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1. Media Use and Societal Perceptions: The Dual Role of Media Trust

Author

European Research Council (ERC), Swedish Research Council (VR), Shehata, Adam, Strömbäck, Jesper, European Research Council (ERC), Swedish Research Council (VR), Shehata, Adam, and Strömbäck, Jesper

Abstract

How citizens’ perceptions of societal problems are shaped by media use has been a critical question in media effects research for decades. This study addresses a specific puzzle concerning media effects in contemporary fragmented media environments: the dual role of media trust as both (a) an antecedent variable guiding news selection and (b) a moderator variable conditioning the effects of news use on perceptions of societal problems. Building upon the differential susceptibility to media effects model, we analyze the role of media trust for citizens’ orientation towards mainstream and alternative news media—and how such usage influences perceptions of two major societal issues: health care and school. Findings from a four-wave panel survey conducted in Sweden suggest that public service and alternative news use matter for citizens’ perceptions of societal problems and that media trust influences news choices and may, partly, condition media effects.

Published
2022

2. Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], Integrated BioBank of Luxembourg - IBBL [research center], Science for Life Laboratory [research center], Centre Hospitalier de Luxembourg [research center], Fonds National de la Recherche - FnR [sponsor], Integrated BioBank of Luxembourg [sponsor], Fondation André et Henriette Losch [sponsor], Swedish Research Council VR [sponsor], Wampach, Linda, Heintz, Anna, Hogan, Angela, Muller, Emilie, Narayanasamy, Shaman, Laczny, Cedric Christian, Hugerth, Luisa, Bindl, Lutz, Bottu, Jean, Andersson, Anders, de Beaufort, Carine, Wilmes, Paul, Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], Integrated BioBank of Luxembourg - IBBL [research center], Science for Life Laboratory [research center], Centre Hospitalier de Luxembourg [research center], Fonds National de la Recherche - FnR [sponsor], Integrated BioBank of Luxembourg [sponsor], Fondation André et Henriette Losch [sponsor], Swedish Research Council VR [sponsor], Wampach, Linda, Heintz, Anna, Hogan, Angela, Muller, Emilie, Narayanasamy, Shaman, Laczny, Cedric Christian, Hugerth, Luisa, Bindl, Lutz, Bottu, Jean, Andersson, Anders, de Beaufort, Carine, and Wilmes, Paul

Abstract

Perturbations to the colonization process of the human gastrointestinal tract have been suggested to result in adverse health effects later in life. Although much research has been performed on bacterial colonization and succession, much less is known about the other two domains of life, archaea, and eukaryotes. Here we describe colonization and succession by bacteria, archaea and microeukaryotes during the first year of life (samples collected around days 1, 3, 5, 28, 150, and 365) within the gastrointestinal tract of infants delivered either vaginally or by cesarean section and using a combination of quantitative real-time PCR as well as 16S and 18S rRNA gene amplicon sequencing. Sequences from organisms belonging to all three domains of life were detectable in all of the collected meconium samples. The microeukaryotic community composition fluctuated strongly over time and early diversification was delayed in infants receiving formula milk. Cesarean section-delivered (CSD) infants experienced a delay in colonization and succession, which was observed for all three domains of life. Shifts in prokaryotic succession in CSD infants compared to vaginally delivered (VD) infants were apparent as early as days 3 and 5, which were characterized by increased relative abundances of the genera Streptococcus and Staphylococcus, and a decrease in relative abundance for the genera Bifidobacterium and Bacteroides. Generally, a depletion in Bacteroidetes was detected as early as day 5 postpartum in CSD infants, causing a significantly increased Firmicutes/Bacteroidetes ratio between days 5 and 150 when compared to VD infants. Although the delivery mode appeared to have the strongest influence on differences between the infants, other factors such as a younger gestational age or maternal antibiotics intake likely contributed to the observed patterns as well. Our findings complement previous observations of a delay in colonization and succession of CSD infants, which affects not on

Published
2017

3. Single cell RNA sequencing identifies early diversity of sensory neurons forming via bi-potential intermediates

Author

Helen C. Lai, Charles Petitpré, Laura Croci, G. Giacomo Consalez, Lynn Linyu Sun, Antoine de Chevigny, Saida Hadjab, Karen Runge, Paula Fontanet, Kylie K. Y. Cheung, Francois Lallemend, Yiqiao Wang, Haohao Wu, Mark A. Landy, Igor Adameyko, Maria Eleni Kastriti, Louis Faure, Faure, L., Wang, Y., Kastriti, M. E., Fontanet, P., Cheung, K. K. Y., Petitpre, C., Wu, H., Sun, L. L., Runge, K., Croci, L., Landy, M. A., Lai, H. C., Consalez, G. G., de Chevigny, A., Lallemend, F., Adameyko, I., Hadjab, S., Medizinische Universität Wien = Medical University of Vienna, Karolinska Institutet [Stockholm], Institut de Neurobiologie de la Méditerranée [Aix-Marseille Université] (INMED - INSERM U1249), Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU), Universita Vita Salute San Raffaele = Vita-Salute San Raffaele University [Milan, Italie] (UniSR), University of Texas Southwestern Medical Center [Dallas], I.A. was supported by ERC Consolidator grant 'STEMMING-FROM-NERVE', Bertil Hallsten Foundation, Swedish Research Council, Paradifference Foundation. F.L. was supported by the Swedish Research Council (VR), the Ragnar Söderberg Foundation, Knut and Alice Wallenberg Foundation, Swedish Brain Foundation, Karolinska Institutet, the Karolinska Institutet Strategic Research program in Neuroscience (StratNeuro) and the Ming Wai Lau Foundation. L.F. is supported by the Austrian Science Fund DOC 33-B27. S.H. is supported by the Swedish Research Council (VR), the Swedish Brain Foundation and Karolinska Institutet. Open access funding provided by Karolinska Institute., Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Bodescot, Myriam

Subjects
0301 basic medicine, Gene regulatory network, General Physics and Astronomy, 02 engineering and technology, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Somatosensory system, Mice, Single-cell analysis, Gene Regulatory Networks, 10. No inequality, lcsh:Science, ComputingMilieux_MISCELLANEOUS, Regulation of gene expression, Mice, Knockout, Neurons, Multidisciplinary, Stem Cells, Neurogenesis, Gene Expression Regulation, Developmental, Cell Differentiation, respiratory system, 021001 nanoscience & nanotechnology, medicine.anatomical_structure, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Female, Single-Cell Analysis, 0210 nano-technology, Sensory Receptor Cells, Science, Developmental neurogenesis, Sensory system, Cell fate determination, Biology, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, medicine, Animals, [SDV.NEU] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Cell fate and cell lineage, Sequence Analysis, RNA, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, General Chemistry, Sensory neuron, Mice, Inbred C57BL, Disease Models, Animal, 030104 developmental biology, Core Binding Factor Alpha 3 Subunit, nervous system, lcsh:Q, Neuroscience, human activities
Abstract

Somatic sensation is defined by the existence of a diversity of primary sensory neurons with unique biological features and response profiles to external and internal stimuli. However, there is no coherent picture about how this diversity of cell states is transcriptionally generated. Here, we use deep single cell analysis to resolve fate splits and molecular biasing processes during sensory neurogenesis in mice. Our results identify a complex series of successive and specific transcriptional changes in post-mitotic neurons that delineate hierarchical regulatory states leading to the generation of the main sensory neuron classes. In addition, our analysis identifies previously undetected early gene modules expressed long before fate determination although being clearly associated with defined sensory subtypes. Overall, the early diversity of sensory neurons is generated through successive bi-potential intermediates in which synchronization of relevant gene modules and concurrent repression of competing fate programs precede cell fate stabilization and final commitment., The diversity of primary sensory neurons and how fate choice is determined is unclear. Here, the authors use single cell RNA sequencing analysis of early murine somatosensory neurons to show that sensory neuron diversity is achieved by a transition through a bi-potential intermediate state.

Published
2020

4. Autophagy-related approaches for improving nutrient use efficiency and crop yield protection

Author

Céline Masclaux-Daubresse, Tamar Avin-Wittenberg, Gad Galili, Elena A. Minina, Luisa M. Sandalio, Erika Isono, Núria S. Coll, Hadas Peled-Zehavi, Henri Batoko, Alisdair R. Fernie, Ammar Hassan, Romain Le Bars, Pilar S. Testillano, Pernilla H. Elander, František Baluška, Daniel Hofius, Peter V. Bozhkov, Agnieszka Sirko, Béatrice Satiat-Jeunemaitre, Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP), Weizmann Institute of Science [Rehovot, Israël], Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences (SLU), Linnean Center for Plant Biology, Microscopie Photonique (PHOT), Département Plateforme (PF I2BC), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris-Saclay, Department of Plant and Environmental Sciences, Institut des Sciences du Végétal, Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Département Biologie Cellulaire (BioCell), Dynamique de la Compartimentation cellulaire dans les cellules de plantes supérieures (DYNBSJ), Cytométrie (CYTO), Laboratory of Plant Development and Nuclear Organization, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), COST action TRANSAUTOPHAGY [CA15138], Swedish Foundation for Strategic Research (SSF), Swedish Research Council (VR), Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (Formas), Knut and Alice Wallenberg Foundation, Research Programme 'Trees and Crops for the Future', Swedish Research Council VR, Swedish Research Council FORMAS, Carl-Tryggers Stiftelse (CTS), Israeli Science Foundation [1899/16, 612/16], Spanish Ministry of Economy and Competitiveness (MINECO) [AGL2014-52028-R, AGL2017-82447-R, AGL2016-78002-R, RyC 2014–16158], European Regional Development Fund (ERDF/FEDER), Wallonia-Brussels Federation Joint Research Action (ARC) [11/16-036], Belgian Funds for Scientific Research (FRS-FNRS) (CDR) [19516174], Belgian Funds for Scientific Research (FRS-FNRS) (FRFC) [6794930], Israel Science Foundation, Ministerio de Economía y Competitividad (España), European Commission, Fonds de la Recherche Scientifique (Fédération Wallonie-Bruxelles), aDepartment of Plant Biology, Uppsala BioCenter, Weizmann Institute of Science, Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, and Consejo Superior de Investigaciones Científicas [Spain] (CSIC)

Subjects
Crops, Agricultural, 0301 basic medicine, Plant growth, Physiology, Plant autophagy, [SDV]Life Sciences [q-bio], Context (language use), Plant Science, Biology, 03 medical and health sciences, Nutrient, Autophagy regulation, biotic stress, Biotic stress, phagophore initiation, plant autophagy, Autophagy, Phagophore initiation, Nutrient deficiency, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Crop Protection, business.industry, Abiotic stress, Crop yield, Nutrients, 15. Life on land, Crop Production, Biotechnology, 030104 developmental biology, Agriculture, nutrient deficiency, autophagy regulation, business
Abstract

Autophagy is a eukaryotic catabolic pathway essential for growth and development. In plants, it is activated in response to environmental cues or developmental stimuli. However, in contrast to other eukaryotic systems, we know relatively little regarding the molecular players involved in autophagy and the regulation of this complex pathway. In the framework of the COST (European Cooperation in Science and Technology) action TRANSAUTOPHAGY (2016-2020), we decided to review our current knowledge of autophagy responses in higher plants, with emphasis on knowledge gaps. We also assess here the potential of translating the acquired knowledge to improve crop plant growth and development in a context of growing social and environmental challenges for agriculture in the near future., Research of the Avin-Wittenberg Group is supported by the Israeli Science Foundation, grant number 1899/16.The Testillano group is supported by project AGL2014-52028-R and AGL2017-82447-R funded by the Spanish Ministry of Economy and Competitiveness (MINECO) and the European Regional Development Fund (ERDF/FEDER). Autophagy research at the Galili lab is supported by The Israel Science Foundation (grant 612/16). Research in the Batoko laboratory was funded by the Wallonia-Brussels Federation Joint Research Action (ARC grant #11/16-036), the Belgian Funds for Scientific Research (FRS-FNRS)(CDR grant #19516174 and FRFC grant #6794930).

Published
2018

5. A novel IRE1 kinase inhibitor for adjuvant glioblastoma treatment

Author

Diana Pelizzari-Raymundo, Dimitrios Doultsinos, Raphael Pineau, Chloé Sauzay, Thodoris Koutsandreas, Timothy Langlais, Antonio Carlesso, Elena Gkotsi, Luc Negroni, Tony Avril, Aristotelis Chatziioannou, Eric Chevet, Leif A. Eriksson, Xavier Guillory, Oncogenesis, Stress, Signaling (OSS), Université de Rennes (UR)-CRLCC Eugène Marquis (CRLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Biomedical Research Foundation of the Academy of Athens (BRFAA), Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), University of Gothenburg (GU), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre for Integrative Biology - CBI (Inserm U964 - CNRS UMR7104 - IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), We thank Dr Frédéric Delom, Dr Delphine Fessart, Pr Reynald Gillet, Dr David Gillot, Dr Élodie Lafont, Dr Eric Ogier-Denis, and Pr Afshin Samali for the critical reading of the manuscript. Part of this work was carried out using the Spectroscopies-CDTP core facility, the animal facility ARCHE, and the immunohistochemistry platform H2P2 (UMS Biosit, Université de Rennes 1- Campus de Villejean - 35043 RENNES Cedex, FRANCE). This work was supported by grants from Institut National du Cancer (INCa, PLBIO), Agence Nationale de la Recherche (ANR, ERAAT), Fondation pour la Recherche Médicale (FRM, DEQ20180339169), the EU COST action 861952 \'Proteocure\' and Cancéropôle Grand-Ouest (Gliotreat) to E.C., EU H2020 MSCA ITN-675448 (TRAINERS) and MSCA RISE-734749 (INSPIRED) grants to E.C., A.C., and L.A.E., INSERM (International Research Project – TUPRIC) to A.C. and E.C., La Ligue contre le Cancer (comités 22, 35, 36, 56 et 85), INSERM, Région Bretagne and from the institut des Neurosciences Cliniques de Rennes (INCR) to T.A. The Swedish Research Council (VR, grant no 2019-3684)), the Swedish Cancer Foundation (grant no 21-1447 Pj) and the Swedish National Infrastructure for Computing (SNIC, funded in part through VR grant agreement 2018-05973) are gratefully acknowledged for funding and allocations of computing time, respectively (L.A.E.). D.P.R. was funded by grants from INSERM (LA VANNETAISE) and the Brittany Region, D.D. was funded by EU H2020 MSCA ITN-675448, C.S. was funded by a Plan Cancer post-doctoral fellowship, X.G. was funded by the Fondation ARC pour la recherche sur le cancer, grant PDF20191209830, C.S. was funded by a post-doctoral fellowship from INSERM-plan cancer., and ANR-17-RAR3-0003,ERAAT,Enhancing Endoplasmic Reticulum Proteostasis to Rescue Alpha1 Antitrypsin Deficiency(2017)

Subjects
Biological sciences, Multidisciplinary, Medicine, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, Molecular neuroscience, Neuroscience
Abstract

International audience; Inositol-requiring enzyme 1 (IRE1) is a major mediator of the unfolded protein response (UPR), which is activated upon endoplasmic reticulum (ER) stress. Tumor cells experience ER stress due to adverse microenvironmental cues, a stress overcome by relying on IRE1 signaling as an adaptive mechanism. Herein, we report the discovery of structurally new IRE1 inhibitors identified through the structural exploration of its kinase domain. Characterization in in vitro and in cellular models showed that they inhibit IRE1 signaling and sensitize glioblastoma (GB) cells to the standard chemotherapeutic, temozolomide (TMZ). Finally, we demonstrate that one of these inhibitors, Z4P, permeates the blood-brain barrier (BBB), inhibits GB growth, and prevents relapse in vivo when administered together with TMZ. The hit compound disclosed herein satisfies an unmet need for targeted, non-toxic IRE1 inhibitors and our results support the attractiveness of IRE1 as an adjuvant therapeutic target in GB.

Published
2023

6. Photothermal Conversion of Solar Infrared Radiation by Plasmonic Nanoantennas for Photovoltaic-Thermoelectric Hybrid Devices

Author

Sébastien Hanauer, Inès Massiot, Adnen Mlayah, Franck Carcenac, Jean-Baptiste Doucet, Sélyan Beldjoudi, Ihar Faniayeu, Alexandre Dmitriev, Équipe Photonique (LAAS-PHOTO), Laboratoire d'analyse et d'architecture des systèmes (LAAS), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-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 Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT), Service Techniques et Équipements Appliqués à la Microélectronique (LAAS-TEAM), University of Gothenburg (GU), Swedish Research Council (VR) (Project No. 2017-04828)Swedish Research Council for Sustainable Development (Formas) (Project No. 2021-01390), and ANR-21-CE50-0003,HYDRES,Systèmes hybrides photovoltaïques-thermoélectriques pour la récupération d'énergie solaire(2021)

Subjects
photothermal conversion, thermoplasmonics, photovoltaics, [SPI]Engineering Sciences [physics], Materials Chemistry, Electrochemistry, Energy Engineering and Power Technology, Chemical Engineering (miscellaneous), Electrical and Electronic Engineering, interface layer, hybrid energy harvesting, thermoelectricity
Abstract

International audience; Photovoltaics have become one of the low-cost options for electricity generation. However, the lack of absorption of the near-infrared and infrared solar spectrum intrinsically limits its efficiency. Here, we present an approach for photothermal conversion of solar infrared radiation in photovoltaic-thermoelectric systems using plasmonic nanoantennas. Through numerical calculations-driven shape engineering we identified Ni diabolo nanoantennas as efficient solar infrared spectrum harvesters. Nanofabrication with electron-beam lithography further revealed its impact on nanoantennas optical properties at single-nanoantenna level. In the large-scale low-cost approach, however, photothermal surfaces of nanocone plasmonic antennas, made with a simple and robust fabrication process, still deliver a significant 6.1°C temperature increase under solar 1 infrared illumination. The reported results pave the way towards the development of hybrid photovoltaic-thermoelectric systems with an optimal utilization of the solar spectrum.

Published
2023

7. Rapid amplitude-modulation of a diarylethene photoswitch: en route to contrast-enhanced fluorescence imaging†

Author

Ezequiel Perez-Inestrosa, Shiming Li, Carlos Benitez-Martin, Gaowa Naren, Joakim Andréasson, Wera Larsson, Bo Albinsson, [Naren,G, Larsson,W, Li,S, Albinsson,B, Andréasson,J] Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Göteborg, Sweden. [Benitez-Martin,C, Pérez-Inestrosa,E] Universidad de Malaga-IBIMA, Departamento de Química Organica, E-29071 Málaga, Spain. [Benitez-Martin,C, Pérez-Inestrosa,E] Centro Andaluz de Nanomedicina y Biotecnología (BIONAND), Malaga, Spain., and Support from the Swedish Research Council VR (Grant # 2016-0360 and Grant # 2018-03998, respectively). E. P.-I. acknowledges the Spanish Ministry for Science, Innovation, and Universities (RD16/0006/0012, PCI2019-111825-2, and PID2019-104293GB-I00), Universidad de Málaga-Junta de Andalucía (UMA18-FEDERJA-007), and FEDER. C. B.-M. is grateful for a FPU fellowship (FPU16/02516).

