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1. Chemical composition of the essential oil of Phlomis linearis Boiss.Bal., and biological effects on the CAM-assay: a safety evaluation

Author

Mehmet Yaşar Dadandi, D. H. Paper, Kemal Hüsnü Can Başer, Betül Demirci, Gerhard Franz, Anadolu Üniversitesi, Eczacılık Fakültesi, Farmakognozi Anabilim Dalı, Demirci, Betül, and Başer, K. Hüsnü Can

Subjects
Turkey, General Biochemistry, Genetics and Molecular Biology, Gas Chromatography-Mass Spectrometry, law.invention, Phlomis, Sesquiterpenes, Germacrane, law, Allantois, Botany, Oils, Volatile, Animals, Phlomis Linearis, Cam-Assay, Chemical composition, Phlomis linearis, Essential oil, Polycyclic Sesquiterpenes, biology, Traditional medicine, Chemistry, Anti-Inflammatory Agents, Non-Steroidal, Biological activity, Chorion, biology.organism_classification, Essential Oil, Lamiaceae, Cattle, Gas chromatography–mass spectrometry, Hydro distillation, Cam assay, Sesquiterpenes
Abstract

WOS: 000188262800014, PubMed ID: 14713159, Phlomis linearis Boiss. & Bal. of the Lamiaceae family growing in central, east and southeast Anatolia is an endemic species for Turkey. The essential oil obtained from the aerial parts by hydro distillation was subsequently analyzed by GC/MS. The main components of the oil were found as beta-caryophyllene (24.2%), germacrene D (22.3%) and caryophyllene oxide (9.2%), among 49 identified compounds, representing 94.5% of the total essential oil. The overall biological activity of the essential oil (100 mug/pellet) was tested on the chorioallantoic membrane (CAM) of the fertilized hen's egg in order to examine the anti-angiogenic and anti-inflammatory activity. None of the tests showed pronounced activity, toxicity or irritation at the tested concentration.

