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1. Convergent vews on disordered protein dynamics from NMR and computational approaches

Author: Nicola, Salvi, Vojtěch, Zapletal, Zuzana, Jaseňáková, Milan, Zachrdla, Petr, Padrta, Subhash, Narasimhan, Thorsten, Marquardsen, Jean-Max, Tyburn, Lukáš, Žídek, Martin, Blackledge, Fabien, Ferrage, Pavel, Kadeřávek, Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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)-Université Grenoble Alpes (UGA), Masaryk University [Brno] (MUNI), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Laboratoire des biomolécules (LBM UMR 7203), Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - 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), Bruker BioSpin MRI GmbH [Ettlingen, Germany], ANR-18-CE29-0003,NANO-DISPRO,Une méthode intégrative pour déterminer les mouvements nanométriques des protéines désordonnées(2018), Ferrage, Fabien, and APPEL À PROJETS GÉNÉRIQUE 2018 - Une méthode intégrative pour déterminer les mouvements nanométriques des protéines désordonnées - - NANO-DISPRO2018 - ANR-18-CE29-0003 - AAPG2018 - VALID
Subjects: Intrinsically Disordered Proteins, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [CHIM.THEO] Chemical Sciences/Theoretical and/or physical chemistry, Magnetic Resonance Spectroscopy, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Protein Conformation, [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Biophysics, [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, DNA-Directed RNA Polymerases, Molecular Dynamics Simulation, Amides
Abstract: International audience; Intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs) is a class of biologically important proteins exhibiting specific biophysical characteristics. They lack a hydrophobic core, and their conformational behavior is strongly influenced by electrostatic interactions. IDPs and IDRs are highly dynamic, and a characterization of the motions of IDPs and IDRs is essential for their physically correct description. NMR together with molecular dynamics simulations are the methods best suited to such a task because they provide information about dynamics of proteins with atomistic resolution. Here, we present a study of motions of a disordered C-terminal domain of the delta subunit of RNA polymerase from Bacillus subtilis. Positively and negatively charged residues in the studied domain form transient electrostatic contacts critical for the biological function. Our study is focused on investigation of ps-ns dynamics of backbone of the delta subunit based on analysis of amide 15N NMR relaxation data and molecular dynamics simulations. In order to extend an informational content of NMR data to lower frequencies, which are more sensitive to slower motions, we combined standard (high-field) NMR relaxation experiments with high-resolution relaxometry. Altogether, we collected data reporting the relaxation at 12 different magnetic fields, resulting in an unprecedented data set. Our results document that the analysis of such data provides a consistent description of dynamics and confirms the validity of so far used protocols of the analysis of dynamics of IDPs also for a partially folded protein. In addition, the potential to access detailed description of motions at the timescale of tens of ns with the help of relaxometry data is discussed. Interestingly, in our case, it appears to be mostly relevant for a region involved in the formation of temporary contacts within the disordered region, which was previously proven to be biologically important.
Published: 2022
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2. Acknowledging and citing core facilities

Author: Kivinen, Katja, GAM van Luenen, Henri, Alcalay, Myriam, Bock, Christoph, Dodzian, Joanna, Hoskova, Katerina, Hoyle, Danielle, Hradil, Ondrej, Christensen, Sofie Kjellerup, Korn, Bernhard, Kosteas, Theodoros, Morales, Mònica, Skowronek, Krzysztof, Theodorou, Vasiliki, van Minnebruggen, Geert, Salamero, Jean, Premvardhan, Lavanya, Institute for Molecular Medicine Finland [Helsinki] (FIMM), Helsinki Institute of Life Science (HiLIFE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Netherlands Cancer Institute (NKI), Antoni van Leeuwenhoek Hospital, European Institute of Oncology [Milan] (ESMO), Research Center for Molecular Medicine of the Austrian Academy of Sciences [Vienna, Austria] (CeMM ), Austrian Academy of Sciences (OeAW), International Institute of Molecular and Cell Biology [Warsaw] (IIMCB), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), The Babraham Institute [Cambridge, UK], EU-LIFE Alliance [Barcelona], Friedrich Miescher Institute for Biomedical Research (FMI), Novartis Research Foundation, Institute of Molecular Biology and Biotechnology (IMBB-FORTH), Foundation for Research and Technology - Hellas (FORTH), Center for Genomic Regulation (CRG-UPF), CIBER de Epidemiología y Salud Pública (CIBERESP), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Space-timE RePresentation, Imaging and cellular dynamics of molecular COmplexes (SERPICO), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), and Institut Curie [Paris]
Subjects: [SDV]Life Sciences [q-bio], [SHS]Humanities and Social Sciences
Abstract: International audience
Published: 2022
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3. Reproducibility and accuracy of microscale thermophoresis in the NanoTemper Monolith: a multi laboratory benchmark study

Author: Caroline Mas, Grzegorz Piszczek, Marjetka Podobnik, Kathryn Perez, Timothy Sharpe, Stephen H. McLaughlin, Roland Montserret, Stefan H. Knauer, Bruno Baron, Christopher M. Johnson, Quyen Nguyen, Mark A. Williams, Katja Pirc, Arthur Sedivy, Celeste Abreu, Tina Daviter, David Ortega-Alarcon, Daumantas Matulis, Rouba Nasreddine, Carlo Carolis, Thomas A. Jowitt, Stephan Uebel, David Staunton, Andrew P. Leech, Maria Garcia-Alai, June Southall, Alexander Fish, Jitka Holková, Alexander K. Buell, Michael Weyand, Jasmina Rokov-Plavec, Blanca López-Méndez, Sylvie Berger, Josef Houser, Natalia Rodrigo, Wojciech Bal, Chad A. Brautigam, Josef Hamacek, Reine Nehmé, Olga Abian, Christian Guenther, Ondrej Vanek, Susanne Schaefer, Sharon M. Kelly, Malgorzata Adamczyk, Di Wu, Pedro Tavares, University of Copenhagen = Københavns Universitet (KU), Biophysique Moléculaire (plateforme) - Molecular Biophysics (platform), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), University of Texas Southwestern Medical Center [Dallas], University of Manchester [Manchester], Universität Bayreuth, Max Planck Institute of Biochemistry (MPIB), Max-Planck-Gesellschaft, University of London [London], Vienna Biocenter Core Facilities, Partenaires INRAE, University of Zaragoza - Universidad de Zaragoza [Zaragoza], Charles University [Prague] (CU), Warsaw University of Technology [Warsaw], Institute of Biochemistry and Biophysics, Polish Academy of Sciences (PAN), Institut de Recherches SERVIER (IRS), Technical University of Denmark [Lyngby] (DTU), Centre for Genomic Regulation [Barcelona] (CRG), Universitat Pompeu Fabra [Barcelona] (UPF)-Centro Nacional de Analisis Genomico [Barcelona] (CNAG), The institute of cancer research [London], Netherlands Cancer Institute (NKI), Antoni van Leeuwenhoek Hospital, EMBL Hamburg, Centre de biophysique moléculaire (CBM), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), MRC Laboratory of Molecular Biology [Cambridge, UK] (LMB), University of Cambridge [UK] (CAM)-Medical Research Council, University of Glasgow, University of York [York, UK], Integrated Structural Biology Grenoble (ISBG - UMS 3518 ), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-European Molecular Biology Laboratory [Grenoble] (EMBL)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Vilnius University [Vilnius], Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie Organique et Analytique (ICOA), Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut de Chimie du CNRS (INC)-Institut National de la Santé et de la Recherche Médicale (INSERM), EMBL Heidelberg, National Institute of Chemistry, National Heart, Lung, and Blood Institute [Bethesda] (NHLBI), University of Zagreb, University of Bayreuth, University of Basel (Unibas), University of Oxford [Oxford], Faculdade de Ciências e Tecnologia [Faro] (FCT), Universidade do Algarve (UAlg), This research was funded by Fondo de Investigaciones Sanitarias from Instituto de Salud Carlos III and European Union (ERDF/ESF, 'Investing in your future' PI18/00349 and Diputación General de Aragón Digestive Pathology Group B25_17R to O.A. Spanish Ministry of Science, Innovation and Universities, FPI Predoctoral Research Contract BES-2017-080739 to D.O.A. This research was funded by project no 2015/17/B/NZ2/01160 (granted to MA), we also acknowledge financial support, from the Faculty of Chemistry at Warsaw University of Technology. As part of the Federal FTI strategy, this work was generously supported by the City of Vienna and the Austrian Ministry for Education, Science and Research., Frapart, Isabelle, University of Copenhagen = Københavns Universitet (UCPH), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Max-Planck-Institut für Biochemie = Max Planck Institute of Biochemistry (MPIB), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Integrated Structural Biology Grenoble (ISBG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and University of Oxford
Subjects: 0301 basic medicine, 030103 biophysics, Materials science, Thermophoresis, Interaction, Biophysics, [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Calorimetry, Benchmark, 03 medical and health sciences, Biomolècules, MST, TRIC, KD, [PHYS.PHYS.PHYS-INS-DET]Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], Surface plasmon resonance, Monolith, Reliability (statistics), Reproducibility, geography, geography.geographical_feature_category, K D, Microscale thermophoresis, Intensity change, Temperature, Reproducibility of Results, Correction, General Medicine, Biofísica, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Benchmarking, 030104 developmental biology, [PHYS.PHYS.PHYS-INS-DET] Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], Benchmark (computing), Original Article, Biological system, Laboratories
Abstract: Microscale thermophoresis (MST), and the closely related Temperature Related Intensity Change (TRIC), are synonyms for a recently developed measurement technique in the field of biophysics to quantify biomolecular interactions, using the (capillary-based) NanoTemper Monolith and (multiwell plate-based) Dianthus instruments. Although this technique has been extensively used within the scientific community due to its low sample consumption, ease of use, and ubiquitous applicability, MST/TRIC has not enjoyed the unambiguous acceptance from biophysicists afforded to other biophysical techniques like isothermal titration calorimetry (ITC) or surface plasmon resonance (SPR). This might be attributed to several facts, e.g., that various (not fully understood) effects are contributing to the signal, that the technique is licensed to only a single instrument developer, NanoTemper Technology, and that its reliability and reproducibility have never been tested independently and systematically. Thus, a working group of ARBRE-MOBIEU has set up a benchmark study on MST/TRIC to assess this technique as a method to characterize biomolecular interactions. Here we present the results of this study involving 32 scientific groups within Europe and two groups from the US, carrying out experiments on 40 Monolith instruments, employing a standard operation procedure and centrally prepared samples. A protein-small molecule interaction, a newly developed protein-protein interaction system and a pure dye were used as test systems. We characterized the instrument properties and evaluated instrument performance, reproducibility, the effect of different analysis tools, the influence of the experimenter during data analysis, and thus the overall reliability of this method. All authors acknowledge the COST Action project ARBRE-MOBIEU CA15126 under the auspices of whose Working Group 4 this study was carried out. ARBRE-MOBIEU COST Action CA15126 funded meetings in the Center for Protein Research, University of Copenhagen (ECOST-MEETING-CA15126-280618-098884) to organize this study and in the Vienna Biocenter Core Facilities GmbH (ECOST-MEETING-CA15126-121119-111544) to discuss the results of the benchmark. Ondřej Vaněk acknowledges support from the Ministry of Education, Youth and Sports of the Czech Republic (LTC17065 in frame of the COST Action CA15126). Jitka Holková and Josef Houser acknowledge CF Biomolecular Interactions and Crystallization of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127). Jasmina Rokov-Plavec acknowledges support from the Croatian Science Foundation (IP-2016-06-6272). Alexander K. Buell thanks the Novo Nordisk Foundation (grant number NNFSA170028392) for funding. Li Peng Lundgren acknowledges for preliminary MST/TRIC experiments (STMS 37745 in the frame of the COST Action CA15126) and the COST Action (CA15126) for a STMS (STMS 44783) for the data analysis. The Novo Nordisk Foundation Center for Protein Research is supported financially by the Novo Nordisk Foundation (Grant agreement NNF14CC0001). Katja Pirc and Marjetka Podobnik acknowledge the grant by the Slovenian Research Agency P1-0391 (Title: Molecular Interactions). This research was funded by Fondo de Investigaciones Sanitarias from Instituto de Salud Carlos III and European Union (ERDF/ESF, “Investing in your future” PI18/00349 and Diputación General de Aragón Digestive Pathology Group B25_17R to O.A. Spanish Ministry of Science, Innovation and Universities, FPI Predoctoral Research Contract BES-2017-080739 to D.O.A. This research was funded by project no 2015/17/B/NZ2/01160 (granted to MA)
Published: 2021
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4. Visualization of hydrogen atoms in a perdeuterated lectin-fucose complex reveals key details of protein-carbohydrate interactions

Author: V. Trevor Forsyth, Anne Imberty, Matthew P. Blakeley, Michael Haertlein, Lukas Gajdos, Michaela Wimmerová, Juliette M. Devos, Atul Kumar, Centre de Recherches sur les Macromolécules Végétales (CERMAV), Institut de Chimie du CNRS (INC)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Institut Laue-Langevin (ILL), ILL, Central European Institute of Technology [Brno] (CEITEC MU), and Brno University of Technology [Brno] (BUT)
Subjects: Glycan, Stereochemistry, Stacking, Q1, Fucose, 03 medical and health sciences, chemistry.chemical_compound, Bacterial Proteins, Structural Biology, Lectins, Aromatic amino acids, Protein–carbohydrate interactions, [CHIM]Chemical Sciences, QD, Binding site, Molecular Biology, 030304 developmental biology, 0303 health sciences, biology, Hydrogen bond, Chemistry, 030302 biochemistry & molecular biology, Ligand (biochemistry), 3. Good health, biology.protein, lipids (amino acids, peptides, and proteins), Photorhabdus, Hydrogen, Protein Binding, QD415
Abstract: Summary Carbohydrate-binding proteins from pathogenic bacteria and fungi have been shown to be implicated in various pathological processes, where they interact with glycans present on the surface of the host cells. These interactions are part of the initial processes of infection of the host and are very important to study at the atomic level. Here, we report the room temperature neutron structures of PLL lectin from Photorhabdus laumondii in its apo form and in complex with deuterated L-fucose, which is, to our knowledge, the first neutron structure of a carbohydrate-binding protein in complex with a fully deuterated carbohydrate ligand. A detailed structural analysis of the lectin-carbohydrate interactions provides information on the hydrogen bond network, the role of water molecules, and the extent of the CH-π stacking interactions between fucose and the aromatic amino acids in the binding site.
Published: 2021
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5. Comparative analysis of targeted next-generation sequencing panels for the detection of gene mutations in chronic lymphocytic leukemia: an ERIC multi-center study

Author: Sutton, Lesley-Ann, Ljungström, Viktor, Enjuanes, Anna, Cortese, Diego, Skaftason, Aron, Tausch, Eugen, Kozubik, Katerina Stano, Nadeu, Ferran, Armand, Marine, Malcikova, Jikta, Djureinovic, Tatjana, Forster, Jade, Davis, Zadie, Oscier, David, Rossi, Davide, Ghia, Paolo, Strefford, Jonathan C., Pospisilova, Sarka, Stilgenbauer, Stephan, Davi, Frederic, Campo, Elias, Stamatopoulos, Kostas, Rosenquist, Richard, Karolinska Institutet [Stockholm], Uppsala University, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), University of Ulm (UUlm), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Service d'Hématologie clinique [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Sorbonne Université - Faculté de Médecine (SU FM), Sorbonne Université (SU), University of Southampton, Oncology Institute of Southern Switzerland (IOSI), Universita Vita Salute San Raffaele = Vita-Salute San Raffaele University [Milan, Italie] (UniSR), IRCCS Ospedale San Raffaele [Milan, Italy], Karolinska University Hospital [Stockholm], Sutton, Lesley-Ann, Ljungström, Viktor, Enjuanes, Anna, Cortese, Diego, Skaftason, Aron, Tausch, Eugen, Stano Kozubik, Katerina, Nadeu, Ferran, Armand, Marine, Malcikova, Jikta, Pandzic, Tatjana, Forster, Jade, Davis, Zadie, Oscier, David, Rossi, Davide, Ghia, Paolo, Strefford, Jonathan C, Pospisilova, Sarka, Stilgenbauer, Stephan, Davi, Frederic, Campo, Elia, Stamatopoulos, Kosta, and Rosenquist, Richard
Subjects: Cytogenetics and Molecular Genetics, [SDV]Life Sciences [q-bio], Mutation, Next-generation sequencing, High-Throughput Nucleotide Sequencing, Humans, Chronic Lymphocytic Leukemia, Hematology, Hematologi, Genomics, Precision Medicine, Leukemia, Lymphocytic, Chronic, B-Cell, Article
Abstract: International audience; Next-generation sequencing (NGS) has transitioned from research to clinical routine, yet the comparability of different technologies for mutation profiling remains an open question. We performed a European multicenter (n=6) evaluation of three amplicon-based NGS assays targeting 11 genes recurrently mutated in chronic lymphocytic leukemia. Each assay was assessed by two centers using 48 pre-characterized chronic lymphocytic leukemia samples; libraries were sequenced on the Illumina MiSeq instrument and bioinformatics analyses were centralized. Across all centers the median percentage of target reads ≥100x ranged from 94.2- 99.8%. In order to rule out assay-specific technical variability, we first assessed variant calling at the individual assay level i.e., pairwise analysis of variants detected amongst partner centers. After filtering for variants present in the paired normal sample and removal of PCR/sequencing artefacts, the panels achieved 96.2% (Multiplicom), 97.7% (TruSeq) and 90% (HaloPlex) concordance at a variant allele frequency (VAF) >0.5%. Reproducibility was assessed by looking at the inter-laboratory variation in detecting mutations and 107 of 115 (93% concordance) mutations were detected by all six centers, while the remaining eight variants (7%) were undetected by a single center. Notably, 6 of 8 of these variants concerned minor subclonal mutations (VAF 5%, after rigorous validation, the use of unique molecular identifiers may be necessary to reach a higher sensitivity and ensure consistent and accurate detection of low-frequency variants.
Published: 2020
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6. Tailoring the Oxygen Reduction Activity of Pt Nanoparticles through Surface Defects: A Simple Top-Down Approach

Author: Regina M. Kluge, Weijin Li, Jan Michalička, Hany A. El-Sayed, Raphaël Chattot, Thomas Gigl, Aliaksandr S. Bandarenka, Felix Haimerl, Batyr Garlyyev, Di Wang, Christoph Hugenschmidt, Wu Wang, Jan M. Macak, Johannes Fichtner, Sebastian Watzele, Laetitia Dubau, Frédéric Maillard, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Electrochimie Interfaciale et Procédés (EIP), Laboratoire d'Electrochimie et de Physico-chimie des Matériaux et des Interfaces (LEPMI), Institut de Chimie du CNRS (INC)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Institut de Chimie du CNRS (INC)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), European Synchrotron Radiation Facility (ESRF), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Institute of Nanotechnology [Karlsruhe] (INT), Karlsruhe Institute of Technology (KIT), and Forschungszentrum Julich, Heinz Maier Leibnitz Zentrum MLZ, JCNS, Lichtenbergstr 1, D-85747 Garching, Germany
Subjects: Surface (mathematics), Technology, Materials science, 010405 organic chemistry, Kinetics, food and beverages, [CHIM.CATA]Chemical Sciences/Catalysis, [CHIM.MATE]Chemical Sciences/Material chemistry, General Chemistry, 2019-022-025989, 010402 general chemistry, Platinum nanoparticles, Electrocatalyst, 01 natural sciences, Catalysis, Oxygen reduction, 0104 chemical sciences, Chemical engineering, TEM, Oxygen reduction reaction, Pt nanoparticles, ddc:600, ComputingMilieux_MISCELLANEOUS
Abstract: Results from Pt model catalyst surfaces have demonstrated that surface defects, in particular surface concavities, can improve the oxygen reduction reaction (ORR) kinetics. It is, however, a challe...
Published: 2020
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7. Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study