Subjects
Phenomena and Processes::Chemical Phenomena::Physicochemical Phenomena::Solubility [Medical Subject Headings], Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Culture Techniques::Cell Culture Techniques [Medical Subject Headings], Fluorescence-lifetime imaging microscopy, Materials science, Context (language use), Colorantes fluorescentes, 010402 general chemistry, Photochemistry, 01 natural sciences, Fluorescence, Fluorescent dyes, Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Microscopy::Microscopy, Fluorescence [Medical Subject Headings], 03 medical and health sciences, chemistry.chemical_compound, Rayos ultravioleta, Chemicals and Drugs::Chemical Actions and Uses::Specialty Uses of Chemicals::Coloring Agents::Fluorescent Dyes [Medical Subject Headings], Diarylethene, Microscopía fluorescente, Fluorescence microscope, Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Microscopy [Medical Subject Headings], Spectroscopy, Microscopy, fluorescence, 030304 developmental biology, 0303 health sciences, Photoswitch, Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Chemistry Techniques, Analytical::Photometry::Luminescent Measurements::Fluorometry::Spectrometry, Fluorescence [Medical Subject Headings], Phenomena and Processes::Physical Phenomena::Optical Phenomena::Light [Medical Subject Headings], General Chemistry, Phenomena and Processes::Physical Phenomena::Radiation::Electromagnetic Radiation::Light::Ultraviolet Rays [Medical Subject Headings], UV, 0104 chemical sciences, Autofluorescence, Chemistry, chemistry, Fluorescencia
Abstract

A water soluble diarylethene (DAE) derivative that displays exceptionally intense fluorescence from the colorless open form has been synthesized and characterized using UV/vis spectroscopy and fluorescence microscopy. We show that the bright emission from the open form can be rapidly switched using amplitude modulated red light, that is, by light at wavelengths longer than those absorbed by the fluorescent species. This is highly appealing in any context where undesired background fluorescence disturbs the measurement, e.g., the autofluorescence commonly observed in fluorescence microscopy. We show that this scheme is conveniently applicable using lock-in detection, and that robust amplitude modulation of the probe fluorescence is indeed possible also in cell studies using fluorescence microscopy., A water soluble diarylethene derivative displaying exceptionally bright fluorescence in the open isomeric form has been used for emission amplitude-modulation. We apply this scheme in fluorescence microscopy, aiming to suppress undesired background.

Published
2021

8. Stress-induced tyrosine phosphorylation of RtcB modulates IRE1 activity and signaling outputs

Author

Alexandra Papaioannou, Federica Centonze, Alice Metais, Marion Maurel, Luc Negroni, Matías Gonzalez-Quiroz, Sayyed Jalil Mahdizadeh, Gabriella Svensson, Ensieh Zare, Alice Blondel, Albert C Koong, Claudio Hetz, Rémy Pedeux, Michel L Tremblay, Leif A Eriksson, Eric Chevet, Chemistry, Oncogenesis, Stress and Signaling (COSS), Université de Rennes (UR)-CRLCC Eugène Marquis (CRLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM), CRLCC Eugène Marquis (CRLCC), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Gothenburg (GU), The University of Texas M.D. Anderson Cancer Center [Houston], Universidad de Chile = University of Chile [Santiago] (UCHILE), McGill University = Université McGill [Montréal, Canada], This work was funded by grants from Institut National du Cancer (PLBIO), SIRIC-ILIAD/Cancéropôle Grand Ouest to E Chevet, Fondation pour la Recherche Médicale (équipe labellisée 2018) to E Chevet and R Pedeux, by European Union (EU) H2020 MSCA ITN-675448 (TRAINERS), and MSCA RISE-734749 (INSPIRED) grants to E Chevet and LA Eriksson. The Swedish Research Council (VR) and the Swedish National Infrastructure for Computing are gratefully acknowledged for funding and allocations of computing time at the C3SE and PDC supercomputing centers, respectively (LA Eriksson). A Papaioannou is a Marie Curie early-stage researcher funded by EU H2020 MSCA ITN-675448 (TRAINERS). A Metais was funded by the Fondation ARC pour la recherche contre le cancer. SJ Mahdizadeh was funded by the Vinnova Seal-of-Excellence programme 2019-02205 (CaTheDRA)., and European Project: 675448,H2020,H2020-MSCA-ITN-2015,TRAIN-ERS(2015)

Subjects
X-Box Binding Protein 1, Ribonucleases, Ecology, Health, Toxicology and Mutagenesis, Endoribonucleases, Tyrosine, [SDV.CAN]Life Sciences [q-bio]/Cancer, Plant Science, RNA, Messenger, Phosphorylation, Protein Serine-Threonine Kinases, Biochemistry, Genetics and Molecular Biology (miscellaneous)
Abstract

International audience; ER stress is mediated by three sensors and the most evolutionary conserved IRE1α signals through its cytosolic kinase and endoribonuclease (RNase) activities. IRE1α RNase activity can either catalyze the initial step of XBP1 mRNA unconventional splicing or degrade a number of RNAs through regulated IRE1-dependent decay. Until now, the biochemical and biological outputs of IRE1α RNase activity have been well documented; however, the precise mechanisms controlling whether IRE1α signaling is adaptive or pro-death (terminal) remain unclear. We investigated those mechanisms and hypothesized that XBP1 mRNA splicing and regulated IRE1-dependent decay activity could be co-regulated by the IRE1α RNase regulatory network. We identified that RtcB, the tRNA ligase responsible for XBP1 mRNA splicing, is tyrosine-phosphorylated by c-Abl and dephosphorylated by PTP1B. Moreover, we show that the phosphorylation of RtcB at Y306 perturbs RtcB interaction with IRE1α, thereby attenuating XBP1 mRNA splicing. Our results demonstrate that the IRE1α RNase regulatory network is dynamically fine-tuned by tyrosine kinases and phosphatases upon various stresses and that the extent of RtcB tyrosine phosphorylation determines cell adaptive or death outputs.

Published
2022

9. Structural and molecular bases to IRE1 activity modulation

Author

Nicolas Gouault, Timothy Langlais, Xavier Guillory, Eric Chevet, François Carreaux, Diana Pelizzari-Raymundo, Leif A. Eriksson, Sayyed Jalil Mahdizadeh, Institut des Sciences Chimiques de Rennes (ISCR), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-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), Chemistry, Oncogenesis, Stress and Signaling (COSS), Institut National de la Santé et de la Recherche Médicale (INSERM)-CRLCC Eugène Marquis (CRLCC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), University of Gothenburg (GU), Institut National du Cancer (INCa PLBIO) Institut National du Cancer (INCA) France, Fondation pour la Recherche Medicale (FRM) Fondation pour la Recherche Medicale [DEQ20180339169], ERANET, Agence Nationale de la Recherche (ERAAT) French National Research Agency (ANR), EU European Commission [H2020 MSCA ITN-675448, MSCA RISE-734749], Swedish Research Council (VR) Swedish Research Council [2019-3684], Vinnova Seal-of-Excellence programVinnova [2019-02205], Ecole Doctorale 3M, university of Rennes 1, Region BretagneRegion Bretagne, Fondation ARC pour la recherche sur le cancerFondation ARC pour la Recherche sur le Cancer [PDF20191209830], Vinnova Seal-of-Excellence program Vinnova [2019-02205], Region Bretagne Region Bretagne, Fondation ARC pour la recherche sur le cancer Fondation ARC pour la Recherche sur le Cancer [PDF20191209830], European Project: 675448,H2020,H2020-MSCA-ITN-2015,TRAIN-ERS(2015), European Project: 777657,H2020-EU.1.3.3. - Stimulating innovation by means of cross-fertilisation of knowledge,777657,MSCA-RISE(2018), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Oncogenesis, Stress, Signaling (OSS), Université de Rennes (UR)-CRLCC Eugène Marquis (CRLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM), and CRLCC Eugène Marquis (CRLCC)

Subjects
Protein Folding, RNase P, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, IRE1, Protein Serine-Threonine Kinases, Endoplasmic Reticulum, Biochemistry, 03 medical and health sciences, 0302 clinical medicine, Endoribonucleases, Animals, Homeostasis, Humans, [CHIM]Chemical Sciences, Enzyme Inhibitors, Mode of action, Molecular Biology, 030304 developmental biology, 0303 health sciences, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Kinase, Chemistry, Endoplasmic reticulum, structure activity relationship (SAR), Cell Biology, unfolded protein response, Endoplasmic Reticulum Stress, Transmembrane protein, Cell biology, Cytosol, structure-based drug design (SBDD), 030220 oncology & carcinogenesis, Unfolded protein response, Protein folding, ER stress, Signal Transduction
Abstract

International audience; The Unfolded Protein response is an adaptive pathway triggered upon alteration of endoplasmic reticulum (ER) homeostasis. It is transduced by three major ER stress sensors, among which the Inositol Requiring Enzyme 1 (IRE1) is the most evolutionarily conserved. IRE1 is an ER-resident type I transmembrane protein exhibiting an ER luminal domain that senses the protein folding status and a catalytic kinase and RNase cytosolic domain. In recent years, IRE1 has emerged as a relevant therapeutic target in various diseases including degenerative, inflammatory and metabolic pathologies and cancer. As such several drugs altering IRE1 activity were developed that target either catalytic activity and showed some efficacy in preclinical pathological mouse models. In this review, we describe the different drugs identified to target IRE1 activity as well as their mode of action from a structural perspective, thereby identifying common and different modes of action. Based on this information we discuss on how new IRE1-targeting drugs could be developed that outperform the currently available molecules.

Published
2021

10. Lie–Trotter Splitting for the Nonlinear Stochastic Manakov System

Author

André Berg, Guillaume Dujardin, David Cohen, Umeå University, Department of Mathematical Sciences (Chalmers), Chalmers University of Technology [Göteborg], Systèmes de particules et systèmes dynamiques (Paradyse), Laboratoire Paul Painlevé (LPP), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), This work was partially supported by the Swedish Research Council (VR) (project nr. 2018-04443), FRO the mobility programs of the French Embassy/Institut français de Suède, and INRIA Lille Nord-Europe. G. Dujardin was partially supported by the Labex CEMPI (ANR-11-LABX-0007-01)., ANR-11-LABX-0007,CEMPI,Centre Européen pour les Mathématiques, la Physique et leurs Interactions(2011), Paradyse, and Laboratoire Paul Painlevé - UMR 8524 (LPP)

Subjects
FOS: Physical sciences, Pattern Formation and Solitons (nlin.PS), Stochastic Manakov equation, Convergence rates, Convergence in probability, Coupled system of stochastic nonlinear Schrödinger equations, 01 natural sciences, Almost sure convergence, Theoretical Computer Science, Mathematics - Analysis of PDEs, [NLIN.NLIN-PS]Nonlinear Sciences [physics]/Pattern Formation and Solitons [nlin.PS], Strong convergence, Convergence (routing), FOS: Mathematics, [MATH.MATH-AP]Mathematics [math]/Analysis of PDEs [math.AP], Applied mathematics, Mathematics - Numerical Analysis, 0101 mathematics, Mathematics, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], Numerical Analysis, Applied Mathematics, General Engineering, Stochastic partial differential equations, Order (ring theory), Numerical Analysis (math.NA), Blowup, 65C30, 65C50, 65J08, 60H15, 60M15, 60-08, 35Q55, Lipschitz continuity, Nonlinear Sciences - Pattern Formation and Solitons, 010101 applied mathematics, Stochastic partial differential equation, Numerical schemes, Splitting scheme, Computational Mathematics, Nonlinear system, Computational Theory and Mathematics, Convergence of random variables, Lie–Trotter scheme, Scheme (mathematics), Manakov system, [MATH.MATH-NA]Mathematics [math]/Numerical Analysis [math.NA], Software, Physics - Optics, Analysis of PDEs (math.AP), Optics (physics.optics)
Abstract

This article analyses the convergence of the Lie-Trotter splitting scheme for the stochastic Manakov equation, a system arising in the study of pulse propagation in randomly birefringent optical fibers. First, we prove that the strong order of the numerical approximation is 1/2 if the nonlinear term in the system is globally Lipschitz. Then, we show that the splitting scheme has convergence order 1/2 in probability and almost sure order 1/2- in the case of a cubic nonlinearity. We provide several numerical experiments illustrating the aforementioned results and the efficiency of the Lie-Trotter splitting scheme. Finally, we numerically investigate the possible blowup of solutions for some power-law nonlinearities., Comment: arXiv admin note: text overlap with arXiv:2005.04978

