2015], LTFCOFUND2013 [PCOFUND-GA-2013-609409].

Subjects
0301 basic medicine, Genetic Markers, Science, Population, General Physics and Astronomy, 02 engineering and technology, Biology, Genome, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Phylogenetics, Cluster Analysis, Humans, lcsh:Science, education, Relative species abundance, Phylogeny, education.field_of_study, Multidisciplinary, Genes, Essential, Phylogenetic tree, Host Microbial Interactions, Gene Expression Profiling, Microbiota, Computational Biology, Molecular Sequence Annotation, General Chemistry, Sequence Analysis, DNA, 021001 nanoscience & nanotechnology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Housekeeping gene, Gene expression profiling, 030104 developmental biology, Evolutionary biology, Metagenomics, Cardiovascular and Metabolic Diseases, lcsh:Q, Microbiome, 0210 nano-technology, Sequence Alignment, Algorithms, Software
Abstract

Metagenomic sequencing has greatly improved our ability to profile the composition of environmental and host-associated microbial communities. However, the dependency of most methods on reference genomes, which are currently unavailable for a substantial fraction of microbial species, introduces estimation biases. We present an updated and functionally extended tool based on universal (i.e., reference-independent), phylogenetic marker gene (MG)-based operational taxonomic units (mOTUs) enabling the profiling of >7700 microbial species. As more than 30% of them could not previously be quantified at this taxonomic resolution, relative abundance estimates based on mOTUs are more accurate compared to other methods. As a new feature, we show that mOTUs, which are based on essential housekeeping genes, are demonstrably well-suited for quantification of basal transcriptional activity of community members. Furthermore, single nucleotide variation profiles estimated using mOTUs reflect those from whole genomes, which allows for comparing microbial strain populations (e.g., across different human body sites)., Nature Communications, 10 (1), ISSN:2041-1723

Published
2019

5. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

Author

Guillem Salazar, Lucas Paoli, Adriana Alberti, Jaime Huerta-Cepas, Hans-Joachim Ruscheweyh, Miguelangel Cuenca, Christopher M. Field, Luis Pedro Coelho, Corinne Cruaud, Stefan Engelen, Ann C. Gregory, Karine Labadie, Claudie Marec, Eric Pelletier, Marta Royo-Llonch, Simon Roux, Pablo Sánchez, Hideya Uehara, Ahmed A. Zayed, Georg Zeller, Margaux Carmichael, Céline Dimier, Joannie Ferland, Stefanie Kandels, Marc Picheral, Sergey Pisarev, Julie Poulain, Silvia G. Acinas, Marcel Babin, Peer Bork, Chris Bowler, Colomban de Vargas, Lionel Guidi, Pascal Hingamp, Daniele Iudicone, Lee Karp-Boss, Eric Karsenti, Hiroyuki Ogata, Stephane Pesant, Sabrina Speich, Matthew B. Sullivan, Patrick Wincker, Shinichi Sunagawa, Emmanuel Boss, Guy Cochrane, Michael Follows, Gabriel Gorsky, Nigel Grimsley, Olivier Jaillon, Stefanie Kandels-Lewis, Fabrice Not, Nicole Poulton, Jeroen Raes, Christian Sardet, Lars Stemmann, European Commission, Ministerio de Economía y Competitividad (España), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Takuvik Joint International Laboratory ULAVAL-CNRS, Université Laval [Québec] (ULaval)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Instituto de Fisica [Mexico] (UASLP), Universidad Autonoma de San Luis Potosi [México] (UASLP), Institute of Microbiology and Swiss Institute of Bioinformatics, CNS, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Center for Genomic Regulation (CRG-UPF), CIBER de Epidemiología y Salud Pública (CIBERESP), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), European Molecular Biology Laboratory [Heidelberg] (EMBL), Bayer Cropscience, Immunobiologie Cellulaire et Moléculaire des Infections Parasitaires, Université Pierre et Marie Curie - Paris 6 (UPMC)-IFR113-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire d'Océanographie Physique et Spatiale (LOPS), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Ohio State University [Columbus] (OSU), Institut de Chimie de Clermont-Ferrand - Clermont Auvergne (ICCF), Sigma CLERMONT (Sigma CLERMONT)-Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), European Molecular Biology Laboratory [Grenoble] (EMBL), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Takuvik Joint ULaval/CNRS Laboratory, Centre National de la Recherche Scientifique (CNRS)-Laval University [Québec], Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique d'Evry (IG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), University of Maine, European Molecular Biology Laboratory European Bioinformatics Institute, Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Department of Earth, Atmospheric and Planetary Sciences [MIT, Cambridge] (EAPS), Massachusetts Institute of Technology (MIT), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Biologie intégrative des organismes marins (BIOM), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Sezione Ecologia Marina Integrata, Stazione Zoologica Anton Dohrn (SZN), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Bigelow Laboratory for Ocean Sciences, Department of Bioscience Engineering, Vrije Universiteit Brussel (VUB), Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Laboratoire de physique des océans (LPO), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Université Paris-Saclay, Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Centro de Investigaciones Biológicas (CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Kyoto University, Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Kyoto University [Kyoto], Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), and Centre National de la Recherche Scientifique (CNRS)-Université Laval [Québec] (ULaval)