Author: Brüggemann, Monika, Kotrova, Michaela, Knecht, Henrik, Bartram, Jack, Boudjogrha, Myriam, Bystry, Vojtech, Fazio, Grazia, Froňková, Eva, Giraud, Mathieu, Grioni, Andrea, Hancock, Jeremy, Herrmann, Dietrich, Jimenez, Cristina, Krejci, Adam, Moppett, John, Reigl, Tomas, Salson, Mikaël, Scheijen, Blanca, Schwarz, Martin, Songia, Simona, Svaton, Michael, van Dongen, Jacques, Villarese, Patrick, Wakeman, Stephanie, Wright, Gary, Cazzaniga, Giovanni, Davi, Frédéric, García-Sanz, Ramón, Davi, David, Groenen, Patricia, Hummel, Michael, Macintyre, Elizabeth, Stamatopoulos, Kostas, Pott, Christiane, Trka, Jan, Darzentas, Nikos, Langerak, Anton, Gonzalez, David, Bruggemann, M, Kotrova, M, Knecht, H, Bartram, J, Boudjogrha, M, Bystry, V, Fazio, G, Fronkova, E, Giraud, M, Grioni, A, Hancock, J, Herrmann, D, Jimenez, C, Krejci, A, Moppett, J, Reigl, T, Salson, M, Scheijen, B, Schwarz, M, Songia, S, Svaton, M, van Dongen, J, Villarese, P, Wakeman, S, Wright, G, Cazzaniga, G, Davi, F, Garcia-Sanz, R, Gonzalez, D, Groenen, P, Hummel, M, Macintyre, E, Stamatopoulos, K, Pott, C, Trka, J, Darzentas, N, Langerak, A, Immunology, University Medical Center of Schleswig–Holstein = Universitätsklinikum Schleswig-Holstein (UKSH), Kiel University, Childhood Leukaemia Investigation Prague (CLIP), University Hospital Motol [Prague], Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189 (CRIStAL), Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Ecole Centrale de Lille, Facultad de Quimica, Universidad Nacional Autonoma de Mexico, Bioinformatics and Sequence Analysis (BONSAI), Laboratoire d'Informatique Fondamentale de Lille (LIFL), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria), Liebherr-Werk Nenzing GmbH, Department of Immunology, Laboratory of molecular mechanisms of hematologic disorders and therapeutic implications (ERL 8254 - Equipe Inserm U1163), Imagine - Institut des maladies génétiques (IMAGINE - U1163), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Bristol Genetics Laboratory, Southmead Hospital, North Bristol NHS Trust, Great Ormond Street Hospital for Children [London] (GOSH), Service d'Hématologie Clinique [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Pitié-Salpêtrière [APHP], Haematology Department, University Hospital of Salamanca, Hematology Department and University Pierre et Marie Curie, Hopital Pitie-Salpetriere, Paris, France, Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands., Charité - Universitätsmedizin Berlin / Charite - University Medicine Berlin, CHU Necker - Enfants Malades [AP-HP], Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden, University Hospital Schleswig–Holstein, Department of Paediatric Haematology/Oncology, Charles University [Prague], Central European Institute of Technology, Masaryk University, Brno, Czech Republic, Erasmus University Medical Center [Rotterdam] (Erasmus MC), Department of Paediatric Haematology, Department of Hematology, University Hospital Schleswig-Holstein [Kiel, Germany], Service d'Hématologie clinique [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Centro Ricerca Tettamanti, Clinica Pediatrica, Ospedale S. Gerardo-Ospedale S. Gerardo, Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Bristol Genetics Laboratory (Southmead Hospital), Southmead Hospital, Instituto de Investigación Biomédica de Salamanca (IBSAL), Department of Pediatric Haematology, Bristol Royal Hospital for Children, Department of Pathology [Nijmegen], Radboud University Medical Center [Nijmegen], Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Unité d'Immunologie et d'Hématologie Pédiatrique (CHU Necker - Enfants Malades [AP-HP]), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Institute of Applied Biosciences, Thessaloniki, Greece., Charles University [Prague] (CU), Centre for Cancer Research and Cell Biology, Queen's University [Belfast] (QUB), and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)
Subjects: Genetic Markers, 0301 basic medicine, Cancer Research, Neoplasm, Residual, Cancer development and immune defence Radboud Institute for Molecular Life Sciences [Radboudumc 2], Receptors, Antigen, T-Cell, Immunoglobulins, Computational biology, Rare cancers Radboud Institute for Molecular Life Sciences [Radboudumc 9], Gene Rearrangement, T-Lymphocyte, Article, DNA sequencing, 03 medical and health sciences, symbols.namesake, All institutes and research themes of the Radboud University Medical Center, 0302 clinical medicine, Genetics research, Multiplex polymerase chain reaction, Humans, Cancer genetics, Recombination, Genetic, Sanger sequencing, minimal residual disease, next generation sequencing immunoglobulin and T-cell receptor, Genes, Immunoglobulin, biology, Computational Biology, High-Throughput Nucleotide Sequencing, Reproducibility of Results, [SDV.MHEP.HEM]Life Sciences [q-bio]/Human health and pathology/Hematology, Hematology, Gene rearrangement, Precursor Cell Lymphoblastic Leukemia-Lymphoma, Reference Standards, Amplicon, Minimal residual disease, 3. Good health, Genes, T-Cell Receptor, 030104 developmental biology, [SDV.IMM.IA]Life Sciences [q-bio]/Immunology/Adaptive immunology, Oncology, 030220 oncology & carcinogenesis, symbols, biology.protein, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Antibody, Primer (molecular biology)
Abstract: International audience; Amplicon-based next-generation sequencing (NGS) of immunoglobulin (IG) and T-cell receptor (TR) gene rearrangements for clonality assessment, marker identification and quantification of minimal residual disease (MRD) in lymphoid neoplasms has been the focus of intense research, development and application. However, standardization and validation in a scientifically controlled multicentre setting is still lacking. Therefore, IG/TR assay development and design, including bioinformatics, was performed within the EuroClonality-NGS working group and validated for MRD marker identification in acute lymphoblastic leukaemia (ALL). Five EuroMRD ALL reference laboratories performed IG/TR NGS in 50 diagnostic ALL samples, and compared results with those generated through routine IG/TR Sanger sequencing. A central polytarget quality control (cPT-QC) was used to monitor primer performance, and a central in-tube quality control (cIT-QC) was spiked into each sample as a library-specific quality control and calibrator. NGS identified 259 (average 5.2/sample, range 0–14) clonal sequences vs. Sanger-sequencing 248 (average 5.0/sample, range 0–14). NGS primers covered possible IG/TR rearrangement types more completely compared with local multiplex PCR sets and enabled sequencing of bi-allelic rearrangements and weak PCR products. The cPT-QC showed high reproducibility across all laboratories. These validated and reproducible quality-controlled EuroClonality-NGS assays can be used for standardized NGS-based identification of IG/TR markers in lymphoid malignancies.
Published: 2019
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8. MZ lymphoproliferations: shared and unique characteristics

Author: Xochelli, Aliki, Bikos, Vasilis, Polychronidou, Eleftheria, Galigalidou, Chrysi, Agathangelidis, Andreas, Charlotte, Frédéric, Moschonas, Panagiotis, Davis, Zadie, Colombo, Monica, Roumelioti, Maria, Sutton, Lesley-Ann, Groenen, Patricia, van den Brand, Michiel, Boudjoghra, Myriam, Algara, Patricia, Traverse-Glehen, Alexandra, Ferrer, Ana, Stalika, Evangelia, Karypidou, Maria, Kanellis, George, Kalpadakis, Christina, Mollejo, Manuella, Pangalis, Gerasimos, Vlamos, Panayiotis, Amini, Rose-Marie, Pospisilova, Sarka, Gonzalez, David, Ponzoni, Maurilio, Anagnostopoulos, Achilles, Giudicelli, Véronique, Lefranc, Marie-Paule, Espinet, Blanca, Panagiotidis, Panagiotis, Piris, Miguel Angel, Du, Ming-Qing, Rosenquist, Richard, Papadaki, Theodora, Belessi, Chrysoula, Ferrarini, Manlio, Oscier, David, Tzovaras, Dimitrios, Ghia, Paolo, Davi, Frederic, Hadzidimitriou, Anastasia, Stamatopoulos, Kostas, Apollo - University of Cambridge Repository, Institute of Applied Biosciences, CERTH, Thessaloniki, Greece., Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden, Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Information Technologies Institute, CERTH, Thessaloniki, Greece., Department of Informatics, Ionian University, Corfu, Greece, Division of Experimental Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milan, Italy., Service d'anatomie et cytologie pathologiques [CHU Saint-Antoine], Université Pierre et Marie Curie - Paris 6 (UPMC)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Service de pathologie [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Information Technologies Institute, CERTH, Thessaloniki, Greece, Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK., Molecular Pathology, Ospedale Policlinico SanMartino, Genoa, Italy., First Department of Propaedeutic Medicine, University of Athens, Athens, Greece, Uppsala Universitet [Uppsala], Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden, Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands., Université Pierre et Marie Curie - Paris 6 (UPMC), Service d'Hématologie Biologique [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Hospital Virgen de la Salud, Toledo, Spain, Department of Pathology and Hematology, Hospices Civils de Lyon (HCL), Laboratori de Citologia Hematològica i Citogenètica Molecular, Servei de Patologia, Hospital del Mar, Barcelona, Spain, Centre for Research and Technology Hellas (CERTH), Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece, Hematopathology Department, Evangelismos Hospital, Athens, Greece., Department of Haematology, University of Crete, Heraklion, Greece., Department of Haematology, Athens Medical Center, Athens, Greece, Department of Informatics [Ionian University], Ionian University [Corfu], Department of Informatics, Ionian University, Corfu, Greece., Department of Genetics and Pathology, Uppsala University Hospital, CEITEC-Central European Institute of Technology, MasarykBrno, Czech Republic., Pathology Unit, Unit of Lymphoid Malignancies, San Raffaele H Scientific Institute, Pathology Unit, San Raffaele Scientific Institute, Milan, Italy, Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoris de Citologia Hematológica/Citogenética Molecular. Servei de Patologia, GRETNHE, IMIM-Hospital del Mar, Laboratori de Citologia Hematològica i Citogenètica Molecular, Servei de Patologia, Hospital del Mar, Barcelona, Spain., Pathology Department, IIS 'Fundacion Jimenez Diaz', Madrid, Spain, Pathology, University of Cambridge [UK] (CAM), Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK, Hematology Department, Nikea General Hospital, Piraeus, Greece, Direzione Scientifica, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliera Universitaria (AOU) San Martino-IST, Genoa, Italy., Informatics & Telematics Institute (ITI), CERTH, Università Vita e Salute, San Raffaele, Milano, Italy, Division of Experimental Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milan, Italy, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institute of Applied Biosciences, Centre for Research and Technology-Hellas, Thessaloniki, Greece, Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden, Xochelli, Aliki, Bikos, Vasili, Polychronidou, Eleftheria, Galigalidou, Chrysi, Agathangelidis, Andrea, Charlotte, Frédéric, Moschonas, Panagioti, Davis, Zadie, Colombo, Monica, Roumelioti, Maria, Sutton, Lesley-Ann, Groenen, Patricia, van den Brand, Michiel, Boudjoghra, Myriam, Algara, Patricia, Traverse-Glehen, Alexandra, Ferrer, Ana, Stalika, Evangelia, Karypidou, Maria, Kanellis, George, Kalpadakis, Christina, Mollejo, Manuella, Pangalis, Gerasimo, Vlamos, Panayioti, Amini, Rose-Marie, Pospisilova, Sarka, Gonzalez, David, Ponzoni, Maurilio, Anagnostopoulos, Achille, Giudicelli, Véronique, Lefranc, Marie-Paule, Espinet, Blanca, Panagiotidis, Panagioti, Piris, Miguel Angel, Du, Ming-Qing, Rosenquist, Richard, Papadaki, Theodora, Belessi, Chrysoula, Ferrarini, Manlio, Oscier, David, Tzovaras, Dimitrio, Ghia, Paolo, Davi, Frederic, Hadzidimitriou, Anastasia, and Stamatopoulos, Kostas
Subjects: [SDV.GEN]Life Sciences [q-bio]/Genetics, Genes, Immunoglobulin, Genes, Immunoglobulin Heavy Chain, Cancer development and immune defence Radboud Institute for Molecular Life Sciences [Radboudumc 2], [SDV]Life Sciences [q-bio], Immunoglobulin Variable Region, Receptors, Antigen, B-Cell, Lymphoma, B-Cell, Marginal Zone, Rare cancers Radboud Institute for Molecular Life Sciences [Radboudumc 9], Complementarity Determining Regions, marginal zone lymphoma, immunoglobulin gene, antigen, ontogeny, Marginal zone lymphoma, Mutation, Tumor Microenvironment, Humans, Gene Rearrangement, B-Lymphocyte
Abstract: Contains fulltext : 203155.pdf (Publisher’s version ) (Closed access) The B cell receptor immunoglobulin (Ig) gene repertoires of marginal zone (MZ) lymphoproliferations were analyzed in order to obtain insight into their ontogenetic relationships. Our cohort included cases with MZ lymphomas (n = 488), i.e. splenic (SMZL), nodal (NMZL) and extranodal (ENMZL), as well as provisional entities (n = 76), according to the WHO classification. The most striking Ig gene repertoire skewing was observed in SMZL. However, restrictions were also identified in all other MZ lymphomas studied, particularly ENMZL, with significantly different Ig gene distributions depending on the primary site of involvement. Cross-entity comparisons of the MZ Ig sequence dataset with a large dataset of Ig sequences (MZ-related or not; n = 65 837) revealed four major clusters of cases sharing homologous ('public') heavy variable complementarity-determining region 3. These clusters included rearrangements from SMZL, ENMZL (gastric, salivary gland, ocular adnexa), chronic lymphocytic leukemia, but also rheumatoid factors and non-malignant splenic MZ cells. In conclusion, different MZ lymphomas display biased immunogenetic signatures indicating distinct antigen exposure histories. The existence of rare public stereotypes raises the intriguing possibility that common, pathogen-triggered, immune-mediated mechanisms may result in diverse B lymphoproliferations due to targeting versatile progenitor B cells and/or operating in particular microenvironments. Copyright (c) 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Published: 2019
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9. Thermal and pH stabilities of i-DNA: confronting in vitro experiments with models and in-cell NMR data

Author: Aurore Guédin, Jun Zhou, Lukáš Trantírek, Laurent Lacroix, Dehui Qiu, Mingpan Cheng, Liezel Tamon, Aleksandr B. Sahakyan, Huangxian Ju, Jielin Chen, Jean-Louis Mergny, Samir Amrane, Pavlína Víšková, Eva Ištvánková, State Key Laboratory of Analytical Chemistry for Life Science [School of Chemistry and Chemical Engineering, Nanjing University], Nanjing University of Science and Technology (NJUST), MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Acides Nucléiques : Régulations Naturelle et Artificielle (ARNA), Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), 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), Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - 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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Mergny, Jean-Louis, École normale supérieure - Paris (ENS-PSL), and 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)
Subjects: 2019-20 coronavirus outbreak, [CHIM.ANAL] Chemical Sciences/Analytical chemistry, [SDV]Life Sciences [q-bio], [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, 010402 general chemistry, 01 natural sciences, Stability (probability), Catalysis, chemistry.chemical_compound, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, [CHIM] Chemical Sciences, Thermal, [CHIM]Chemical Sciences, Thermal stability, ComputingMilieux_MISCELLANEOUS, 010405 organic chemistry, General Chemistry, Nmr data, In vitro, 0104 chemical sciences, [SDV] Life Sciences [q-bio], [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, chemistry, Chemical physics, Large size, DNA
Abstract: Recent studies indicate that i-DNA, a four-stranded cytosine-rich DNA also known as the i-motif, is actually formed in vivo ; however, a systematic study on sequence effects on stability has been missing. Herein, an unprecedented number of different sequences (271) bearing four runs of 3-6 cytosines with different spacer lengths has been tested. While i-DNA stability is nearly independent on total spacer length, the central spacer plays a special role on stability. Stability also depends on the length of the C-tracts at both acidic and neutral pHs. This study provides a global picture on i-DNA stability thanks to the large size of the introduced data set; it reveals unexpected features and allows to conclude that determinants of i-DNA stability do not mirror those of G-quadruplexes. Our results illustrate the structural roles of loops and C-tracts on i-DNA stability, confirm its formation in cells, and allow establishing rules to predict its stability.
Published: 2021
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10. Spin Crossover Metal-Organic Frameworks with Inserted Photoactive Guests: On the Quest to Control the Spin State by Photoisomerization

Author: Francisco Javier Valverde-Muñoz, Ján Moncoľ, Azzedine Bousseksou, Ivan Šalitroš, Gábor Molnár, Lionel Salmon, Barbora Brachňaková, Sébastien Bonhommeau, Ján Pavlik, Lucie Routaboul, Laboratoire de chimie de coordination (LCC), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Slovak University of Technology in Bratislava, Faculty of Science [Univ Palacký], Palacky University Olomouc, Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Institut des Sciences Moléculaires (ISM), Université Montesquieu - Bordeaux 4-Université Sciences et Technologies - Bordeaux 1-École Nationale Supérieure de Chimie et de Physique de Bordeaux (ENSCPB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Instituto de Ciencia Molecular (ICMol), Universitat de València (UV), Slovak grant agencies (APVV-18-0197, APVV-18-0016, APVV-19-0087, VEGA 1/0125/18, KEGA 018-STU-4), European Regional Development Fund : Operational Program Integrated Infrastructure for the project: 'Strategic research in the field of SMART monitoring, treatment and preventive protection against coronavirus (SARS-CoV-2)', project no. 313011ASS8, National Scholarship Programme of the Slovak Republic, Department of Inorganic Chemistry, Palacký University Olomouc, Czech Republic, Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601), Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Université Montesquieu - Bordeaux 4-Université Sciences et Technologies - Bordeaux 1 (UB)-École Nationale Supérieure de Chimie et de Physique de Bordeaux (ENSCPB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Materials science, Spin states, Photoisomerization, 02 engineering and technology, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, 0104 chemical sciences, Inorganic Chemistry, Thermogravimetry, Crystallography, chemistry.chemical_compound, symbols.namesake, Acetylene, chemistry, Spin crossover, symbols, [CHIM.CRIS]Chemical Sciences/Cristallography, Molecule, Metal-organic framework, [CHIM.COOR]Chemical Sciences/Coordination chemistry, 0210 nano-technology, Raman spectroscopy
Abstract: International audience; Three Hofmann-like metal-organic frameworks {Fe(bpac)[Pt(CN)4]}•G (bpac=1,2-bis(4-pyridyl)acetylene) were synthesized with photoisomerizable guest molecules (G = trans-azobenzene, trans-stilbene or cis-stilbene) and were characterized by elemental analysis, thermogravimetry and powder X-ray diffraction. The insertion of guest molecules and their conformation were inferred from Raman and FTIR spectra and from single-crystal X-ray diffraction and confronted with computational simulation. The magnetic and photomagnetic behaviors of the framework are significantly altered by the different guest molecules and different conformations. On the other hand, photoisomerization of the guest molecules becomes strongly hindered by the framework.
Published: 2021
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11. Theoretical study of current-induced domain wall motion in magnetic nanotubes with azimuthal domains

Author: Arnaud De Riz, Jérôme Hurst, Michal Staňo, Olivier Fruchart, Jean-Christophe Toussaint, Daria Gusakova, SPINtronique et TEchnologie des Composants (SPINTEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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)-Université Grenoble Alpes (UGA), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Micro et NanoMagnétisme (MNM), Institut Néel (NEEL), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), ANR-17-CE24-0017,MATEMAC-3D,Manipulation de textures magnétiques par courant – modélisation 3D par éléments finis(2017), Micro et NanoMagnétisme (NEEL - MNM), and ANR-18-CE92-0045,C3DS,Chimie pour une spintronique 3D(2018)
Subjects: Physics, Magnetic domain, Field (physics), Condensed matter physics, Exchange interaction, 02 engineering and technology, 021001 nanoscience & nanotechnology, 01 natural sciences, Magnetic anisotropy, Magnetization, Domain wall (magnetism), [PHYS.COND.CM-GEN]Physics [physics]/Condensed Matter [cond-mat]/Other [cond-mat.other], 0103 physical sciences, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Electric current, 010306 general physics, 0210 nano-technology, Anisotropy
Abstract: We report a theoretical overview of the magnetic domain wall behavior under an electric current in infinitely long nanotubes with azimuthal magnetization, combining the one-dimensional analytic model and micromagnetic simulations. We highlight effects that, besides spin-transfer torques already largely understood in flat strips, arise specifically in the tubular geometry: the \OE{}rsted field and curvature-induced magnetic anisotropy resulting both from the exchange interaction and material growth. Depending on both the geometry of the tube and the strength of the azimuthal anisotropy, Bloch or N\'eel walls arise at rest, resulting in two regimes of motion largely dominated by either spin-transfer torques or the \OE{}rsted field. We determine the Walker breakdown current in all cases, and highlight the most suitable parameters to achieve high domain wall speed.
Published: 2021
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12. Classification of challenging Laser-Induced Breakdown Spectroscopy soil sample data - EMSLIBS contest