Published
2021

11. Causal effects of lifetime smoking on breast and colorectal cancer risk:Mendelian randomization study

Author

Marc J. Gunter, Inger T. Gram, Elisabete Weiderpass, Hilary A. Tindle, Sun-Seog Kweon, Renée T. Fortner, Rudolf Kaaks, Sarah J Lewis, James Yarmolinsky, Stephen B. Gruber, Marije F. Bakker, Li Hsu, Yi Lin, Neil Murphy, Polly A. Newcomb, Konstantinos K. Tsilidis, Noralane M. Lindor, Rosario Tumino, Gianluca Severi, Hermann Brenner, Emmanouil Bouras, Jane C. Figueiredo, Niki Dimou, Richard M. Martin, Bethany Van Guelpen, María-José Sánchez-Pérez, Centre International de Recherche contre le Cancer - International Agency for Research on Cancer (CIRC - IARC), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Cancerfonden Cancer Research Foundation in Northern Sweden Deutsche Krebshilfe Vetenskapsrådet, VR Australian Lions Childhood Cancer Research Foundation, ALCCRF Knut och Alice Wallenbergs Stiftelse State of Maryland Vetenskapsrådet, VR: VR 2017-00650 Centers for Disease Control and Prevention, CDC Institut National Du Cancer, INCa National Institutes of Health, NIH National Cancer Institute, NCI: P30 CA015704 Centre Hospitalier Universitaire de Nantes, CHU de Nantes Conseil Régional des Pays de la Loire Association Anne de Bretagne Genetique Centre Hospitalier Universitaire de Nantes, CHU de Nantes U.S. Public Health Service, USPHS: HHSN261201500005C U.S. Department of Health and Human Services, HHS National Institutes of Health, NIH National Cancer Institute, NCI National Institute on Aging, NIA: U01 AG18033 Institut National Du Cancer, INCa: P30 CA006973, U01 CA86308 American Institute for Cancer Research, AICR European Commission, EC National Institutes of Health, NIH: R01 CA189184, 2P30CA015704-40, R01 CA207371, U01 CA206110 Matthias Lackas-Stiftung Johns Hopkins University, JHU: HHSN268201200008I National Cancer Institute, NCI National Institutes of Health, NIH: R01 CA143247, R01 CA81488, U01 CA122839, U19 CA148107, U01 CA167551 National Institutes of Health, NIH National Institute of Environmental Health Sciences, NIEHS: T32 ES013678 National Cancer Institute, NCI U.S. Department of Health and Human Services, HHS: R01 CA197350, R01 CA81488, R01 CA201407, P01 CA196569, U19 CA148107, P30 CA014089 Österreichische Forschungsförderungsgesellschaft, FFG: 829675 Instituto de Salud Carlos III, ISCIII European Regional Development Fund, ERDF: PI14-613, PI09-1286 Xarxa de Bancs de Tumors de Catalunya, XBTC: PT13/0010/0013 Generalitat de Catalunya: 2017SGR723 Junta de Castilla y León: LE22A10-2 Agència de Gestió d'Ajuts Universitaris i de Recerca, AGAUR Ministerstvo Zdravotnictví Ceské Republiky, MZCR: AZV 17-30920A, AZV 15-27580A Grantová Agentura České Republiky, GA ČR: CZ GA CR: GAP304/10/1286, 1585 Deutsche Forschungsgemeinschaft, DFG: HO 5117/2-1, BR 1704/6-1, KL 2354/3-1, BR 1704/6-4, BR 1704/6-3, CH 117/1-1, HE 5998/2-1, RO 2270/8-1, BR1704/17-1 Bundesministerium für Bildung und Forschung, BMBF: 01ER0814, 01KH0404, 01ER0815, 01ER1505A, 01ER1505B U01 CA 84968-06 National Cancer Institute, NCI University of Maryland School of Public Health, SPH NIHR Imperial Biomedical Research Centre, BRC Imperial College London NIHR Imperial Biomedical Research Centre, BRC Centre International de Recherche sur le Cancer, CIRC Ministerie van Volksgezondheid, Welzijn en Sport, VWS Deutsche Krebshilfe Cancer Research UK, CRUK: C8221/A29017 Ministerie van Volksgezondheid, Welzijn en Sport, VWS Vetenskapsrådet, VR Ligue Contre le Cancer Bundesministerium für Bildung und Forschung, BMBF Bundesministerium für Bildung und Forschung, BMBF Kræftens Bekæmpelse, DCS Associazione Italiana per la Ricerca sul Cancro, AIRC Instituto de Salud Carlos III, ISCIII Deutsches Krebsforschungszentrum, DKFZ Institut National de la Santé et de la Recherche Médicale, Inserm National Research Council, NRC Institut Gustave-Roussy Deutsches Krebsforschungszentrum, DKFZ Cancerfonden World Cancer Research Fund, WCRF Medical Research Council, MRC: MR/M012190/1 Generalitat de Catalunya: 2017SGR653, 2014SGR135, 2014SGR255, 2017SGR21 SAF2014-54453R, SAF07-64873, SAF 2010-19273 Xunta de Galicia: PGIDIT07PXIB9101209PR Instituto de Salud Carlos III, ISCIII European Regional Development Fund, ERDF: PS09/02368, PI14/00230, 17/00878, PI08/1276, PI17/00509, PI08/0024, PI11/00681, P111/00219, PI14/00173 Xarxa de Bancs de Tumors de Catalunya, XBTC: SLT002/ 16/00398 GCB13131592CAST European Cooperation in Science and Technology, COST: CA17118, BM1206 Deutsche Krebshilfe National Institutes of Health, NIH: K07 CA190673, P01 CA055075, K07CA190673, R35CA197735, U01 CA167552, UM1 CA167552, R01 CA042182, P01 CA087969, R01 CA151993, P50 CA127003, UM1 CA186107, R35 CA197735, R01 CA137178 HCRI15011-1 National Cancer Institute, NCI: R01CA136726 Damon Runyon Cancer Research Foundation, DRCRF: CI-8 Food Standards Agency, FSA Cancer Research UK, CRUK: C588/A19167 VicHealth Cancer Council Victoria National Health and Medical Research Council, NHMRC: 251553, 209057, 509348, 504711 National Institutes of Health, NIH U.S. Department of Health and Human Services, HHS: R01 CA81488 Florida Department of Health: 09BN-13 National Institutes of Health, NIH: R01 CA189184, P30 CA076292 National Institutes of Health, NIH: P30 DK034987, R01 CA66635 18226, 18223 Canadian Institutes of Health Research, CIHR: CRT 43821 National Institutes of Health, NIH U.S. Department of Health and Human Services, HHS: U01 CA74783 Cancerfonden Cancer Research Foundation, CRF Vetenskapsrådet, VR Australian Lions Childhood Cancer Research Foundation, ALCCRF Canadian Cancer Society National Institutes of Health, NIH: U01/ U24 CA074783, U01 CA167551 Pelotonia CA16058, CA67941 Canadian Institutes of Health Research, CIHR: 112746 Ontario Research Foundation, ORF: GL201-043 National Cancer Institute, NCI U.S. Department of Health and Human Services, HHS: U01 HG004446, GEI U01 HG 004438, Z01 CP 010200 Division of Cancer Epidemiology and Genetics, National Cancer Institute, DCEG Institut National Du Cancer, INCa National Institutes of Health, NIH Division of Cancer Prevention, National Cancer Institute, DCP, NCI National Institutes of Health, NIH: U24 CA074794, U01 CA074794, R01 CA076366, U01 CA167551 National Cancer Institute, NCI National Institutes of Health, NIH: UM1 CA182883, U10 CA37429 National Cancer Institute, NCI Institut National Du Cancer, INCa: R03 CA153323, P01 CA074184, K05 CA152715, R01 CA097325 National Institutes of Health, NIH: KL2 TR000421 National Center for Advancing Translational Sciences, NCATS Stockholms Läns Landsting Vetenskapsrådet, VR: K2015-55X-22674-01-4, K2008-55X-20157-03-3, K2006-72X-20157-01-2 Karolinska Institutet, KI National Institutes of Health, NIH: K05 CA154337 Swedish Cancer Foundation National Heart, Lung, and Blood Institute, NHLBI National Institutes of Health, NIH U.S. Department of Health and Human Services, HHS: HHSN268201100004C, HHSN268201100003C, HHSN268201100001C, HHSN271201100004C, HHSN268201100046C, HHSN268201100002C, R.M. Martin reports grants from Cancer Research UK during the conduct of the study. R.T. Fortner reports that grants from German Cancer Aid and from German Ministry of Education and Research supported the conduct of EPIC Heidelberg. S.B. Gruber reports other from Brogent International LLC outside the submitted work. B. van Guelpen reports grants from Swedish Research Council, Swedish Cancer Society, Knut and Alice Wallenberg Foundation, Lion’s Cancer Research Foundation at Umea° University, and Cancer Research Foundation in Northern Sweden during the conduct of the study. No disclosures were reported by the other authors., CLUE: We appreciate the continued efforts of the staff members at the Johns Hopkins George W. Comstock Center for Public Health Research and Prevention in the conduct of the CLUE II study. We thank the participants in CLUE. Cancer incidence data for CLUE were provided by the Maryland Cancer Registry, Center for Cancer Surveillance and Control, Maryland Department of Health, 201 W. Preston Street, Room 400, Baltimore, MD 21201, http://phpa.dhmh.maryland.gov/cancer, 410-767-4055. We acknowledge the State of Maryland, the Maryland Cigarette Restitution Fund, and the National Program of Cancer Registries of the Centers for Disease Control and Prevention for the funds that support the collection and availability of the cancer registry data., CPS-II: The authors thank the CPS-II participants and Study Management Group for their invaluable contributions to this research. The authors would also like to acknowledge the contribution to this study from central cancer registries supported through the Centers for Disease Control and Prevention National Program of Cancer Registries, and cancer registries supported by the National Cancer Institute Surveillance Epidemiology and End Results program., NSHDS investigators thank the Biobank Research Unit at Umea° University, the V€asterbotten Intervention Programme, the Northern Sweden MONICA study and Region V€asterbotten for providing data and samples and acknowledge the contribution from Biobank Sweden, supported by the Swedish Research Council (VR 2017-00650)., Cancer incidence data have been provided by the District of Columbia Cancer Registry, Georgia Cancer Registry, Hawaii Cancer Registry, Minnesota Cancer Surveillance System, Missouri Cancer Registry, Nevada Central Cancer Registry, Pennsylvania Cancer Registry, Texas Cancer Registry, Virginia Cancer Registry, and Wisconsin Cancer Reporting System. All are supported in part by funds from the Center for Disease Control and Prevention, National Program for Central Registries, local states or by the National Cancer Institute, Surveillance, Epidemiology, and End Results program. The results reported here and the conclusions derived are the sole responsibility of the authors., Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO): National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services (U01 CA137088, R01 CA059045, R01CA201407). This research was funded in part through the NIH/NCI Cancer Center Support Grant P30 CA015704., ASTERISK: a Hospital Clinical Research Program (PHRC-BRD09/C) from the University Hospital Center of Nantes (CHU de Nantes) and supported by the Regional Council of Pays de la Loire, the Groupement des EntreprisesFranc¸aises dans la Luttecontre le Cancer (GEFLUC), the Association Anne de Bretagne Génétique and the Ligue RégionaleContre le Cancer (LRCC)., The ATBC Study is supported by the Intramural Research Program of the U.S. National Cancer Institute, National Institutes of Health, and by U.S. Public Health Service contract HHSN261201500005C from the National Cancer Institute, Department of Health and Human Services., CLUE funding was from the National Cancer Institute (U01 CA86308, Early Detection Research Network, and P30 CA006973), National Institute on Aging (U01 AG18033), and the American Institute for Cancer Research. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the US government. COLO2&3: NIH (R01 CA60987).

Subjects
Male, 0301 basic medicine, Oncology, medicine.medical_specialty, Epidemiology, medicine.drug_class, Colorectal cancer, Breast Neoplasms, Article, 03 medical and health sciences, 0302 clinical medicine, Breast cancer, Risk Factors, Internal medicine, Mendelian randomization, Genetic predisposition, Humans, Medicine, Risk factor, 11 Medical and Health Sciences, business.industry, Smoking, Odds ratio, Mendelian Randomization Analysis, medicine.disease, Confidence interval, 3. Good health, Causality, 030104 developmental biology, Estrogen, 030220 oncology & carcinogenesis, Female, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, ICEP, Colorectal Neoplasms, business, Genome-Wide Association Study
Abstract

Background: Observational evidence has shown that smoking is a risk factor for breast and colorectal cancer. We used Mendelian randomization (MR) to examine causal associations between smoking and risks of breast and colorectal cancer. Methods: Genome-Wide Association Study summary data were used to identify genetic variants associated with lifetime amount of smoking (n = 126 variants) and ever having smoked regularly (n = 112 variants). Using two-sample MR, we examined these variants in relation to incident breast (122,977 cases/105,974 controls) and colorectal cancer (52,775 cases/45,940 controls). Results: In inverse-variance weighted models, a genetic predisposition to higher lifetime amount of smoking was positively associated with breast cancer risk [OR per 1-SD increment: 1.13; 95% confidence interval (CI): 1.00–1.26; P = 0.04]; although heterogeneity was observed. Similar associations were found for estrogen receptor–positive and estrogen receptor–negative tumors. Higher lifetime amount of smoking was positively associated with colorectal cancer (OR per 1-SD increment, 1.21; 95% CI, 1.04–1.40; P = 0.01), colon cancer (OR, 1.31; 95% CI, 1.11–1.55; P < 0.01), and rectal cancer (OR, 1.36; 95% CI, 1.07–1.73; P = 0.01). Ever having smoked regularly was not associated with risks of breast (OR, 1.01; 95% CI, 0.90–1.14; P = 0.85) or colorectal cancer (OR, 0.97; 95% CI, 0.86–1.10; P = 0.68). Conclusions: These findings are consistent with prior observational evidence and support a causal role of higher lifetime smoking amount in the development of breast and colorectal cancer. Impact: The results from this comprehensive MR analysis indicate that lifetime smoking is a causal risk factor for these common malignancies.

Published
2021

12. Atlas Optimization for Deep Brain Stimulation

Author

Vogel, Dorian, Wårdell, Karin, Coste, Jerome, Lemaire, Jean-Jacques, Hemm, Simone, Institute for Medical and Analytical Technologies, School of Life Sciences (IMAT), University of Applied Sciences and Arts Northwestern Switzerland (HES-SO), Department of Biomedical Engineering [Linköping], Linköping University (LIU), Institut Pascal (IP), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)-Institut national polytechnique Clermont Auvergne (INP Clermont Auvergne), Université Clermont Auvergne (UCA)-Université Clermont Auvergne (UCA), Service de Neurochirurgie [CHU Clermont-Ferrand], CHU Gabriel Montpied [Clermont-Ferrand], CHU Clermont-Ferrand-CHU Clermont-Ferrand, This work was financially supported by the Swedish Foundation for Strategic Research (SSF BD15-0032), Swedish Research Council (VR 2016-03564), and the University of Applied Sciences and Arts Northwestern Switzerland (FHNW)., Service de Neurochirurgie [Clermont-Ferrand], CHU Clermont-Ferrand-CHU Gabriel Montpied [Clermont-Ferrand], and CHU Clermont-Ferrand

Subjects
Registration, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Patient normalization, Optimisation, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Atlas, [SDV.MHEP.CHI]Life Sciences [q-bio]/Human health and pathology/Surgery, Deep Brain Stimulation (DBS), Movement disorders, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing
Abstract

International audience; Electrical stimulation of the deep parts of the brain is the standard answer for patients subject to drug-refractory movement disorders. Collective analysis of data collected during surgeries are crucial in order to provide more systematic planning assistance and understanding the physiological mechanisms of action. To that end, the process of normalizing anatomies captured with Magnetic Resonance imaging across patients is a key component. In this work, we present the optimization of a workflow designed to create group-specific anatomical templates: a group template is refined iteratively using the results of successive non-linear image registrations with refinement steps in the in the basal-ganglia area. All non-linear registrations were executed using the Advanced Normalization Tools (ANTs) and the quality of the nor-malization was measured using spacial overlap of anatomical structures manually delineated during the planning of the surgery. The parameters of the workflow evaluated were: the use of multiple modalities sequentially or together during each registration to the template, the number of iterations in the template creation and the fine settings of the non-linear registration tool. Using the T1 and white matter attenuated inverse recovery modalities (WAIR) together produced the best results, especially in the center of the brain. The optimal numbers of iterations of the template creation were higher than those from the literature and our previous works. Finally, the setting of the non-linear registration tool that improved results the most was the activation of the registration with the native voxel sizes of images, as opposed to down-sampled version of the images. The normalization process was optimized over our previous study and allowed to obtain the best possible anatomical nor-malization of this specific group of patient. It will be used to summarize and analyze peri-operative measurements during test stimulation. The aim is that the conclusions obtained from this analysis will be useful for assistance during the planning of new surgeries.

Published
2021

13. A functional connection between translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae

Author

Rodríguez-Galán, Olga, García-Gómez, Juan J, Rosado, Iván V, Wei, Wu, Méndez-Godoy, Alfonso, Pillet, Benjamin, Alekseenko, Alisa, Steinmetz, Lars M, Pelechano, Vicent, Kressler, Dieter, de la Cruz, Jesús, Ministerio de Economía y Competitividad (España), European Commission, Swiss National Science Foundation, Ragnar Söderberg Foundation, Swedish Research Council, Wallenberg Academy, Karolinska Institute, National Key Research and Development Program (China), National Natural Science Foundation of China, National Institutes of Health (US), German Research Foundation, European Research Council, University of Fribourg, Universidad de Sevilla. Departamento de Genética, [Rodríguez-Galán,O, García-Gómez,JJ, Rosado,IV, de la Cruz,J] Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain. [Rodríguez-Galán,O, de la Cruz,J] Departamento de Genetica, Universidad de Sevilla, Seville, Spain. [Wei,W, Steinmetz,LM] Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA. [Wei,W] CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. [Méndez-Godoy,A, Pillet,B, Kressler,D] Unit of Biochemistry, Department of Biology, University of Fribourg, Fribourg, Switzerland. [Alekseenko,A, Pelechano,V] SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden. [Steinmetz,LM] European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany. [Steinmetz,LM] Department of Genetics, School of Medicine, Stanford, CA, USA., Spanish Ministry of Economy and Competitiveness (MINECO), European Regional Development Fund (ERDF) [BFU2016-75352-P, PID2019-103850-GB-I00 to J.d.l.C.], Swiss National Science Foundation [31003A_156764, 31003A_175547 to D.K.], Swedish Research Council [VR 2016-01842], Wallenberg Academy [fellowship KAW 2016.0123], Karolinska Institutet (SFO SciLifeLab fellowship, KID and KI funds) (to V.P.), National Key R&D Program of China [2017YFC0908405], National Natural Science Foundation of China [81870187 to W.W.], US National Institutes of Health (NIH) [P01 HG000205], German Research Foundation (DFG) [1422/4-1], European Research Council (ERC Advanced Investigator Grant) (to L.M.S.), J.J.G.-G. was recipient of a FPI fellowship from MINECO, and Funding for open access charge: SNSF or University of Fribourg.

Subjects
Diseases::Nutritional and Metabolic Diseases::Metabolic Diseases::Proteostasis Deficiencies [Medical Subject Headings], Ribosomal Proteins, Protein Folding, Chemicals and Drugs::Amino Acids, Peptides, and Proteins::Proteins::Molecular Chaperones [Medical Subject Headings], Saccharomyces cerevisiae Proteins, Anatomy::Cells::Cellular Structures::Intracellular Space::Cytoplasm::Cytoplasmic Structures::Organelles::Ribosomes [Medical Subject Headings], Phenomena and Processes::Chemical Phenomena::Biochemical Phenomena::Biochemical Processes::Peptide Biosynthesis::Protein Biosynthesis::Peptide Chain Elongation, Translational [Medical Subject Headings], AcademicSubjects/SCI00010, Chemicals and Drugs::Amino Acids, Peptides, and Proteins::Proteins::Ribosomal Proteins [Medical Subject Headings], Chemicals and Drugs::Amino Acids, Peptides, and Proteins::Proteins::Fungal Proteins::Saccharomyces cerevisiae Proteins [Medical Subject Headings], Chemicals and Drugs::Enzymes and Coenzymes::Enzymes::Transferases::Acyltransferases::Aminoacyltransferases::Peptidyl Transferases [Medical Subject Headings], Mutation, Missense, Peptide Chain Elongation, Translational, Saccharomyces cerevisiae, Chemicals and Drugs::Chemical Actions and Uses::Specialty Uses of Chemicals::Solvents [Medical Subject Headings], Phenomena and Processes::Physical Phenomena::Biophysical Phenomena::Biophysical Processes::Protein Folding [Medical Subject Headings], Chemicals and Drugs::Amino Acids, Peptides, and Proteins::Proteins::Recombinant Proteins [Medical Subject Headings], Loss of Function Mutation, Chemicals and Drugs::Amino Acids, Peptides, and Proteins::Peptides [Medical Subject Headings], Point Mutation, Organisms::Eukaryota::Fungi::Ascomycota::Saccharomycetales::Saccharomyces::Saccharomyces cerevisiae [Medical Subject Headings], Chaperonas moleculares, Phenomena and Processes::Genetic Phenomena::Genetic Structures::Genome::Genome Components::Genes::Alleles [Medical Subject Headings], Alleles, Chemicals and Drugs::Macromolecular Substances::Multiprotein Complexes [Medical Subject Headings], Mutación, Pliegue de proteína, Gene regulation, Chromatin and Epigenetics, Chemicals and Drugs::Nucleic Acids, Nucleotides, and Nucleosides::Nucleic Acids::RNA::RNA, Messenger [Medical Subject Headings], Recombinant Proteins, Phenomena and Processes::Genetic Phenomena::Genetic Variation::Mutation::Mutation, Missense [Medical Subject Headings], Multiprotein Complexes, Mutation, Peptidyl Transferases, Proteostasis, Ribosomas, Proteínas de saccharomyces cerevisiae, Phenomena and Processes::Genetic Phenomena::Genetic Variation::Mutation::Point Mutation [Medical Subject Headings], Alelos, Ribosomes, Molecular Chaperones
Abstract

Proteostasis needs to be tightly controlled to meet the cellular demand for correctly de novo folded proteins and to avoid protein aggregation. While a coupling between translation rate and co-translational folding, likely involving an interplay between the ribosome and its associated chaperones, clearly appears to exist, the underlying mechanisms and the contribution of ribosomal proteins remain to be explored. The ribosomal protein uL3 contains a long internal loop whose tip region is in close proximity to the ribosomal peptidyl transferase center. Intriguingly, the rpl3[W255C] allele, in which the residue making the closest contact to this catalytic site is mutated, affects diverse aspects of ribosome biogenesis and function. Here, we have uncovered, by performing a synthetic lethal screen with this allele, an unexpected link between translation and the folding of nascent proteins by the ribosome-associated Ssb-RAC chaperone system. Our results reveal that uL3 and Ssb-RAC cooperate to prevent 80S ribosomes from piling up within the 5′ region of mRNAs early on during translation elongation. Together, our study provides compelling in vivo evidence for a functional connection between peptide bond formation at the peptidyl transferase center and chaperone-assisted de novo folding of nascent polypeptides at the solvent-side of the peptide exit tunnel., Spanish Ministry of Economy and Competitiveness (MINECO); European Regional Development Fund (ERDF) [BFU2016-75352-P, PID2019-103850-GB-I00 to J.d.l.C.]; Swiss National Science Foundation [31003A_156764, 31003A_175547 to D.K.]; Ragnar Söderberg Foundation; Swedish Research Council [VR 2016-01842]; Wallenberg Academy [fellowship KAW 2016.0123]; Karolinska Institutet (SFO SciLifeLab fellowship, KID and KI funds) (to V.P.); National Key R&D Program of China [2017YFC0908405]; National Natural Science Foundation of China [81870187 to W.W.]; US National Institutes of Health (NIH) [P01 HG000205]; German Research Foundation (DFG) [1422/4-1]; European Research Council (ERC Advanced Investigator Grant) (to L.M.S.); J.J.G.-G. was recipient of a FPI fellowship from MINECO; Funding for open access charge: SNSF or University of Fribourg.