Published
2004

2. Zika virus enhances monocyte adhesion and transmigration favoring viral dissemination to neural cells

Author

Emma Partiot, Nilda Vanesa Ayala-Nunez, Jacky G. Goetz, Gautier Follain, Judith R.E. Roels, Anita Eckly, Béatrice Uring-Lambert, Maxime Chazal, Raphael Gaudin, Gillian Hale, Frank M. J. Jacobs, Sandrine Bourdoulous, Orestis Faklaris, Sherif R. Zaki, Aurélie Hirschler, Nolwenn Jouvenet, Margot Carocci, Florian Bakoa, Sarah Cianférani, Christine Carapito, Frédéric Doussau, Brigid C. Bollweg, François Delalande, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA), Institut National de la Santé et de la Recherche Médicale (INSERM), Immuno-Rhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Strasbourg (UNISTRA), Fédération de Médecine Translationnelle de Strasbourg (FMTS), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, Swammerdam Institute for Life Sciences, University of Amsterdam [Amsterdam] (UvA)-Center for Neurosciences, Génomique virale et vaccination, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Université Paris Descartes - Paris 5 (UPD5), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), BioCampus Montpellier (BCM), Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Biologie et pharmacologie des plaquettes sanguines: hémostase, thrombose, transfusion, Université de Strasbourg (UNISTRA)-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM), Les Hôpitaux Universitaires de Strasbourg (HUS), Institut des Neurosciences Cellulaires et Intégratives (INCI), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), This work has received funding from the French State via the French National Research Agency (ANR) as part of the program Investissements d’avenir (IdEx Université de Strasbourg) to RG. This work was supported by an ATIP-AVENIR starting grant to RG. The research leading to these results has received funding from the People Program (Marie Curie Actions) of the European Union’s Seventh Framework Program (FP7/2007–2013) under REA grant agreement no. PCOFUND-GA-2013-609102, through the PRESTIGE program coordinated by Campus France, and from the French Agency for Research on AIDS and Viral Hepatitis (ANRS), both attributed to NVAN. Experiments conducted by G.F. and J.G.G. were funded by Plan Cancer (OptoMetaTrap), Ligue contre le Cancer, Idex Attractivités (University of Strasbourg), and by institutional funds from INSERM and University of Strasbourg. G.F. was supported by a doctoral fellowship from Ligue Contre le Cancer. Mass spectrometry experiments were supported by the French Proteomic Infrastructure (ProFI, ANR-10-INBS-08-03). F.B. is a recipient of a PhD grant provided by ANRT (Association Nationale de la Recherche et de la Technologie). N.J. is funded by Agence Nationale pour la Recherche (ANR-16-CE15-0025-01), Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur. CDC contributions to this paper written and edited by G.L.H. and B.C.B. in their private capacity. No official support or endorsement by the Centers for Disease Control and Prevention, Department of Health and Human Services is intended, nor should be inferred. All authors read, provided feedback, and approved the paper. The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention. The following reagent was obtained through the NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH: HIV-1 NL4-3 AD8 Infectious Molecular Clone (pNL(AD8)) from Dr. Eric O. Freed (cat# 11346)., ANR-16-CE15-0025,Viro-Storm,Mécanismes de production incontrôlée de cytokines au cours de l'infection virale(2016), European Project: 609102,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,PRESTIGE(2014), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), EFS-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), jouvenet, nolwenn, Mécanismes de production incontrôlée de cytokines au cours de l'infection virale - - Viro-Storm2016 - ANR-16-CE15-0025 - AAPG2016 - VALID, PRES Towards International Gain of Excellence - PRESTIGE - - EC:FP7:PEOPLE2014-09-01 - 2019-08-31 - 609102 - VALID, Equipe Direction scientifique, Sciences et Technologies de la Musique et du Son (STMS), Université Pierre et Marie Curie - Paris 6 (UPMC)-IRCAM-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-IRCAM-Centre National de la Recherche Scientifique (CNRS), École pratique des hautes études (EPHE), Neuro-Immunologie Virale, Virologie UMR1161 (VIRO), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de Photonique Quantique et Moléculaire (LPQM), Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-École normale supérieure - Cachan (ENS Cachan), Biologie et pharmacologie des plaquettes sanguines: hémostase, thrombose, transfusion (http://www.u949.inserm.fr/), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-EFS, Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de Masse BioOrganique, Département des Sciences Analytiques, Institut Pluridisciplinaire Hubert Curien, Strasbourg, France (LSMBO-DSA-IPHC), Centre National de la Recherche Scientifique (CNRS), Immunorhumathologie moléculaire, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and Molecular Neuroscience (SILS, FNWI)

Subjects
Central Nervous System, 0301 basic medicine, MESH: Neurons, General Physics and Astronomy, MESH: Organoids, MESH: Monocytes, Monocytes, Zika virus, 0302 clinical medicine, MESH: Transendothelial and Transepithelial Migration, Cerebellum, MESH: Animals, lcsh:Science, MESH: Embryonic Stem Cells, ComputingMilieux_MISCELLANEOUS, Zebrafish, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Neurons, Multidisciplinary, Zika Virus Infection, Cell adhesion molecule, food and beverages, Sciences du Vivant [q-bio]/Microbiologie et Parasitologie, Phenotype, 3. Good health, Cell biology, Organoids, Mechanisms of disease, medicine.anatomical_structure, MESH: Cell Survival, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Female, Endothelium, Cell Survival, Science, MESH: Zika Virus, Biology, MESH: Endothelium, Article, General Biochemistry, Genetics and Molecular Biology, Virus, MESH: Cell Adhesion, 03 medical and health sciences, Virology, medicine, Animals, Humans, MESH: Central Nervous System, Cellular microbiology, Cell adhesion, MESH: Zebrafish, Embryonic Stem Cells, MESH: Humans, Monocyte, fungi, Transendothelial and Transepithelial Migration, Zika Virus, General Chemistry, biology.organism_classification, Embryonic stem cell, MESH: Cerebellum, Disease Models, Animal, 030104 developmental biology, lcsh:Q, MESH: Disease Models, Animal, Cell Adhesion Molecules, MESH: Female, 030217 neurology & neurosurgery
Abstract