Author: Erik Képeš, Frederik Schreckenberg, Vincent Motto-Ros, Cécile Fabre, Manoj Kumar Gundawar, Paul Prasse, Ludovic Duponchel, Jakub Vrábel, Xiaofeng Tan, Sven Connemann, Jozef Kaiser, Daniel Riebe, Rajendhar Junjuri, Pavel Pořízka, Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement - UMR 8516 (LASIRE), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille Institut (CLIL), Spectrométrie des biomolécules et agrégats (SPECTROBIO), Institut Lumière Matière [Villeurbanne] (ILM), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, GeoRessources, Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre de recherches sur la géologie des matières premières minérales et énergétiques (CREGU)-Institut national des sciences de l'Univers (INSU - CNRS), Fraunhofer-Institut für Lasertechnik (ILT), Fraunhofer Institute for Manufacturing Engineering and Automation (Fraunhofer IPA), Fraunhofer (Fraunhofer-Gesellschaft)-Fraunhofer (Fraunhofer-Gesellschaft), Institut für informatik [Potsdam], Universität Potsdam, Institute of Chemistry (Physical Chemistry), University of Potsdam, Advanced Centre of Research in High Energy Materials (ARCHEM), University of Hyderabad, X Scientific, Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Centre de recherches sur la géologie des matières premières minérales et énergétiques (CREGU)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), and University of Potsdam = Universität Potsdam
Subjects: Computer science, Sample (statistics), CONTEST, computer.software_genre, 01 natural sciences, Analytical Chemistry, Chemometrics, [SPI]Engineering Sciences [physics], 0103 physical sciences, Machine learning, [CHIM]Chemical Sciences, Laser-induced breakdown spectroscopy, Instrumentation, Spectroscopy, Classification benchmark, 010302 applied physics, [PHYS]Physics [physics], Elemental composition, Data processing, 010401 analytical chemistry, Atomic and Molecular Physics, and Optics, 0104 chemical sciences, Data set, EMSLIBS contest, Laser-induced breakdown spectroscopy (LIBS), Data mining, computer
Abstract: International audience; We present results of the classification contest organized for the EMSLIBS 2019 conference. For this publication, we chose only the five best approaches and discussed their algorithm in detail. The main focus of the contest reflected both recent and long-term challenges of Laser-Induced Breakdown Spectroscopy (LIBS) data processing. The contest was designed with a purpose to raise a challenge in handling and processing a very large dataset, containing high-dimensional elemental spectra. For the contest, 138 samples were measured using a lab-based LIBS system. In total, the data set consisted of 70,000 spectra, separated into 12 classes according to their elemental composition. Due to its extensivity and complexity, the data set is unique within the LIBS community. The central idea was to simulate the so-called “out-of-sample” classification (i.e. according to similar elemental composition), implying various real-world applications. Even more, it reflects the current level of expertise in the LIBS community and the capability of the LIBS method itself.
Published: 2020
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13. KIF14 controls ciliogenesis via regulation of Aurora A and is important for Hedgehog signaling

Author: Alexandre Benmerah, Petra Pejskova, Linda Dolanska, Ranjani Sri Ganji, Zbynek Zdrahal, Madeline Louise Reilly, Lucia Binó, Ondrej Bernatik, Lukas Cajanek, Benmerah, Alexandre, Masaryk University [Brno] (MUNI), Laboratoire des Maladies Rénales Héréditaires, Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Central European Institute of Technology [Brno] (CEITEC MU), and Brno University of Technology [Brno] (BUT)
Subjects: Kinesins, Mitosis, [SDV.GEN] Life Sciences [q-bio]/Genetics, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Protein Serine-Threonine Kinases, Biology, [SDV.MHEP.UN]Life Sciences [q-bio]/Human health and pathology/Urology and Nephrology, Article, Sodium Channels, Motor protein, 03 medical and health sciences, 0302 clinical medicine, Tandem Mass Spectrometry, Ciliogenesis, [SDV.BDD] Life Sciences [q-bio]/Development Biology, CEP164, Humans, Basal body, Hedgehog Proteins, Cilia, Sonic hedgehog, Interphase, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Hedgehog, Adaptor Proteins, Signal Transducing, Aurora Kinase A, 030304 developmental biology, Oncogene Proteins, [SDV.GEN]Life Sciences [q-bio]/Genetics, 0303 health sciences, Cilium, Cell Cycle, Intracellular Signaling Peptides and Proteins, Cell Biology, [SDV.MHEP.UN] Life Sciences [q-bio]/Human health and pathology/Urology and Nephrology, Basal Bodies, Hedgehog signaling pathway, Cell biology, HEK293 Cells, biology.protein, RNA Interference, 030217 neurology & neurosurgery, Chromatography, Liquid, Signal Transduction
Abstract: Pejskova et al. find that KIF14 is required for cilia formation and KIF14 loss leads to Hedgehog signaling defects. The study pinpoints deregulated Aurora A activity as a downstream mediator of KIF14 deficiency and thus reveals a connection between cell cycle regulation and ciliogenesis., Primary cilia play critical roles in development and disease. Their assembly and disassembly are tightly coupled to cell cycle progression. Here, we present data identifying KIF14 as a regulator of cilia formation and Hedgehog (HH) signaling. We show that RNAi depletion of KIF14 specifically leads to defects in ciliogenesis and basal body (BB) biogenesis, as its absence hampers the efficiency of primary cilium formation and the dynamics of primary cilium elongation, and disrupts the localization of the distal appendage proteins SCLT1 and FBF1 and components of the IFT-B complex. We identify deregulated Aurora A activity as a mechanism contributing to the primary cilium and BB formation defects seen after KIF14 depletion. In addition, we show that primary cilia in KIF14-depleted cells are defective in response to HH pathway activation, independently of the effects of Aurora A. In sum, our data point to KIF14 as a critical node connecting cell cycle machinery, effective ciliogenesis, and HH signaling.
Published: 2020
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14. Unravelling local environments in mixed TiO2–SiO2 thin films by XPS and ab initio calculations

Author: Lenka Zajíčková, Michèle Carette, Pavel Ondračka, David Holec, Agnès Granier, David Nečas, Mireille Richard-Plouet, Antoine Goullet, Stéphane Elisabeth, Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), Bio-Micro-Electro-Mechanical Systems - IEMN (BIOMEMS - IEMN), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), Institut des Matériaux Jean Rouxel (IMN), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Syst Plus Consulting, University of Leoben (MU), Faculty of Science [Brno] (SCI / MUNI), Masaryk University [Brno] (MUNI), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN), Central European Institute of Technology [Brno] (CEITEC), Brno University of Technology [Brno], Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Institut d’Électronique, de Microélectronique et de Nanotechnologie (IEMN) - UMR 8520 (IEMN), Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Université Polytechnique Hauts-de-France (UPHF)-Ecole Centrale de Lille-Université Polytechnique Hauts-de-France (UPHF)-Institut supérieur de l'électronique et du numérique (ISEN), University of science (Masaryk University), and Masaryk University
Subjects: 010302 applied physics, Materials science, Binding energy, General Physics and Astronomy, Infrared spectroscopy, 02 engineering and technology, Surfaces and Interfaces, General Chemistry, 021001 nanoscience & nanotechnology, Condensed Matter Physics, 01 natural sciences, 7. Clean energy, Surfaces, Coatings and Films, Amorphous solid, X-ray photoelectron spectroscopy, Core electron, Ab initio quantum chemistry methods, Chemical physics, 0103 physical sciences, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Density functional theory, Thin film, 0210 nano-technology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; Mixed TixSi1−xO2 oxide can exhibit a partial phase separation of the TiO2 and SiO2 phases at the atomic level. The quantification of TiO2-SiO2 mixing in the amorphous material is complicated and was so far done mostly by infrared spectroscopy. We developed a new approach to the fitting of X-ray photoelectron spectroscopy data for the quantification of partial phase separation in amorphous TixSi1-xO2 thin films deposited by plasma enhanced chemical vapour deposition. Several fitting constraints reducing the total number of degrees of freedom in the fits and thus the fit uncertainty were obtained by using core electron binding energies predicted by density functional theory calculations on TixSi1-xO2 amorphous supercells. Consequently, a decomposition of the O1s peak into TiO2, SiO2 and mixed components was possible. The component areas ratios were compared with the ratios predicted by older theoretical models based on the atomic environment statistics and we also developed several new models corresponding to more realistic atomic structure and partial mixing. Based on the comparison we conclude that the studied films are mostly disordered, with only a moderate phase separation.
Published: 2020
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15. Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response

Author: Picart-Picolo, Ariadna, Grob, Stefan, Picault, Nathalie, Franek, Michal, Llauro, Christel, Halter, Thierry, Maier, Tom R, Jobet, Edouard, Descombin, Julie, Zhang, Panpan, Paramasivan, Vijayapalani, Baum, Thomas J, Navarro, Lionel, Dvořáčková, Martina, Mirouze, Marie, Pontvianne, Frédéric, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Universität Zürich [Zürich] = University of Zurich (UZH), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), 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), Iowa State University (ISU), Cent European Inst Technol CEITEC, Masaryk University [Brno] (MUNI), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), ANR-15-CE12-0013,NucleoReg,Régulation transcriptionnelle par séquestration nucléolaire(2015), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), 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), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), University of Zurich, and Pontvianne, Frédéric
Subjects: [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, arabidopsis, 2716 Genetics (clinical), duplication, CAF1, 10126 Department of Plant and Microbial Biology, 1311 Genetics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Genetics(clinical), 580 Plants (Botany), 10211 Zurich-Basel Plant Science Center, TDDO
Abstract: International audience; Rapid plant genome evolution is crucial to adapt to environmental changes. Chromosomal rearrangements and gene copy number variation (CNV) are two important tools for genome evolution and sources for the creation of new genes. However, their emergence takes many generations. In this study, we show that in Arabidopsis thaliana, a significant loss of ribosomal RNA (rRNA) genes with a past history of a mutation for the chromatin assembly factor 1 (CAF1) complex causes rapid changes in the genome structure. Using long-read sequencing and microscopic approaches, we have identified up to 15 independent large tandem duplications in direct orientation (TDDOs) ranging from 60 kb to 1.44 Mb. Our data suggest that these TDDOs appeared within a few generations, leading to the duplication of hundreds of genes. By subsequently focusing on a line only containing 20% of rRNA gene copies (20rDNA line), we investigated the impact of TDDOs on 3D genome organization, gene expression, and cytosine methylation. We found that duplicated genes often accumulate more transcripts. Among them, several are involved in plant–pathogen response, which could explain why the 20rDNA line is hyper-resistant to both bacterial and nematode infections. Finally, we show that the TDDOs create gene fusions and/or truncations and discuss their potential implications for the evolution of plant genomes.
Published: 2020
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16. The frequency and consequences of multipolar mitoses in undifferentiated embryonic stem cells

Author: Milan Ešner, Jean-Yvez Tinevez, Veronika Pospíšilová, Radek Fedr, Aleš Hampl, Martin Anger, Iveta Červenková, Department of Histology and Embryology [Brno] (MED / MUNI), Faculty of Medicine [Brno] (MED / MUNI), Masaryk University [Brno] (MUNI)-Masaryk University [Brno] (MUNI), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Institute of Biophysics of the Czech Academy of Sciences (IBP / CAS), Czech Academy of Sciences [Prague] (CAS), Hub d'analyse d'images - Image Analysis Hub (Platform) (IAH), Institut Pasteur [Paris], St. Anne’s University Hospital [Brno], This work was supported by Czech Science Foundation projects 15-11707S and 15-04844S andthe European Regional Development Fund-Project 'National infrastructure for biological and medical imaging' (No.CZ.02.1.01/0.0/0.0/16_013/000 1775)., We thank Drs. Anthony Hyman and Ina Poser (MPICBG, Dresden, Germany) for providing the H2A-GFP BAC construct, Dr. Ronald Naumann (MPI-CBG, Dresden, Germany) for providing the JM8.A mouse ES cells, and Dr. Klara Koudelkova for her excellent technical assistance, and Institut Pasteur [Paris] (IP)
Subjects: Genome instability, Multipolar division, Cell division, Health, Toxicology and Mutagenesis, [SDV]Life Sciences [q-bio], Cell, Biomedical Engineering, Spindle assembly checkpoint (SAC), Biology, Single-cell tracking, General Biochemistry, Genetics and Molecular Biology, Time-lapse microscopy, 03 medical and health sciences, 0302 clinical medicine, Tissue engineering, Artificial Intelligence, medicine, General Pharmacology, Toxicology and Pharmaceutics, Mitosis, General Immunology and Microbiology, General Neuroscience, General Medicine, Embryonic stem cell, 030205 complementary & alternative medicine, Cell biology, Mitosis length, medicine.anatomical_structure, 030220 oncology & carcinogenesis, General Agricultural and Biological Sciences, Embryonic stem (ES) cells, Multipolar spindles
Abstract: International audience; Embryonic stem (ES) cells are pluripotent cells widely used in cell therapy and tissue engineering. However, the broader clinical applications of ES cells are limited by their genomic instability and karyotypic abnormalities. Thus, understanding the mechanisms underlying ES cell karyotypic abnormalities is critical to optimizing their clinical use. In this study, we focused on proliferating human and mouse ES cells undergoing multipolar divisions. Specifically, we analyzed the frequency and outcomes of such divisions using a combination of time-lapse microscopy and cell tracking. This revealed that cells resulting from multipolar divisions were not only viable, but they also frequently underwent subsequent cell divisions. Our novel data also showed that in human and mouse ES cells, multipolar spindles allowed more robust escape from chromosome segregation control mechanisms than bipolar spindles. Considering the frequency of multipolar divisions in proliferating ES cells, it is conceivable that cell division errors underlie ES cell karyotypic instability.
Published: 2019
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17. An interactive and intuitive visualisation method for X-ray computed tomography data of biological samples in 3D Portable Document Format

Author: Glenda Comai, Markéta Tesařová, Shahragim Tajbakhsh, Eglantine Heude, Jozef Kaiser, Marketa Kaucka, Tomáš Zikmund, Igor Adameyko, Cellules Souches et Développement / Stem Cells and Development, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institute of Experimental Biology, Masaryk University [Brno] (MUNI), Biologie Moléculaire du Développement, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Physiologie moléculaire et adaptation (PhyMA), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 3D PDF, Models, Anatomic, Embryology, Computer science, [SDV]Life Sciences [q-bio], ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION, lcsh:Medicine, 3D rendering, Facial Bones, Article, Rendering (computer graphics), 03 medical and health sciences, Disk formatting, Mice, 0302 clinical medicine, Data acquisition, Software, Imaging, Three-Dimensional, Computer graphics (images), Animals, Portable Document Format, lcsh:Science, 030304 developmental biology, 0303 health sciences, Electronic Data Processing, Multidisciplinary, business.industry, Information Dissemination, lcsh:R, Skull, imaging, X-Ray Microtomography, File format, Data Compression, Visualization, Data sharing, Radiographic Image Interpretation, Computer-Assisted, lcsh:Q, business, Biomedical engineering, 030217 neurology & neurosurgery, CT, 3D
Abstract: 3D imaging approaches based on X-ray microcomputed tomography (microCT) have become increasingly accessible with advancements in methods, instruments and expertise. The synergy of material and life sciences has impacted biomedical research by proposing new tools for investigation. However, data sharing remains challenging as microCT files are usually in the range of gigabytes and require specific and expensive software for rendering and interpretation. Here, we provide an advanced method for visualisation and interpretation of microCT data with small file formats, readable on all operating systems, using freely available Portable Document Format (PDF) software. Our method is based on the conversion of volumetric data into interactive 3D PDF, allowing rotation, movement, magnification and setting modifications of objects, thus providing an intuitive approach to analyse structures in a 3D context. We describe the complete pipeline from data acquisition, data processing and compression, to 3D PDF formatting on an example of craniofacial anatomical morphology in the mouse embryo. Our procedure is widely applicable in biological research and can be used as a framework to analyse volumetric data from any research field relying on 3D rendering and CT-biomedical imaging.
Published: 2019
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18. Electrodeposition of silver amalgam particles on ITO – Towards novel electrode material

Author: Filip Ligmajer, Miroslav Fojta, Alain Walcarius, Ales Danhel, Tomáš Šikola, Institute of Biophysics of the Czech Academy of Sciences (IBP / CAS), Czech Academy of Sciences [Prague] (CAS), Brno University of Technology [Brno] (BUT), Central European Institute of Technology [Brno] (CEITEC MU), Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l'Environnement (LCPME), and Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Chemistry, Scanning electron microscope, General Chemical Engineering, Inorganic chemistry, Oxide, 02 engineering and technology, Electrolyte, Chronoamperometry, 010402 general chemistry, 021001 nanoscience & nanotechnology, Electrochemistry, 7. Clean energy, 01 natural sciences, 0104 chemical sciences, Analytical Chemistry, chemistry.chemical_compound, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Elemental analysis, Electrode, Amalgam (chemistry), 0210 nano-technology
Abstract: International audience; Silver solid amalgam represents up to now the most suitable alternative electrode material to metallic mercury in electroanalytical chemistry. Controlled electrodeposition of variable (sub)micrometer-sized silver amalgam particles (AgAP) on the surface of transparent indium-tin oxide (ITO) electrode from an electrolyte containing Ag+ and Hg2+ ions is reported here, as a novel perspective method suitable for preparation of nano-structured silver amalgam electrode material. Elemental analysis of the composition and morphology of the AgAP decorating the ITO was studied by scanning electron microscopy including energy-disperse X-ray spectroscopy and by image processing software. Particle composition, size, and surface coverage are controllable by selection of the Ag+/Hg2+ ratio in the electrodeposition solution and by setting of individual parameters of applied double pulsed/potential chronoamperometry. Applicable potential window of thus prepared ITO-AgAP electrode was found to be within +0.2 to −1.0 V in 0.2 acetate buffer pH 5.0. Utilized voltammetric and chronoamperometric methods revealed significant enhancement in electrochemical reducibility of selected model organic nitro-compound (shift of the peak potential about 300 mV to more positive potentials). Its further employment in UV/Vis spectroelectrochemical cell provided information about number of consumed electrons and kinetic characteristics. Furthermore preferential adsorption of calf thymus DNA at AgAP than ITO was observed by fluorescence microscopy indicating its potential applicability in (bio-)spectroelectrochemical methods. Further advantages and potential applications are also proposed and discussed.
Published: 2018
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19. Community curation of bioinformatics software and data resources

Author: Ison, Jon, Ménager, Hervé, Brancotte, Bryan, Jaaniso, Erik, Salumets, Ahto, Raček, Tomáš, Lamprecht, Anna-Lena, Palmblad, Magnus, Kalaš, Matúš, Chmura, Piotr, Hancock, John M, Schwämmle, Veit, Ienasescu, Hans-Ioan, Sub Software Technology, Software Technology, Sub Software Technology, Software Technology, National Life Science Supercomputing Center [Kongens Lyngby, Denmark] (Computerome), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institute of Computer Science [University of Tartu, Estonie], University of Tartu, Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Faculty of Informatics [Brno] (FI / MUNI), Masaryk University [Brno] (MUNI), Department of Information and Computing Sciences [Utrecht], Utrecht University [Utrecht], Center for Proteomics and Metabolomics [Leiden] (CPM), Leiden University Medical Center (LUMC), Universiteit Leiden-Universiteit Leiden, Department of Informatics [Bergen] (UiB), University of Bergen (UiB), Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), ELIXIR Hub [Cambridge], University of Southern Denmark (SDU), We acknowledge with gratitude the support of our funders: The Danish Ministry of Higher Education and Science and ELIXIR-EXCELERATE under the European Union’s Horizon 2020 research and innovation programme (grant agreement number 676559), European Project: 676559,H2020,H2020-INFRADEV-1-2015-1,ELIXIR-EXCELERATE(2015), Technical University of Denmark [Lyngby] (DTU), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)
Subjects: AcademicSubjects/SCI01060, Computer science, community driven, registry, 03 medical and health sciences, Software, Bioinformatics software, Humans, Molecular Biology, database, 030304 developmental biology, Life Scientists, 0303 health sciences, business.industry, software, 030302 biochemistry & molecular biology, Community Participation, Computational Biology, bioinformatics, curation, Service provider, Data science, Data resources, Europe, Database Management Systems, Problem Solving Protocol, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, Information Systems
Abstract: The corpus of bioinformatics resources is huge and expanding rapidly, presenting life scientists with a growing challenge in selecting tools that fit the desired purpose. To address this, the European Infrastructure for Biological Information is supporting a systematic approach towards a comprehensive registry of tools and databases for all domains of bioinformatics, provided under a single portal (https://bio.tools). We describe here the practical means by which scientific communities, including individual developers and projects, through major service providers and research infrastructures, can describe their own bioinformatics resources and share these via bio.tools.
Published: 2019
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20. Self-supported sulphurized TiO2 nanotube layers as positive electrodes for lithium microbatteries