Subjects
ASSEMBLY PROCESSES, Effects of global warming on oceans, DIVERSITY, microbial ecology, global ocean microbiome, CARBON, 0302 clinical medicine, biogeochemistry, Gene expression, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, CLIMATE-CHANGE, Geography, Microbiota, Temperature, CYANOBACTERIA, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], GENOME, BACTERIA, community turnover, Life Sciences & Biomedicine, Biochemistry & Molecular Biology, SURFACE, Oceans and Seas, Tara Oceans, Biology, Article, metagenome, General Biochemistry, Genetics and Molecular Biology, ocean warming, 03 medical and health sciences, eco-systems biology, Microbial ecology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], metatranscriptome, Seawater, RNA, Messenger, 14. Life underwater, Gene, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 030304 developmental biology, Science & Technology, Biogeochemistry, Molecular Sequence Annotation, Cell Biology, Environmental variation, Gene Expression Regulation, Cardiovascular and Metabolic Diseases, 13. Climate action, Metagenomics, Evolutionary biology, BIODIVERSITY, sense organs, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Transcriptome, 030217 neurology & neurosurgery, gene expression change, BIOGEOGRAPHY
Abstract

This article is contribution number 94 of Tara Oceans.-- 37 pages, 20 figures, 1 table, supplementary information https://doi.org/10.1016/j.cell.2019.10.014.-- All raw reads are available through ENA at https://www.ebi.ac.uk/ena using the identifiers listed in https://doi.org/10.5281/zenodo.3473199. Processed data are accessible at https://www.ebi.ac.uk/biostudies/studies/S-BSST297, and additional information is provided in https://doi.org/10.5281/zenodo.3473199 and at the companion website: https://www.ocean-microbiome.org. Scripts used in this manuscript are available through a Github repository at https://github.com/SushiLab/omrgc_v2_scripts, Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms, Tara Oceans (that includes both the Tara Oceans and Tara Oceans Polar Circle expeditions) would not exist without the leadership of the Tara Expeditions Foundation and the continuous support of 23 institutes (https://oceans.taraexpeditions.org). We further thank the commitment of the following sponsors: CNRS (in particular Groupement de Recherche GDR3280 and the Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE); European Molecular Biology Laboratory (EMBL); Genoscope/CEA; the French Ministry of Research; the French Government “Investissements d’Avenir” programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), and PSL∗ Research University (ANR-11-IDEX-0001-02); Gordon and Betty Moore Foundation (award 3790); the US National Science Foundation (OCE#1536989 and OCE#1829831 to M.B.S.); the European Union’s Horizon 2020 research and innovation programme (grant agreement 686070); and the Ohio Supercomputer and the EMBL and ETH Zürich HPC facilities for computational support. Funding for the collection and processing of the TARA data set was provided by NASA Ocean Biology and Biogeochemistry program under grants NNX11AQ14G, NNX09AU43G, NNX13AE58G, and NNX15AC08G to the University of Maine and Canada Excellence Research Chair on Remote sensing of Canada’s new Arctic frontier Canada Foundation for Innovation. C.B. acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement 835067). S.G.A. thanks the Spanish Ministry of Economy and Competitiveness (CTM2017-87736-R). S. Sunagawa. is supported by the ETH and the Helmut Horten Foundation and by funding from the Swiss National Foundation (205321_184955)