Published
2021

14. From NiMoO 4 to γ-NiOOH: Detecting the Active Catalyst Phase by Time Resolved in Situ and Operando Raman Spectroscopy

Author

Pierfrancesco Maltoni, Robin N. Dürr, Bruno Jousselme, Haining Tian, Leif Hammarström, Tomas Edvinsson, Uppsala University, Laboratoire Innovation en Chimie des Surfaces et NanoSciences (LICSEN UMR 3685), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Departement of engineering sciences, the Angstrom Laboratory, the Swedish Research Council (VR) Grant 2015-03814, European Project: 765376,eSCALED, Department of Chemistry – Ångström Laboratory, UPPSALA University, Box 538, 75120, Uppsala, Sweden, Laboratoire Innovation en Chimie des Surfaces et NanoSciences (LICSEN), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut Rayonnement Matière de Saclay (IRAMIS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)

Subjects
Materials science, General Physics and Astronomy, chemistry.chemical_element, Materialkemi, 02 engineering and technology, engineering.material, nickel molybdate, 010402 general chemistry, Electrocatalyst, 01 natural sciences, 7. Clean energy, Physical Chemistry, Article, Catalysis, time-resolved operando Raman spectroscopy, symbols.namesake, Phase (matter), nanostructures, Materials Chemistry, electrocatalysis, General Materials Science, molybdenum leaching, Fysikalisk kemi, General Engineering, Oxygen evolution, in situ catalyst formation, [CHIM.MATE]Chemical Sciences/Material chemistry, [CHIM.CATA]Chemical Sciences/Catalysis, 021001 nanoscience & nanotechnology, 0104 chemical sciences, Chemical engineering, chemistry, 13. Climate action, Molybdenum, symbols, engineering, alkaline water splitting, Noble metal, Nanorod, Additions and Corrections, 0210 nano-technology, Raman spectroscopy
Abstract

Water electrolysis powered by renewable energies is a promising technology to produce sustainable fossil free fuels. The development and evaluation of effective catalysts are here imperative; however, due to the inclusion of elements with different redox properties and reactivity, these materials undergo dynamical changes and phase transformations during the reaction conditions. NiMoO4 is currently investigated among other metal oxides as a promising noble metal free catalyst for the oxygen evolution reaction. Here we show that at applied bias, NiMoO4·H2O transforms into γ-NiOOH. Time resolved operando Raman spectroscopy is utilized to follow the potential dependent phase transformation and is collaborated with elemental analysis of the electrolyte, confirming that molybdenum leaches out from the as-synthesized NiMoO4·H2O. Molybdenum leaching increases the surface coverage of exposed nickel sites, and this in combination with the formation of γ-NiOOH enlarges the amount of active sites of the catalyst, leading to high current densities. Additionally, we discovered different NiMoO4 nanostructures, nanoflowers, and nanorods, for which the relative ratio can be influenced by the heating ramp during the synthesis. With selective molybdenum etching we were able to assign the varying X-ray diffraction (XRD) pattern as well as Raman vibrations unambiguously to the two nanostructures, which were revealed to exhibit different stabilities in alkaline media by time-resolved in situ and operando Raman spectroscopy. We advocate that a similar approach can beneficially be applied to many other catalysts, unveiling their structural integrity, characterize the dynamic surface reformulation, and resolve any ambiguities in interpretations of the active catalyst phase. Addition/correction: This article has been corrected. Correction in: ACS Nano 2021, 15, 12, 20693-20693. DOI: 10.1021/acsnano.1c10145Title in Web of Science: From NiMoO4 to gamma-NiOOH: Detecting the Active Catalyst Phase by Time Resolved in Situ and Operando Raman Spectroscopy

Published
2021

15. Optimization of group-specific template generation for deep brain stimulation

Author

Dorian Vogel, Ashesh Shah, Jérôme Coste, Jean-Jacques Lemaire, Karin Wårdell, Simone Hemm, Linköping University (LIU), University of Applied Sciences and Arts Northwestern Switzerland (FHNW), CHU Clermont-Ferrand, Institut Pascal (IP), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)-Institut national polytechnique Clermont Auvergne (INP Clermont Auvergne), Université Clermont Auvergne (UCA)-Université Clermont Auvergne (UCA), This work was financially supported by the Swedish Foundation for Strategic Research (SSF BD15-0032), Swedish Research Council (VR 2016-03564), and the University of Applied Sciences and Arts Northwestern Switzerland (FHNW)., and Coste, Jérôme

Subjects
[SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, [SDV.NEU.NB] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, [INFO.INFO-IM] Computer Science [cs]/Medical Imaging, [INFO.INFO-IM]Computer Science [cs]/Medical Imaging, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2020

16. A Survey on the Fine-grained Complexity of Constraint Satisfaction Problems Based on Partial Polymorphisms

Author

Miguel Couceiro, Lucien Haddad, Victor Lagerkvist, Knowledge representation, reasonning (ORPAILLEUR), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Natural Language Processing & Knowledge Discovery (LORIA - NLPKD), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Royal Military College of Canada, Department of Computer and Information Science - Linköping University, Linköping University (LIU), and We thank the anonymous reviewer for several helpful comments. The third author is partially supported by the Swedish Research Council (VR) under grant 2019-03690.

Subjects
TheoryofComputation_MATHEMATICALLOGICANDFORMALLANGUAGES, ComputingMethodologies_SYMBOLICANDALGEBRAICMANIPULATION, [INFO]Computer Science [cs], Computer Science::Computational Complexity, [MATH]Mathematics [math]
Abstract

International audience; Constraint satisfaction problems (CSPs) are combinatorial problems with strong ties to universal algebra and clone theory. The recently proved CSP dichotomy theorem states that each finite-domain CSP is either solvable in polynomial time, or that it is NP-complete. However, among the intractable CSPs there is a seemingly large variance in how fast they can be solved by exponential-time algorithms, which cannot be explained by the classical algebraic approach based on polymorphisms. In this contribution we will survey an alternative approach based on partial polymorphisms, which is useful for studying the fine-grained complexity of NP-complete CSPs. Moreover, we will state and discuss some challenging open problems in this research field.

Published
2020

17. A cell fitness selection model for neuronal survival during development

Author

Wang, Yiqiao, Wu, Haohao, Fontanet, Paula, Codeluppi, Simone, Akkuratova, Natalia, Petitpré, Charles, Xue-Franzén, Yongtao, Niederreither, Karen, Sharma, Anil, Da Silva, Fabio, Comai, Glenda, Agirman, Gulistan, Palumberi, Domenico, Linnarsson, Sten, Adameyko, Igor, Moqrich, Aziz, Schedl, Andreas, La Manno, Gioele, Hadjab, Saida, Lallemend, François, Karolinska Institutet [Stockholm], Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Valrose (IBV), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Cellules Souches et Développement / Stem Cells and Development, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Swedish Research Council (VR), the Ragnar Söderberg Foundation, Knut and Alice Wallenberg Foundation, Swedish Brain Foundation, Karolinska Institutet, the Karolinska Institutet Strategic Research program in Neuroscience (StratNeuro), the Ming Wai Lau Foundation and Åke Wiberg Foundation (F.L.), by RARENET V No. 1.7 EU Regional Development Fund, University of Strasbourg Institute of Advanced Studies (USIAS) (K.N.), and by ERC (BRAINCELL grant 261063), VR, the Wellcome Trust (grant 108726/Z/15/Z), and the EU (FP7/DDPDGENES), ANR-17-CE16-0020,Myochronic,Etude des mécanismes moléculaires qui sous-tendent la chronicisation de la douleur. Ce qu'une Myosine non conventionnelle nous apprend(2017), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)

Subjects
nervous-system, animal structures, Sensory Receptor Cells, Cell Survival, Science, Tretinoin, Chick Embryo, Models, Biological, Article, death, expression, trkc, Animals, Receptor, trkC, gene, lcsh:Science, [SDV.BDD]Life Sciences [q-bio]/Development Biology, mouse, dorsal-root-ganglia, Cell Death, Neurotrophic factors, differentiation, Proprioception, Mice, Inbred C57BL, Core Binding Factor Alpha 3 Subunit, sensory neurons, nervous system, retinoic acid synthesis, Neuronal development, lcsh:Q, Signal Transduction
Abstract

Developmental cell death plays an important role in the construction of functional neural circuits. In vertebrates, the canonical view proposes a selection of the surviving neurons through stochastic competition for target-derived neurotrophic signals, implying an equal potential for neurons to compete. Here we show an alternative cell fitness selection of neurons that is defined by a specific neuronal heterogeneity code. Proprioceptive sensory neurons that will undergo cell death and those that will survive exhibit different molecular signatures that are regulated by retinoic acid and transcription factors, and are independent of the target and neurotrophins. These molecular features are genetically encoded, representing two distinct subgroups of neurons with contrasted functional maturation states and survival outcome. Thus, in this model, a heterogeneous code of intrinsic cell fitness in neighboring neurons provides differential competitive advantage resulting in the selection of cells with higher capacity to survive and functionally integrate into neural networks., Programmed cell death is an important part of tissue development, and traditionally it is considered that neuronal death is a stochastic process in response to neurotrophic factor deprivation. Here the authors show that for TrkC+ proprioreceptors, which neurons die is predetermined molecularly by how much TrkC is present, as well as by a gene expression signature.

Published
2019

18. Increasing Access to Science and Engineering—the Role of Multimodality

Author

John Airey, Zachary Simpson, and Swedish Research Council VR 2016-04113

Subjects
050101 languages & linguistics, Other Physics Topics, Science and engineering, 05 social sciences, Perspective (graphical), Didactics, Equity (finance), 050301 education, engineering education, Annan fysik, Didaktik, Science education, access to science, Multimodality, multimodality, equity, science education, Engineering education, 0501 psychology and cognitive sciences, Engineering ethics, Sociology, lcsh:L, 0503 education, lcsh:Education
Abstract

The idea for this special issue of Designs for Learning emerged during the 8th International Conference on Multimodality (8ICOM), held in Cape Town in December 2016. During that conference, a special stream of papers was organised, all of which addressed the question of science and/or engineering teaching from a multimodal perspective. In this editorial we discuss the issue of multimodal access to science and engi- neering and introduce the papers in the special issue.

Published
2019

19. Unpacking the Hertzsprung-Russell Diagram: A Social Semiotic Analysis of the Disciplinary and Pedagogical Affordances of a Central Resource in Astronomy

Author

John Airey, Urban Eriksson, and Swedish Research Council VR 2016-04113

Subjects
Unpacking, Other Physics Topics, Astronomy education, Social semiotics, Representation (arts), Disciplinary learning, Disciplinary affordance, Pedagogical affordance, Graphs, Resource (project management), Astronomi, astrofysik och kosmologi, Semiotics, Astronomy, Astrophysics and Cosmology, Sociology, Affordance, Counterintuitive, Didactics, Annan fysik, Didaktik, undergraduate physics, Epistemology, semiotics, lcsh:L, Discipline, lcsh:Education
Abstract

In this paper we are interested in the relationship between disciplinary knowledge and its representation. We carry out a social semiotic analysis of a central tool used in astronomy—the Hertzsprung-Russell (H-R) diagram—in order to highlight its disciplinary and pedagogical affordances. By analysing the relationship between disciplinary knowledge and its representation in this way we claim that it becomes possible to identify potential barriers to student learning—instances where semiotic resources with high disciplinary affordance have low pedagogical affordance for newcomers to the discipline. The astronomy resource that we have chosen to analyse has played a pivotal role in our understanding of stellar evolution and as such it features prominently on all undergraduate astronomy programs. However, like most disciplinary-specific semiotic resources, today’s H-R diagram is the culmination of many years of work by numerous disciplinary experts. Over time, the H-R diagram has been revised and reworked by a number of different actors in order to reconcile it with developing observational and theoretical advances. As a consequence, the H-R diagram that we know today combines many layers of astronomical knowledge, whilst still retaining some rather quirky traces of its historical roots. In this paper we adopt a social semiotic lens to analyse these ‘layers of knowledge’ and ‘historical anomalies’ showing how they have resulted in a number of counterintuitive aspects within the diagram that have successively lowered its pedagogical affordance. We claim that the counterintuitive aspects we identify in our analysis give rise to potential barriers to student disciplinary learning. Using our analysis as a case study, we generalise our findings suggesting four types of barrier to understanding that are potentially at work when meeting disciplinary-specific semiotic resources for the first time. We finish the paper by making some general suggestions about the wider use of our analysis method and ways of dealing with any barriers to learning identified. In the specific case of the H-R diagram, we suggest that lecturers should explicitly tease out its disciplinary affordances by the use of ‘unpacked’ resources that have a higher pedagogical affordance.

Published
2019

20. Advances in therapeutic applications of extracellular vesicles

Author

Oscar P. B. Wiklander, Jan Lötvall, Meadhbh Á. Brennan, Xandra O. Breakefield, Samir El Andaloussi, Karolinska Institutet [Stockholm], Evox Therapeutics Limited, Partenaires INRAE, Sarcomes osseux et remodelage des tissus calcifiés - Phy-Os [Nantes - INSERM U1238] (Phy-Os), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Bretagne Loire (UBL)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN), Harvard John A. Paulson School of Engineering and Applied Sciences (SEAS), Harvard University [Cambridge], Massachusetts General Hospital [Boston], Harvard Medical School [Boston] (HMS), M.A.B. was supported by Marie Skłodowska Curie Individual Fellowship PARAGEN H2020-MSCA-IF-2015-708711. J.L. was supported by the Swedish Cancer Foundation (Dnr 2014/844 and 2017/739), the Swedish Heart and Lung Foundation (Dnr 20150588), the Swedish Research Council (Dnr 2016-02854), and the VBG Group Herman Krefting Foundation for Asthma and Allergy Research. X.O.B. was supported by NIH NCI grants U19 CA179563, P01 CA069246, and R35 CA232103-01. S.EL.A. was supported by Swedish Research Council (VR-Med) and Swedish Strategic Science Foundation (SSF-IRC)., Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Bretagne Loire (UBL)-Centre hospitalier universitaire de Nantes (CHU Nantes), and brennan, meadhbh

Subjects
[SDV]Life Sciences [q-bio], medicine.medical_treatment, Cell, Bioengineering, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Extracellular vesicles, Article, Extracellular Vesicles, 03 medical and health sciences, Drug Delivery Systems, 0302 clinical medicine, medicine, Animals, Humans, Disease, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, 030304 developmental biology, 0303 health sciences, Chemistry, Vesicle, General Medicine, Stem-cell therapy, Immunotherapy, Immune modulation, Cell biology, [SDV] Life Sciences [q-bio], medicine.anatomical_structure, 030220 oncology & carcinogenesis, Function (biology), Intracellular
Abstract

International audience; Extracellular vesicles (EVs) are nanometer-sized, lipid membrane-enclosed vesicles secreted by most, if not all, cells and contain lipids, proteins, and various nucleic acid species of the source cell. EVs act as important mediators of intercellular communication that influence both physiological and pathological conditions. Given their ability to transfer bioactive components and surmount biological barriers, EVs are increasingly being explored as potential therapeutic agents. EVs can potentiate tissue regeneration, participate in immune modulation, and function as potential alternatives to stem cell therapy, and bioengineered EVs can act as delivery vehicles for therapeutic agents. Here, we cover recent approaches and advances of EV-based therapies.

Published
2019

21. Evidence for molecular structural variations in the cytoarchitectures of a Jurassic plant

Author

Vivi Vajda, Anders Engdahl, Martin J. Whitehouse, Yuangao Qu, Nicola McLoughlin, Mark A. van Zuilen, Institute of Deep-Sea Science and Engineering [Chinese Academy of Sciences] [Sanya] (IDSSE), Chinese Academy of Sciences [Beijing] (CAS), Swedish Museum of Natural History, 114 18 Stockholm, Sweden, Department of Geology, Rhodes University, Grahamstown 6139, South Africa, Albany Museum, Grahamstown 6139, South Africa, Institut de Physique du Globe de Paris (IPGP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-IPG PARIS-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), MAX IV Laboratory, Lund University, SE-221 00 Lund, Sweden, Department of Earth and Ecosystem Sciences [Lund], Lund University [Lund], and This project is financially supported by the National Key R&D Program of China (2018YFC0309800), the Hundred Talent Program C of China (Y810011BRC), the Swedish Research Council (VR 2015-04264), the Bergen Research Foundation (Norway), the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement 646894), and the Department of Science and Technology–National Research Foundation Centre for Excellence in Palaeosciences at the University of Witwatersrandthe (South Africa). The NordSIM laboratory at the Swedish Museum of Natural History is a Vetenskapsrådet (VR)-funded research infrastructure, of which this is publication 593. We highly appreciate the technical assistance of the University of Bergen, the Institut de Physique du Globe de Paris, the MAX Lab at Lund University, and the NordSIM lab. Many thanks to Gang Lü for helping us with data processing, and to the Botanical Garden in Lund for providing extant royal fern samples

Subjects
Sweden, Permineralization, Taphonomy, 010504 meteorology & atmospheric sciences, biology, Osmunda, Lineage (evolution), Osmundaceae, Annan geovetenskap och miljövetenskap, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Geology, 010502 geochemistry & geophysics, biology.organism_classification, 01 natural sciences, Fossilization, Geochemistry, Evolutionary biology, [SDU]Sciences of the Universe [physics], Organelle, Fern, Mitosis, 0105 earth and related environmental sciences, Osmunda regalis, Other Earth and Related Environmental Sciences
Abstract

In this study, we investigate the molecular structural characteristics of organic remains in various cellular organelles from a 180 Ma Jurassic royal fern belonging to the Osmundaceae family of ferns, and compare their carbon isotopic compositions to a now-living species of royal fern (Osmunda regalis). We discovered molecular structural variations indicated by Raman and infrared spectral parameters obtained from various fossilized cellular organelles. The organic remains preserved in the chromosomes and cell nuclei show marked structural heterogeneities compared to the cell walls during different stages of the cell cycle. The fossil and extant fern have similar δ13C values obtained from bulk samples, supporting evolutionary stasis in this plant lineage and an unchanged metabolic pathway of carbon assimilation since the Jurassic. The organic remains in the cellular organelles of the fossil seem to be less heterogeneous than those in the extant fern, likely due to the preferential preservation of certain cellular compounds during fossilization. Taphonomic processes appear to have diminished the subcellular isotopic heterogeneities. Our research sheds light on the functioning of ancient plant cellular organelles during mitosis, provides insights to the taphonomic processes operating at molecular and isotopic levels, and shows the practicability of in situ techniques in studying the evolution and behaviors of ancient cells. This project is also financially supported by the National Key R&D Program of China (2018YFC0309800), the Hundred Talent Program C of China (Y810011BRC), the Swedish Research Council (VR 2015-04264), the Bergen Research Foundation (Norway), the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement 646894), and the Department of Science and Technology–National Research Foundation Centre for Excellence in Palaeosciences at the University of Witwatersrandthe (South Africa). The NordSIM laboratory at the Swedish Museum of Natural History is a Vetenskapsrådet (VR)-funded research infrastructure.