Author: Girish D. Salian, Jan Michalička, Milos Krbal, Chrystelle Lebouin, Jan M. Macak, Hanna Sopha, Alexander T. Tesfaye, Marie-Vanessa Coulet, Ludek Hromadko, Thierry Djenizian, Département d’Électronique Flexible (FEL-ENSMSE), CMP-GC-Ecole des Mines de Saint-Etienne (Institut Mines-Télécom (IMT)) (Mines Saint-Etienne ), Center of Materials and Nanotechnologies [University of Pardubice] (CEMNAT ), Faculty of Chemical Technology [University of Pardubice], University of Pardubice-University of Pardubice, Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Matériaux divisés, interfaces, réactivité, électrochimie (MADIREL), Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Centre Microélectronique de Provence - Site Georges Charpak (CMP-GC) (CMP-ENSMSE), École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), and Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-CMP-GC
Subjects: Thermogravimetric analysis, Nanotube, Materials science, samonosné, Scanning electron microscope, 02 engineering and technology, 010402 general chemistry, 7. Clean energy, 01 natural sciences, law.invention, Li-ion microbatteries, X-ray photoelectron spectroscopy, law, General Materials Science, Thermal stability, Li-iontové mikrobatarie, Self-supported, Sulphurization, Titania nanotubes, [CHIM.MATE]Chemical Sciences/Material chemistry, 021001 nanoscience & nanotechnology, katoda, Self-supported Cathode, Cathode, 0104 chemical sciences, síření, Chemical engineering, Electrode, Cyclic voltammetry, 0210 nano-technology, TiO2 nanotrubičky
Abstract: We report the synthesis and characterization of self-supported sulphurized TiO2 nanotube layers as a cathode material for Li microbatteries. Sulphurized TiO2 nanotubes were obtained by annealing of selfsupported TiO2 nanotubes in sulphur atmosphere. The morphology, structure, composition and thermal stability of the TixOySz nanotube layers were studied by scanning electron microscopy, transmission electron microscopy, X-ray diffraction, X-ray photoelectron spectroscopy and thermogravimetric analysis. The electrochemical behaviors of the chemically modified nanotubes were investigated by cyclic voltammetry and chronopotentiometry techniques. This nanostructured electrode used as a cathode material showed high rate capabilities even at very fast kinetics. Remarkably, a high discharge capacity (340 mu Ah cm(-2)) has been retrieved after 100 cycles with 100% coulombic efficiency attesting the excellent stability of the electrode. (C) 2019 The Authors. Published by Elsevier Ltd. Popisujeme syntézu a charakterizaci samonosných sířených vrstev TiO2 nanotrubic jako katod pro lithiové mikrobaterie. Sířené TiO2 nanotrubice byly získány žíháním samonosných TiO2 nanotrubiček v atmosféře síry. Morfologie, struktura, složení a tepelná stabilita vrstev TixOySz nanotrubic byly studovány skenovací elektronovou mikroskopií, transmisní elektronovou mikroskopií, rentgenovou difrakcí, rentgenovou fotoelektronovou spektroskopií a termogravimetrickou analýzou. Elektrochemické chování chemicky modifikovaných nanotrubic bylo zkoumáno technikami cyklické voltametrie a chronopotenciometrie. Tato nanostrukturovaná elektroda použitá jako katoda vykazovala vysoké rychlosti i při velmi rychlé kinetice. Je pozoruhodné, že po 100 cyklech byla získána vysoká vybíjecí kapacita (340 μAh cm−2) se 100% coulombickou účinností, což svědčí o vynikající stabilitě elektrody.
Published: 2019
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21. Directly Sequenced Genomes of Contemporary Strains of Syphilis Reveal Recombination-Driven Diversity in Genes Encoding Predicted Surface-Exposed Antigens

Author: Linda Grillová, Jan Oppelt, Lenka Mikalová, Markéta Nováková, Lorenzo Giacani, Anežka Niesnerová, Angel A. Noda, Ariel E. Mechaly, Petra Pospíšilová, Darina Čejková, Philippe A. Grange, Nicolas Dupin, Radim Strnadel, Marcus Chen, Ian Denham, Natasha Arora, Mathieu Picardeau, Christopher Weston, R. Allyn Forsyth, David Šmajs, Biologie des Spirochètes / Biology of Spirochetes, Institut Pasteur [Paris], Masaryk University [Brno] (MUNI), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Departments of Medicine and Global Health, University of Washington [Seattle], Instituto de Medicina Tropical Pedro Kouri, Cristallographie (Plateforme) - Crystallography (Platform), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Veterinary Research Institute [Brno] (VRI), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Service de Dermatologie [CHU Cochin], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Masaryk University and University Hospital Brno, University Hospital Brno, Monash University [Melbourne], Melbourne Sexual Health Centre [Australia], Alfred Health, Universität Zürich [Zürich] = University of Zurich (UZH), GeneticPrime Dx, Department of Biology [San Diego], San Diego State University (SDSU), This research was supported by funds from the Faculty of Medicine, Masaryk University to junior researchers (LGr, MN, and PP), the Grant Agency of the Czechia (GA17-25455S) and by the Ministry of Health of the Czechia (17-31333A) to DŠ. Core Facility Bioinformatics of CEITEC Masaryk University is gratefully acknowledged for the obtaining of the scientific data presented in this manuscript. Computational resources were provided by the CESNET LM2015042 and the CERIT Scientific Cloud LM2015085, provided under the program 'Projects of Large Research, Development, and Innovations Infrastructures'., University of Zurich, Šmajs, David, Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP)-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)-Université Paris Cité (UPCité), Department of Biology [San Diego State Univ] (Biology SDSU), and MURGUET, SYLVIE
Subjects: Microbiology (medical), [SDV]Life Sciences [q-bio], Population, lcsh:QR1-502, syphilis, 340 Law, 610 Medicine & health, direct whole genome sequencing, Genome, Genetic recombination, Microbiology, 2726 Microbiology (medical), lcsh:Microbiology, 03 medical and health sciences, 510 Mathematics, Treponema pallidum subsp. pallidum, medicine, Genetic variability, education, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Gene, Original Research, 030304 developmental biology, Genetics, 0303 health sciences, education.field_of_study, Genetic diversity, Treponema, biology, 030306 microbiology, culture-independent bacterial enrichment, 2404 Microbiology, Treponema pallidum subsp pallidum, medicine.disease, biology.organism_classification, 10218 Institute of Legal Medicine, 3. Good health, [SDV] Life Sciences [q-bio], [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, recombination- driven diversity, Syphilis, recombination-driven diversity
Abstract: We would like to thank Prof. Nicholas Robert Thomson (Wellcome Sanger Institute) for his valuable insights during the preparation of the manuscript. We also thank Robert Anthony Gaultney for his assistance with the English revision of the manuscript.; International audience; Syphilis, caused by Treponema pallidum subsp. pallidum (TPA), remains an important public health problem with an increasing worldwide prevalence. Despite recent advances in in vitro cultivation, genetic variability of this pathogen during infection is poorly understood. Here, we present contemporary and geographically diverse complete treponemal genome sequences isolated directly from patients using a methyl-directed enrichment prior to sequencing. This approach reveals that approximately 50% of the genetic diversity found in TPA is driven by inter- and/or intra-strain recombination events, particularly in strains belonging to one of the defined genetic groups of syphilis treponemes: Nichols-like strains. Recombinant loci were found to encode putative outer-membrane proteins and the recombination variability was almost exclusively found in regions predicted to be at the host-pathogen interface. Genetic recombination has been considered to be a rare event in treponemes, yet our study unexpectedly showed that it occurs at a significant level and may have important impacts in the biology of this pathogen, especially as these events occur primarily in the outer membrane proteins. This study reveals the existence of strains with different repertoires of surface-exposed antigens circulating in the current human population, which should be taken into account during syphilis vaccine development.
Published: 2019
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22. Structure and functions of microtubule associated proteins tau and MAP2c: Similarities and differences

Author: Malene Ringkjøbing Jensen, Rostislav Skrabana, Subhash Narasimhan, Kateřina Melková, Lukáš Žídek, Markus Zweckstetter, Vojtěch Zapletal, Martin Blackledge, Jozef Hritz, Séverine Jansen, Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Department of NMR-based Structural Biology [Göttingen], Max Planck Institute for Biophysical Chemistry (MPI-BPC), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: 0301 basic medicine, Gene isoform, Microtubule-associated protein, metabolism [Microtubules], lcsh:QR1-502, tau Proteins, Review, Biochemistry, Filamentous actin, Microtubules, lcsh:Microbiology, chemistry [Microtubule-Associated Proteins], 03 medical and health sciences, 0302 clinical medicine, Molecular recognition, Microtubule, ddc:570, Animals, Humans, tau, Structural motif, Cytoskeleton, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Chemistry, phosphorylation, chemistry [tau Proteins], metabolism [Microtubule-Associated Proteins], intrinsically disordered protein, metabolism [tau Proteins], [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, nuclear magnetic resonance, 030104 developmental biology, Biophysics, chemistry [Microtubules], microtubule associated protein, Sequence motif, Microtubule-Associated Proteins, 030217 neurology & neurosurgery
Abstract: The stability and dynamics of cytoskeleton in brain nerve cells are regulated by microtubule associated proteins (MAPs), tau and MAP2. Both proteins are intrinsically disordered and involved in multiple molecular interactions important for normal physiology and pathology of chronic neurodegenerative diseases. Nuclear magnetic resonance and cryo-electron microscopy recently revealed propensities of MAPs to form transient local structures and long-range contacts in the free state, and conformations adopted in complexes with microtubules and filamentous actin, as well as in pathological aggregates. In this paper, we compare the longest, 441-residue brain isoform of tau (tau40), and a 467-residue isoform of MAP2, known as MAP2c. For both molecules, we present transient structural motifs revealed by conformational analysis of experimental data obtained for free soluble forms of the proteins. We show that many of the short sequence motifs that exhibit transient structural features are linked to functional properties, manifested by specific interactions. The transient structural motifs can be therefore classified as molecular recognition elements of tau40 and MAP2c. Their interactions are further regulated by post-translational modifications, in particular phosphorylation. The structure-function analysis also explains differences between biological activities of tau40 and MAP2c.
Published: 2019
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23. Microbe-focused glycan array screening platform

Author: Peter H. Seeberger, Xiaoqiang Guo, Jana Mrázková, Franck Fieschi, You Yang, Hidenori Tanaka, Bernd Lepenies, Chakkumkal Anish, Frank Schuhmacher, Michaela Wimmerová, Christoph Rademacher, Daniele Leonori, Heung Sik Hahm, João T. Monteiro, Claney L. Pereira, Anika Reinhardt, Sandip Pasari, Sharavathi Guddehalli Parameswarappa, Mark K. Schlegel, Dan Grünstein, Jeyakumar Kandasamy, Guozhi Xiao, Andreas Geissner, Timo Johannssen, Sebastian Götze, Christopher E. Martin, Michel Thépaut, Department of Biomolecular Systems [Potsdam], Max Planck Institute of Colloids and Interfaces, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Immunology Unit and Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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)-Centre National de la Recherche Scientifique (CNRS), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: Glycan, Carbohydrate synthesis, Oligosaccharides, Computational biology, Plasma protein binding, glycan arrays, CHO Cells, 01 natural sciences, antiglycan antibodies, Glycomics, 03 medical and health sciences, Cricetulus, Species Specificity, microbial antigens, Polysaccharides, Lectins, Animals, Humans, immune receptors, 030304 developmental biology, 0303 health sciences, Antigens, Bacterial, Multidisciplinary, Innate immune system, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], 010405 organic chemistry, Microarray analysis techniques, Chemistry, Microarray Analysis, Mammalian Glycan, Recombinant Proteins, 0104 chemical sciences, carbohydrates (lipids), PNAS Plus, Immune System, biology.protein, bacterial lectins, DNA microarray, Carrier Proteins, Protein Binding
Abstract: International audience; Interactions between glycans and glycan binding proteins are essential for numerous processes in all kingdoms of life. Glycan microarrays are an excellent tool to examine protein-glycan interactions. Here, we present a microbe-focused glycan microarray platform based on oligosaccharides obtained by chemical synthesis. Glycans were generated by combining different carbohydrate synthesis approaches including automated glycan assembly, solution-phase synthesis, and chemoenzymatic methods. The current library of more than 300 glycans is as diverse as the mammalian glycan array from the Consortium for Functional Glycomics and, due to its microbial focus, highly complementary. This glycan platform is essential for the characterization of various classes of glycan binding proteins. Applications of this glycan array platform are highlighted by the characterization of innate immune receptors and bacterial virulence factors as well as the analysis of human humoral immunity to pathogenic glycans.
Published: 2019
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24. The bio.tools registry of software tools and data resources for the life sciences

Author: Piotr Jaroslaw Chmura, Salvador Capella, Rob Hooft, Søren Brunak, Tomáš Raček, Inge Jonassen, Rodrigo Lopez, Jacques van Helden, Bengt Persson, Hedi Peterson, Brane Leskošek, Alfonso Valencia, Heinz Stockinger, Hervé Ménager, Emil Karol Rydza, Matúš Kalaš, Josep Lluís Gelpí, Tommi Nyrönen, Hans Ienasescu, Christophe Blanchet, Rafael C. Jimenez, Björn Grüning, Jon Ison, Babis Savakis, Radka Svobodová Vařeková, Arlindo L. Oliveira, Peter Løngreen, Niall Beard, Gert Vriend, Veit Schwämmle, Jiří Vondrášek, Séverine Duvaud, Federico Zambelli, Ahto Salumets, Kristoffer Rapacki, Olivier Collin, Technical University of Denmark [Lyngby] (DTU), University of Copenhagen = Københavns Universitet (KU), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], University of Bergen (UIB), University of Southern Denmark (SDU), Albert-Ludwigs-Universität Freiburg, University of Manchester [Manchester], European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Swiss Institute of Bioinformatics - Lausanne (SIB), Swiss Institute of Bioinformatics, Uppsala University, Central European Institute of Technology [Brno] (CEITEC), Czech Academy of Sciences [Prague] (ASCR), University of Tartu, Dutch Techcentre for Life Sciences [Utrecht], Center for Science (CSC-IT), CSC-IT Center for Science, Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Università degli studi di Milano [Milano], Biomedical Sciences Research Centre Alexander Fleming [Vari, Greece] (BSRC), University of Ljubljana, Institut Français de Bioinformatique - UMS CNRS 3601 (IFB-CORE), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA), ELIXIR Hub [Cambridge], Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa (INESC-ID), Instituto Superior Técnico, Universidade Técnica de Lisboa (IST)-Instituto de Engenharia de Sistemas e Computadores (INESC), Nijmegen Medical Centre [Nijmegen], Plateforme bioinformatique GenOuest [Rennes], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Danish Ministry of Higher Education and Science, European Project: 676559,H2020,H2020-INFRADEV-1-2015-1,ELIXIR-EXCELERATE(2015), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), University of Bergen (UiB), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Czech Academy of Sciences [Prague] (CAS), Università degli Studi di Milano [Milano] (UNIMI), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Plateforme Génomique Santé Biogenouest®-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), University of Copenhagen = Københavns Universitet (UCPH), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université de Lausanne = University of Lausanne (UNIL), Università degli Studi di Milano = University of Milan (UNIMI), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), and Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1)
Subjects: lcsh:QH426-470, Databases, Factual, Bioinformatics, [SDV]Life Sciences [q-bio], MEDLINE, Biology, Biological Science Disciplines, 03 medical and health sciences, 0302 clinical medicine, Software, Bioinformàtica, lcsh:QH301-705.5, 030304 developmental biology, 0303 health sciences, Internet, business.industry, Biochemistry and Molecular Biology, Data science, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Data resources, Variety (cybernetics), lcsh:Genetics, Workflow, lcsh:Biology (General), The Internet, Open Letter, business, Nanomedicine Radboud Institute for Molecular Life Sciences [Radboudumc 19], Biokemi och molekylärbiologi, 030217 neurology & neurosurgery
Abstract: Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue (https://bio.tools) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information. Electronic supplementary material The online version of this article (10.1186/s13059-019-1772-6) contains supplementary material, which is available to authorized users.
Published: 2019
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25. Cytogenetic complexity in chronic lymphocytic leukemia: definitions, associations and clinical impact

Author: Blanca Espinet, M. Jose Calasanz, Marie Jarošová, Carolina Moreno, Julio Delgado, Andrea Visentin, Niki Stavroyianni, Rosa Collado, Florence Cymbalista, Helena Podgornik, Kostas Stamatopoulos, Zadie Davis, Michael Doubek, Claudia Haferlach, Fred Davi, Achilles Anagnostopoulos, Arnon P. Kater, Šárka Pospíšilová, Panayiotis Panayiotidis, Sabine Jeromin, David Oscier, Florence Nguyen-Khac, Maria Dimou, Neus Ruiz-Xivillé, Antonio Cuneo, Anna Puiggros, Panagiotis Baliakas, Theodoros Iliakis, Aliki Xochelli, Anastasia Athanasiadou, Alexander C. Leeksma, Paolo Ghia, Pau Abrisqueta, Karla Plevová, Virginie Eclache, George Papaioannou, Livio Trentin, Gian Matteo Rigolin, Michalis Iskas, Kristina Durechova, Evangelia Stalika, Fanny Baran-Marszak, Graduate School, CCA - Cancer biology and immunology, Clinical Haematology, Experimental Immunology, Uppsala University, MLL Münchner Leukämielabor GmbH / MLL Munich Leukemia Laboratory [Munich, Germany], General Hospital of Thessaloniki George Papanikolaou, IMIM-Hospital del Mar, Generalitat de Catalunya, Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Masaryk University [Brno] (MUNI), University Hospital Brno, Centre de Recherche des Cordeliers (CRC (UMR_S_1138 / U1138)), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris Cité (UPCité), Royal Bournemouth Hospital, Università degli Studi di Ferrara = University of Ferrara (UniFE), Università degli Studi di Padova = University of Padua (Unipd), Centre for Research and Technology Hellas (CERTH), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), Hôpital Avicenne [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Vall d'Hebron University Hospital [Barcelona], National and Kapodistrian University of Athens (NKUA), Consorcio Hospital General Universitario de Valencia, Universidad de Navarra [Pamplona] (UNAV), Universitat Autònoma de Barcelona (UAB), Hospital de la Santa Creu i Sant Pau, Academic Medical Center - Academisch Medisch Centrum [Amsterdam] (AMC), University of Amsterdam [Amsterdam] (UvA), Amsterdam institute for Infection and Immunity [Amsterdam, The Netherlands] (A3I), University Medical Centre Ljubljana [Ljubljana, Slovenia] (UMCL), Universita Vita Salute San Raffaele = Vita-Salute San Raffaele University [Milan, Italie] (UniSR), Lambert, Mélanie, Baliakas, P., Jeromin, S., Iskas, M., Puiggros, A., Plevova, K., Nguyen-Khac, F., Davis, Z., Matteo Rigolin, G., Visentin, A., Xochelli, A., Delgado, J., Baran-Marszak, F., Stalika, E., Abrisqueta, P., Durechova, K., Papaioannou, G., Eclache, V., Dimou, M., Iliakis, T., Collado, R., Doubek, M., Calasanz, M. J., Ruiz-Xiville, N., Moreno, C., Jarosova, M., Leeksma, A. C., Panayiotidis, P., Podgornik, H., Cymbalista, F., Anagnostopoulos, A., Trentin, L., Stavroyianni, N., Davi, F., Ghia, P., Kater, A. P., Cuneo, A., Pospisilova, S., Espinet, B., Athanasiadou, A., Oscier, D., Haferlach, C., and Stamatopoulos, K.
Subjects: Male, Chronic lymphocytic leukemia, cytogenetics, complex karyotype, prognosis, Oncology, complex karyotype, medicine.medical_specialty, [SDV]Life Sciences [q-bio], Chronic lymphocytic leukemia, Immunology, Somatic hypermutation, Biochemistry, Somatic evolution in cancer, cytogenetics, NO, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, Biomarkers, Tumor, Humans, Medicine, Survival rate, Aged, Retrospective Studies, Chromosome Aberrations, Hematology, business.industry, Cytogenetics, Cell Biology, Middle Aged, medicine.disease, Leukemia, Lymphocytic, Chronic, B-Cell, 3. Good health, Survival Rate, [SDV] Life Sciences [q-bio], Leukemia, 030220 oncology & carcinogenesis, Mutation, Chromosome abnormality, Female, Somatic Hypermutation, Immunoglobulin, prognosis, Tumor Suppressor Protein p53, business, Follow-Up Studies, 030215 immunology
Abstract: Recent evidence suggests that complex karyotype (CK) defined by the presence of =3 chromosomal aberrations (structural and/or numerical) identified by chromosome banding analysis (CBA) may be relevant for treatment decision-making in chronic lymphocytic leukemia (CLL). However, many challenges towards routine clinical application of CBA remain. In a retrospective study of 5290 patients with available CBA data, we explored both clinicobiological associations and the clinical impact of CK in CLL. We found that patients with =5 abnormalities, defined as high-CK, exhibit uniformly dismal clinical outcome, independently of clinical stage, TP53 aberrations (deletion of chromosome 17p and or TP53 mutations, TP53abs) and the expression of somatically hypermutated (M-CLL) or unmutated (U-CLL) immunoglobulin heavy variable genes (IGHV). Thus, they contrasted CK cases with 3 or 4 aberrations (low-CK and intermediate-CK, respectively) who followed aggressive disease courses only in the presence of TP53abs. At the other end of the spectrum, patients with CK and +12,+19 displayed an exceptionally indolent profile. Building upon CK, TP53abs and IGHV gene somatic hypermutation status, we propose a novel hierarchical model where patients with high-CK exhibit the worst prognosis, while M-CLL lacking CK or TP53abs as well as CK with +12,+19 show the longest overall survival. In conclusion, CK should not be axiomatically considered unfavorable in CLL, representing a heterogeneous group with variable clinical behavior. High-CK with =5 chromosomal aberrations emerges as prognostically adverse, independently of other biomarkers. Prospective clinical validation is warranted before finally incorporating high-CK in risk stratification of CLL.
Published: 2019
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26. Adaptive hysteresis compensation on an experimental nanopositioning platform