Published
2019
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6. Determinants of community structure in the global plankton interactome

Author

Colomban de Vargas, Stéphane Audic, Isabel Ferrera, Gabriel Gorsky, Jean Weissenbach, Guillem Salazar, Johan Decelle, Pablo Sánchez, Marta Royo-Llonch, Patrick Wincker, Francesco d'Ovidio, Jun Wang, Léo Berline, Ana María Cabello, Tara Oceans Coordinators, Marie-José Garet-Delmas, Simon Roux, Silvia G. Acinas, J. Cesar Ignacio-Espinosa, Peer Bork, Fabrice Not, Fabrizio Carcillo, Lars Stemmann, Hiroyuki Ogata, Marc Picheral, Chris Bowler, Céline Dimier, Nicolas Henry, Luc De Meester, Youssef Darzi, Eric Karsenti, Elena Lara, Shinichi Sunagawa, Francisco M. Cornejo-Castillo, Sébastien Colin, Stephane Pesant, Sabrina Speich, Karoline Faust, Marta Sebastián, Samuel Chaffron, Lionel Guidi, Caroline Souffreau, Jeroen Raes, Laurent Coppola, Sarah Searson, Stefanie Kandels-Lewis, Gipsi Lima-Mendez, Flora Vincent, Lucie Bittner, Gianluca Bontempi, Matthew B. Sullivan, Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Rega Institute - VIB Center for the Biology of Disease, Department of Microbiology and Immunology, Bioinformatics and (eco-)systems Biology Laboratory, Louvain, Belgique, Université Catholique de Louvain = Catholic University of Louvain (UCL), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Processus de couplage à Petite Echelle, Ecosystèmes et Prédateurs Supérieurs (PEPS), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Department of Marine Biology and Oceanography [Barcelone], Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Pangea, Instituto de Fisica [Mexico] (UASLP), Universidad Autonoma de San Luis Potosi [México] (UASLP), Universidad de Granada = University of Granada (UGR), European Molecular Biology Laboratory [Heidelberg] (EMBL), Diversité et Interactions au sein du Plancton Océanique (DIPO), Institute for Chemical Research, Kyoto University, Laboratoire de physique des océans (LPO), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology, Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Department of Marine Biology and Oceanography, Universidad de Granada (UGR), Kyoto University [Kyoto], Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, and Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS)

Subjects
Abiotic component, Biotic component, Multidisciplinary, Primary producers, Ecology, fungi, Community structure, [PHYS.PHYS.PHYS-GEO-PH]Physics [physics]/Physics [physics]/Geophysics [physics.geo-ph], 15. Life on land, Biology, Plankton, Interactome, Food chain, 13. Climate action, Abundance (ecology), 14. Life underwater, ComputingMilieux_MISCELLANEOUS
Abstract

Lima-Mendez, Gipsi ... et. al.-- 9 pages, 4 figures, 1 table, supplementary materials www.sciencemag.org/content/348/6237/1262073/suppl/DC1, Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied the photic zone interactome using environmental factors and organismal abundance profiles and found that environmental factors are incomplete predictors of community structure. We found associations across plankton functional types and phylogenetic groups to be nonrandomly distributed on the network and driven by both local and global patterns. We identified interactions among grazers, primary producers, viruses, and (mainly parasitic) symbionts and validated networkgenerated hypotheses using microscopy to confirm symbiotic relationships. We have thus provided a resource to support further research on ocean food webs and integrating biological components into ocean models. © 2015, American Association for the Advancement of Science. All rights reserved, We thank the commitment of the following people and sponsors:Centre National de la Recherche Scientifique (CNRS) (in particular, Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, Fund for Scientific Research – Flanders (G.L.M., K.F., S.C., and J.R.), Rega Institute (J.R.), KU Leuven(J.R.), The French Ministry of Research, the French Government “Investissements d’Avenir” programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), PSL* Research University (ANR-11-IDEX-0001-02), ANR (projects POSEIDON/ANR-09-BLAN-0348, PHYTBACK/ANR-2010-1709-01, PROMETHEUS/ANR-09-PCSGENM- 217, TARA GIRUS/ANR-09-PCS-GENM-218, European Union FP7 (MicroB3/No.287589, IHMS/HEALTH-F4-2010-261376, ERC Advanced Grant Awards to CB (Diatomite: 294823), Gordon and Betty Moore Foundation grant (3790) to M.B.S., Spanish Ministry of Science and Innovation grant CGL2011-26848/BOS MicroOcean PANGENOMICS to S.G.A., TANIT (CONES 2010-0036) from the Agència de Gestió d´Ajusts Universitaris i Reserca funded to S.G.A., JSPS KAKENHI grant number 26430184 to H.O., FWO, BIO5, Biosphere 2, Agnès b., the Veolia Environment Foundation, Region Bretagne, Lorient Agglomeration, World Courier, Illumina, the EDF Foundation, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Tara schooner, and its captain and crew. We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries that graciously granted sampling permissions. Tara Oceans would not exist without continuous support from 23 institutes (http://oceans.taraexpeditions.org)