Zika virus (ZIKV) invades and persists in the central nervous system (CNS), causing severe neurological diseases. However the virus journey, from the bloodstream to tissues through a mature endothelium, remains unclear. Here, we show that ZIKV-infected monocytes represent suitable carriers for viral dissemination to the CNS using human primary monocytes, cerebral organoids derived from embryonic stem cells, organotypic mouse cerebellar slices, a xenotypic human-zebrafish model, and human fetus brain samples. We find that ZIKV-exposed monocytes exhibit higher expression of adhesion molecules, and higher abilities to attach onto the vessel wall and transmigrate across endothelia. This phenotype is associated to enhanced monocyte-mediated ZIKV dissemination to neural cells. Together, our data show that ZIKV manipulates the monocyte adhesive properties and enhances monocyte transmigration and viral dissemination to neural cells. Monocyte transmigration may represent an important mechanism required for viral tissue invasion and persistence that could be specifically targeted for therapeutic intervention., Zika virus (ZIKV) can infect the central nervous system, but it is not clear how it reaches the brain. Here, Ayala-Nunez et al. show in ex vivo and in vivo models that ZIKV can hitch a ride in monocytes in a Trojan Horse manner to cross the endothelium and disseminate the virus.

Published
2019

3. The Flemmingsome reveals an ESCRT-to-membrane coupling via ALIX/syntenin/syndecan-4 required for completion of cytokinesis

Author

Quentin Giai Gianetto, Neetu Gupta-Rossi, Mariette Matondo, Stéphane Frémont, Frédérique Cuvelier, Audrey Salles, Julia Chamot-Rooke, Hervé Ménager, Florine Milin, Sandrine Schmutz, Cyril Addi, Murielle Rocancourt, Magalie Duchateau, Arnaud Echard, Thibaut Douché, Adrien Presle, Pascale Zimmermann, Trafic membranaire et Division cellulaire - Membrane Traffic and Cell Division, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Collège doctoral [Sorbonne universités], Sorbonne Université (SU), Cytometrie et Biomarqueurs – Cytometry and Biomarkers (UTechS CB), Institut Pasteur [Paris], Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Plateforme de Protéomique / Proteomics platform, Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, BioImagerie Photonique – Photonic BioImaging (UTechS PBI), Centre de Recherche en Cancérologie de Marseille (CRCM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Aix Marseille Université (AMU), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), This work has been supported by Institut Pasteur, CNRS, and ANR (AbCyStem, Cytosign) to A.E. C.A. received a fellowship from the Doctoral School Complexité du Vivant ED515, contrat n° 2412/2016 and AMX. A.P. received a fellowship from the Doctoral School Complexité du Vivant ED515, contrat n°2611 bis/2016 and Fondation ARC pour la recherche sur le cancer (DOC20190508876)., We thank R. Basto, G. Hickson, J. Mathieu, J.-R. Huyhn, R. Shaughnessy, M. Serres, and T. Wai for critical reading of the paper, the Echard Lab members for helpful discussions, the Recombinant antibodies platform (TAb-IP, Institut Curie, Paris) and the DSHB (University of Iowa) for antibodies. GFP-MKLP2 cells were from the Hyman Lab MPI-MCBG Dresden45., UTechS PBI is part of the France–BioImaging infrastructure network (FBI) supported by the French National Research Agency (ANR-10-INSB-04, Investments for the Future), and acknowledges support from ANR/FBI and the Région Ile-de-France (program 'Domaine d’Intérêt Majeur-Malinf') for the use of the Zeiss LSM 780 Elyra PS1 microscope. We thank P.H. Commere from the Utechs CB, Institut Pasteur for FACS sorting., Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Collège Doctoral, Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Salles, Audrey