Author: Gildas Besancon, Jakub Dokoupil, Łukasz Ryba, Alina Voda, GIPSA - Systèmes linéaires et robustesse (GIPSA-SLR), Département Automatique (GIPSA-DA), Grenoble Images Parole Signal Automatique (GIPSA-lab ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Grenoble Images Parole Signal Automatique (GIPSA-lab ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), and GIPSA - Systèmes non linéaires et complexité (GIPSA-SYSCO)
Subjects: 0209 industrial biotechnology, Engineering, business.industry, 020208 electrical & electronic engineering, 02 engineering and technology, Tracking (particle physics), [SPI.AUTO]Engineering Sciences [physics]/Automatic, Computer Science Applications, Compensation (engineering), Nonlinear system, Hysteresis, 020901 industrial engineering & automation, Amplitude, Polynomial and rational function modeling, Control and Systems Engineering, Control theory, Path (graph theory), Parametric model, 0202 electrical engineering, electronic engineering, information engineering, business
Abstract: International audience; This paper presents a novel adaptive approach for hysteresis compensation applied to a piezoelectric actuator in one axis of an STM-like lab-made micro-/nanopositioning platform. The idea is to identify a compensating static parametric model, which imitates directly the inverse model of the nonlinearity. In this way, the approach is less complex than those based on model inversion. In addition, the identification is made online, allowing to consider a simple polynomial model, and to adapt its parameters according to the actual hysteresis curve which is faced (ascending or descending path, varying input amplitude, etc.). In order to be able to track possibly fast parameter variations, an original adaptation algorithm is proposed within the Bayesian framework, and including an exponential forgetting factor with optimal data-driven tuning. Illustrative experimental results are finally presented for tracking both triangular and sinusoidal reference signals with varying amplitude.
Published: 2016
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27. Unique morphogenetic signatures define mammalian neck muscles and associated connective tissues

Author: Estelle Jullian, Alexandre Grimaldi, Marketa Tesarova, Elizabeth M. Sefton, Gabrielle Kardon, Shahragim Tajbakhsh, Jozef Kaiser, Eglantine Heude, Tomáš Zikmund, Robert G. Kelly, Noritaka Adachi, Département Adaptations du vivant (AdV), Evolution des régulations endocriniennes (ERE), Muséum National d'Histoire Naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Muséum National d'Histoire Naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Mécanismes adaptatifs : des organismes aux communautés (MECADEV), Centre National de la Recherche Scientifique (CNRS)-Muséum National d'Histoire Naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Muséum National d'Histoire Naturelle (MNHN)-Molécules de Communication et Adaptation des Micro-organismes (MCAM) (MCAM), Muséum National d'Histoire Naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Structure et Instabilité des Génomes (STRING), Muséum National d'Histoire Naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum National d'Histoire Naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), First Faculty of Medicine, Charles University [Prague], Department of Human Genetics [Salt Lake City], University of Utah, Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Collège de France (CdF)-Centre National de la Recherche Scientifique (CNRS), Cellules Souches et Développement, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Central European Institute of Technology [Brno, Czech Republic], Brno University of Technology [Brno], Department of Human Genetics, Département de Biologie du Développement, Institut Pasteur [Paris], Cellules Souches et Développement / Stem Cells and Development, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS), and Poulain, Sébastien
Subjects: Male, 0301 basic medicine, Mouse, [SDV]Life Sciences [q-bio], Mesoderm, somite, 0302 clinical medicine, Neck Muscles, Morphogenesis, Biology (General), [SDV.BDD]Life Sciences [q-bio]/Development Biology, ComputingMilieux_MISCELLANEOUS, Mammals, Mice, Knockout, 0303 health sciences, Microscopy, Confocal, Myogenesis, General Neuroscience, [SDV.BA]Life Sciences [q-bio]/Animal biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], 030302 biochemistry & molecular biology, Gene Expression Regulation, Developmental, Neural crest, General Medicine, Cell biology, [SDV] Life Sciences [q-bio], medicine.anatomical_structure, Somites, Connective Tissue, embryonic structures, Medicine, Female, neural crest, Research Article, TBX1, animal structures, QH301-705.5, Science, Connective tissue, Mice, Transgenic, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, neck myogenesis, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, medicine, Animals, Muscle, Skeletal, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, General Immunology and Microbiology, Lateral plate mesoderm, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, X-Ray Microtomography, Somite, 030104 developmental biology, cranial mesoderm, T-Box Domain Proteins, Developmental biology, 030217 neurology & neurosurgery, Developmental Biology
Abstract: In vertebrates, head and trunk muscles develop from different mesodermal populations and are regulated by distinct genetic networks. Neck muscles at the head-trunk interface remain poorly defined due to their complex morphogenesis and dual mesodermal origins. Here, we use genetically modified mice to establish a 3D model that integrates regulatory genes, cell populations and morphogenetic events that define this transition zone. We show that the evolutionary conserved cucullaris-derived muscles originate from posterior cardiopharyngeal mesoderm, not lateral plate mesoderm, and we define new boundaries for neural crest and mesodermal contributions to neck connective tissue. Furthermore, lineage studies and functional analysis ofTbx1-andPax3-null mice reveal a unique genetic program for somitic neck muscles that is distinct from that of somitic trunk muscles. Our findings unveil the embryological and developmental requirements underlying tetrapod neck myogenesis and provide a blueprint to investigate how muscle subsets are selectively affected in some human myopathies.
Published: 2018
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28. Determination of Protein ps-ns Motions by High-Resolution Relaxometry

Author: Samuel F. Cousin, Fabien Ferrage, Pavel Kadeřávek, Nicolas Bolik-Coulon, Structure et Dynamique des Biomolécules (LBM-E3), Laboratoire des biomolécules (LBM UMR 7203), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), and Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Relaxometry, Materials science, Spectrometer, 010405 organic chemistry, Protein dynamics, Relaxation (NMR), Rotational diffusion, Nanosecond, 010402 general chemistry, 01 natural sciences, Molecular physics, 0104 chemical sciences, Magnetic field, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Nuclear magnetic resonance, Picosecond, ComputingMilieux_MISCELLANEOUS
Abstract: Many of the functions of biomacromolecules can be rationalized by the characterization of their conformational energy landscapes: the structures of the dominant states, transitions between states and motions within states. Nuclear magnetic resonance (NMR) spectroscopy is the technique of choice to study internal motions in proteins. The determination of motions on picosecond to nanosecond timescales requires the measurement of nuclear spin relaxation rates at multiple magnetic fields. High sensitivity and resolution are obtained only at high magnetic fields, so that, until recently, site-specific relaxation rates in biomolecules were only measured over a narrow range of high magnetic fields. This limitation was particularly striking for the quantification of motions on nanosecond timescales, close to the correlation time for overall rotational diffusion. High-resolution relaxometry is an emerging technique to investigate picosecond-nanosecond motions of proteins. This approach uses a high-field NMR spectrometer equipped with a sample shuttle device, which allows for the measurement of the relaxation rate constants at low magnetic fields, while preserving the sensitivity and resolution of a high-field NMR spectrometer. The combined analysis of high-resolution relaxometry and standard high-field relaxation data provides a more accurate description of the dynamics of proteins, in particular in the nanosecond range. The purpose of this chapter is to describe how to perform high-resolution relaxometry experiments and how to analyze the rates measured with this technique.
Published: 2018
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29. Functionally specific binding regions of microtubule-associated protein 2c exhibit distinct conformations and dynamics

Author: Martin Blackledge, Jozef Hritz, Vojtěch Zapletal, Séverine Jansen, Markus Zweckstetter, Malene Ringkjøbing Jensen, Jiří Nováček, Kateřina Melková, Erik Nomilner, Milan Zachrdla, Lukáš Žídek, Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Department of NMR-based Structural Biology [Göttingen], Max Planck Institute for Biophysical Chemistry (MPI-BPC), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: 0301 basic medicine, Protein Conformation, Microtubule-associated protein, nuclear magnetic resonance (NMR), Protein subunit, small-angle X-ray scattering (SAXS), microtubule-associated protein (MAP), chemistry [Plectin], MAP2 protein, human, Biochemistry, chemistry [Microtubule-Associated Proteins], paramagnetic relaxation enhancement (PRE), src Homology Domains, 03 medical and health sciences, FYN, Protein structure, X-Ray Diffraction, protein conformation, Scattering, Small Angle, Humans, Phosphorylation, Binding site, Protein kinase A, Molecular Biology, Polyproline helix, NMR relaxation, Tau protein (Tau), Binding Sites, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Chemistry, metabolism [Plectin], metabolism [Microtubule-Associated Proteins], Cell Biology, PLEC protein, human, 030104 developmental biology, ddc:540, Biophysics, Plectin, Microtubule-Associated Proteins, Molecular Biophysics, Protein Binding
Abstract: International audience; Microtubule-associated protein 2c (MAP2c) is a 49-kDa intrinsically disordered protein regulating the dynamics of microtubules in developing neurons. MAP2c differs from its sequence homologue Tau in the pattern and kinetics of phosphorylation by cAMP-dependent protein kinase (PKA). Moreover, the mechanisms through which MAP2c interacts with its binding partners and the conformational changes and dynamics associated with these interactions remain unclear. Here, we used NMR relaxation and paramagnetic relaxation enhancement techniques to determine the dynamics and long-range interactions within MAP2c. The relaxation rates revealed large differences in flexibility of individual regions of MAP2c, with the lowest flexibility observed in the known and proposed binding sites. Quantitative conformational analyses of chemical shifts, small-angle X-ray scattering (SAXS), and paramagnetic relaxation enhancement measurements disclosed that MAP2c regions interacting with important protein partners, including Fyn tyrosine kinase, plectin, and PKA, adopt specific conformations. High populations of polyproline II and α-helices were found in Fyn- and plectin-binding sites of MAP2c, respectively. The region binding the regulatory subunit of PKA consists of two helical motifs bridged by a more extended conformation. Of note, although MAP2c and Tau did not differ substantially in their conformations in regions of high sequence identity, we found that they differ significantly in long-range interactions, dynamics, and local conformation motifs in their N-terminal domains. These results highlight that the N-terminal regions of MAP2c provide important specificity to its regulatory roles and indicate a close relationship between MAP2c's biological functions and conformational behavior.
Published: 2018
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30. Field-cycling long-lived-state NMR of 15N2 spin pairs

Author: Malcolm H. Levitt, Daniel J. O'Leary, Pavel Kadeřávek, Stuart J. Elliott, Fabien Ferrage, Stefan Glöggler, Mohamed Sabba, Richard C. D. Brown, Lynda J. Brown, School of Chemistry [Southampton, UK], University of Southampton, Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Institut des Sciences Moléculaires (ISM), Université Montesquieu - Bordeaux 4-Université Sciences et Technologies - Bordeaux 1-École Nationale Supérieure de Chimie et de Physique de Bordeaux (ENSCPB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Range (particle radiation), Materials science, 010304 chemical physics, Field cycling, Biophysics, Nuclear magnetic resonance spectroscopy, 010402 general chemistry, Condensed Matter Physics, 01 natural sciences, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Magnetization, 0103 physical sciences, Physical and Theoretical Chemistry, Atomic physics, Spin (physics), Molecular Biology, ComputingMilieux_MISCELLANEOUS
Abstract: A range of nuclear magnetic resonance spectroscopy and imaging applications are limited by the short lifetimes of magnetisation in solution. Long-lived states, which are slowly relaxing configurations of nuclear spins, have been shown to alleviate this limitation. Long-lived states have decay lifetimes TLLS significantly exceeding the longitudinal relaxation time T1, in some cases by an order of magnitude. Here we present an experimental case of a long-lived state for a 15N labelled molecular system in solution. We observe a strongly biexponential decay for the long-lived state, with the lifetime of the slowly relaxing component exceeding 40 minutes, ∼21 times longer than the spin-lattice relaxation time T1. The lifetime of the long-lived state was revealed by using a dedicated two-field NMR spectrometer capable of fast sample shuttling between high and low magnetic fields, and the application of a resonant radiofrequency field at low magnetic field. The relaxation characteristics of the long-lived state are examined.
Published: 2018
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31. No improvement in long-term survival over time for chronic lymphocytic leukemia patients in stereotyped subsets #1 and #2 treated with chemo(immuno)therapy

Author: Tatiana Tzenou, Richard Rosenquist, Marie-Paule Lefranc, Karla Plevová, Charles C. Chu, Yorick Sandberg, Gunnar Juliusson, Véronique Giudicelli, Livio Trentin, Mark Catherwood, Frederic Davi, Šárka Pospíšilová, Xiao-Jie Yan, Silvio Veronese, Lesley-Ann Sutton, Carsten Utoft Niemann, Nikos Darzentas, Kostas Stamatopoulos, Achilles Anagnostopoulos, Diane F. Jelinek, David Oscier, Mattias Mattsson, Nicholas Chiorazzi, Karin E. Smedby, Panagiotis Panagiotidis, Chrysoula Belessi, Florence Nguyen-Khac, Marco Montillo, Eva Minga, Paolo Ghia, Anton W. Langerak, Lydia Scarfò, Andreas Agathangelidis, Tait D. Shanafelt, Panagiotis Baliakas, Niki Stavroyianni, Larry Mansouri, Anastasia Hadzidimitriou, Zadie Davis, Fie Juhl Vojdeman, Uppsala Universitet [Uppsala], Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden, Institute of Applied Biosciences, Centre for Research and Technology-Hellas, Thessaloniki, Greece, Department of Immunology, Genetics and Pathology [Uppsala, Sueden] (IGP), Uppsala University, Department of Hematology [Uppsala], Università Vita-Salute San Raffaele, Milan, Italy., Strategic Research Program in CLL, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy, Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden, Università Vita e Salute, San Raffaele, Milano, Italy, Strategic Research Program in CLL, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy., Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK., The Feinstein Institute for Medical Research, CEITEC-Central European Institute of Technology, MasarykBrno, Czech Republic., Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Erasmus University Medical Center [Rotterdam] (Erasmus MC), Department of Hematology, Rigshospitalet, Copenhagen, Denmark, First Department of Propaedeutic Medicine, University of Athens, Athens, Greece, Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinico, Department of Medicine Solna, Clinical Epidemiology Unit, Karolinska Institutet, and Hematology Center, Karolinska University Hospital, Stockholm, Sweden, Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Service d'Hématologie clinique [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Hematology and Transplantation, Lund Strategic Research Center for Stem Cell Biology and Cell Therapy, Lund University and Hospital Department of Hematology, Lund Stem Cell Center, Lund, Sweden, Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece, Universita degli Studi di Padova, Venetian Institute Molecular Medicine (VIMM), Department of Hemato-Oncology, Belfast City Hospital, Belfast, UK, University Hospital Brno, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Department of Immunology, Mayo Clinic, Rochester, MV, USA, Mayo Clinic [Rochester], Hematology Department, Nikea General Hospital, Piraeus, Greece, Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden., Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden, Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece., Institute of Applied Biosciences, Thessaloniki, Greece., Department of Immunology, Baliakas, Panagioti, Mattsson, Mattia, Hadzidimitriou, Anastasia, Minga, Eva, Agathangelidis, Andrea, Sutton, Lesley-Ann, Scarfo, Lydia, Davis, Zadie, Yan, Xiao-Jie, Plevova, Karla, Sandberg, Yorick, Vojdeman, Fie J, Tzenou, Tatiana, Chu, Charles C, Veronese, Silvio, Mansouri, Larry, Smedby, Karin E, Giudicelli, Véronique, Nguyen-Khac, Florence, Panagiotidis, Panagioti, Juliusson, Gunnar, Anagnostopoulos, Achille, Lefranc, Marie-Paule, Trentin, Livio, Catherwood, Mark, Montillo, Marco, Niemann, Carsten U, Langerak, Anton W, Pospisilova, Sarka, Stavroyianni, Niki, Chiorazzi, Nichola, Oscier, David, Jelinek, Diane F, Shanafelt, Tait, Darzentas, Niko, Belessi, Chrysoula, Davi, Frederic, Ghia, Paolo, Rosenquist, Richard, Stamatopoulos, Kostas, and Immunology
Subjects: Adult, Male, chemorefractorine, Oncology, medicine.medical_specialty, Cyclophosphamide, Chronic lymphocytic leukemia, [SDV]Life Sciences [q-bio], Young Adult, 03 medical and health sciences, 0302 clinical medicine, Drug Therapy, Chemoimmunotherapy, Internal medicine, medicine, Humans, Chronic Lymphocytic Leukemia, [INFO]Computer Science [cs], stereotyped subsets, Online Only Articles, Survival rate, ComputingMilieux_MISCELLANEOUS, Aged, Retrospective Studies, Aged, 80 and over, [SDV.GEN]Life Sciences [q-bio]/Genetics, Hematology, business.industry, Middle Aged, medicine.disease, Leukemia, Lymphocytic, Chronic, B-Cell, 3. Good health, Fludarabine, Survival Rate, Leukemia, 030220 oncology & carcinogenesis, Female, Rituximab, Immunotherapy, business, 030215 immunology, medicine.drug
Abstract: The overall survival (OS) of patients with chronic lymphocytic leukemia (CLL) has improved over the last decades mainly due to advances in the understanding of the disease biology and the introduction of novel therapeutic approaches(1). In the present retrospective study we investigated trends in OS in subgroups of cases defined by genetic and immunogenetic features aiming at addressing the question whether advances in chemoimmunotherapy had a uniform impact across all CLL patients. We found that such advances have translated into prolonged OS in all prognostic subgroups examined except those carrying TP53 abnormalities, as expected, but also those assigned to stereotyped subsets #1 and #2, that are generally devoid of such gene aberrations. This latter finding, reported here for the first time, indicates the need for alternative treatment options for these patients.
Published: 2018
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32. Magnetic Nanowires and Nanotubes

Author: Olivier Fruchart, Michal Stano, Brno University of Technology [Brno] (BUT), Central European Institute of Technology [Brno] (CEITEC MU), SPINtronique et TEchnologie des Composants (SPINTEC), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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), Ekkes Brück, ANR-10-LABX-0051,LANEF,Laboratory of Alliances on Nanosciences - Energy for the Future(2010), and European Project: 309589,EC:FP7:NMP,FP7-NMP-2012-SMALL-6,M3D(2012)
Subjects: Physics, domain-wall, Nanowire, Nanotechnology, 02 engineering and technology, 021001 nanoscience & nanotechnology, 01 natural sciences, Characterization (materials science), Micrometre, Magnetization, core-shell, Domain wall (magnetism), Spin wave, [PHYS.COND.CM-GEN]Physics [physics]/Condensed Matter [cond-mat]/Other [cond-mat.other], 0103 physical sciences, Nano, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], magnetic nanowire, Single domain, 010306 general physics, 0210 nano-technology, magnetic nanotube
Abstract: Review, 124 pages, 23 figures, 496 references.; International audience; We propose a review of the current knowledge about the synthesis, magnetic properties and applications of magnetic cylindrical nanowires and nanotubes. By nano we consider diameters reasonably smaller than a micrometer. At this scale, comparable to micromagnetic and transport length scales, novel properties appear. At the same time, this makes the underlying physics easier to understand due to the limiter number of degrees of freedom involved. The three-dimensional nature and the curvature of these objects contribute also to their specific properties, compared to patterns flat elements. While the topic of nanowires and later nanotubes started now decades ago, it is nevertheless flourishing, thanks to the progress of synthesis, theory and characterization tools. These give access to ever more complex and thus functional structures, and also shifting the focus from material-type measurements of large assemblies, to single-object investigations. We first provide an overview of common fabrication methods yielding nanowires, nanotubes and structures engineered in geometry (change in diameter, shape) or material (segments, core-shell structures), shape or core-shell. We then review their magnetic properties: global measurements, magnetization states and switching, single domain wall statics and dynamics, and spin waves. For each aspect, both theory and experiments are surveyed. We also mention standard characterization techniques useful for these. We finally mention emerging applications of magnetic nanowires and nanotubes, along with the foreseen perspectives in the topic.
Published: 2018
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33. High-Resolution NMR of Folded Proteins in Hyperpolarized Physiological Solvents