Published
2019

22. A molecular framework for the control of adventitious rooting by TIR1/AFB2-Aux/IAA-dependent auxin signaling in Arabidopsis

Author

Zahra Raneshan, Alok Ranjan, Laurent Gutierrez, Emilie Cavel, Catherine Bellini, Ondřej Novák, Salma Chaabouni, Rozenn Le Hir, François Jobert, Daniel Ioan Pacurar, Abdellah Lakehal, László Bakó, Irene Perrone, Umeå University, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Shahid Bahonar University of Kerman, Czech Academy of Sciences [Prague] (CAS), Palacky University Olomouc, Swedish University of Agricultural Sciences (SLU), Université de Picardie Jules Verne (UPJV), Swedish Research Council (VR)Swedish Research Council, Swedish Research Council for Research and Innovation for Sustainable Growth (VINNOVA), K. & A. Wallenberg FoundationKnut & Alice Wallenberg Foundation, Carl Trygger Foundation, Carl Kempe Foundation, University of Picardie Jules Verne, Regional Council of PicardieRegion Hauts-de-France, European Regional Development FundEuropean Union (EU), and Ministry of Education, Youth and Sports of the Czech Republic (European Regional Development Fund-Project 'Plants as a tool for sustainable global development') [CZ.02.1.01/0.0/0.0/16_019/0000827

Subjects
0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Arabidopsis, Receptors, Cell Surface, Plant Science, Biology, adventitious roots, 01 natural sciences, Plant Roots, 03 medical and health sciences, chemistry.chemical_compound, Auxin, Transcription (biology), Gene Expression Regulation, Plant, Arabidopsis thaliana, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, heterocyclic compounds, Jasmonate, Molecular Biology, Transcription factor, chemistry.chemical_classification, Regulation of gene expression, Indoleacetic Acids, Arabidopsis Proteins, Protein Stability, AuxIAA, Jasmonic acid, F-Box Proteins, fungi, food and beverages, biology.organism_classification, Hypocotyl, jasmonate, Cell biology, 030104 developmental biology, chemistry, TIR1/AFB, 010606 plant biology & botany, Signal Transduction
Abstract

International audience; In Arabidopsis thaliana, canonical auxin-dependent gene regulation is mediated by 23 transcription factors from the AUXIN RESPONSE FACTOR (ARF) family that interact with auxin/indole acetic acid repressors (Aux/IAAs), which themselves form co-receptor complexes with one of six TRANSPORT INHIBITOR1/AUXIN-SIGNALLING F-BOX (TIR1/AFB) proteins. Different combinations of co-receptors drive specific sensing outputs, allowing auxin to control a myriad of processes. ARF6 and ARF8 are positive regulators of adventitious root initiation upstream of jasmonate, but the exact auxin co-receptor complexes controlling the transcriptional activity of these proteins has remained unknown. Here, using loss-of-function mutants we show that three Aux/IAA genes, IAA6, IAA9, and IAA17, act additively in the control of adventitious root (AR) initiation. These three IAA proteins interact with ARF6 and/or ARF8 and likely repress their activity in AR development. We show that TIR1 and AFB2 are positive regulators of AR formation and TIR1 plays a dual role in the control of jasmonic acid (JA) biosynthesis and conjugation, as several JA biosynthesis genes are up-regulated in the tir1-1 mutant. These results lead us to propose that in the presence of auxin, TIR1 and AFB2 form specific sensing complexes with IAA6, IAA9, and/or IAA17 to modulate JA homeostasis and control AR initiation.

Published
2019

23. Stable antiferromagnetic nanocrystals for room temperature applications: The case of iron nitride

Author

Kowalik I.A., Gonzalez Szwacki N., Niño M.A., Luque F.J., Arvanitis D. and We would like to acknowledge the Polish National Science Centre (NSC) under Grant No. 2011/03/D/ST3/02654 for the main support. We acknowledge the access to the computing facilities of the Interdisciplinary Centre of Modelling at the University of Warsaw. Additional financial support is acknowledged from the Carl Tryggers foundation for Science Research under No. CTS 16:32. MAN acknowledeges the support of the MICCINN/ MINECO (Spain) through the programmes MAT2013-49893-EXP and MAT2014-59315-R. We acknowledge Andrea Navarro-Quezada, Bogdan Faina, Mauro Rovezzi and Alberta Bonanni for providing the samples and for interesting discussions. We acknowledge Tomasz Dietl for reviewing the manuscript and for interesting discussions. The research leading to these results has received funding through the MAX IV-lab and Elettra Synchrotrons from the European Community’s Seventh Framework Programme (FP7/ 2007-2013) under grant agreement no. 226716 (ELISA) and 312284 (CALIPSO). I. A. Kowalik acknowledges the support from the Baltic Science Link project coordinated by the Swedish Research Council, VR. Some of the XAS and XMCD experiments were performed at the beamline 29 at ALBA Synchrotron with the collaboration of ALBA staff. We acknowledge the Nanospectroscopy beamline staff for carrying out the XMCD-PEEM measurements.

Published
2019

24. A DAO1-mediated circuit controls auxin and jasmonate crosstalk robustness during adventitious root initiation in Arabidopsis

Author

Catherine Bellini, Ondřej Novák, Abdellah Lakehal, Asma Dob, Department of Plant Physiology, Umeå University, Czech Academy of Sciences [Prague] (CAS), Swedish University of Agricultural Sciences (SLU), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Centre National de la Recherche Scientifique (CNRS), Swedish Research Council (VR), and Swedish Governmental Agency for Innovation Agency (VINNOVA)

Subjects
0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Mutant, Arabidopsis, Plant Roots, 01 natural sciences, lcsh:Chemistry, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Jasmonate, lcsh:QH301-705.5, Spectroscopy, chemistry.chemical_classification, biology, General Medicine, Computer Science Applications, Cell biology, Crosstalk (biology), Utvecklingsbiologi, Oxidoreductases, Signal Transduction, organogenesis, Organogenesis, Cyclopentanes, adventitious roots, Article, Catalysis, Inorganic Chemistry, 03 medical and health sciences, Auxin, auxin oxidation, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Oxylipins, Physical and Theoretical Chemistry, Molecular Biology, Indoleacetic Acids, Arabidopsis Proteins, Organic Chemistry, Wild type, biology.organism_classification, 030104 developmental biology, chemistry, lcsh:Biology (General), lcsh:QD1-999, jasmonates, auxin, Developmental biology, 010606 plant biology & botany, Developmental Biology
Abstract

Adventitious rooting is a post-embryonic developmental program governed by a multitude of endogenous and environmental cues. Auxin, along with other phytohormones, integrates and translates these cues into precise molecular signatures to provide a coherent developmental output. Auxin signaling guides every step of adventitious root (AR) development from the early event of cell reprogramming and identity transitions until emergence. We have previously shown that auxin signaling controls the early events of AR initiation (ARI) by modulating the homeostasis of the negative regulator jasmonate (JA). Although considerable knowledge has been acquired about the role of auxin and JA in ARI, the genetic components acting downstream of JA signaling and the mechanistic basis controlling the interaction between these two hormones are not well understood. Here we provide evidence that COI1-dependent JA signaling controls the expression of DAO1 and its closely related paralog DAO2. In addition, we show that the dao1-1 loss of function mutant produces more ARs than the wild type, probably due to its deficiency in accumulating JA and its bioactive metabolite JA-Ile. Together, our data indicate that DAO1 controls a sensitive feedback circuit that stabilizes the auxin and JA crosstalk during ARI.

Published
2019

25. Genome Sequence of Listeria innocua Strain MEZLIS26, Isolated from a Goat in South Africa

Author

Marc Lecuit, Josef D. Järhult, Mohamed E. El Zowalaty, Oliver T. Zishiri, Rachel A. Hickman, Alexandra Moura, Noelle R. Noyes, DIAKITE, andrée, St Jude Children's Research Hospital, University of KwaZulu-Natal [Durban, Afrique du Sud] (UKZN), University of Sharjah (UoS), Uppsala University, Biologie des Infections - Biology of Infection, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre collaborateur de l'OMS Listeria / WHO Collaborating Centre Listeria (CC-OMS / WHO-CC), Institut Pasteur [Paris] (IP)-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Université Paris Descartes - Paris 5 (UPD5), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service des Maladies infectieuses et tropicales [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), University of Minnesota System, The whole-genome sequencing work is supported by the National Institutes of Health/Food and Drug Administration under award number 1U18FD006780-01., We thank the South African National Research Foundation for supporting this research through the Thuthuka Funding Instrument (grant number TTK170411226583) and the Swedish Research Council (VR) through grant number 2016-02606. We thank Lyndy Harden and Siddhartha Thakur from Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University (Raleigh, NC). We thank the Genome Trakr Network and the Whole Genome Sequencing Program for foodborne pathogen traceback and the Center for Food Safety and Applied Nutrition (CFSAN), U.S. Food and Drug Administration (FDA), for support in the whole-genome sequencing (WGS) of the strain MEZLIS26 as part of the US Food and Drug Administration's WGS surveillance effort., University of KwaZulu-Natal (UKZN), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris]-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)

Subjects
[SDV]Life Sciences [q-bio], Biology, Microbiology, Genome, 03 medical and health sciences, Immunology and Microbiology (miscellaneous), [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Genetics, Molecular Biology, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, 030306 microbiology, Strain (biology), Genome Sequences, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV] Life Sciences [q-bio], Mikrobiologi, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Listeria, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

Here, we report the draft genome sequence of Listeria innocua strain MEZLIS26, isolated from a healthy goat in Flagstaff, Eastern Cape Province, South Africa. The genome was sequenced using the Illumina MiSeq platform and had a length of 2,800,777 bp, with a G+C content of 37.4%, 2,755 coding DNA sequences (CDSs), 49 transfer RNAs (tRNAs), and 4 noncoding RNAs (ncRNAs).

Published
2019

26. Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution

Author

Hill, Jason, Rastas, Pasi, Hornett, Emily A., Neethiraj, Ramprasad, Clark, Nathan, Morehouse, Nathan, de la Paz Celorio-Mancera, Maria, Cols, Jofre Carnicer, Dircksen, Heinrich, Meslin, Camille, Keehnen, Naomi, Pruisscher, Peter, Sikkink, Kristin, Vives, Maria, Vogel, Heiko, Wiklund, Christer, Woronik, Alyssa, Boggs, Carol L., Nylin, Sören, Wheat, Christopher W., Stockholm University, Department of Medical Biochemistry and Microbiology, Uppsala University, Institute of Biotechnology, Royal Institute of Technology [Stockholm] (KTH )-Albanova University Center, Department of Zoology, University of Cambridge [UK] (CAM), Institute of Integrative Biology, Liverpool School of Tropical Medicine (LSTM), Department of Computational and Systems Biology, University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE)-Pennsylvania Commonwealth System of Higher Education (PCSHE), Department of Biological Sciences, The Open University [Milton Keynes] (OU), University of Barcelona, Universitat Autònoma de Barcelona (UAB), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Department of Ecology, Evolution, and Behavior, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, Department of Biology, The University of Mississippi [Oxford], Department of Entomology, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, New York University, New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), University of South Carolina [Columbia], Funding was provided by the Swedish Research Council [VR grant numbers 2012-3715 (to S.N.), 2010-5341 (to S.N.), and 621-2012-4001 (to C.W.W.)], the Academy of Finland [grant number 131155 (to C.W.W.)], the Knut and Alice Wallenberg Foundation (grant number 2012.0058), and MINECO-FEDER [project number CGL2016- 78093-R (to J.C.C.)], Albanova University Center-Royal Institute of Technology [Stockholm] (KTH ), Department ofComputationaland Systems Biology, Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours-Centre National de la Recherche Scientifique (CNRS), Pennsylvania Commonwealth System of Higher Education (PCSHE), Institut d'écologie et des sciences de l'environnement de Paris (IEES), Max Planck Institute for Chemical Ecology, and Max-Planck-Gesellschaft

Subjects
Male, endocrine system, GENES, DATABASE, Genetic Linkage, [SDV]Life Sciences [q-bio], NEO-SEX CHROMOSOMES, Genome, Insect, GENOMES, SYSTEMATICS, lepidopteran chromosome evolution, ANNOTATION, CLASSIFICATION, Chromosomes, Evolution, Molecular, qx_560, Collinearity, Chromosome structure, Genome Size, Genetics, Animals, Genetik, Selection, Genetic, Research Articles, Phylogeny, FUSIONS, Evolutionary Biology, Ploidies, qu_500, Chromosome evolution, reorganization of holocentric chromosomes, fungi, 1184 Genetics, developmental biology, physiology, SciAdv r-articles, KARYOTYPE, Chromosome Mapping, Gene content, Bombyx, Chromosome numbers, Cromosomes, Chromosomes, Insect, Lepidoptera, [SDE]Environmental Sciences, qu_550, Female, DIVERSIFICATION, Lepidòpters, Butterflies, Research Article
Abstract

Unprecedented reorganization in a butterfly genome sheds light on the enigma of holocentric chromosome evolution., Chromosome evolution presents an enigma in the mega-diverse Lepidoptera. Most species exhibit constrained chromosome evolution with nearly identical haploid chromosome counts and chromosome-level gene collinearity among species more than 140 million years divergent. However, a few species possess radically inflated chromosomal counts due to extensive fission and fusion events. To address this enigma of constraint in the face of an exceptional ability to change, we investigated an unprecedented reorganization of the standard lepidopteran chromosome structure in the green-veined white butterfly (Pieris napi). We find that gene content in P. napi has been extensively rearranged in large collinear blocks, which until now have been masked by a haploid chromosome number close to the lepidopteran average. We observe that ancient chromosome ends have been maintained and collinear blocks are enriched for functionally related genes suggesting both a mechanism and a possible role for selection in determining the boundaries of these genome-wide rearrangements.

Published
2019

27. When the Grafting of Double Decker Phthalocyanines on Si(100)-2 × 1 Partly Affects the Molecular Electronic Structure

Author

Johann Lüder, Niklas Mårtensson, Cesare Grazioli, Nadine Witkowski, Carla Puglia, Marcel Bouvet, Barbara Brena, Ieva Bidermane, Sareh Ahmadi, Department of Physics and Astronomy [Uppsala], Uppsala University, Materialfysik, KTH-Electrum, Laboratorio TASC ( IOM CNR ), Consiglio Nazionale delle Ricerche ( CNR ), Institut de Chimie Moléculaire de l'Université de Bourgogne [Dijon] ( ICMUB ), Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Institut des Nanosciences de Paris ( INSP ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Swedish Research Council (VR), European Research Council under the European Union 321319, Gender Equality Group, Department of Physics and Astronomy, Uppsala University, Knut and Alice Wallenberg Foundation KAW-2013.0020, Swedish Research Council 2014-3776, European Project : 321319,ERC 321319, Laboratorio TASC (IOM CNR), Consiglio Nazionale delle Ricerche (CNR), Institut de Chimie Moléculaire de l'Université de Bourgogne [Dijon] (ICMUB), Université de Bourgogne (UB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut des Nanosciences de Paris (INSP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), European Project: 321319,ERC 321319, and National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR)

Subjects
lutetium bi-phthalocyanine, Silicon, XAS, Atom and Molecular Physics and Optics, STM, Analytical chemistry, chemistry.chemical_element, 02 engineering and technology, 010402 general chemistry, DFT, [ CHIM ] Chemical Sciences, 01 natural sciences, Si(100), law.invention, Adsorption, X-ray photoelectron spectroscopy, scanning tunneling microscope, law, basis-set, XPS, [CHIM]Chemical Sciences, surface, Molecule, Physical and Theoretical Chemistry, Basis set, metal-free phthalocyanine, field-effect transistors, Phthalocyanine, bis-phthalocyanine, 021001 nanoscience & nanotechnology, 0104 chemical sciences, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials, total-energy calculations, General Energy, Electronic Structure, chemistry, si(001), Chemical physics, thin-films, augmented-wave method, Atom- och molekylfysik och optik, Density functional theory, Scanning tunneling microscope, Absorption (chemistry), 0210 nano-technology
Abstract

International audience; A combined X-ray photoelectron spectroscopy (XPS), scanning tunneling microscopy (STM), and density functional theory (DFT) study has been performed to characterize the adsorbate interaction of lutetium biphthalocyanine (LuPc2) molecules on the Si(100)-2 × 1 surface. Large molecule–substrate adsorption energies are computed and are found to compete with the molecule–molecule interactions of the double decker molecules. A particularly good matching between STM images and computed ones confirms the deformation of the molecule upon the absorption process. The comparison between DFT calculations and XP spectra reveals that the electronic distribution in the two plateaus of the biphthalocyanine are not affected in the same manner upon the adsorption onto the silicon surface. This finding can be of particular importance in the implementation of organic molecules in hybrid devices.

Published
2016

28. Grazer-induced transcriptomic and metabolomic response of the chain-forming diatom Skeletonema marinoi

Author

Johanna Bergkvist, Erik Selander, Swaraj Basu, Valeria Sabatino, Alberto Amato, Anna Godhe, Thomas Kiørboe, Maria Immacolata Ferrante, Remo Sanges, Mats X. Andersson, Göran M. Nylund, Physiologie cellulaire et végétale (LPCV), Institut National de la Recherche Agronomique (INRA)-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), Integrative Marine Ecology, Stazione Zoologica Anton Dohrn (SZN), Department of Marine Sciences [Gothenburg], University of Gothenburg (GU), Department of Biological and Environmental Sciences [Gothenburg], National Institute of Aquatic Resources, Technical University of Denmark [Lyngby] (DTU), Swedish Research Council VR 2015-05491, European Union under FP7-People 600407, Swedish Research Council Formas VR 217-2008-1719, European Project: 227799,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2008-1,ASSEMBLE(2009), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Stazione Zoologica Anton Dohrn, and Danmarks Tekniske Universitet = Technical University of Denmark (DTU)

Subjects
0106 biological sciences, 0301 basic medicine, Food Chain, Frustule, Nitrogen, Calanus finmarchicus, [SDV]Life Sciences [q-bio], Down-Regulation, 01 natural sciences, Microbiology, Article, Receptors, G-Protein-Coupled, Copepoda, Transcriptome, 03 medical and health sciences, Metabolomics, Skeletonema marinoi, Settore BIO/13 - Biologia Applicata, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Oxylipins, SDG 14 - Life Below Water, 14. Life underwater, Ecosystem, Phylogeny, Ecology, Evolution, Behavior and Systematics, Trophic level, Diatoms, biology, Gene Expression Profiling, 010604 marine biology & hydrobiology, Cell Cycle, fungi, Lipid Metabolism, biology.organism_classification, Lipids, Cell biology, Gene expression profiling, Phenotype, 030104 developmental biology, Diatom, Metabolome, Signal Transduction
Abstract

International audience; Diatoms and copepods are main actors in marine food webs. The prey–predator interactions between them affect bloom dynamics, shape marine ecosystems and impact the energy transfer to higher trophic levels. Recently it has been demonstrated that the presence of grazers may affect the diatom prey beyond the direct effect of grazing. Here, we investigated the response of the chain-forming centric diatom Skeletonema marinoi to grazer cues, including changes in morphology, gene expression and metabolic profile. S. marinoi cells were incubated with Calanus finmarchicus or with Centropages typicus and in both cases responded by reducing the chain length, whereas changes in gene expression indicated an activation of stress response, changes in the lipid and nitrogen metabolism, in cell cycle regulation and in frustule formation. Transcripts linked to G protein-coupled receptors and to nitric oxide synthesis were differentially expressed suggesting involvement of these signalling transduction pathways in the response. Downregulation of a lipoxygenase in the transcriptomic data and of its products in the metabolomic data also indicate an involvement of oxylipins. Our data contribute to a better understanding of the gene function in diatoms, providing information on the nature of genes implicated in the interaction with grazers, a crucial process in marine ecosystems.