Published
2015

7. Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

Author

Logares, Ramiro, Sunagawa, Shinichi, Salazar, Guillem, Cornejo-Castillo, Francisco M., Ferrera, Isabel, Sarmento, Hugo, Hingamp, Pascal, Ogata, Hiroyuki, de Vargas, Colomban, Lima-Mendez, Gipsi, Raes, Jeroen, Poulain, Julie, Jaillon, Olivier, Wincker, Patrick, Kandels-Lewis, Stefanie, Karsenti, Eric, Bork, Peer, Acinas, Silvia G., Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), European Molecular Biology Laboratory, Instituto de Fisica [Mexico] (UASLP), Universidad Autonoma de San Luis Potosi [México] (UASLP), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Education academy of computational life sciences, Tokyo Institute of Technology [Tokyo] (TITECH), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Bioscience Engineering, Vrije Universiteit Brussel (VUB), Rega Institute - Department of Microbiology and Immunology, Université Catholique de Louvain = Catholic University of Louvain (UCL), VIB Center for the Biology of Disease, Flanders Institute for Biotechnology, Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), European Molecular Biology Laboratory [Heidelberg] (EMBL), Max Delbrück Center for Molecular Medicine [Berlin] (MDC), Helmholtz-Gemeinschaft = Helmholtz Association, CNRD, EMBL, Biosphere 2, agnes b., Veolia Environmental Foundation, Region Bretagne, World Courier, Cap L'Orient, Foundation EDF Diversiterre, FRB, Prince Albert II de Monaco Foundation, Etienne Bourgois, Genoscope/CEA, Tara Foundations teams and crew, Spanish Ministry of Science and Innovation, FP7-OCEAN-2011 `Micro B3', Agencia de Gestio d'Ajusts Universitaris i Reserca [CTM2010-12317-E, CONES 2010-0036], MicroOcean PANGENOMICS [CGL2011-26848/BOS], Spanish Ministry of Science and Innovation (MICINN), Marie Curie Intra European Fellowship (MASTDIEV) [PIEF-GA-2009-235365], Marie Curie Intra European Fellowship (EU), Spanish Ministry of Science and Innovation [JCI-2010-06594], PhD JAE-Predoc (CSIC), UPMC, FPI (MICINN), Agence Nationale de la Recherche, ANR [ANR-09-GENM-031, ANR-09-BLAN-0348, ANR-11-BTBR-0008, Tara-GirusANR-09-PCS-GENM-218], Fund for Scientific Research Flanders (FWO), [BCV-2010-3-0003], [2011-2-0003/3-0005], VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR, FWO, BIO5, Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)

Subjects
[SDV]Life Sciences [q-bio], [SDE]Environmental Sciences
Abstract

International audience; Sequencing of 16S rDNA polymerase chain reaction (PCR) amplicons is the most common approach for investigating environmental prokaryotic diversity, despite the known biases introduced during PCR. Here we show that 16S rDNA fragments derived from Illumina-sequenced environmental metagenomes (mitags) are a powerful alternative to 16S rDNA amplicons for investigating the taxonomic diversity and structure of prokaryotic communities. As part of the TaraOceans global expedition, marine plankton was sampled in three locations, resulting in 29 subsamples for which metagenomes were produced by shotgun Illumina sequencing (ca. 700Gb). For comparative analyses, a subset of samples was also selected for Roche-454 sequencing using both shotgun (m454tags; 13 metagenomes, ca. 2.4Gb) and 16S rDNA amplicon (454tags; ca. 0.075Gb) approaches. Our results indicate that by overcoming PCR biases related to amplification and primer mismatch, mitags may provide more realistic estimates of community richness and evenness than amplicon 454tags. In addition, mitags can capture expected beta diversity patterns. Using mitags is now economically feasible given the dramatic reduction in high-throughput sequencing costs, having the advantage of retrieving simultaneously both taxonomic (Bacteria, Archaea and Eukarya) and functional information from the same microbial community.