Subjects
0301 basic medicine, Syntenins, SYNDECAN, [SDV]Life Sciences [q-bio], General Physics and Astronomy, Cell Cycle Proteins, Plasma protein binding, ABSCISSION, 0302 clinical medicine, ALIX, SYNTENIN, lcsh:Science, Multidisciplinary, Chemistry, MOLECULAR-MECHANISMS, Transmembrane protein, 3. Good health, Cell biology, [SDV] Life Sciences [q-bio], Multidisciplinary Sciences, Midbody, Science & Technology - Other Topics, MACHINERY, LATE STEPS, Protein Binding, Cell division, Science, BIOGENESIS, SCISSION, HIV Budding, Endosomes, macromolecular substances, General Biochemistry, Genetics and Molecular Biology, ESCRT, Article, 03 medical and health sciences, Abscission, Humans, Cytokinesis, Organelles, MIDBODY, Science & Technology, Endosomal Sorting Complexes Required for Transport, Calcium-Binding Proteins, Cell Membrane, General Chemistry, 030104 developmental biology, Membrane protein, Syndecan-4, lcsh:Q, 030217 neurology & neurosurgery, HeLa Cells
Abstract

Cytokinesis requires the constriction of ESCRT-III filaments on the side of the midbody, where abscission occurs. After ESCRT recruitment at the midbody, it is not known how the ESCRT-III machinery localizes to the abscission site. To reveal actors involved in abscission, we obtained the proteome of intact, post-abscission midbodies (Flemmingsome) and identified 489 proteins enriched in this organelle. Among these proteins, we further characterized a plasma membrane-to-ESCRT module composed of the transmembrane proteoglycan syndecan-4, ALIX and syntenin, a protein that bridges ESCRT-III/ALIX to syndecans. The three proteins are highly recruited first at the midbody then at the abscission site, and their depletion delays abscission. Mechanistically, direct interactions between ALIX, syntenin and syndecan-4 are essential for proper enrichment of the ESCRT-III machinery at the abscission site, but not at the midbody. We propose that the ESCRT-III machinery must be physically coupled to a membrane protein at the cytokinetic abscission site for efficient scission, uncovering common requirements in cytokinesis, exosome formation and HIV budding., ESCRT filaments drive the final abscission between two daughter cells but how they physically interact with the membrane is unclear. Using proteomics, the authors show that syndecan-4/syntenin/ALIX couples the ESCRT machinery to the abscission site and thus promotes efficient abscission.

Published
2020

4. Agent-based modelling of reactive vaccination of workplaces and schools against COVID-19

Author

Benjamin Faucher, Rania Assab, Jonathan Roux, Daniel Levy-Bruhl, Cécile Tran Kiem, Simon Cauchemez, Laura Zanetti, Vittoria Colizza, Pierre-Yves Boëlle, Chiara Poletto, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Centre de Recherches sur l'Action Politique en Europe (ARENES), Université de Rennes (UR)-Institut d'Études Politiques [IEP] - Rennes-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Centre National de la Recherche Scientifique (CNRS), École des Hautes Études en Santé Publique [EHESP] (EHESP), Santé publique France - French National Public Health Agency [Saint-Maurice, France], Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Collège Doctoral, Sorbonne Université (SU), Haute Autorité de Santé [Saint-Denis La Plaine] (HAS), Tokyo Institute of Technology [Tokyo] (TITECH), We acknowledge financial support from Haute Autorité de Santé, the ANR and Fondation de France through the project NoCOV (00105995), the Municipality of Paris (https://www.paris.fr/) through the programme Emergence(s), EU H2020 grants MOOD(H2020-874850, paper MOOD 035) and RECOVER (H2020-101003589) (the contents of this publication do not necessarily reflect the views of the European Commission), the ANRS through the project EMERGEN (ANRS0151), and the Institut des Sciences duCalcul et de la Donnée., ANR-20-COVI-0070,NoCOV,Prévisions au court et moyen terme de la diffusion de COVID-19 dans la population générale française(2020), European Project: 874850,H2020-SC1-2019-Single-Stage-RTD,MOOD(2020), European Project: 101003589, H2020-SC1-PHE-CORONAVIRUS-2020,RECOVER(2020), EHESP, SCD, Prévisions au court et moyen terme de la diffusion de COVID-19 dans la population générale française - - NoCOV2020 - ANR-20-COVI-0070 - COVID-19 - VALID, MOnitoring Outbreak events for Disease surveillance in a data science context - MOOD - 874850 - INCOMING, Rapid European COVID-19 Emergency Response research - RECOVER - - H2020-SC1-PHE-CORONAVIRUS-20202020-02-14 - 2022-02-13 - 101003589 - VALID, and European Project: 874850,MOOD