Published
2018

29. Vast diversity of prokaryotic virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis

Author

Disa Bäckström, Mart Krupovic, Eugene V. Koonin, Natalya Yutin, Thijs J. G. Ettema, National Center for Biotechnology Information (NCBI), Uppsala University, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), National Institutes of Health [Bethesda] (NIH), NY and EVK are supported by intramural funds of the US Department of Health and Human Services (to the National Library of Medicine). TJGE is supported by grants of the European Research Council (ERC Starting Grant 310039-PUZZLE_CELL), the Swedish Foundation for Strategic Research (SSF-FFL5) and the Swedish Research Council (VR grant 2015–04959). MK is supported by l’Agence Nationale de la Recherche (France) project ENVIRA., We acknowledge the help from chief scientist R. B. Pedersen, the scientific party and the entire crew on board the Norwegian research vessel G.O. Sars for providing marine sediment samples from the Loki’s Castle hydrothermal vent area during the summer 2010 expedition., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), European Project: 310039,EC:FP7:ERC,ERC-2012-StG_20111109,PUZZLE_CELL(2012), and Institut Pasteur [Paris]

Subjects
0301 basic medicine, Archaeal Viruses, [SDV]Life Sciences [q-bio], Genome, MESH: Archaeal Viruses, Databases, Genetic, MESH: Genetic Variation, MESH: Phylogeny, Phylogeny, MESH: Capsid Proteins, MESH: Databases, Genetic, Genetics, MESH: Genomics, Genomics, Infectious Diseases, MESH: Archaea, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Genome, Viral, MESH: Metagenomics, Tectiviridae, Sequence analysis, Bioinformatik och systembiologi, Genome, Viral, Biology, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Phylogenetics, Virology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Life Science, Human virome, lcsh:RC109-216, Gene, MESH: Tectiviridae, Bioinformatics and Systems Biology, Bacteria, Research, Genetic Variation, Archaea, Mikrobiologi, MESH: Bacteria, 030104 developmental biology, Metagenomics, Capsid Proteins
Abstract

Background Analysis of metagenomic sequences has become the principal approach for the study of the diversity of viruses. Many recent, extensive metagenomic studies on several classes of viruses have dramatically expanded the visible part of the virosphere, showing that previously undetected viruses, or those that have been considered rare, actually are important components of the global virome. Results We investigated the provenance of viruses related to tail-less bacteriophages of the family Tectiviridae by searching genomic and metagenomics sequence databases for distant homologs of the tectivirus-like Double Jelly-Roll major capsid proteins (DJR MCP). These searches resulted in the identification of numerous genomes of virus-like elements that are similar in size to tectiviruses (10–15 kilobases) and have diverse gene compositions. By comparison of the gene repertoires, the DJR MCP-encoding genomes were classified into 6 distinct groups that can be predicted to differ in reproduction strategies and host ranges. Only the DJR MCP gene that is present by design is shared by all these genomes, and most also encode a predicted DNA-packaging ATPase; the rest of the genes are present only in subgroups of this unexpectedly diverse collection of DJR MCP-encoding genomes. Only a minority encode a DNA polymerase which is a hallmark of the family Tectiviridae and the putative family "Autolykiviridae". Notably, one of the identified putative DJR MCP viruses encodes a homolog of Cas1 endonuclease, the integrase involved in CRISPR-Cas adaptation and integration of transposon-like elements called casposons. This is the first detected occurrence of Cas1 in a virus. Many of the identified elements are individual contigs flanked by inverted or direct repeats and appear to represent complete, extrachromosomal viral genomes, whereas others are flanked by bacterial genes and thus can be considered as proviruses. These contigs come from metagenomes of widely different environments, some dominated by archaea and others by bacteria, suggesting that collectively, the DJR MCP-encoding elements have a broad host range among prokaryotes. Conclusions The findings reported here greatly expand the known host range of (putative) viruses of bacteria and archaea that encode a DJR MCP. They also demonstrate the extreme diversity of genome architectures in these viruses that encode no universal proteins other than the capsid protein that was used as the marker for their identification. From a supposedly minor group of bacterial and archaeal viruses, these viruses are emerging as a substantial component of the prokaryotic virome. Electronic supplementary material The online version of this article (10.1186/s12985-018-0974-y) contains supplementary material, which is available to authorized users.

Published
2018

30. Application of Py-GC/MS coupled with PARAFAC2 and PLS-DA to study fast pyrolysis of genetically engineered poplars

Author

Ruben Vanholme, Frederik Ronsse, Gilles Pilate, Guy B. Marin, Victor Abrahamsson, Rebecca Van Acker, Kevin Van Geem, Wout Boerjan, Hilal Ezgi Toraman, Laboratory for Chemical Technology, Universiteit Gent = Ghent University [Belgium] (UGENT), Lund University [Lund], Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Department of Biosystems Engineering [Ghent], Biologie intégrée pour la valorisation de la diversité des arbres et de la forêt (BioForA), Institut National de la Recherche Agronomique (INRA)-Office National des Forêts (ONF), Funding from the European Research Council under the European Union's Seventh Framework Programme FP7/2007-2013/ERC grant agreement n° 290793. SBO proposal 'Bioleum' supported by the Institute for promotion of Innovation through Science and Technology in Flanders (IWT) and the EU-funded project ENERGYPOPLAR (FB7-211917). V.A. acknowledges the support from Swedish Research Council VR (2010-5439, 2010-333, 2013-4356, 2014-4052) and the Royal Physiographic Society in Lund., European Project: 290793,EC:FP7:ERC,ERC-2011-ADG_20110209,MADPII(2012), Universiteit Gent = Ghent University (UGENT), and Institut National de la Recherche Agronomique (INRA)-Office national des forêts (ONF)

Subjects
0106 biological sciences, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, 020209 energy, Lignocellulosic biomass, Bio-oil, Gas-chromatography, 02 engineering and technology, PLS-DA, 01 natural sciences, Analytical Chemistry, chemistry.chemical_compound, Thermochemical conversion, PARAFAC2, Partial least squares regression, 0202 electrical engineering, electronic engineering, information engineering, Lignin, Organic chemistry, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Phenylpropanoid, Lignin biosynthesis, Phenolic compounds, Fuel Technology, chemistry, Biosynthetic-pathway, Environmental chemistry, Field-grown transgenic plants, Principal component analysis, Cinnamoyl-CoA reductase, Gas chromatography–mass spectrometry, Pyrolysis, 010606 plant biology & botany
Abstract

International audience; Field-grown genetically engineered and wild-type poplars were pyrolyzed in a micro-pyrolysis (Py-GC/MS) setup under fast pyrolysis conditions. Poplars (Populus tremula x P. alba) down-regulated for cirmamoyl-CoA reductase (CCR), which catalyzes the first step of the monolignol-specific branch of the phenylpropanoid biosynthetic pathway, were grown in field trials in France and harvested after a full rotation of 2 years. The effect of small compositional differences, specifically small shifts in lignin composition and their impact on the bio-oil composition, could not be identified using principal component analysis (PCA), necessitating the use of more advanced analysis techniques. The combination of parallel factor analysis 2 (PARAFAC2) and partial least squares discriminant analysis (PLS-DA) for detailed characterization and classification of the pyrolysis data enabled the classification of the poplars with a success rate above 99% using the PARAFAC2 scores. This methodology proved to be extremely valuable to identify subtle information in complex datasets, such as the one used in this study. The obtained PLS-DA models were validated by cross-validation, jackknifing and permutation tests in order to ensure that the model was not overfitting the data. PLS-DA showed that down-regulation of CCR dis-favored the relative amount of both guaiacyl and syringyl lignin-derived compounds. This study shows that lignin engineering can be a promising strategy to alter the lignin composition of the biomass for the production of high value-added phenolic compounds.

Published
2018

31. Drought legacy effects on the composition of soil fungal and prokaryote communities

Author

Annelein Meisner, Samuel Jacquiod, Basten L. Snoek, Freddy C. ten Hooven, Wim H. van der Putten, Meisner, Annelein, Lund University [Lund], University of Copenhagen = Københavns Universitet (UCPH), Department of Microbial Ecology, Netherlands Institute of Ecology, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Department of Terrestrial Ecology, Netherlands Institute for Ecology (NIOO-KNAW), Utrecht University [Utrecht], Laboratory of Nematology, Wageningen University and Research [Wageningen] (WUR), Swedish Research Council (VR) [330-2014-6430], ERC-Adv grant [26055290] (SPECIALS), European Project: 600398,EC:FP7:PEOPLE,FP7-PEOPLE-2012-COFUND,INCA(2014), Microbial Ecology (ME), Terrestrial Ecology (TE), University of Copenhagen = Københavns Universitet (KU), Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Sub Bioinformatics, and Theoretical Biology and Bioinformatics

Subjects
0301 basic medicine, Microbiology (medical), Rare biosphere, [SDV]Life Sciences [q-bio], lcsh:QR1-502, Microbial communities, Biology, Microbiology, lcsh:Microbiology, Mesocosm, 03 medical and health sciences, Soil, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Groep Koornneef, Climate change, Ecosystem, Global environmental change, Water content, Laboratorium voor Nematologie, Original Research, climate change, soil, Birch effect, re-wetting, bacteria, fungi, microbial communities, 2. Zero hunger, Bacteria, Ecology, Community structure, Fungi, Microbiomes, 15. Life on land, PE&RC, Re-wetting, 030104 developmental biology, Microbial population biology, 13. Climate action, international, [SDE]Environmental Sciences, Terrestrial ecosystem, Species richness, EPS, Laboratory of Nematology
Abstract

International audience; It is increasingly acknowledged that climate change is influencing terrestrial ecosystems by increased drought and rainfall intensities. Soil microbes are key drivers of many processes in terrestrial systems and rely on water in soil pores to fulfill their life cycles and functions. However, little is known on how drought and rainfall fluctuations, which affect the composition and structure of microbial communities, persist once original moisture conditions have been restored. Here, we study how simulated short-term drying and re-wetting events shape the community composition of soil fungi and prokaryotes. In a mesocosm experiment, soil was exposed to an extreme drought, then re-wetted to optimal moisture (50% WHC, water holding capacity) or to saturation level (100% WHC). Composition, community structure and diversity of microbes were measured by sequencing ITS and 16S rRNA gene amplicons 3 weeks after original moisture content had been restored. Drying and extreme re-wetting decreased richness of microbial communities, but not evenness. Abundance changes were observed in only 8% of prokaryote OTUs, and 25% of fungal OTUs, whereas all other OTUs did not differ between drying and re-wetting treatments. Two specific legacy response groups (LRGs) were observed for both prokaryotes and fungi. OTUs belonging to the first LRG decreased in relative abundance in soil with a history of drought, whereas OTUs that increased in soil with a history of drought formed a second LRG. These microbial responses were spread among different phyla. Drought appeared to be more important for the microbial community composition than the following extreme re-wetting. 16S profiles were correlated with both inorganic N concentration and basal respiration and ITS profiles correlated with fungal biomass. We conclude that a drying and/or an extreme re-wetting history can persist in soil microbial communities via specific response groups composed of members with broad phylogenetic origins, with possible functional consequences on soil processes and plant species. As a large fraction of OTUs responding to drying and re-wetting belonged to the rare biosphere, our results suggest that low abundant microbial species are potentially important for ecosystem responses to extreme weather events.

Published
2018

32. Exponential integrators for nonlinear Schrödinger equations with white noise dispersion

Author

David Cohen, Guillaume Dujardin, Umeå University, Quantitative methods for stochastic models in physics (MEPHYSTO), Laboratoire Paul Painlevé (LPP), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université libre de Bruxelles (ULB), This work was partially supported by UMIT Research Lab at Umeå University, the Swedish Research Council (VR) (Project No. 2013-4562), the The G S Magnuson Foundation at KVA (Project No. MG2015-0080), the Agence Nationale de la Recherche in the framework of the Labex CEMPI (ANR-11-LABX-0007-01), and Inria (EPI MEPHYSTO). The computational results presented have been achieved (in part) using the HPC infrastructure LEO of the University of Innsbruck. The computations were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC) at HPC2N, Umeå University., ANR-11-LABX-0007,CEMPI,Centre Européen pour les Mathématiques, la Physique et leurs Interactions(2011), Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université libre de Bruxelles (ULB)-Laboratoire Paul Painlevé - UMR 8524 (LPP), Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Laboratoire Paul Painlevé - UMR 8524 (LPP), and Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Inria Lille - Nord Europe

Subjects
Statistics and Probability, Beräkningsmatematik, 010103 numerical & computational mathematics, Exponential integrator, Exponential integrators, 01 natural sciences, Schrödinger equation, Geometric numerical integration, symbols.namesake, Nonlinear Schrödinger equation, Mean-square convergence, [MATH.MATH-AP]Mathematics [math]/Analysis of PDEs [math.AP], 0101 mathematics, Geometric Numerical Integration, White noise dispersion, Mathematics, Partial differential equation, Applied Mathematics, Mathematical analysis, Stochastic partial differential equations, White noise, Numerical integration, 010101 applied mathematics, Stochastic partial differential equation, [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], Computational Mathematics, Nonlinear system, Modeling and Simulation, symbols, Numerical methods, [MATH.MATH-NA]Mathematics [math]/Numerical Analysis [math.NA]
Abstract

International audience; This article deals with the numerical integration in time of the nonlinear Schrödinger equation with power law nonlinearity and random dispersion. We introduce a new explicit exponential integrator for this purpose that integrates the noisy part of the equation exactly. We prove that this scheme is of mean-square order 1 and we draw consequences of this fact. We compare our exponential integrator with several other numerical methods from the literature. We finally propose a second exponential integrator, which is implicit and symmetric and, in contrast to the first one, preserves the $L 2-norm$ of the solution.

Published
2017

33. Ibuprofen and ketoprofen potentiate UVA-induced cell death by a photosensitization process

Author

Bignon, Emmanuelle, Marazzi, Marco, Besancenot, Vanessa, Gattuso, Hugo, Drouot, Guillaume, Morell, Christophe, Eriksson, Leif A., Grandemange, Stephanie, Dumont, Elise, Monari, Antonio, 0000-0001-7158-7994, 0000-0001-5654-3109, 0000-0001-9464-1463, Laboratoire de Chimie - UMR5182 (LC), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)-Institut de Chimie du CNRS (INC), Chemometrics and Theoretical Chemistry - Chimiométrie et chimie théorique, Institut des Sciences Analytiques (ISA), Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Centre de Recherche en Automatique de Nancy (CRAN), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Dept Chem & Mol Biol, University of Gothenburg (GU), This research was supported by the COST action 'MOLIM: Molecules in Motion'. M.M. is thankful to the French and Austrian National Research Agencies (ANR and FWF, respectively) for a grant under the 'DeNeTheor' project. Support from the COST 'Action Biomimetic Radical Chemistry' in the form of a STSM is also acknowledged. L.A.E. gratefully acknowledges financial support from the Faculty of Science at University of Gothenburg, and the Swedish Research Council (VR). We acknowledge grants of computing time at the C3SE supercomputing center, via the Swedish National Infrastructure for Computing (SNIC)., ANR-15-CE29-0027,DeNeTheor,Etats Excités et Dynamique de Complexes de Re(I) Fonctionnalisés en Interaction avec des Métalloprotéines: Nouvelles Méthodes Théoriques pour la Simulation et le Contrôle des Propriétés à l'Etat Excité dans un Environnement Biologique(2015), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Chemometrics and theoretical chemistry. - Chimiométrie et chimie théorique, Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL)

Subjects
Models, Molecular, Photosensitizing Agents, Cell Death, Molecular Structure, Cell Survival, Ultraviolet Rays, Science, Apoptosis, Drug Synergism, Ibuprofen, Article, Structure-Activity Relationship, Ketoprofen, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Cell Line, Tumor, Humans, Medicine
Abstract

International audience; Nonsteroidal 2-arylproprionic acids are widely used, over-the-counter, anti-inflammatory drugs. Photosensitivity is a commonly overlooked adverse effect of these drugs. Based on the combined use of cell viability assays and molecular modeling, we prove and rationalize the photochemical pathways triggering photosensitization for two drugs, ibuprofen and ketoprofen. As its parent compound benzophenone, ketoprofen produces singlet oxygen, upon triplet manifold population. However, ibuprofen and ketoprofen photodissociate and hence may generate two highly reactive radicals. The formation of metastable aggregates between the two drugs and B-DNA is also directly probed by molecular dynamics. Our approach characterizes the coupled influence of the drug's intrinsic photochemistry and the interaction pattern with DNA. The photosensitization activity of nonsteroidal 2-arylproprionic acids, being added to gels and creams for topical use, should be crucially analyzed and rationalized to enact the proper preventive measures.