Author: Dennis Kurzbach, Geoffrey Bodenhausen, Pavel Kadeřávek, Fabien Ferrage, Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Masaryk University [Brno] (MUNI), Structure et Dynamique des Biomolécules (LBM-E3), Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: 0301 basic medicine, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Chemistry, Organic Chemistry, General Chemistry, 010402 general chemistry, Photochemistry, 01 natural sciences, Catalysis, Spectral line, 0104 chemical sciences, Solvent, 03 medical and health sciences, chemistry.chemical_compound, 030104 developmental biology, Amide, Molecule, Target protein, Hyperpolarization (physics), Two-dimensional nuclear magnetic resonance spectroscopy, Dissolution
Abstract: International audience; Hyperpolarized 2D exchange spectroscopy (HYPEX) to obtain high‐resolution nuclear magnetic resonance (NMR) spectra of folded proteins under near‐physiological conditions is reported. The technique is based on hyperpolarized water, which is prepared by dissolution dynamic nuclear polarization and mixed in situ in an NMR spectrometer with a protein in a physiological saline buffer at body temperature. Rapid exchange of labile protons with the hyperpolarized solvent, combined with cross‐relaxation effects (NOEs), leads to boosted signal intensities for many amide 1H–15N correlations in the protein ubiquitin. As the introduction of hyperpolarization to the target protein is mediated via the solvent, the method is applicable to a broad spectrum of target molecules.
Published: 2018
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34. Not all IGHV3-21 chronic lymphocytic leukemias are equal: prognostic considerations

Author: Eva Minga, Karin E. Smedby, Lesley-Ann Sutton, Nicholas Chiorazzi, Myriam Boudjogra, Kostas Stamatopoulos, Karla Plevová, Lone Bredo Pedersen, Zadie Davis, Lydia Scarfò, Andreas Agathangelidis, Monica Facco, Achilles Anagnostopoulos, Maria Chatzouli, Chrysoula Belessi, Athina Tsanousa, Panagiotis Baliakas, Kirsten van Lom, Lefteris Angelis, Yorick Sandberg, Gunnar Juliusson, Diane F. Jelinek, Fie Juhl Vojdeman, Anne Gardiner, Panagiotis Panagiotidis, Anton W. Langerak, Florence Nguyen-Khac, Hana Skuhrová Francová, Frederic Davi, Denis Moreno, Silvio Veronese, Richard Rosenquist, Marie-Paule Lefranc, Nikos Darzentas, Šárka Pospíšilová, Véronique Giudicelli, Xiao-Jie Yan, Charles C. Chu, Christian H. Geisler, Larry Mansouri, David Oscier, Mark Catherwood, Marco Montillo, Anastasia Hadzidimitriou, Livio Trentin, Paolo Ghia, Tait D. Shanafelt, Tatiana Tzenou, Baliakas, P, Agathangelidis, A, Hadzidimitriou, A, Sutton, La, Minga, E, Tsanousa, A, Scarfò, L, Davis, Z, Yan, Xj, Shanafelt, T, Plevova, K, Sandberg, Y, Vojdeman, Fj, Boudjogra, M, Tzenou, T, Chatzouli, M, Chu, Cc, Veronese, S, Gardiner, A, Mansouri, L, Smedby, Ke, Pedersen, Lb, Moreno, D, Van Lom, K, Giudicelli, V, Francova, H, Nguyen Khac, F, Panagiotidis, P, Juliusson, G, Angelis, L, Anagnostopoulos, A, Lefranc, Mp, Facco, M, Trentin, L, Catherwood, M, Montillo, M, Geisler, Ch, Langerak, Aw, Pospisilova, S, Chiorazzi, N, Oscier, D, Jelinek, Df, Darzentas, N, Belessi, C, Davi, F, Ghia, PAOLO PROSPERO, Rosenquist, R, Stamatopoulos K. Ghia P., is Co senior author, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden, Università Vita-Salute San Raffaele, Milan, Italy, Division of Molecular Oncology and Department of Onco-Hematology, Istituto di Ricovero e Cura a Carattere Scientifico, San Raffaele Scientific Institute, Milan, Italy, Institute of Applied Biosciences, Centre for Research and Technology-Hellas, Thessaloniki, Greece, Department of Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece, Department of Haematology, Royal Bournemouth Hospital, Bournemouth, United Kingdom, The Feinstein Institute for Medical Research, Mayo Clinic [Rochester], Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Erasmus University Medical Center [Rotterdam] (Erasmus MC), Department of Hematology, Rigshospitalet, Copenhagen, Denmark, Service d'Hématologie Biologique [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), First Department of Propaedeutic Medicine, University of Athens, Athens, Greece, Hematology Department, Nikea General Hospital, Piraeus, Greece, Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinico, Department of Medicine, Solna, Clinical Epidemiology Unit, Karolinska Institutet, Stockholm, Sweden, Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Lund University and Hospital Department of Hematology, Lund Stem Cell Center, Lund, Sweden, Hematology Department and Hematopoietic Cell Transplantation Unit, Georgios Papanicolaou Hospital, Thessaloniki, Greece, Universita degli Studi di Padova, Department of Hemato-Oncology, Belfast City Hospital, Belfast, United Kingdom, Immunology, and Hematology
Subjects: Male, Oncology, medicine.medical_specialty, Chronic lymphocytic leukemia, Immunology, B-cell receptor, Gene Rearrangement, B-Lymphocyte, Heavy Chain, Antineoplastic Agents, Biology, Biochemistry, Time-to-Treatment, Genetic Heterogeneity, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, medicine, Humans, 10. No inequality, ComputingMilieux_MISCELLANEOUS, Survival analysis, Aged, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, B-Lymphocytes, 0303 health sciences, Lymphoid Neoplasia, Hematology, Gene Expression Regulation, Leukemic, Genetic heterogeneity, Cell Biology, Middle Aged, Prognosis, medicine.disease, Leukemia, Lymphocytic, Chronic, B-Cell, Survival Analysis, Treatment Outcome, 030220 oncology & carcinogenesis, biology.protein, Immunoglobulin heavy chain, Female, Somatic Hypermutation, Immunoglobulin, Antibody, Immunoglobulin Heavy Chains, IGHV@
Abstract: An unresolved issue in chronic lymphocytic leukemia (CLL) is whether IGHV3-21 gene usage, in general, or the expression of stereotyped B-cell receptor immunoglobulin defining subset # 2 (IGHV3-21/IGLV3-21), in particular, determines outcome for IGHV3-21-utilizing cases. We reappraised this issue in 8593 CLL patients of whom 437 (5%) used the IGHV3-21 gene with 254/437 (58%) classified as subset # 2. Within subset # 2, immunoglobulin heavy variable (IGHV)-mutated cases predominated, whereas non-subset # 2/IGHV3-21 was enriched for IGHV-unmutated cases (P =.002). Subset # 2 exhibited significantly shorter time-to-first-treatment (TTFT) compared with non-subset # 2/IGHV3-21 (22 vs 60 months, P =.001). No such difference was observed between non-subset # 2/IGHV3-21 vs the remaining CLL with similar IGHV mutational status. In conclusion, IGHV3-21 CLL should not be axiomatically considered a homogeneous entity with adverse prognosis, given that only subset # 2 emerges as uniformly aggressive, contrasting non-subset # 2/IGVH3-21 patients whose prognosis depends on IGHV mutational status as the remaining CLL.
Published: 2015
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35. High-Throughput Immunogenetics for Clinical and Research Applications in Immunohematology: Potential and Challenges

Author: Marie-Paule Lefranc, Gianni Cazzaniga, Christiane Pott, Elizabeth Macintyre, Nikos Darzentas, Mathieu Giraud, Patricia J. T. A. Groenen, David Gonzalez, Frederic Davi, Monika Brüggemann, Jacques J.M. van Dongen, Véronique Giudicelli, Kostas Stamatopoulos, Anton W. Langerak, Michael Hummel, Department of Immunology, University Hospital Schleswig–Holstein, CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Centre for Cancer Research and Cell Biology, Queen's University [Belfast] (QUB), Centro Ricerca Tettamanti, Clinica Pediatrica, Ospedale S. Gerardo-Ospedale S. Gerardo, Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Bioinformatics and Sequence Analysis (BONSAI), Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut für Pathologie [Berlin], Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Department of Pathology [Nijmegen], Radboud University Medical Center [Nijmegen], Institute of Applied Biosciences, Centre for Research and Technology-Hellas, Thessaloniki, Greece, University Medical Center Rotterdam, Hôpital Universitaire Pitié Salpêtrière, Assistance Publique - Hôpitaux de Paris (AP - HP), Central European Institute of Technology, Masaryk University, Brno, Czech Republic, Queen's University Belfast [Belfast] (QUB), Ospedale S. Gerardo - Ospedale S. Gerardo, Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier, 34396 Montpellier Cedex 05, France, Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL), Université de Lille, Sciences et Technologies - Ecole Centrale de Lille - Institut National de Recherche en Informatique et en Automatique (Inria) - Université de Lille, Sciences Humaines et Sociales - Centre National de la Recherche Scientifique (CNRS), AP-HP Hôpital Necker - Enfants Malades [Paris], Charite-Universitatsmedizin Berlin [Berlin], Immunology, Langerak, A, Brüggemann, M, Davi, F, Darzentas, N, Van Dongen, J, Gonzalez, D, Cazzaniga, G, Giudicelli, V, Lefranc, M, Giraud, M, Macintyre, E, Hummel, M, Pott, C, Groenen, P, Stamatopoulos, K, Centre National de la Recherche Scientifique (CNRS)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)
Subjects: [SDV.MHEP.HEM] Life Sciences [q-bio]/Human health and pathology/Hematology, 0301 basic medicine, MED/03 - GENETICA MEDICA, [SDV.IMM] Life Sciences [q-bio]/Immunology, Immunology, Computational biology, Immunogenetics, Rare cancers Radboud Institute for Molecular Life Sciences [Radboudumc 9], Bioinformatics, Immunogenetic, 03 medical and health sciences, Repertoire analysis, Humans, Immunology and Allergy, Medicine, Throughput (business), Alleles, Allele, Gene Rearrangement, Immunologic Technique, Genes, Immunoglobulin, business.industry, Computational Biology, High-Throughput Nucleotide Sequencing, [SDV.MHEP.HEM]Life Sciences [q-bio]/Human health and pathology/Hematology, Hematology, 3. Good health, Genes, T-Cell Receptor, 030104 developmental biology, Immunologic Techniques, [SDV.IMM]Life Sciences [q-bio]/Immunology, business, Human
Abstract: Analysis and interpretation of Ig and TCR gene rearrangements in the conventional, low-throughput way have their limitations in terms of resolution, coverage, and biases. With the advent of high-throughput, next-generation sequencing (NGS) technologies, a deeper analysis of Ig and/or TCR (IG/TR) gene rearrangements is now within reach, which impacts on all main applications of IG/TR immunogenetic analysis. To bridge the generation gap from low- to high-throughput analysis, the EuroClonality-NGS Consortium has been formed, with the main objectives to develop, standardize, and validate the entire workflow of IG/TR NGS assays for 1) clonality assessment, 2) minimal residual disease detection, and 3) repertoire analysis. This concerns the preanalytical (sample preparation, target choice), analytical (amplification, NGS), and postanalytical (immunoinformatics) phases. Here we critically discuss pitfalls and challenges of IG/TR NGS methodology and its applications in hemato-oncology and immunology.
Published: 2017
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36. Membrane-Depolarizing Channel Blockers Induce Selective Glioma Cell Death by Impairing Nutrient Transport and Unfolded Protein/Amino Acid Responses

Author: Lene Uhrbom, Shimei Wee, Sten Linnarsson, Anna-Lena Gustavsson, Michaela Krafčíková, Annika Jenmalm Jensen, Petra Sekyrova, Ercan Mutlu, Lars Hammarström, Ivar Dehnisch, A. F. Maarten Altelaar, Sven Nelander, Per Uhlén, Mia Niklasson, Lukáš Trantírek, Michael Andäng, Anna Segerman, C. Theresa Vincent, Voichita D. Marinescu, Linnéa Schmidt, Brittany Carson, Per Øyvind Enger, Nicolas Fritz, Zuzana Sramkova, Jennifer M. Feenstra, Gregorios Kyriatzis, Martin Haraldsson, Gianluca Maddalo, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden, Department of Physiology and Pharmacology Karolinska Institute, Department of Biomolecular Mass Spectrometry and Proteomics Group [Utrecht, The Netherlands], Utrecht University [Utrecht]-Utrecht Institute for Pharmaceutical Sciences (UIPS)-Bijvoet Centre for Biomolecular Research [Utrecht, The Netherlands], Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Univ Bergen, Dept Biomed, Bergen, Norway, iDepartment of Materials and Engineering, Applied Materials Physics, Royal Institute of Technology, Royal Institute of Technology [Stockholm] (KTH ), Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17165 Sweden., Department of Physiology and Biophysics, Weill Cornell Medical College, Weill Medical College of Cornell University [New York], Haukeland University Hospital, University of Bergen (UiB), Afd Biomol.Mass Spect. and Proteomics, and Biomolecular Mass Spectrometry and Proteomics
Subjects: 0301 basic medicine, Proteomics, Programmed cell death, Dihydropyridines, Cancer Research, Population, Cell, [SDV.CAN]Life Sciences [q-bio]/Cancer, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, 03 medical and health sciences, Calcium Channels, T-Type, Mice, Potassium Channels, Calcium-Activated, Cancer stem cell, Cell Line, Tumor, Taverne, medicine, Animals, Humans, Amino Acids, education, education.field_of_study, Cancer och onkologi, Voltage-dependent calcium channel, Cell Death, Brain Neoplasms, Sodium, Depolarization, Biological Transport, Glioma, Mycotoxins, Calcium Channel Blockers, 3. Good health, Cell biology, 030104 developmental biology, medicine.anatomical_structure, Biochemistry, Oncology, Cancer and Oncology, Unfolded protein response, Neoplastic Stem Cells, Unfolded Protein Response, Intracellular
Abstract: Glioma-initiating cells (GIC) are considered the underlying cause of recurrences of aggressive glioblastomas, replenishing the tumor population and undermining the efficacy of conventional chemotherapy. Here we report the discovery that inhibiting T-type voltage-gated Ca2+ and KCa channels can effectively induce selective cell death of GIC and increase host survival in an orthotopic mouse model of human glioma. At present, the precise cellular pathways affected by the drugs affecting these channels are unknown. However, using cell-based assays and integrated proteomics, phosphoproteomics, and transcriptomics analyses, we identified the downstream signaling events these drugs affect. Changes in plasma membrane depolarization and elevated intracellular Na+, which compromised Na+-dependent nutrient transport, were documented. Deficits in nutrient deficit acted in turn to trigger the unfolded protein response and the amino acid response, leading ultimately to nutrient starvation and GIC cell death. Our results suggest new therapeutic targets to attack aggressive gliomas. Cancer Res; 77(7); 1741–52. ©2017 AACR.
Published: 2017

37. Identification of Nucleolus-Associated Chromatin Domains Reveals a Role for the Nucleolus in 3D Organization of the A. thaliana Genome

Author: Frédéric Pontvianne, Jiří Fajkus, Julio Sáez-Vásquez, Hugues Parrinello, Marie-Christine Carpentier, Marine Rohmer, Veronika Pavlištová, Karin Jaške, Šárka Schořová, Miloslava Fojtová, Nathalie Durut, Craig S. Pikaard, Goetschy, Elisabeth, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-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), BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Indiana University [Bloomington], Indiana University System, Mendel Centre for Plant Genomics and Proteomics [Brno, Czech Republic], Masaryk University [Brno] (MUNI)-CEITEC - Central European Institute of Technology [Brno, Czech Republic], Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), BioCampus Montpellier (BCM), and Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Transcription, Genetic, Nucleolus, Heterochromatin, [SDV]Life Sciences [q-bio], Arabidopsis, Gene Expression, Ribosome biogenesis, Biology, DNA, Ribosomal, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, nucleolus, RRNA processing, lcsh:QH301-705.5, Ribosomal DNA, Genetics, nucleolus-associated chromatin domains, telomere, heterochromatin, RNA-Binding Proteins, Phosphoproteins, Chromatin, nuclear architecture, [SDV] Life Sciences [q-bio], 030104 developmental biology, lcsh:Biology (General), RNA, Ribosomal, Nucleolus organizer region, Nucleolin, Cell Nucleolus, Genome, Plant
Abstract: The nucleolus is the site of ribosomal RNA (rRNA) gene transcription, rRNA processing and ribosome biogenesis. However, the nucleolus also plays additional roles in the cell. We isolated nucleoli by Fluorescence Activated Cell Sorting (FACS) and identified Nucleolus-Associated Chromatin Domains (NADs) by deep sequencing, comparing wild-type plants and null mutants for the nucleolar protein, NUCLEOLIN 1 (NUC1). NADs are primarily genomic regions with heterochromatic signatures and include transposable elements (TEs), sub-telomeric regions and mostly inactive protein-coding genes. However, NADs also include active ribosomal RNA genes, and the entire short arm of chromosome 4 adjacent to them. In nuc1 null mutants, which alter rRNA gene expression and overall nucleolar structure, NADs are altered, telomere association with the nucleolus is decreased and telomeres become shorter. Collectively, our studies reveal roles for NUC1 and the nucleolus in the spatial organization of chromosomes as well as telomere maintenance.
Published: 2016
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38. Magneto-optical signature of massless Kane electrons in Cd3As2

Author: Akrap, A., Hakl, M., Tchoumakov, S., Crassee, I., Kuba, J., Goerbig, M., Homes, C. c., Caha, O., Novák, J., Teppe, F., Desrat, W., Koohpayeh, S., Wu, L., Armitage, N. p., Nateprov, A., Arushanov, E., Gibson, Q. d., Cava, J., van Der Marel, D., Piot, B., Faugeras, C., Martinez Garcia, Gines, Potemski, M., Orlita, M., Department of Quantum Matter Physics [Geneva] (DQMP), University of Geneva [Switzerland], Laboratoire national des champs magnétiques intenses - Grenoble (LNCMI-G ), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Laboratoire de Physique des Solides (LPS), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Group of Applied Physics - Biophotonics [Geneva] (GAP-Biophotonics), Group of Applied Physics [Geneva] (GAP), University of Geneva [Switzerland]-University of Geneva [Switzerland], CEITEC BUT, Brno University of Technology, Purkynova 123, 612 00 Brno, Czech Republic, Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11), Department of Condensed Matter Physics and Materials Science [TIFR] (CMPMS), Tata Institute for Fundamental Research (TIFR), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Johns Hopkins University (JHU), University of California [Berkeley], University of California, Academy of Sciences of Moldova, Academy of Sciences of Moldova (ASM), Department of Physics, Princeton University (DPPU), Princeton University, and Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Condensed Matter - Other Condensed Matter, Condensed Matter - Materials Science, Condensed Matter - Mesoscale and Nanoscale Physics, [PHYS.COND.CM-GEN]Physics [physics]/Condensed Matter [cond-mat]/Other [cond-mat.other], Mesoscale and Nanoscale Physics (cond-mat.mes-hall), [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences, ddc:500.2, [PHYS.COND.CM-MSQHE]Physics [physics]/Condensed Matter [cond-mat]/Mesoscopic Systems and Quantum Hall Effect [cond-mat.mes-hall], Other Condensed Matter (cond-mat.other)
Abstract: We report on optical reflectivity experiments performed on Cd3As2 over a broad range of photon energies and magnetic fields. The observed response clearly indicates the presence of 3D massless charge carriers. The specific cyclotron resonance absorption in the quantum limit implies that we are probing massless Kane electrons rather than symmetry-protected 3D Dirac particles. The latter may appear at a smaller energy scale and are not directly observed in our infrared experiments., Comment: 5 pages, 4 figures + supplementary materials (17 pages), to be published in Phys. Rev. Lett
Published: 2016
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39. Plastidic P2 glucose-6P dehydrogenase from poplar is modulated by thioredoxin m-type: Distinct roles of cysteine residues in redox regulation and NADPH inhibition