Published
2014

8. The Erdős-Sós conjecture for geometric graphs

Author

Gelasio Salazar, Jesús Leaños, Francisco Zaragoza, Cynthia Rodríguez, Dolores Lara, Ruy Fabila-Monroy, Luis F. Barba, Département d'Informatique, Université libre de Bruxelles (ULB), Centro de Investigacion y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Departament de Matemàtica Aplicada II, Universitat Politècnica de Catalunya [Barcelona] (UPC), Unidad Académica de Matemáticas [Mexico], Universidad Autonoma de Zacatecas [Autonomous University of Zacatecas] (UAZ), Departamento de Sistemas [Azcapotzalco], Universidad Autonoma Metropolitana-Azcapotzalco, Department of Combinatorics and Optimization, University of Waterloo [Waterloo], Instituto de Fisica [Mexico] (UASLP), and Universidad Autonoma de San Luis Potosi [México] (UASLP)

Subjects
Combinatorics, Discrete mathematics, Set (abstract data type), [INFO.INFO-DM] Computer Science [cs]/Discrete Mathematics [cs.DM], Spatial network, Conjecture, General Computer Science, Discrete Mathematics and Combinatorics, Convex position, [INFO.INFO-DM]Computer Science [cs]/Discrete Mathematics [cs.DM], Tree (graph theory), Theoretical Computer Science, Mathematics
Abstract

Combinatorics, Let f(n,k) be the minimum number of edges that must be removed from some complete geometric graph G on n points, so that there exists a tree on k vertices that is no longer a planar subgraph of G. In this paper we show that ( 1 / 2 )n2 / k-1-n / 2≤f(n,k) ≤2 n(n-2) / k-2. For the case when k=n, we show that 2 ≤f(n,n) ≤3. For the case when k=n and G is a geometric graph on a set of points in convex position, we completely solve the problem and prove that at least three edges must be removed.

Published
2013

9. Scattering of dilute thermal atom clouds on optical Weber beams

Author

H. Hattermann, Simon Bernon, Rocío Jáuregui, C. L. Hernández-Cedillo, József Fortágh, Instituto de Fisica [Mexico] (UASLP), Universidad Autonoma de San Luis Potosi [México] (UASLP), Physikalisches Institut [Tübingen], and Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen

Subjects
Electromagnetic field, Physics, Angular momentum, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], [PHYS.COND.GAS]Physics [physics]/Condensed Matter [cond-mat]/Quantum Gases [cond-mat.quant-gas], Scattering, 01 natural sciences, Atomic and Molecular Physics, and Optics, Symmetry (physics), 010309 optics, [PHYS.QPHY]Physics [physics]/Quantum Physics [quant-ph], Phase space, 0103 physical sciences, Atom, [SPI.OPTI]Engineering Sciences [physics]/Optics / Photonic, Atomic physics, 010306 general physics, Beam (structure), ComputingMilieux_MISCELLANEOUS, Structured light
Abstract

We report the experimental observation and a theoretical description of the scattering of free falling dilute thermal clouds of ${}^{87}$Rb atoms by microscopically structured light beams with parabolic-cylindrical symmetry. These structured beams are known in the literature as Weber beams. High-fidelity Weber beams are generated by means of a spatial light modulator and an annular spatial filtering process, which yields a quasipropagation-invariant electromagnetic field in the region of interaction with the atom cloud. The dynamics of the atomic density profile and the phase space distribution of the scattered atoms is explored. A natural dynamical variable of Weber modes is the product of the angular momentum along the axis of propagation of the beam with a component of linear momentum perpendicular to that axis. To pave the way of the understanding about the transfer of this variable, we study the evolution of the analogous atomic variable.

Published
2013

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