Subjects
Multidisciplinary, Schools, Systems Analysis, Vaccination, General Physics and Astronomy, COVID-19, General Chemistry, General Biochemistry, Genetics and Molecular Biology, [SDV.IMM.VAC] Life Sciences [q-bio]/Immunology/Vaccinology, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Humans, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.IMM.VAC]Life Sciences [q-bio]/Immunology/Vaccinology, Workplace, COVID 19
Abstract

With vaccination against COVID-19 stalled in some countries, increasing vaccine accessibility and distribution could help keep transmission under control. Here, we study the impact of reactive vaccination targeting schools and workplaces where cases are detected, with an agent-based model accounting for COVID-19 natural history, vaccine characteristics, demographics, behavioural changes and social distancing. In most scenarios, reactive vaccination leads to a higher reduction in cases compared with non-reactive strategies using the same number of doses. The reactive strategy could however be less effective than a moderate/high pace mass vaccination program if initial vaccination coverage is high or disease incidence is low, because few people would be vaccinated around each case. In case of flare-ups, reactive vaccination could better mitigate spread if it is implemented quickly, is supported by enhanced test-trace-isolate and triggers an increased vaccine uptake. These results provide key information to plan an adaptive vaccination rollout.

Published
2021

5. Single-molecule localization microscopy

Author

Markus Sauer, Florian Schueder, Melike Lakadamyali, Gerti Beliu, Melina Theoni Gyparaki, Suliana Manley, Ralf Jungmann, Juliette Griffié, Mickaël Lelek, Christophe Zimmer, Imagerie et Modélisation - Imaging and Modeling, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), University of Pennsylvania, University of Würzburg = Universität Würzburg, Ludwig Maximilian University [Munich] (LMU), Max-Planck-Institut für Biochemie = Max Planck Institute of Biochemistry (MPIB), Max-Planck-Gesellschaft, Ecole Polytechnique Fédérale de Lausanne (EPFL), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), C.Z. acknowledges funding by Institut Pasteur, Fondation pour la Recherche Médicale (grant DEQ 20150331762), Région Ile de France, Agence Nationale de la Recherche and Investissement d’Avenir grant ANR-16-CONV-0005. M.La. acknowledges funding from the National Institutes of Health/National Institutes of General Medical Sciences (NIH/NIGMS) under grant RO1 GM133842-01. G.B. and M.S. acknowledge funding by the German Research Foundation (DFG) (SA829/19-1) and the European Regional Development Fund (EFRE project ‘Center for Personalized Molecular Immunotherapy’). F.S. and R.J. acknowledge support by the DFG through SFB1032 (project A11) and the Max Planck Society. J.G. and S.M. acknowledge funding by the European Union’s H2020 programme under the Marie Skłodowska-Curie grant BALTIC (to J.G.) and ERC Piko (to S.M.)., The authors apologize to the authors of numerous papers that could not be cited owing to limited space. M.Le. and C.Z. thank B. Lelandais for excellent comments on the manuscript and M. Singh for acquiring the image shown in Fig. 3b., ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), University of Pennsylvania [Philadelphia], Max Planck Institute of Biochemistry (MPIB), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPC)

Subjects
Single molecule localization, light-microscopy, Computer science, business.industry, General Medicine, Article, General Biochemistry, Genetics and Molecular Biology, optical reconstruction microscopy, diffraction-limit, Fluorescent labelling, 3-dimensional superresolution, live-cell, correlative superresolution fluorescence, Microscopy, Time course, Image acquisition, colocalization analysis, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Computer vision, Artificial intelligence, business, living cells, intramolecular spirocyclization, Image resolution, electron-microscopy
Abstract