Published
2017

34. Quenched mass transport of particles towards a target

Author

Bruno Bouchard, Idris Kharroubi, Boualem Djehiche, CEntre de REcherches en MAthématiques de la DEcision (CEREMADE), Université Paris Dauphine-PSL, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Department of Mathematics [Sweden] (KTH), Stockholm University, Laboratoire de Probabilités, Statistiques et Modélisations (LPSM UMR 8001), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU), Swedish Research Council (VR) Grant no. 2016-04086 is gratefully acknowledged, ANR-15-CE05-0024,CAESARS,Contrôle et simulation des systèmes électriques, interaction et robustesse(2015), Centre National de la Recherche Scientifique (CNRS)-Université Paris Dauphine-PSL, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Laboratoire de Probabilités, Statistiques et Modélisations (LPSM (UMR_8001)), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)

Subjects
Control and Optimization, viscosity solutions, 0211 other engineering and technologies, stochastic target, 010103 numerical & computational mathematics, 02 engineering and technology, Management Science and Operations Research, MSC (2010): 93E20, 60K35, 49L25, 01 natural sciences, Stochastic differential equation, Reachability, Bellman equation, FOS: Mathematics, 0101 mathematics, Brownian motion, Mathematics, dynamic programming, McKean-Vlasov SDEs, 021103 operations research, Partial differential equation, Applied Mathematics, Mathematical analysis, Probability (math.PR), 16. Peace & justice, mass trans- portation, Dynamic programming, [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], Probability distribution, Viscosity solution, Mathematics - Probability
Abstract

International audience; We consider the stochastic target problem of finding the collection of initial laws of a mean-field stochastic differential equation such that we can control its evolution to ensure that it reaches a prescribed set of terminal probability distributions, at a fixed time horizon. Here, laws are considered conditionally to the path of the Brownian motion that drives the system. We establish a version of the geometric dynamic programming principle for the associated reachability sets and prove that the corresponding value function is a viscosity solution of a geometric partial differential equation. This provides a characterization of the initial masses that can be almost-surely transported towards a given target, along the paths of a stochastic differential equation. Our results extend [16] to our setting.

Published
2017

35. Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life

Author

Luisa W. Hugerth, Jean Bottu, Anna Heintz-Buschart, Angela Hogan, Linda Wampach, Carine de Beaufort, Paul Wilmes, Lutz Bindl, Anders F. Andersson, Shaman Narayanasamy, Emilie E. L. Muller, Cedric Christian Laczny, Fonds National de la Recherche - FnR [sponsor], Integrated BioBank of Luxembourg [sponsor], Fondation André et Henriette Losch [sponsor], Swedish Research Council VR [sponsor], Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], Integrated BioBank of Luxembourg - IBBL [research center], Science for Life Laboratory [research center], Centre Hospitalier de Luxembourg [research center], Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg [Luxembourg], Laboratoire Hétéroéléments et Coordination (DCPH), and École polytechnique (X)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Microbiology (medical), microbial colonization, Microbiologie [F11] [Sciences du vivant], Firmicutes, 030106 microbiology, lcsh:QR1-502, Biology, Microbiology, lcsh:Microbiology, delivery mode, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Colonization, Microbiology [F11] [Life sciences], Microbiome, quantitative real-time PCR, ComputingMilieux_MISCELLANEOUS, Bifidobacterium, Original Research, 2. Zero hunger, [SDV.MHEP.PED]Life Sciences [q-bio]/Human health and pathology/Pediatrics, amplicon sequencing, Bacteroidetes, biology.organism_classification, Delivery mode, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], succession, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, infant gut microbiome, fungi, Bacteroides, Bacteria
Abstract

Perturbations to the colonization process of the human gastrointestinal tract have been suggested to result in adverse health effects later in life. Although much research has been performed on bacterial colonization and succession, much less is known about the other two domains of life, archaea, and eukaryotes. Here we describe colonization and succession by bacteria, archaea and microeukaryotes during the first year of life (samples collected around days 1, 3, 5, 28, 150, and 365) within the gastrointestinal tract of infants delivered either vaginally or by cesarean section and using a combination of quantitative real-time PCR as well as 16S and 18S rRNA gene amplicon sequencing. Sequences from organisms belonging to all three domains of life were detectable in all of the collected meconium samples. The microeukaryotic community composition fluctuated strongly over time and early diversification was delayed in infants receiving formula milk. Cesarean section-delivered (CSD) infants experienced a delay in colonization and succession, which was observed for all three domains of life. Shifts in prokaryotic succession in CSD infants compared to vaginally delivered (VD) infants were apparent as early as days 3 and 5, which were characterized by increased relative abundances of the genera Streptococcus and Staphylococcus, and a decrease in relative abundance for the genera Bifidobacterium and Bacteroides. Generally, a depletion in Bacteroidetes was detected as early as day 5 postpartum in CSD infants, causing a significantly increased Firmicutes/Bacteroidetes ratio between days 5 and 150 when compared to VD infants. Although the delivery mode appeared to have the strongest influence on differences between the infants, other factors such as a younger gestational age or maternal antibiotics intake likely contributed to the observed patterns as well. Our findings complement previous observations of a delay in colonization and succession of CSD infants, which affects not only bacteria but also archaea and microeukaryotes. This further highlights the need for resolving bacterial, archaeal, and microeukaryotic dynamics in future longitudinal studies of microbial colonization and succession within the neonatal gastrointestinal tract.

Published
2017

36. The redox control of photorespiration: from biochemical and physiological aspects to biotechnological considerations

Author

Per Gardeström, Nicolas Rouhier, Olivier Keech, Leszek A. Kleczkowski, Umeå University, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Swedish Research Council (VR - 621-2014-4688), Kempe Foundations, French National Research Agency ANR (ANR-11-LABX-0002-01), and Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL)

Subjects
0106 biological sciences, 0301 basic medicine, photorespiration, Light, Physiology, Cellular respiration, Cell Respiration, Plant Science, Oxidative phosphorylation, Biology, Photosynthesis, 01 natural sciences, Redox, 03 medical and health sciences, chemistry.chemical_compound, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Amino Acid Sequence, cysteine, Glycine cleavage system, post-translational regulation, Reducing equivalent, Plants, redox proteomics, 030104 developmental biology, chemistry, Biochemistry, reducing equivalent, Photorespiration, Oxidation-Reduction, régulation redox, 010606 plant biology & botany, Glycerate kinase, Biotechnology
Abstract

Photorespiration is a complex and tightly regulated process occurring in photosynthetic organisms. This process can alter the cellular redox balance, notably via the production and consumption of both reducing and oxidizing equivalents. Under certain circumstances, these equivalents, as well as reactive oxygen or nitrogen species, can become prominent in subcellular compartments involved in the photorespiratory process, eventually promoting oxidative post-translational modifications of proteins. Keeping these changes under tight control should therefore be of primary importance. In order to review the current state of knowledge about the redox control of photorespiration, we primarily performed a careful description of the known and potential redox-regulated or oxidation sensitive photorespiratory proteins, and examined in more details two interesting cases: the glycerate kinase and the glycine cleavage system. When possible, the potential impact and subsequent physiological regulations associated with these changes have been discussed. In the second part, we reviewed the extent to which photorespiration contributes to cellular redox homeostasis considering, in particular, the set of peripheral enzymes associated with the canonical photorespiratory pathway. Finally, some recent biotechnological strategies to circumvent photorespiration for future growth improvements are discussed in the light of these redox regulations.

Published
2017

37. In-situ evaluation of dye adsorption on TiO 2 using QCM

Author

Besharat Z., Alvarez-Asencio R., Tian H., Yu S., Johnson C.M., Göthelid M., Rutland M.W. and The financial support from the Swedish Research Council (VR) is gratefully acknowledged. S.Y. acknowledges the financial support from Knut and Alice Wallenberg Foundation. The authors thank Prof Licheng Sun for valuable discussions.

Published
2017

38. Brassinosteroid signaling-dependent root responses to prolonged elevated ambient temperature

Author

Martins, Sara, Montiel-Jorda, Alvaro, Cayrel, Anne, Huguet, Stéphanie, Roux, Christine Paysant-Le, Ljung, Karin, Vert, Grégory, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Signalisation Cellulaire et Ubiquitination chez les plantes (UBINET), Département Biologie Cellulaire (BioCell), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), PhD fellowship from the Saclay Plant Sciences LabEx initiative - French government [ANR-10-LABX-0040-SPS], Agence Nationale de la Recherche [ANR-11-IDEX-0003-02, ANR-13-JSV2-0004-01], Swedish Governmental Agency for Innovation Systems (VINNOVA), Swedish Research Council (VR), Kempestiftelserna, CNRS (ATIP), and Marie Curie Action [PCIG-GA-2012-334021]

Subjects
Microscopy, Confocal, Indoleacetic Acids, Arabidopsis Proteins, Science, Gene Expression Profiling, [SDV]Life Sciences [q-bio], Blotting, Western, fungi, Arabidopsis, Temperature, Gene Expression Regulation, Developmental, food and beverages, Plants, Genetically Modified, Plant Roots, Article, Gene Expression Regulation, Plant, Brassinosteroids, Mutation, Protein Kinases, Plant Shoots, Signal Transduction
Abstract

Due to their sessile nature, plants have to cope with and adjust to their fluctuating environment. Temperature elevation stimulates the growth of Arabidopsis aerial parts. This process is mediated by increased biosynthesis of the growth-promoting hormone auxin. How plant roots respond to elevated ambient temperature is however still elusive. Here we present strong evidence that temperature elevation impinges on brassinosteroid hormone signaling to alter root growth. We show that elevated temperature leads to increased root elongation, independently of auxin or factors known to drive temperature-mediated shoot growth. We further demonstrate that brassinosteroid signaling regulates root responses to elevated ambient temperature. Increased growth temperature specifically impacts on the level of the brassinosteroid receptor BRI1 to downregulate brassinosteroid signaling and mediate root elongation. Our results establish that BRI1 integrates temperature and brassinosteroid signaling to regulate root growth upon long-term changes in environmental conditions associated with global warming., Moderate heat stimulates the growth of Arabidopsis shoots in an auxin-dependent manner. Here, Martins et al. show that elevated ambient temperature modifies root growth by reducing the BRI1 brassinosteroid-receptor protein level and downregulating brassinosteroid signaling.

Published
2017

39. Photoelectron and Absorption Spectroscopy Studies of Metal-Free Phthalocyanine on Au(111): Experiment and Theory

Author

Olle Eriksson, Johann Lüder, Pål Palmgren, Sareh Ahmadi, Barbara Brena, Ieva Bidermane, Biplab Sanyal, Carla Puglia, Emmanuelle Göthelid, Maria Novella Piancastelli, Masumeh-Nina Shariati, Institut des Nanosciences de Paris (INSP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Department of Physics and Astronomy [Uppsala], Uppsala University, Swedish Foundation for Strategic Research (SSF), Swedish Research Council (VR), Goran Gustafsson Foundation, and Uppsala University Unimolecular Center (U3MEC)

Subjects
Absorption spectroscopy, Inorganic chemistry, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials, chemistry.chemical_compound, General Energy, Adsorption, chemistry, Metal free, X-ray photoelectron spectroscopy, Monolayer, Phthalocyanine, Molecule, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], Physical and Theoretical Chemistry
Abstract

International audience; The adsorption of monolayers and multilayers of metal-free phthalocyanine molecules on the Au(111) (root 3 x 22) reconstructed surface has been investigated by X-ray photoelectron spectroscopy (XPS) and X-ray absorption spectroscopy (XAS). Our results for the monolayer show that the molecules are arranged tightly onto the surface with their molecular plane parallel to it. In addition, the X-ray absorption spectra of the monolayer have been modeled by density functional theory, which could enlighten new aspect of the interaction between molecules and substrate. The XAS results evidence that also in the multilayer the molecules keep the orientation with the molecular plane parallel to the surface. These results are discussed in the framework of moleculemolecule/moleculeadsorbate interactions.

Published
2013

40. Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors

Author

Jana Braesel, César Nicolás, Anders Tunlid, Tomas Johansson, Dag Ahrén, Francois Rineau, Dimitrios Floudas, Björn Canbäck, Firoz Shah, Bernard Henrissat, Magnus Ellström, David S. Hibbett, Francis Martin, Per Persson, Mark M. Smits, Robert Carleer, Gerald Lackner, Johan Bentzer, Dirk Hoffmeister, Lund University [Lund], Hasselt University (UHasselt), Clark University, Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Architecture et fonction des macromolécules biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), King Abdulaziz University, Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), LabEx ARBRE : Advanced Research on the Biology of Tree and Forest Ecosystems ([LabEx ARBRE]), Office National des Forêts (ONF)-AgroParisTech-Institut National de la Recherche Agronomique (INRA)-Centre National de la Propriété Forestière-CRITT Bois-European Forest Institute = Institut Européen de la Forêt = Euroopan metsäinstituutti (EFI)-Université de Lorraine (UL), Swedish Research Council (VR), Knut and Alice Wallenberg Foundation, strategic research programme Biodiversity and Ecosystem Services in a Changing Climate (BECC), French National Research Agency through the Laboratory of Excellence ARBRE [ANR-11-LABX-0002-01], Office of Science of the US Department of Energy, ANR-11-LABX-0002,ARBRE,Recherches Avancées sur l'Arbre et les Ecosytèmes Forestiers(2011), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech-CRITT Bois-Office national des forêts (ONF)-Université de Lorraine (UL)-Centre National de la Propriété Forestière-European Forest Institute = Institut Européen de la Forêt = Euroopan metsäinstituutti (EFI), Hasselt University, Friedrich-Schiller-Universität Jena, Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Office National des Forêts (ONF)-Université de Lorraine (UL)-Centre National de la Propriété Forestière-CRITT Bois-European Forest Institute = Institut Européen de la Forêt = Euroopan metsäinstituutti (EFI)

Subjects
0301 basic medicine, spectroscopy, Transcription, Genetic, Physiology, ectomycorrhizal fungi, Genes, Fungal, Secondary Metabolism, Plant Science, Biology, Lignin, Fungal Proteins, Transcriptome, Soil, 03 medical and health sciences, Symbiosis, Phylogenetics, Gene Expression Regulation, Fungal, Mycorrhizae, soil organic matter, Botany, evolution, Organic matter, Organic Chemicals, Secondary metabolism, Gene, Phylogeny, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, chemistry.chemical_classification, Fungal protein, decomposition, Full Paper, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Research, Soil organic matter, Laccase, Fungi, Full Papers, 15. Life on land, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], 030104 developmental biology, transcriptome, chemistry, 13. Climate action, Oxidation-Reduction
Abstract

Ectomycorrhizal fungi are thought to have a key role in mobilizing organic nitrogen that is trapped in soil organic matter (SOM). However, the extent to which ectomycorrhizal fungi decompose SOM and the mechanism by which they do so remain unclear, considering that they have lost many genes encoding lignocellulose-degrading enzymes that are present in their saprotrophic ancestors. Spectroscopic analyses and transcriptome profiling were used to examine the mechanisms by which five species of ectomycorrhizal fungi, representing at least four origins of symbiosis, decompose SOM extracted from forest soils. In the presence of glucose and when acquiring nitrogen, all species converted the organic matter in the SOM extract using oxidative mechanisms. The transcriptome expressed during oxidative decomposition has diverged over evolutionary time. Each species expressed a different set of transcripts encoding proteins associated with oxidation of lignocellulose by saprotrophic fungi. The decomposition 'toolbox' has diverged through differences in the regulation of orthologous genes, the formation of new genes by gene duplications, and the recruitment of genes from diverse but functionally similar enzyme families. The capacity to oxidize SOM appears to be common among ectomycorrhizal fungi. We propose that the ancestral decay mechanisms used primarily to obtain carbon have been adapted in symbiosis to scavenge nutrients instead. This work was supported by grants from the Swedish Research Council (VR) (to A.T. and P.P.), the Knut and Alice Wallenberg Foundation (to A.T.), the strategic research programme Biodiversity and Ecosystem Services in a Changing Climate (BECC) (to A.T.) and the French National Research Agency through the Laboratory of Excellence ARBRE (ANR-11-LABX-0002-01) (to F.M.). Genome sequencing was conducted by the US Department of Energy Joint Genome Institute, supported by the Office of Science of the US Department of Energy. We also thank Annegret Kohler and Nicolas Cichocki for handling the fungal cultures, and principal investigators from the Mycorrhizal Genomics Initiative Consortium for providing the strain cultures and access to the genome sequences before publication.

Published
2016

41. Large effects of subtle electronic correlations on the energetics of vacancies in alpha-Fe

Author

Silke Biermann, Leonid Pourovskii, Sergei I. Simak, Olivier Parcollet, Pascal Delange, Michel Ferrero, Thomas Ayral, Centre de Physique Théorique [Palaiseau] (CPHT), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Institut de Physique Théorique - UMR CNRS 3681 (IPHT), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Chaire Physique de la matière condensée (A. Georges), Collège de France (CdF (institution)), Japan Science and Technology Agency (JST), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Linköping University (LIU), NUST MISiS (No. K3-2015-038) (Ru),The Swedish Research Council (VR) Project No. 2014-4750, LiLi-NFM,the Swedish Government Strategic Research Area in Materials Science on Functional Materials at Link¨oping University (FacultyGrant SFO-Mat-LiU No. 2009 00971),IDRIS/GENCI Orsay under project t2016091393, European Project: 319286,EC:FP7:ERC,ERC-2012-SyG,Q-MAC(2013), European Project: 278472,EC:FP7:ERC,ERC-2011-StG_20101014,MOTTMETALS(2012), European Project: 617196,EC:FP7:ERC,ERC-2013-CoG,CORRELMAT(2014), and Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)

Subjects
[PHYS]Physics [physics], Materials science, Condensed matter physics, Pacs : 61.72.jd, 71.10.-w, 71.27.+a, 75.50.Bb, Strongly Correlated Electrons (cond-mat.str-el), Energetics, Ab initio, FOS: Physical sciences, 02 engineering and technology, 021001 nanoscience & nanotechnology, 01 natural sciences, 3. Good health, Condensed Matter - Strongly Correlated Electrons, Condensed Matter::Materials Science, Vacancy defect, Lattice (order), 0103 physical sciences, Teoretisk kemi, Coulomb, Spectral function, 010306 general physics, 0210 nano-technology, Theoretical Chemistry, ComputingMilieux_MISCELLANEOUS
Abstract

We study the effect of electronic Coulomb correlations on the vacancy formation energy in paramagnetic alpha-Fe within ab initio dynamical mean-field theory. The calculated value for the formation energy is substantially lower than in standard density-functional calculations and in excellent agreement with experiment. The reduction is caused by an enhancement of electronic correlations at the nearest neighbors of the vacancy. This effect is explained by subtle changes in the corresponding spectral function of the d-electrons. The local lattice relaxations around the vacancy are substantially increased by many-body effects., Comment: Supplementary material included at the end of the file

Published
2016
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42. Investigation of cobalt redox mediators and effects of TiO2 film topology in dye-sensitized solar cells

Author

Safdari M., Lohse P.W., Häggman L., Frykstrand S., Högberg D., Rutland M., Asencio R.A., Gardner J., Kloo L., Hagfeldt A., Boschloo G. and This work was supported by the European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 246124 of the SANS project, the Swedish Energy Agency, the Swedish Research Council (VR), and the STandUP for Energy program.