Author: Sergio Esposito, Daniela Castiglia, Nicolas Rouhier, José M. Gualberto, Kamel Chibani, Alessia De Lillo, Manuela Cardi, Mirko Zaffagnini, Jean-Pierre Jacquot, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de biologie moléculaire des plantes (IBMP), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Dipartimento Biol, University of Naples Federico II, Dipartimento Farm & Biotecnol, University of Bologna, Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Central European Institute of Technology [Brno] (CEITEC), Université de Strasbourg (UNISTRA), Legge Regionale della Campania CUP E69D15000270002, 5/2002, French Ministry of Foreign Affairs 672700K, Project FORGIARE (Formazione Giovani alla Ricerca) by Compagnia di San Paolo V-10/FORG/ST/2012/5, French National Research Agency (ANR) as part of the 'Investissements d'Avenir' program (Lab of Excellence ARBRE) UMR1136 ANR-11-LABX-0002-01, Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Cardi M, Zaffagnini M, De Lillo A, Castiglia D, Chibani K, Gualberto JM, Rouhier N, Jacquot JP, Esposito S, Cardi, Manuela, Zaffagnini, Mirko, DE LILLO, Alessia, Castiglia, Daniela, Chibani, Kamel, Gualberto, José Manuel, Rouhier, Nicola, Jacquot, Jean Pierre, and Esposito, Sergio
Subjects: 0106 biological sciences, 0301 basic medicine, disulfure, STRESS, [SDV]Life Sciences [q-bio], Amino Acid Motifs, Dehydrogenase, nadph, Plant Science, 01 natural sciences, Pentose Phosphate Pathway, Serine, Thioredoxins, NADPH, poplar, G6PDH, cysteine, redox regulation, déshydrogénase, Glutamate synthase, Plastids, MOLECULAR CHARACTERIZATION, Cloning, Molecular, PENTOSE-PHOSPHATE PATHWAY, ComputingMilieux_MISCELLANEOUS, Plant Proteins, biology, food and beverages, General Medicine, ARABIDOPSIS, Recombinant Proteins, Populus, Biochemistry, glucose 6 phosphate déshydrogénase, Oxidation-Reduction, régulation redox, BARLEY ROOTS, HUMAN GLUCOSE-6-PHOSPHATE-DEHYDROGENASE, ISOFORMS, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Glucosephosphate Dehydrogenase, Pentose phosphate pathway, plante supérieure, Oxidative pentose phosphate pathway, CHLAMYDOMONAS-REINHARDTII, thioredoxine, 03 medical and health sciences, Genetic, Complementary DNA, cystéine, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, PLANTS, Amino Acid Sequence, Cysteine, Binding site, Thioredoxin, Populu, Binding Sites, Active site, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, mécanisme de régulation, 030104 developmental biology, GLUTAMATE SYNTHASE, Mutagenesis, Site-Directed, biology.protein, Sequence Alignment, Agronomy and Crop Science, NADP, 010606 plant biology & botany
Abstract: A cDNA coding for a plastidic P2-type G6PDH isoform from A cDNA coding for a plastidic P2-type G6PDH isoform from poplar (Populus tremula x tremuloides) has been used to express and purify to homogeneity the mature recombinant protein with a N-terminus His-tag. The study of the kinetic properties of the recombinant enzyme showed an in vitro redox sensing modulation exerted by reduced DTT. The interaction with thioredoxins (TRXs) was then investigated. Five cysteine to serine variants (C145S - C175S - C183S - C195S - C242S) and a variant with a double substitution for Cys175 and Cys183 (C175S/C183S) have been generated, purified and biochemically characterized in order to investigate the specific role(s) of cysteines in terms of redox regulation and NADPH-dependent inhibition. Three cysteine residues (C145, C194, C242) are suggested to have a role in controlling the NADP+ access to the active site, and in stabilizing the NADPH regulatory binding site. Our results also indicate that the regulatory disulfide involves residues Cys175 and Cys183 in a position similar to those of chloroplastic P1-G6PDHs, but the modulation is exerted primarily by TRX m-type, in contrast to P1-G6PDH, which is regulated by TRX f. This unexpected specificity indicates differences in the mechanism of regulation, and redox sensing of plastidic P2-G6PDH compared to chloroplastic P1-G6PDH in higher plants. (Populus tremula x tremuloides) has been used to express and purify to homogeneity the mature recombinant protein with a N-terminus His-tag. The study of the kinetic properties of the recombinant enzyme showed an in vitro redox sensing modulation exerted by reduced DTT. The interaction with thioredoxins (TRXs) was then investigated. Five cysteine to serine variants (C145S - C175S - C183S - C195S - C242S) and a variant with a double substitution for Cys175 and Cys183 (C175S/C183S) have been generated, purified and biochemically characterized in order to investigate the specific role(s) of cysteines in terms of redox regulation and NADPH-dependent inhibition. Three cysteine residues (C145, C194, C242) are suggested to have a role in controlling the NADP+ access to the active site, and in stabilizing the NADPH regulatory binding site. Our results also indicate that the regulatory disulfide involves residues Cys175 and Cys183 in a position similar to those of chloroplastic P1-G6PDHs, but the modulation is exerted primarily by TRX m-type, in contrast to P1-G6PDH, which is regulated by TRX f. This unexpected specificity indicates differences in the mechanism of regulation, and redox sensing of plastidic P2-G6PDH compared to chloroplastic P1-G6PDH in higher plants.
Published: 2016
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40. Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation

Author: Florian Maumus, Nora Bujdoso, Christiane Kiefer, I. Mateos, Claudia Chica, Korbinian Schneeberger, Claude Becker, George Coupland, Mathieu Piednoël, Maria C. Albani, Raquel Iglesias-Fernández, Martin A. Lysak, Geo Velikkakam James, Vimal Rawat, Karl Nordström, Thomas Piofczyk, Loren Castaings, Laura de Lorenzo, Cristina Barrero-Sicilia, Matthias Zytnicki, François Roudier, Javier Paz-Ares, Vincent Colot, Julieta L. Mateos, Markus C. Berns, Pilar Carbonero, Eva-Maria Willing, Sara Bergonzi, Bogna Szarzynska, Detlef Weigel, Jörg Hagmann, Norman Warthmann, Seth J. Davis, Ales Pecinka, Romy Chen-Min-Tao, Terezie Mandáková, Stephan C. Schuster, Hadi Quesneville, Carlos Alonso-Blanco, Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research (MPIPZ), Research group Plant Cytogenomics, Central European Institute of Technology [Brno] (CEITEC), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Department of Molecular Biology, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Research School of Biology, Australian National University (ANU), 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), Unité de Biométrie et Intelligence Artificielle (UBIA), Department of Plant Molecular Genetics, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Max-Planck-Gesellschaft, Center for Comparative Genomics and Bioinformatics, Pennsylvania State University (Penn State), Penn State System-Penn State System, ANR, Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT)-Brno University of Technology [Brno] (BUT), Institut de biologie de l'ENS Paris (IBENS), 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)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Center for Comparative Genomics and Bioinformatics (CCBB), Brno University of Technology [Brno] (BUT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - 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), and 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)
Subjects: 0106 biological sciences, Transposable element, Epigenomics, Biología, [SDV]Life Sciences [q-bio], Retrotransposon, Plant Science, Biology, 01 natural sciences, Genome, Ciencias Biológicas, 03 medical and health sciences, Plant evolution, Laboratorium voor Plantenveredeling, Life Science, Ciencias de las Plantas, Botánica, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, Arabis alpina, ARABIS ALPINA, Methylation, biology.organism_classification, Long terminal repeat, GENOME, Phylogenetics, Plant Breeding, DNA methylation, CIENCIAS NATURALES Y EXACTAS, 010606 plant biology & botany
Abstract: Despite evolutionary conserved mechanisms to silence transposable element activity, there are drastic differences in the abundance of transposable elements even among closely related plant species. We conducted a de novo assembly for the 375 Mb genome of the perennial model plant, Arabis alpina. Analysing this genome revealed long-lasting and recent transposable element activity predominately driven by Gypsy long terminal repeat retrotransposons, which extended the low-recombining pericentromeres and transformed large formerly euchromatic regions into repeat-rich pericentromeric regions. This reduced capacity for long terminal repeat retrotransposon silencing and removal in A. alpina co-occurs with unexpectedly low levels of DNA methylation. Most remarkably, the striking reduction of symmetrical CG and CHG methylation suggests weakened DNA methylation maintenance in A. alpina compared with Arabidopsis thaliana. Phylogenetic analyses indicate a highly dynamic evolution of some components of methylation maintenance machinery that might be related to the unique methylation in A. alpina. Fil: Willing, Eva Maria. Max Planck Institute for Plant Breeding Research; Alemania Fil: Rawat, Vimal. Central European Institute of Technology; República Checa Fil: Mandáková, Terezie. Central European Institute of Technology; República Checa Fil: Maumus, Florian. INRA. Research Unit in Genomics; Francia Fil: James, Geo Velikkakam. Max Planck Institute for Plant Breeding Research; Alemania Fil: Nordström, Karl J. V.. Max Planck Institute for Plant Breeding Research; Alemania Fil: Becker, Claude. Max Planck Institute for Developmental Biology; Alemania Fil: Warthmann, Norman. Max Planck Institute for Developmental Biology; Alemania. The Australian National University; Australia Fil: Chica, Claudia. Centre National de la Recherche Scientifique; Francia Fil: Szarzynska, Bogna. Centre National de la Recherche Scientifique; Francia Fil: Zytnicki, Matthias. Max Planck Institute for Developmental Biology; Alemania Fil: Albani, Maria C.. Max Planck Institute for Plant Breeding Research; Alemania Fil: Kiefer, Christiane. Max Planck Institute for Plant Breeding Research; Alemania Fil: Bergonzi, Sara. Max Planck Institute for Plant Breeding Research; Alemania Fil: Castaings, Loren. Max Planck Institute for Plant Breeding Research; Alemania Fil: Mateos, Julieta Lisa. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Max Planck Institute for Plant Breeding Research; Alemania Fil: Berns, Markus C.. Max Planck Institute for Plant Breeding Research; Alemania Fil: Bujdoso, Nora. Max Planck Institute for Plant Breeding Research; Alemania Fil: Piofczyk, Thomas. Max Planck Institute for Plant Breeding Research; Alemania Fil: Roudier, François. Centre National de la Recherche Scientifique; Francia Fil: Carbonero, Pilar. Universidad Politécnica de Madrid; España Fil: Paz Ares, Javier. Consejo Superior de Investigaciones Cientificas; España Fil: Davis, Seth J.. Max Planck Institute for Plant Breeding Research; Alemania Fil: Pecinka, Ales. Max Planck Institute for Plant Breeding Research; Alemania Fil: Quesneville, Hadi. INRA. Research Unit in Genomics; Francia Fil: Colot, Vincent. Centre National de la Recherche Scientifique; Francia Fil: Lysak, Martin A.. Central European Institute of Technology; República Checa Fil: Weigel, Detlef. Max Planck Institute for Developmental Biology; Alemania Fil: Coupland, George. Max Planck Institute for Plant Breeding Research; Alemania Fil: Schneeberger, Korbinian. Max Planck Institute for Plant Breeding Research; Alemania
Published: 2015
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41. Cross-correlated relaxation measurements under adiabatic sweeps: determination of local order in proteins

Author: Kadeřávek, Pavel, Grutsch, Sarina, Salvi, Nicola, Tollinger, Martin, Žídek, Lukáš, Bodenhausen, Geoffrey, Ferrage, Fabien, Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Institut des sciences et d'ingénierie chimiques (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Université Pierre et Marie Curie - Paris 6 (UPMC), Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), University of Innsbruck, National Centre for Biomolecular Research, Masaryk University [Brno] (MUNI), École normale supérieure - Paris (ENS-PSL), and Leopold Franzens Universität Innsbruck - University of Innsbruck
Subjects: Cross-correlated cross relaxation, Adiabatic sweep, Ubiquitin, Humans, Protein Interaction Domains and Motifs, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Protein dynamics, Biochemistry, CREB-Binding Protein, Nuclear Magnetic Resonance, Biomolecular, Spectroscopy, Article, NMR
Abstract: Adiabatically swept pulses were originally designed for the purpose of broadband spin inversion. Later, unexpected advantages of their utilization were also found in other applications, such as refocusing to excite spin echoes, studies of chemical exchange or fragment-based drug design. Here, we present new experiments to characterize fast (ps–ns) protein dynamics, which benefit from little-known properties of adiabatic pulses. We developed a strategy for measuring cross-correlated cross-relaxation (CCCR) rates during adiabatic pulses. This experiment provides a linear combination of longitudinal and transverse CCCR rates, which is offset-independent across a typical amide \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$^{15}\hbox {N}$$\end{document}15N spectrum. The pulse sequence can be recast to provide accurate transverse CCCR rates weighted by the populations of exchanging states. Sensitivity can be improved in systems in slow exchange. Finally, the experiments can be easily modified to yield residue-specific correlation times. The average correlation time of motions can be determined with a single experiment while at least two different experiments had to be recorded until now. Electronic supplementary material The online version of this article (doi:10.1007/s10858-015-9994-8) contains supplementary material, which is available to authorized users.
Published: 2015
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42. Urinary microRNAs as a new class of noninvasive biomarkers in oncology, nephrology, and cardiology

Author: Mlcochova, Hana, Hezova, Renata, Meli, Albano C, Slaby, Ondrej, Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Physiologie & médecine expérimentale du Cœur et des Muscles [U 1046] (PhyMedExp), Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Male, Urologic Diseases, MicroRNAs, Heart Diseases, [SDV]Life Sciences [q-bio], Neoplasms, RNA Stability, Humans, Female, ComputingMilieux_MISCELLANEOUS, Biomarkers
Abstract: MicroRNAs (miRNAs) are small noncoding RNAs that posttranscriptionally regulate gene expression. In the last decade, number of evidences showing miRNAs contribution to the regulation of apoptosis, cellular proliferation, differentiation, and other important cellular processes is constantly growing. Specific miRNA expression signatures have been identified in variety of human cancers as well as pathologies of cardiovascular and urinary systems. Our chapter focuses on the potential of urinary miRNAs to serve as biomarkers in uro-oncology, nephrology, and cardiology. We discuss in detail recent knowledge about the origin of urinary miRNAs, their stability, quality control, and their utility as a potential new class of biomarkers in medicine. Finally, we summarize the studies focusing on detection and characterization of urinary miRNAs as potential biomarkers in urologic cancers, nephrology, and cardiology.
Published: 2014
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43. The path to life's origins. Remaining hurdles

Author: Ernesto Di Mauro, Edward N. Trifonov, Raffaele Saladino, Department of Biology and Biotechnology 'Charles Darwin', Institut Pasteur, Fondation Cenci Bolognetti - Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Dipartimento di Agrobiologia ed Agrochimica, Università della Tuscia, University of Haifa [Haifa], Central European Institute of Technology [Brno] (CEITEC MU), and Brno University of Technology [Brno] (BUT)
Subjects: Genetics, RNA replicator, [SDV]Life Sciences [q-bio], General Medicine, formamide reactions, Biology, Biological Evolution, Models, Biological, self-replication, origin of life, Epistemology, simplissimus, Structural Biology, border chemistry/life, Path (graph theory), abiotic start, Molecular Biology, Simple (philosophy)
Abstract: International audience; Recent progress in abiotic syntheses, especially self-catalytic syntheses, as well as theoretical breakthroughs such as reconstruction of events of early molecular evolution and tracing repeat expansions in contemporary genomes, converge to a rather simple possible scenario of origin of life, notwithstanding the enormity of the problem. The scenario includes self-replicating RNA duplexes, supplemented by monomers and high-energy compounds that, as demonstrated or assumed, can all be synthesized abiotically. The self-replication would proceed with occasional mutational changes, propagated in later cycles. This audacious, as it may seem, walk toward the life origin already involves many laboratories, each exploring its own scenario. The one suggested in this outline seems to the authors well justified to engage in, while bypassing few steps to deal with later.
Published: 2014
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44. $Ortho$-(methylsulfanyl)phenylphosphonates and derivatives: Synthesis and applications as mono- or bidentate ligands for the preparation of platinum complexes

Author: Mathieu Lecinq, Jiří Kozelka, Mihaela Gulea, Matthieu Hamel, Laboratoire de chimie moléculaire et thioorganique (LCMT), Centre National de la Recherche Scientifique (CNRS)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU), Laboratoire Capteurs et Architectures Electroniques (LCAE), Département Métrologie Instrumentation & Information (DM2I), Laboratoire d'Intégration des Systèmes et des Technologies (LIST), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Laboratoire d'Intégration des Systèmes et des Technologies (LIST), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Laboratoire d'Innovation Thérapeutique (LIT), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC), Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (LCBPT - UMR 8601), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), The ' Ministère de la Recherche et des Nouvelles Technologies' for the grant and the 'région Basse Normandie'and the European Union (FEDER funding) support, Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Centre National de la Recherche Scientifique (CNRS)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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 Technologique (CEA) (DRT (CEA)), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), CEITEC-Central European Institute of Technology, MasarykBrno, Czech Republic., The ' Ministère de la Recherche et des Nouvelles Technologies' for the grant and the 'région BasseNormandie'and the European Union (FEDER funding) support, Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Le Havre Normandie (ULH), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Intégration des Systèmes et des Technologies (LIST (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Laboratoire d'Intégration des Systèmes et des Technologies (LIST (CEA)), and Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Denticity, Sulfide, Platinum complexes, Stereochemistry, chemistry.chemical_element, Sigmatropic reaction, 010402 general chemistry, Sigmatropic rearrangement, 01 natural sciences, Biochemistry, Potassium tetrachloroplatinate, Medicinal chemistry, Inorganic Chemistry, chemistry.chemical_compound, Materials Chemistry, [CHIM]Chemical Sciences, [CHIM.COOR]Chemical Sciences/Coordination chemistry, Physical and Theoretical Chemistry, Cis/trans isomerization, chemistry.chemical_classification, 010405 organic chemistry, Ligand, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Organic Chemistry, Sulfoxide, Phosphonate, 0104 chemical sciences, chemistry, S-Bidentate ligands, Platinum
Abstract: International audience; The preparation of six phenylphosphonates (and phosphonic acid derivatives) bearing a sulfur group in $ortho$ position was accomplished $via$ either a [1,3]- or a [1,4]-sigmatropic rearrangement. Their complexation with different platinum sources has been studied and the new platinum complexes obtained were characterized by NMR spectroscopy ($^1$H, $^{13}$C, $^{31}$P and $^{195}$Pt). Three runs of experiments were performed. The first was the reaction of ligands 1 and 2 bearing one sulfide and a phosphonate diester functions with potassium tetrachloroplatinate. In the obtained complexes, two molecules of ligand chelate the metal only by the sulfur atom. We were able to observe by $^{195}$Pt and $^{31}$P NMR spectroscopy the $trans$ to $cis$ rearrangement of a dichloro-methyl-($o$-phosphorylbenzyl)sulfide platinum(II) complex upon time, leading to two new species, which are diastereomers of the cis-complex. The second set of experiments involved ligands 1, 2 and 3 bearing one sulfide or sulfoxide and a phosphonate diester moieties, cisplatin and one equivalent of silver nitrate. In the resulting complexes the platinum is coordinated by the sulfur atom of one molecule of ligand. In the third run, the reaction between ligands 4, 5, and 6 bearing one sulfide or sulfoxide and one phosphonic acid or one phosphonic monoester group and the cisplatin diaqua form led to O,S$-$Pt chelates.
Published: 2013
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45. An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

Author: Zoé Joly-Lopez, J. Chris Pires, Thomas E. Bureau, Christopher D. Town, Erik van den Bergh, John R. Stinchcombe, Ken Dewar, Ewa Forczek, Xiaowu Wang, Douglas R. Hoen, Emilio Vello, Alan M. Moses, Martin A. Lysak, Terezie Mandáková, David E. Jarvis, Daniel J. Schoen, Patrick P. Edger, Jeremy Schmutz, Adrian E. Platts, Karen S. Schumaker, Joshua G. Steffen, M. Eric Schranz, Paul M. Harrison, Mickael Leclercq, Annabelle Haudry, Khaled M. Hazzouri, Robert J. Williamson, Mathieu Blanchette, Stephen I. Wright, Eléments transposables, évolution, populations, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), McGill University and Genome Quebec Innovation Centre, Institute of Vegetables and Flowers (IVF), Chinese Academy of Agricultural Sciences (CAAS), United States Department of Energy, Research group Plant Cytogenomics, Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT)-Brno University of Technology [Brno] (BUT), Psychiatry, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Department of Biology [Montréal], McGill University = Université McGill [Montréal, Canada], and McGill Centre for Bioinformatics (MCB)
Subjects: 0106 biological sciences, Arabidopsis, Regulatory Sequences, Nucleic Acid, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, Genome, Conserved non-coding sequence, Conserved sequence, Population genomics, brassica-oleracea, Gene Expression Regulation, Plant, Gene Duplication, Cluster Analysis, Conserved Sequence, Phylogeny, ComputingMilieux_MISCELLANEOUS, Genetics, 0303 health sciences, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], High-Throughput Nucleotide Sequencing, Genomics, drosophila, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Biosystematiek, annotation, dna elements, Genome, Plant, arabidopsis-thaliana, Biology, size, Evolution, Molecular, 03 medical and health sciences, evolution, human genome, Nucleotide Motifs, Selection, Genetic, Gene, 030304 developmental biology, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Computational Biology, Molecular Sequence Annotation, 15. Life on land, ultraconserved elements, Noncoding DNA, gene-expression, Brassicaceae, Biosystematics, Human genome, EPS, Gene Deletion, 010606 plant biology & botany
Abstract: Despite the central importance of noncoding DNA to gene regulation and evolution, understanding of the extent of selection on plant noncoding DNA remains limited compared to that of other organisms. Here we report sequencing of genomes from three Brassicaceae species (Leavenworthia alabamica, Sisymbrium irio and Aethionema arabicum) and their joint analysis with six previously sequenced crucifer genomes. Conservation across orthologous bases suggests that at least 17% of the Arabidopsis thaliana genome is under selection, with nearly one-quarter of the sequence under selection lying outside of coding regions. Much of this sequence can be localized to approximately 90,000 conserved noncoding sequences (CNSs) that show evidence of transcriptional and post-transcriptional regulation. Population genomics analyses of two crucifer species, A. thaliana and Capsella grandiflora, confirm that most of the identified CNSs are evolving under medium to strong purifying selection. Overall, these CNSs highlight both similarities and several key differences between the regulatory DNA of plants and other species.
Published: 2013
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46. Generic acquisition protocol for quantitative MRI of the spinal cord