Single-molecule localization microscopy (SMLM) describes a family of powerful imaging techniques that dramatically improve spatial resolution over standard, diffraction-limited microscopy techniques and can image biological structures at the molecular scale. In SMLM, individual fluorescent molecules are computationally localized from diffraction-limited image sequences and the localizations are used to generate a super-resolution image or a time course of super-resolution images, or to define molecular trajectories. In this Primer, we introduce the basic principles of SMLM techniques before describing the main experimental considerations when performing SMLM, including fluorescent labelling, sample preparation, hardware requirements and image acquisition in fixed and live cells. We then explain how low-resolution image sequences are computationally processed to reconstruct super-resolution images and/or extract quantitative information, and highlight a selection of biological discoveries enabled by SMLM and closely related methods. We discuss some of the main limitations and potential artefacts of SMLM, as well as ways to alleviate them. Finally, we present an outlook on advanced techniques and promising new developments in the fast-evolving field of SMLM. We hope that this Primer will be a useful reference for both newcomers and practitioners of SMLM. This Primer explains the central concepts of single-molecule localization microscopy (SMLM) before discussing experimental considerations regarding fluorophores, optics and data acquisition, processing and analysis. The Primer further describes recent high-impact discoveries made by SMLM techniques and concludes by discussing emerging methodologies.

Published
2021

6. Forest production efficiency increases with growth temperature

Author

Alessandro Cescatti, Alessio Collalti, Andreas Ibrom, Giorgio Matteucci, Marcos Fernández-Martínez, Ramdane Alkama, Daniel S. Goll, Julia Pongratz, Philippe Ciais, Anders Stockmarr, Vanessa Haverd, Stephen Sitch, Julia E. M. S. Nabel, Iain Colin Prentice, Pierre Friedlingstein, Almut Arneth, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), FOE-2019 College of Natural Resources, University of California Berkeley, CNR: DTA.AD003.474, We thank R.H. Waring, S. Vicca, M. Campioli, F. Pagani and E. Grieco for early constructive comments and thoughtful suggestions, S. Noce for the map of data points. We thank efforts from all site investigators and their funding agencies. This paper contributes to the AXA Chair Programme in Biosphere and Climate Impacts and the Imperial College initiative Grand Challenges in Ecosystems and the Environment. A.C. and G.M. are partially supported by resources available from the Ministry of University and Research (FOE-2019), under the project 'Climate Change' (CNR DTA.AD003.474), M.F.-M. is a postdoctoral fellow of the Research Foundation—Flanders (FWO), AXA Research Fund, and Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)

Subjects
0106 biological sciences, 010504 meteorology & atmospheric sciences, General Physics and Astronomy, adaptation, Atmospheric sciences, 01 natural sciences, Nutrient, Forest production efficiency, ddc:550, SDG 13 - Climate Action, gpp, lcsh:Science, Plant ecology, chemistry.chemical_classification, forest productivity, Carbon dioxide in Earth's atmosphere, Biomass (ecology), Multidisciplinary, Climate-change ecology, Biogeography, [SDE]Environmental Sciences, Engineering sciences. Technology, primary production, biomass production efficienty, Science, carbon use efficiency, chemistry.chemical_element, General Biochemistry, Genetics and Molecular Biology, Article, Latitude, Organic matter, Ecosystem, Precipitation, Biology, 0105 earth and related environmental sciences, Computer. Automation, npp, Primary production, General Chemistry, 15. Life on land, Earth sciences, chemistry, 13. Climate action, Environmental science, lcsh:Q, Forest ecology, Carbon, 010606 plant biology & botany
Abstract

Forest production efficiency (FPE) metric describes how efficiently the assimilated carbon is partitioned into plants organs (biomass production, BP) or—more generally—for the production of organic matter (net primary production, NPP). We present a global analysis of the relationship of FPE to stand-age and climate, based on a large compilation of data on gross primary production and either BP or NPP. FPE is important for both forest production and atmospheric carbon dioxide uptake. We find that FPE increases with absolute latitude, precipitation and (all else equal) with temperature. Earlier findings—FPE declining with age—are also supported by this analysis. However, the temperature effect is opposite to what would be expected based on the short-term physiological response of respiration rates to temperature, implying a top-down regulation of carbon loss, perhaps reflecting the higher carbon costs of nutrient acquisition in colder climates. Current ecosystem models do not reproduce this phenomenon. They consistently predict lower FPE in warmer climates, and are therefore likely to overestimate carbon losses in a warming climate., Many models assume a universal carbon use efficiency across forest biomes, in contrast to assumptions of other process-based models. Here the authors analyse forest production efficiency across a wide range of climates to show a positive relationship with annual temperature and precipitation, indicating that ecosystem models are overestimating forest carbon losses under warming.

