6 results on '"Instituto de Fisica [Mexico] (UASLP)"'
Search Results
2. Microbial abundance, activity and population genomic profiling with mOTUs2
- Author
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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].
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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
3. Determinants of community structure in the global plankton interactome
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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
4. Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities
- Author
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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
5. The Erdős-Sós conjecture for geometric graphs
- Author
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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)
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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
6. Scattering of dilute thermal atom clouds on optical Weber beams
- Author
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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
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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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