Author: René Labounek, Nawal Kinany, Michela Fratini, Laura Barlow, Markus Barth, P Wyss, Marco Battiston, Sean Mackey, Nyoman D. Kurniawan, Deborah Pareto, Kenneth A. Weber, Guillaume Gilbert, Robert L. Barry, Anna Pichiecchio, Eva Alonso-Ortiz, Matthew D. Budde, Mihael Abramovic, Alexandra Tinnermann, Giancarlo Germani, Dimitri Van De Ville, Falk Eippert, Anna J.E. Combes, Igor Nestrasil, Marios C. Yiannakas, Haleh Karbasforoushan, Julien Doyon, Cornelia Laule, Nicole Atcheson, Ali Khatibi, Nico Papinutto, Karla R. Epperson, Marek Dostál, Yazhuo Kong, Loan Mattera, Charley Gros, Paulo Loureiro de Sousa, Pierre-Gilles Henry, Alan C. Seifert, Richard G. Wise, Issei Fukunaga, Alexandru Foias, Shannon H. Kolind, Todd B. Parrish, Akifumi Hagiwara, Daniel Papp, Carina Arneitz, Virginie Callot, Christian Büchel, Maria Marcella Laganà, Tobias Leutritz, Slawomir Kusmia, Ferran Prados, Kevin S. Epperson, Marc J. Ruitenberg, Nikolaus Weiskopf, Kouhei Kamiya, Benjamin De Leener, Adam V. Dvorak, Giovanni Savini, Christine S. Law, Petr Kudlička, Paul Kuntke, Julien Cohen-Adad, Alex Rovira, Jan Valošek, Patrick Freund, George Tackley, Zachary A. Smith, Eloy Martinez-Heras, Maxime Descoteaux, Yaou Liu, Miloš Keřkovský, Joo Won Kim, Kristin P. O’Grady, Elisabeth Solana, Rebecca S. Samson, Junqian Xu, Alex K. Smith, Federico Giove, Maryam Seif, Claudia A. M. Wheeler-Kingshott, Tomáš Horák, James M. Joers, Francesco Grussu, Christophe Lenglet, Jürgen Finsterbusch, Sara Llufriu, Hagen H. Kitzler, Masaaki Hori, Yuichi Suzuki, Seth A. Smith, École Polytechnique de Montréal (EPM), Université du Québec à Montréal = University of Québec in Montréal (UQAM), Mila - Quebec AI Institute, Swiss Paraplegic Research = Schweizer Paraplegiker-Stiftung, University of Queensland [Brisbane], University of British Columbia (UBC), Massachusetts General Hospital [Boston], Harvard Medical School [Boston] (HMS), Massachusetts Institute of Technology (MIT), University College of London [London] (UCL), Universitaetsklinikum Hamburg-Eppendorf = University Medical Center Hamburg-Eppendorf [Hamburg] (UKE), Medical College of Wisconsin [Milwaukee] (MCW), Centre de résonance magnétique biologique et médicale (CRMBM), Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Centre National de la Recherche Scientifique (CNRS), Centre d'Exploration Métabolique par Résonance Magnétique [Hôpital de la Timone - AP-HM] (CEMEREM), Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Centre National de la Recherche Scientifique (CNRS)- Hôpital de la Timone [CHU - APHM] (TIMONE), Vanderbilt University Medical Center [Nashville], Vanderbilt University [Nashville], CHU Sainte Justine [Montréal], Université de Sherbrooke (UdeS), Centre d'Imagerie Moléculaire de Sherbrooke, Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie (ICube), École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Université de Strasbourg (UNISTRA)-Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Masaryk University and University Hospital Brno, McGill University = Université McGill [Montréal, Canada], Max Planck Institute for Human Cognitive and Brain Sciences [Leipzig] (IMPNSC), Max-Planck-Gesellschaft, Stanford University School of Medicine [CA, USA], Universität Zürich [Zürich] = University of Zurich (UZH), IRCCS Santa Lucia Foundation, Juntendo University School of Medicine [Tokyo, Japan], University of Pavia, IRCCS Mondino Foundation, Philips Healthcare [Markham], Museo Storico della Fisica e Centro di Studi e Ricerche 'Enrico Fermi', Roma, Vall d'Hebron University Hospital [Barcelona], Center for Magnetic Resonance Research [Minneapolis] (CMRR), University of Minnesota Medical School, University of Minnesota System-University of Minnesota System, Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Toho University Omori Medical Center [Tokyo], The University of Tokyo (UTokyo), Northwestern University Feinberg School of Medicine, Stanford University, University of Birmingham [Birmingham], Icahn School of Medicine at Mount Sinai [New York] (MSSM), Ecole Polytechnique Fédérale de Lausanne (EPFL), University of Geneva [Switzerland], Technische Universität Dresden = Dresden University of Technology (TU Dresden), Chinese Academy of Sciences [Beijing] (CAS), University of Chinese Academy of Sciences [Beijing] (UCAS), University of Oxford [Oxford], University of Southern Queensland (USQ), Cardiff University, Epilepsy Society [Buckinghamshire] (MRI Unit), Departments of Ophthalmology and Pediatrics, University of Minnesota, Minneapolis, MN, University of Minnesota [Twin Cities] (UMN), University Hospital Olomouc [Czech Republic], Capital University of Medical Sciences [Beijing] (CUMS), Universitat de Barcelona (UB), University of California [San Francisco] (UCSF), University of California, Feinberg School of Medicine, Northwestern University [Evanston], Universitat Oberta de Catalunya [Barcelona] (UOC), University of Oklahoma Health Sciences Center (OUHSC), Palacky University Olomouc, Leipzig University, University 'G. d'Annunzio' of Chieti-Pescara [Chieti and Pescara, Italy], Centre d'Exploration Métabolique par Résonance Magnétique [Hôpital de la Timone - APHM] (CEMEREM), Hôpital de la Timone [CHU - APHM] (TIMONE)-Centre de résonance magnétique biologique et médicale (CRMBM), Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Les Hôpitaux Universitaires de Strasbourg (HUS)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Masaryk University [Brno] (MUNI), Università degli Studi di Pavia = University of Pavia (UNIPV), Enrico Fermi Center for Study and Research | Museo Storico della Fisica e Centro Studi e Ricerche Enrico Fermi, Université de Genève = University of Geneva (UNIGE), University of Oxford, University of California [San Francisco] (UC San Francisco), University of California (UC), Assistance Publique - Hôpitaux de Marseille (APHM)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Assistance Publique - Hôpitaux de Marseille (APHM)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Assistance Publique - Hôpitaux de Marseille (APHM)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)- Hôpital de la Timone [CHU - APHM] (TIMONE), Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Matériaux et nanosciences d'Alsace (FMNGE), and Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Adult, Male, medicine.medical_specialty, Computer science, Neuroimaging, Article, General Biochemistry, Genetics and Molecular Biology, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, 0302 clinical medicine, Image Processing, Computer-Assisted, medicine, Humans, NeuroPoly, Medical physics, health care economics and organizations, Protocol (science), medicine.diagnostic_test, technology, industry, and agriculture, Healthy subjects, Magnetic resonance imaging, Spinal cord, Magnetic Resonance Imaging, White matter microstructure, humanities, 3. Good health, Acquisition Protocol, medicine.anatomical_structure, Spinal Cord, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], 030217 neurology & neurosurgery, Diffusion MRI
Abstract: Quantitative spinal cord (SC) magnetic resonance imaging (MRI) presents many challenges, including a lack of standardized imaging protocols. Here we present a prospectively harmonized quantitative MRI protocol, which we refer to as the spine generic protocol, for users of 3T MRI systems from the three main manufacturers: GE, Philips and Siemens. The protocol provides guidance for assessing SC macrostructural and microstructural integrity: T1-weighted and T2-weighted imaging for SC cross-sectional area computation, multi-echo gradient echo for gray matter cross-sectional area, and magnetization transfer and diffusion weighted imaging for assessing white matter microstructure. In a companion paper from the same authors, the spine generic protocol was used to acquire data across 42 centers in 260 healthy subjects. The key details of the spine generic protocol are also available in an open-access document that can be found at https://github.com/spine-generic/protocols . The protocol will serve as a starting point for researchers and clinicians implementing new SC imaging initiatives so that, in the future, inclusion of the SC in neuroimaging protocols will be more common. The protocol could be implemented by any trained MR technician or by a researcher/clinician familiar with MRI acquisition.
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47. Tools and data services registry: a community effort to document bioinformatics resources

Author: Callum Smith, Paolo Uva, Thomas Gatter, Peter Løngreen, Peter Juvan, Hans Ienasescu, Giuseppe Profiti, Aleksandra Nenadic, Kristoffer Rapacki, Chris Morris, Paola Roncaglia, Steffen Möller, Laura Emery, Søren Brunak, Maria Maddalena Sperotto, Heinz Stockinger, Kristian Davidsen, Federico Zambelli, Helen Parkinson, Olivia Doppelt-Azeroual, Luana Licata, Tatyana Goldberg, Andrea Schafferhans, Elisabeth Gasteiger, Emil Karol Rydza, Camille Laibe, Victor De La Torre, Marie Grosjean, Manuela Helmer-Citterich, Hervé Ménager, Radka Svobodová Vařeková, Rafael C. Jimenez, Martin Closter Jespersen, Anthony Bretaudeau, Jan Brezovsky, Tunca Doğan, Matúš Kalaš, Peter M. Rice, Ivan Mičetić, Rune Møllegaard Friborg, Maximilian Koch, Silvio C. E. Tosatto, Nick Juty, Björn Grüning, Gianmauro Cuccuru, Frederik Coppens, Gianni Cesareni, Jon Ison, Rabie Saidi, Sébastien Moretti, Rita Casadio, Gert Vriend, Guy Yachdav, Niall Beard, Timothy F. Booth, Michael Cornell, Piotr Jaroslaw Chmura, Veit Schwämmle, Karel Berka, Dan Bolser, Vassilios Ioannidis, Jing-Woei Li, Burkhard Rost, Gianluca Della Vedova, Fabien Mareuil, Hedi Peterson, Allegra Via, Paolo Romano, Christian Anthon, Technical University of Denmark [Lyngby] (DTU), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP), University of Bergen (UIB), University of Copenhagen = Københavns Universitet (KU), University of Manchester, Palacky University, European Bioinformatics Institute, NEBC Wallingford, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Masaryk University, University of Bologna, Università degli Studi di Roma Tor Vergata [Roma], Ghent University [Belgium] (UGENT), Flanders Institute for Biotechnology, CRS4 Bioinformat, Università degli studi di Milano-Bicocca, Swiss Institute of Bioinformatics, Universität Bielefeld = Bielefeld University, Tumor Biology Center, Centre National de la Recherche Scientifique (CNRS), University of Freiburg, University of Ljubljana, The Chinese University of Hong Kong [Hong Kong], Universita degli Studi di Padova, Bioinformatics Research Centre, Université de Lausanne, CCLRC Daresbury Laboratory, Universität zu Lübeck [Lübeck] - University of Lübeck [Lübeck], Universität Rostock, University of Tartu, Imperial College London, IRCCS Azienda Ospedaliera Universitaria Integrata San Martino (IRCCS AOU San Martino), University of Southern Denmark (SDU), WTCHG, Central European Institute of Technology [Brno] (CEITEC), Instituto Nacional de Bioinformática, Sapienza University of Rome (DIAG), Consiglio Nazionale delle Ricerche, University of Milan, Radboud University Nijmegen, Ison, J, Rapacki, K, Ménager, H, Kalaš, M, Rydza, E, Chmura, P, Anthon, C, Beard, N, Berka, K, Bolser, D, Booth, T, Bretaudeau, A, Brezovsky, J, Casadio, R, Cesareni, G, Coppens, F, Cornell, M, Cuccuru, G, Davidsen, K, DELLA VEDOVA, G, Dogan, T, Doppelt Azeroual, O, Emery, L, Gasteiger, E, Gatter, T, Goldberg, T, Grosjean, M, Grüning, B, Helmer Citterich, M, Ienasescu, H, Ioannidis, V, Jespersen, M, Jimenez, R, Juty, N, Juvan, P, Koch, M, Laibe, C, Li, J, Licata, L, Mareuil, F, Mičetić, I, Friborg, R, Moretti, S, Morris, C, Möller, S, Nenadic, A, Peterson, H, Profiti, G, Rice, P, Romano, P, Roncaglia, P, Saidi, R, Schafferhans, A, Schwämmle, V, Smith, C, Sperotto, M, Stockinger, H, Vařeková, R, Tosatto, S, de la Torre, V, Uva, P, Via, A, Yachdav, G, Zambelli, F, Vriend, G, Rost, B, Parkinson, H, Løngreen, P, Brunak, S, University of Bergen (UiB), Palacky University Olomouc, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Masaryk University [Brno] (MUNI), Universiteit Gent = Ghent University [Belgium] (UGENT), Università degli Studi di Milano-Bicocca [Milano] (UNIMIB), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), Universität zu Lübeck [Lübeck], Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Danmarks Tekniske Universitet = Technical University of Denmark (DTU), University of Copenhagen = Københavns Universitet (UCPH), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, University of Bologna/Università di Bologna, Universiteit Gent = Ghent University (UGENT), Università degli Studi di Milano-Bicocca = University of Milano-Bicocca (UNIMIB), Université de Lausanne = University of Lausanne (UNIL), Università degli Studi di Padova = University of Padua (Unipd), Universität zu Lübeck = University of Lübeck [Lübeck], Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), Università degli Studi di Milano = University of Milan (UNIMI), Ison, Jon, Rapacki, Kristoffer, Ménager, Hervé, Kalaš, Matúš, Rydza, Emil, Chmura, Piotr, Anthon, Christian, Beard, Niall, Berka, Karel, Bolser, Dan, Booth, Tim, Bretaudeau, Anthony, Brezovsky, Jan, Casadio, Rita, Cesareni, Gianni, Coppens, Frederik, Cornell, Michael, Cuccuru, Gianmauro, Davidsen, Kristian, Vedova, Gianluca Della, Dogan, Tunca, Doppelt-Azeroual, Olivia, Emery, Laura, Gasteiger, Elisabeth, Gatter, Thoma, Goldberg, Tatyana, Grosjean, Marie, Grüning, Björn, Helmer-Citterich, Manuela, Ienasescu, Han, Ioannidis, Vassilio, Jespersen, Martin Closter, Jimenez, Rafael, Juty, Nick, Juvan, Peter, Koch, Maximilian, Laibe, Camille, Li, Jing-Woei, Licata, Luana, Mareuil, Fabien, Mičetić, Ivan, Friborg, Rune Møllegaard, Moretti, Sebastien, Morris, Chri, Möller, Steffen, Nenadic, Aleksandra, Peterson, Hedi, Profiti, Giuseppe, Rice, Peter, Romano, Paolo, Roncaglia, Paola, Saidi, Rabie, Schafferhans, Andrea, Schwämmle, Veit, Smith, Callum, Sperotto, Maria Maddalena, Stockinger, Heinz, Vařeková, Radka Svobodová, Tosatto, Silvio C E, de la Torre, Victor, Uva, Paolo, Via, Allegra, Yachdav, Guy, Zambelli, Federico, Vriend, Gert, Rost, Burkhard, Parkinson, Helen, Løngreen, Peter, and Brunak, Søren
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], registry, Bioinformatics, computer.software_genre, Matematikk og naturvitenskap: 400::Informasjons- og kommunikasjonsvitenskap: 420::Systemutvikling og -arbeid: 426 [VDP], Task (project management), Documentation, Data and Information, Database Issue, Registries, bioinformatique, Data Curation, base de données, Settore BIO/11, gestion de données, tool, SOFTWARE-DEVELOPMENT, bioinformatics, ddc, outil informatique, Tools and data services registry, SEQANSWERS, Web service, MOLECULAR-BIOLOGY, Biology, Ecology and Environment, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Genetics, Implementation, Dissemination, Bioinformatikk / Bioinformatics, Data curation, bioinformatic, business.industry, Computational Biology, Software, Software development, bioinformatics, tools, registry, elixir, Biology and Life Sciences, Mathematics and natural scienses: 400::Information and communication science: 420::System development and design: 426 [VDP], FRAMEWORK, ELIXIR, Settore BIO/18 - Genetica, 030104 developmental biology, tools, Data as a service, COMPILATION, business, COLLECTION, Nanomedicine Radboud Institute for Molecular Life Sciences [Radboudumc 19], computer, WEB SERVICES, LIFE SCIENCES
Abstract: Contains fulltext : 171819.pdf (Publisher’s version ) (Open Access) Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.
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48. High-sensitivity mapping of magnetic induction fields with nanometer-scale resolution: comparison of off-axis electron holography and pixelated differential phase contrast

Author: Olivier Fruchart, Jean-Luc Rouvière, Victor Boureau, Michal Staňo, and David Cooper, Jean-Christophe Toussaint, Centre d'élaboration de matériaux et d'études structurales (CEMES), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie de Toulouse (ICT-FR 2599), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), CIME EPFL, Ecole Polytechnique Fédérale de Lausanne (EPFL), Micro et NanoMagnétisme (MNM), Institut Néel (NEEL), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Laboratoire d'Etude des Matériaux par Microscopie Avancée (LEMMA ), Modélisation et Exploration des Matériaux (MEM), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), SPINtronique et TEchnologie des Composants (SPINTEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives - Laboratoire d'Electronique et de Technologie de l'Information (CEA-LETI), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Nanocharacterisation platform based at Minatec (PFNC), ANR-10-LABX-0051,LANEF,Laboratory of Alliances on Nanosciences - Energy for the Future(2010), European Project: 306535,EC:FP7:ERC,ERC-2012-StG_20111012,HOLOVIEW(2012), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Micro et NanoMagnétisme (NEEL - MNM)
Subjects: Diffraction, Materials science, electron holography, Acoustics and Ultrasonics, Holography, FOS: Physical sciences, Applied Physics (physics.app-ph), 02 engineering and technology, 01 natural sciences, Electron holography, law.invention, Optics, law, Mesoscale and Nanoscale Physics (cond-mat.mes-hall), 0103 physical sciences, Scanning transmission electron microscopy, stem, Image resolution, 010302 applied physics, Condensed Matter - Mesoscale and Nanoscale Physics, detector, business.industry, Resolution (electron density), Detector, pixelated stem, Physics - Applied Physics, 021001 nanoscience & nanotechnology, Condensed Matter Physics, equipment and supplies, pixelated dpc, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials, electric field, lorentz microscopy, Transmission electron microscopy, magnetic induction, specimens, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], 4d-stem, microscopy, precision, 0210 nano-technology, business
Abstract: We compare two transmission electron microscopy (TEM) based techniques that can provide highly spatially resolved quantitative measurements of magnetic induction fields at high sensitivity. To this end, the magnetic induction of a ferromagnetic NiFe nanowire has been measured and compared to micromagnetic modeling. State-of-the-art off-axis electron holography has been performed using the averaging of large series of holograms to improve the sensitivity of the measurements. These results are then compared to those obtained from pixelated differential phase contrast, a technique that belongs to pixelated (or 4D) scanning transmission electron microscopy (STEM) experiments. This emerging technique uses a pixelated detector to image the local diffraction patterns as the beam is scanned over the sample. For each diffraction pattern, the deflection of the beam is measured and converted into magnetic induction, while scanning the beam allows a map to be generated. Aberration corrected Lorentz (field-free) configurations of the TEM and STEM were used for an improved spatial resolution. We show that the pixelated STEM approach, even when performed using an old generation of charge-coupled device camera, provides better sensitivity at the expense of spatial resolution. A more general comparison of the two quantitative techniques is given.
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