Published
2020

7. Stochastic modeling reveals how motor protein and filament properties affect intermediate filament transport

Author

Sandrine Etienne-Manneville, Stéphanie Portet, Cécile Leduc, J. C. Dallon, Brigham Young University (BYU), Polarité cellulaire, Migration et Cancer - Cell Polarity, Migration and Cancer, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), University of Manitoba [Winnipeg], This work was supported by: EPSRC grant numbers EP/K032208/1 and EP/R014604/1 and by La Ligue contre le cancer and the Institut Pasteur., The authors would like to thank the Isaac Newton Institute for Mathematical Sciences for support and hospitality during the programme 'Coupling Geometric PDE’s with Physics for Cell Morphology, Motility and Pattern Formation' when the work on this paper was undertaken., Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and ANR-16-CE13-0019,SiFi2Net,Filaments intermédiaires: du filament unique au réseau(2016)

Subjects
0301 basic medicine, Statistics and Probability, Materials science, [SDV]Life Sciences [q-bio], Dynein, Biological Transport, Active, Kinesins, Catch bond, macromolecular substances, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Microtubules, Models, Biological, General Biochemistry, Genetics and Molecular Biology, Quantitative Biology::Cell Behavior, Protein filament, Motor protein, Quantitative Biology::Subcellular Processes, 03 medical and health sciences, 0302 clinical medicine, Molecular motor, Vimentin, Intermediate filaments, Intermediate filament, Cytoskeleton, Stochastic Processes, General Immunology and Microbiology, Applied Mathematics, Dyneins, Molecular motors, General Medicine, Kinesin, Stochastic, 030104 developmental biology, Modeling and Simulation, Biophysics, General Agricultural and Biological Sciences, 030217 neurology & neurosurgery
Abstract

International audience; Intermediate filaments are a key component of the cytoskeleton. Their transport along microtubules plays an essential role in the control of the shape and structural organization of cells. To identify the key parameters responsible for the control of intermediate filament transport, we generated a model of elastic filament transport by microtubule-associated dynein and kinesin. The model is also applicable to the transport of any elastically-coupled cargoes. We investigate the effect of filament properties such as number of motor binding sites, length, and elasticity on motion of filaments. Additionally, we consider the effect of motor properties, i.e. off rates, on filament transport. When one motor has a catch bond off rate it dictates the motion, whereas when motors have the same type of off rate filaments can alternate between retrograde and anterograde motions. The elasticity of filaments optimizes the filament transport and the coordination of motors along the length of the filament.