Published
2016

43. The epidermis coordinates auxin-induced stem growth in response to shade

Author

Yogev Burko, Karin Ljung, Jeff A. Long, Joanne Chory, Carl Procko, Yvon Jaillais, The Salk Institute for Biological Studies, Reproduction et développement des plantes (RDP), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Department of Molecular, Cell, and Developmental Biology, University of California [Los Angeles] (UCLA), University of California-University of California, Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, NIH-National Cancer Institute Cancer Center P30 014195, Chapman Foundation, Helmsley Charitable Trust, NSF DBI-0735191 DBI-1265383, National Institutes of Health (NIH) 1F32GM101876-01, NIH GM52413 GM94428, National Science Foundation (NSF) EAGER grant IOS-1045256, Swedish Research Council (VR),Marianne and Marcus Wallenberg Foundation, Swedish Governmental Agency for Innovation Systems (Vinnova), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), and University of California (UC)-University of California (UC)

Subjects
0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Arabidopsis, 01 natural sciences, Medical and Health Sciences, Hypocotyl, Plant Epidermis, chemistry.chemical_compound, Gene Expression Regulation, Plant, Brassinosteroid, chemistry.chemical_classification, biology, Brassica rapa, Nuclear Proteins, food and beverages, Biological Sciences, Cell biology, Sunlight, Stem Cell Research - Nonembryonic - Non-Human, Signal transduction, Corrigendum, Signal Transduction, Biotechnology, Cell type, stem growth, 03 medical and health sciences, Shade avoidance, Auxin, epidermis, Brassinosteroids, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, shade avoidance, Epidermis (botany), Indoleacetic Acids, Arabidopsis Proteins, Gene Expression Profiling, Psychology and Cognitive Sciences, fungi, Plant, biology.organism_classification, Stem Cell Research, 030104 developmental biology, chemistry, Gene Expression Regulation, brassinosteroid, Mutation, auxin, 010606 plant biology & botany, Transcription Factors, Developmental Biology
Abstract

Growth of a complex multicellular organism requires coordinated changes in diverse cell types. These cellular changes generate organs of the correct size, shape, and functionality. In plants, the growth hormone auxin induces stem elongation in response to shade; however, which cell types of the stem perceive the auxin signal and contribute to organ growth is poorly understood. Here, we blocked the transcriptional response to auxin within specific tissues to show that auxin signaling is required in many cell types for correct hypocotyl growth in shade, with a key role for the epidermis. Combining genetic manipulations in Arabidopsis thaliana with transcriptional profiling of the hypocotyl epidermis from Brassica rapa, we show that auxin acts in the epidermis in part by inducing activity of the locally acting, growth-promoting brassinosteroid pathway. Our findings clarify cell-specific auxin function in the hypocotyl and highlight the complexity of cell type interactions within a growing organ.

Published
2016

44. Vegetable oil reactions within wood studied by direct 13C excitation with 1H decoupling and magic-angle sample spinning (MAS) NMR

Author

István Furó, Mats Johansson, Guilhem Pages, M Alireza Salehi, Sergey V. Dvinskikh, Qualité des Produits Animaux (QuaPA), Institut National de la Recherche Agronomique (INRA), Royal Institute of Technology in Stockholm (KTH), Wallenberg Laboratory, Göteborgs Universitet (GU), and Knut and Alice Wallenberg Foundation via the Wallenberg Wood Science Center, Swedish Research Council VR, Swedish Research Council Formas, 243-2006-273

Subjects
Materials science, Magic angle, General Chemical Engineering, engineering.material, 010402 general chemistry, 01 natural sciences, methyl linoleate, Coating, oil oxidation, Materials Chemistry, Molecule, Organic chemistry, oil immobilization, Anisotropy, methyl oleate, Spinning, C-13 single-pulse excitation magic-angle spinning, 010405 organic chemistry, Organic Chemistry, technology, industry, and agriculture, 0104 chemical sciences, Surfaces, Coatings and Films, Vegetable oil, Chemical engineering, engineering, SPMAS, [CHIM.OTHE]Chemical Sciences/Other, Excitation, Decoupling (electronics)
Abstract

International audience; Despite having been used for ages to protect wood against the influence of outdoor elements, the chemistry of vegetable oils within wood is poorly known. We propose a method based on solid-state magic-angle sample spinning NMR to in situ characterize oil oxidation as well as its immobilization. To eliminate signal coming from wood molecules but to keep signal from the oil, direct 13C excitation is performed with low-power 1H decoupling during signal acquisition. To suppress the effect of anisotropic spin-interactions and magnetic field inhomogeneity, the sample is spun at the magic-angle. Mono- and polyunsaturated fatty acid derivatives show a difference in their oxidation process: the monounsaturated methyl oleate reacts with wood components and becomes immobilized while the polyunsaturated methyl linoleate becomes oxidized and form oligomers but does not seem to bind to wood. Linola® oil behaves as would be expected on the basis of its composition by monounsaturated and polyunsaturated chains. This method can be generalized to all coating treatments to characterize chemical pathways and reactions. A better understanding of coating effects on wood is a crucial step to design more efficient protective mixtures.

Published
2012

45. Antimicrobial activity of filamentous fungi isolated from highly antibiotic-contaminated river sediment

Author

Erja Chryssanthou, K. Stefan Svahn, D. G. Joakim Larsson, Ulf Göransson, Hesham R. El-Seedi, Bjorn R. Olsen, Lars Bohlin, and Swedish Governmental Agency for Innovation Systems (VINNOVA), Uppsala University, the Swedish International Development Agency (SIDA) and the Swedish Research Council (VR)

Subjects
Aspergillus, biology, Gliotoxin, Epidemiology, medicine.drug_class, secondary metabolites, gliotoxin, Antibiotics, Aspergillus fumigatus, gliotoxin, antimicrobial activity, filamentous fungi, Environmental Science (miscellaneous), Antimicrobial, biology.organism_classification, Enterococcus faecalis, Aspergillus fumigatus, Microbiology, lcsh:Infectious and parasitic diseases, chemistry.chemical_compound, chemistry, medicine, Original Article, lcsh:RC109-216, Candida albicans, Bacteria
Abstract

Background: Filamentous fungi are well known for their production of substances with antimicrobial activities, several of which have formed the basis for the development of new clinically important antimicrobial agents. Recently, environments polluted with extraordinarily high levels of antibiotics have been documented, leading to strong selection pressure on local sentinel bacterial communities. In such microbial ecosystems, where multidrug-resistant bacteria are likely to thrive, it is possible that certain fungal antibiotics have become less efficient, thus encouraging alternative strategies for fungi to compete with bacteria. Methods: In this study, sediment of a highly antibiotic-contaminated Indian river was sampled in order to investigate the presence of cultivable filamentous fungi and their ability to produce substances with antimicrobial activity. Results: Sixty one strains of filamentous fungi, predominantly various Aspergillus spp. were identified. The majority of the Aspergillus strains displayed antimicrobial activity against methicillin-resistant Staphylococcus aureus, extended-spectrum beta-lactamase-producing Escherichia coli, vancomycin-resistant Enterococcus faecalis and Candida albicans. Bioassay-guided isolation of the secondary metabolites of A. fumigatus led to the identification of gliotoxin. Conclusion: This study demonstrated proof of principle of using bioassay-guided isolation for finding bioactive molecules Keywords: secondary metabolites; Aspergillus; gliotoxin (Published: 24 May 2012) Citation: Infection Ecology and Epidemiology 2012, 2 : 11591 - http://dx.doi.org/10.3402/iee.v2i0.11591

Published
2012

46. Polymer Binding to Carbon Nanotubes in Aqueous Dispersions: Residence Time on the Nanotube Surface As Obtained by NMR Diffusometry

Author

István Furó, Guilhem Pages, Michael Shtein, Anton Frise, Oren Regev, Ilan Pri Bar, Royal Institute of Technology in Stockholm (KTH), Department of Chemical Engineering, Ben-Gurion University of the Negev (BGU), Swedish Research Council (VR), Knut and Alice Wallenberg Foundation, and Israeli Ministry of Health 3-00000-6083

Subjects
1h nmr spectroscopy, Nanotube, Magnetic Resonance Spectroscopy, Materials science, Polymers, Surface Properties, Aqueous dispersion, 02 engineering and technology, Carbon nanotube, 010402 general chemistry, Residence time (fluid dynamics), 01 natural sciences, law.invention, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, law, Polymer chemistry, Materials Chemistry, Copolymer, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Physical and Theoretical Chemistry, chemistry.chemical_classification, Nanotubes, Carbon, Water, Polymer, Poloxamer, 021001 nanoscience & nanotechnology, 0104 chemical sciences, Surfaces, Coatings and Films, chemistry, Chemical engineering, 0210 nano-technology
Abstract

International audience; The binding of block copolymer Pluronic F-127 in aqueous dispersions of single- (SWCNT) and multiwalled (MWCNT) carbon nanotubes has been studied by pulsed-field-gradient (PFG) 1H NMR spectroscopy. We show that a major fraction of polymers exist as a free species while a minor fraction is bound to the carbon nanotubes (CNT). The polymers exchange between these two states with residence times on the nanotube surface of 24 ± 5 ms for SWCNT and of 54 ± 11 ms for MWCNT. The CNT concentration in the solution was determined by improved thermal gravimetric analysis (TGA) indicating that the concentration of SWCNT dispersed by F-127 was significantly higher than that for MWCNT. For SWCNT, the area per adsorbed Pluronic F-127 molecule is estimated to be about 40 nm2.

Published
2012

47. Population regulation of territorial species: both site dependence and interference mechanisms matter

Author

Marie Nevoux, Malcolm A. C. Nicoll, Ken Norris, Debora Arlt, Carl G. Jones, Olivier Gimenez, School of Agriculture Policy and Development, Centre for Agri-Environmental Research, University of Reading (UOR), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut de Recherche pour le Développement (IRD [France-Sud]), Durrell Wildlife Conservation Trust, Mauritian Wildlife Foundation, Peregrine Fund, National Parks and Conservation Service, Government of Mauritius, Natural Environment Research Council, Swedish Research Council (VR), and French Research National Agency (ANR) [ANR-08-JCJC-0028-01]

Subjects
Male, 0106 biological sciences, [SDV]Life Sciences [q-bio], media_common.quotation_subject, Population Dynamics, Population, Breeding, Biology, Models, Biological, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Competition (biology), 010605 ornithology, Sexual Behavior, Animal, Animals, Population growth, education, Falconiformes, Research Articles, General Environmental Science, media_common, Population Density, education.field_of_study, General Immunology and Microbiology, Ecology, Mechanism (biology), General Medicine, Spatial heterogeneity, Density dependence, [SDE]Environmental Sciences, Spatial ecology, Female, Vital rates, Territoriality, General Agricultural and Biological Sciences
Abstract

International audience; Spatial patterns of site occupancy are commonly driven by habitat heterogeneity and are thought to shape population dynamics through a site-dependent regulatory mechanism. When examining this, however, most studies have only focused on a single vital rate (reproduction), and little is known about how space effectively contributes to the regulation of population dynamics. We investigated the underlying mechanisms driving density-dependent processes in vital rates in a Mauritius kestrel population where almost every individual was monitored. Different mechanisms acted on different vital rates, with breeding success regulated by site dependence (differential use of space) and juvenile survival by interference (density-dependent competition for resources). Although territorial species are frequently assumed to be regulated through site dependence, we show that interference was the key regulatory mechanism in this population. Our integrated approach demonstrates that the presence of spatial processes regarding one trait does not mean that they necessarily play an important role in regulating population growth, and demonstrates the complexity of the regulatory process.

Published
2010

48. How valence bond theory can help you understand your (bio)chemical reaction

Author

Etienne Derat, Avital Shurki, Shina Caroline Lynn Kamerlin, Alexandre Barrozo, Méthodes et Application en Chimie Organique (MACO), Institut Parisien de Chimie Moléculaire (IPCM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), European Research Council under the European Community's Seventh Framework Programme (FP7)/ERC [306474], Swedish Research Council (VR), Israel Science Foundation [1337/13], CNRS, and MENESR

Subjects
Scope (project management), 010405 organic chemistry, business.industry, Chemistry, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Nobel prizes, Nanotechnology, Hydrogen Bonding, General Chemistry, Kemi, 010402 general chemistry, 01 natural sciences, 0104 chemical sciences, 3. Good health, Models, Chemical, Chemical Sciences, Quantum Theory, Valence bond theory, Computer Simulation, Software engineering, business
Abstract

International audience; Almost a century has passed since valence bond (VB) theory was originally introduced to explain covalent bonding in the H-2 molecule within a quantum mechanical framework. The past century has seen constant improvements in this theory, with no less than two distinct Nobel prizes based on work that is essentially developments in VB theory. Additionally, ongoing advances in both methodology and computational power have greatly expanded the scope of problems that VB theory can address. In this Tutorial Review, we aim to give the reader a solid understanding of the foundations of modern VB theory, using a didactic example of a model S(N)2 reaction to illustrate its immediate applications. This will be complemented by examples of challenging problems that at present can only be efficiently addressed by VB-based approaches. Finally, the ongoing importance of VB theory is demonstrated. It is concluded that VB will continue to be a major driving force for chemistry in the century to come.

Published
2015

49. Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant

Author

Alberto Mendoza Herrera, Philippe Normand, María Antonia Cruz Hernández, Elizabeth G. Wilbanks, Alison M. Berry, Anna M O'Brien, Pascale Fournier, Katharina Pawlowski, Irina V. Demina, Petar Pujic, Theoden Vigil-Stenman, Kai Battenberg, Marc T. Facciotti, Claudine Médigue, Tomas Persson, Brian Vanden Heuvel, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Swedish Research Council [229-2005-679], Swedish Research Council VR [2007-17840-52674-16], CA Experiment Station project [PLS-2173-H], UC Davis Plant Sciences Graduate Fellowship, NSF GRFP [DGE-1148897], NSF [EF-0949453], ANR (BugsInACell) [ANR-13-BSV7-0013-03], ANR (Sesam) [ANR-10-BLAN-1708], UC Mexus-Conacyt [05-24], Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), and Börnke, Frederik

Subjects
General Science & Technology, Science, [SDV]Life Sciences [q-bio], Frankia, plante hôte, medicine.disease_cause, Rhizobium leguminosarum, Actinobacteria, Rhizobia, Bacterial Proteins, protéine bactérienne, Botany, Operon, medicine, Genetics, Datisca glomerata, Symbiosis, ComputingMilieux_MISCELLANEOUS, Phylogeny, régulation de l'expression génique, Multidisciplinary, Genome, biology, opéron, Bacterial, food and beverages, Rosales, Gene Expression Regulation, Bacterial, biology.organism_classification, Cucurbitaceae, Gene Expression Regulation, Candidatus, Medicine, curcubitaceae, Actinorhizal plant, symbiose, Genome, Bacterial, Research Article
Abstract

International audience; Frankia strains are nitrogen-fixing soil actinobacteria that can form root symbioses with actinorhizal plants. Phylogenetically, symbiotic frankiae can be divided into three clusters, and this division also corresponds to host specificity groups. The strains of cluster II which form symbioses with actinorhizal Rosales and Cucurbitales, thus displaying a broad host range, show suprisingly low genetic diversity and to date can not be cultured. The genome of the first representative of this cluster, Candidatus Frankia datiscae Dg1 (Dg1), a microsymbiont of Datisca glomerata, was recently sequenced. A phylogenetic analysis of 50 different housekeeping genes of Dg1 and three published Frankia genomes showed that cluster II is basal among the symbiotic Frankia clusters. Detailed analysis showed that nodules of Datisca glomerata, independent of the origin of the inoculum, contain several closely related cluster II Frankia operational taxonomic units. Actinorhizal plants and legumes both belong to the nitrogen-fixing plant clade, and bacterial signaling in both groups involves the common symbiotic pathway also used by arbuscular mycorrhizal fungi. However, so far, no molecules resembling rhizobial Nod factors could be isolated from Frankia cultures. Alone among Frankia genomes available to date, the genome of Dg1 contains the canonical nod genes nodA, nodB and nodC known from rhizobia, and these genes are arranged in two operons which are expressed in Datisca glomerata nodules. Furthermore, Frankia Dg1 nodC was able to partially complement a Rhizobium leguminosarum A34 nodC::Tn5 mutant. Phylogenetic analysis showed that Dg1 Nod proteins are positioned at the root of both alpha- and beta-rhizobial NodABC proteins. NodA-like acyl transferases were found across the phylum Actinobacteria, but among Proteobacteria only in nodulators. Taken together, our evidence indicates an Actinobacterial origin of rhizobial Nod factors.

Published
2015

50. Characterization of gas phase iron phthalocyanine with X-ray photoelectron and absorption spectroscopies

Author

Bidermane, Ieva, Luder, Johann, Totani, Roberta, Grazioli, Cesare, Simone, Monica, Coreno, Marcello, Kivimaeki, Antti, Ahlund, John, Lozzi, Luca, Brena, Barbara, Puglia, Carla, Institut des Nanosciences de Paris (INSP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Department of Physics and Astronomy [Uppsala], Uppsala University, Swedish Research Council (VR), Carl Trygger Foundation, Uppsala University Unimolecular Electronics Consortium (U3MEC), KAW foundation, Bidermane, Ieva, Lüder, Johann, Totani, Roberta, Grazioli, Cesare, de Simone, Monica, Coreno, Marcello, Kivimäki, Antti, Åhlund, John, Lozzi, Luca, Brena, Barbara, and Puglia, Carla

Subjects
Ligand fields, Ligand field, X-ray photoelectron spectroscopy, FePc, Gas phase, X-ray absorption spectroscopy, Condensed Matter Physics, Electronic, Optical and Magnetic Materials, Electronic, Condensed Matter Physic, Optical and Magnetic Materials, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat]
Abstract

International audience; Despite the numerous studies dedicated to phthalocyanine molecules adsorbed on surfaces, in monolayer or thin film, very few works have been focused on the characterization of vapors of these molecules. In this article we present the C 1s, N 1s and Fe 2p photoemission results as well as N K-edge X-ray absorption data of iron phthalocyanine (FePc) in gas phase. Presented comparison of X-ray photoelectron spectroscopy and X-ray absorption spectroscopy spectra of FePc films show a great similarity with the gas phase results, confirming the molecular character of thick films. The Fe2p photoemission spectrum of the gas phase FePc, shown for the first time, can be considered as a fingerprint of the Fe(II) ionic state of the central metal of the iron phthalocyanine. The performed multiplet calculations for describing the Fe 2p XP spectrum indicate 3Eg (a1g2eg32g1) state as the most probable ground state for thick film of iron phthalocyanine. (C) 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Published
2015

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