Published
2019

8. Social and non-social autism symptoms and trait domains are genetically dissociable

Author

Freddy Cliquet, Varun Warrier, Roberto Toro, Hyejung Won, Richard Delorme, Thomas Bourgeron, Anders D. Børglum, Janita Bralten, Claire S. Leblond, Geert Poelmans, Jakob Grove, Ward De Witte, Bhismadev Chakrabarti, David A. Hinds, Simon Baron-Cohen, Toro, Roberto [0000-0002-6671-858X], Cliquet, Freddy [0000-0002-9989-0685], Chakrabarti, Bhismadev [0000-0002-6649-7895], Børglum, Anders D. [0000-0001-8627-7219], Grove, Jakob [0000-0003-2284-5744], Hinds, David A. [0000-0002-4911-803X], Apollo - University of Cambridge Repository, University of Cambridge [UK] (CAM), Génétique humaine et fonctions cognitives - Human Genetics and Cognitive Functions (GHFC (UMR_3571 / U-Pasteur_1)), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), Child and Adolescent Psychiatry Department [AP- HP Hôpital Robert Debré], AP-HP Hôpital universitaire Robert-Debré [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Radboud University Medical Center [Nijmegen], Radboud University [Nijmegen], University of Reading (UOR), The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus University [Aarhus], 23andMe Inc., V.W. was funded by St. John’s College, Cambridge, and the Cambridge Commonwealth Trust. This study was funded by grants to SBC from the Medical Research Council, the Wellcome Trust, the Autism Research Trust, the Templeton World Charity Foundation, and to T.B. from the Institut Pasteur, the CNRS, the INSERM, The Fondamental Foundation, the APHP, the BioPsy Labex and the University Paris Diderot. The research was conducted in association with the National Institute for Health Research (NIHR) Collaboration for Leadership in Applied Health Research and Care East of England at Cambridgeshire and Peterborough NHS Foundation Trust. We also received support from the NIHR Cambridge Biomedical Research Centre. We acknowledge with gratitude the generous support of Drs Dennis and Mireille Gillings in strengthening the collaboration between S.B.-C. and T.B., and between Cambridge University and the Institut Pasteur. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health. Data obtained from 23andMe was supported by the National Human Genome Research Institute of the National Institutes of Health (grant number R44HG006981). The UK Medical Research Council and Wellcome (grant ref: 102215/2/13/2) and the University of Bristol provide core support for ALSPAC. GWAS data were generated by Sample Logistics and Genotyping Facilities at Wellcome Sanger Institute and LabCorp (Laboratory Corporation of America) using support from 23andMe. This publication is the work of the authors who will serve as guarantors for the content of this paper. The iPSYCH (The Lundbeck Foundation Initiative for Integrative Psychiatric Research) team acknowledges funding from The Lundbeck Foundation (grant nos. R102-A9118 and R155-2014-1724), the Stanley Medical Research Institute, the European Research Council (project no.: 294838), the Novo Nordisk Foundation for supporting the Danish National Biobank resource, and grants from Aarhus and Copenhagen Universities and University Hospitals, including support to the iSEQ Center, the GenomeDK HPC facility, and the CIRRAU Center. The project leading to this application has received funding from the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement no. 777394. The JU receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA and AUTISM SPEAKS, Autistica, SFARI. We thank the iPSCH-Broad Autism Group and the EU-AIMS LEAP group for sharing data. A full list of the authors and affiliations in the iPSYCH-Broad autism group and the EU-AIMS LEAP group is provided in the Supplementary Information., The 23andMe Research Team : Michelle Agee, Babak Alipanahi, Adam Auton, Robert K. Bell, Katarzyna Bryc, Sarah L. Elson, Pierre Fontanillas, Nicholas A. Furlotte, Karen E. Huber, Aaron Kleinman, Nadia K. Litterman, Jennifer C. McCreight, Matthew H. McIntyre, Joanna L. Mountain, Carrie A.M. Northover, Steven J. Pitts, J. Fah Sathirapongsasuti, Olga V. Sazonova, Janie F. Shelton, Suyash Shringarpure, Chao Tian, Joyce Y. Tung, Vladimir Vacic & Catherine H. Wilson, European Project: 294838,EC:FP7:ERC,ERC-2011-ADG_20110310,EIMS(2012), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), and Radboud university [Nijmegen]

Subjects
Male, DIAGNOSTIC OBSERVATION SCHEDULE, LD SCORE REGRESSION, 45/43, Medicine (miscellaneous), Genome-wide association study, Genome-wide association studies, Developmental psychology, FUNCTIONING AUTISM, Cohort Studies, 0302 clinical medicine, Heritability of autism, MESH: Cohort Studies, lcsh:QH301-705.5, GENERAL-POPULATION, 631/208/366/1373, 0303 health sciences, MESH: Genetic Predisposition to Disease, article, Autism spectrum disorders, MESH: Reproducibility of Results, Phenotype, Autistic traits, 631/208/727/2000, Trait, Female, General Agricultural and Biological Sciences, Psychology, MESH: Social Behavior, EMPATHY QUOTIENT, MESH: Autistic Disorder, 631/208/205/2138, Genetic predisposition to disease, MESH: Phenotype, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, PSYCHOMETRIC ANALYSIS, All institutes and research themes of the Radboud University Medical Center, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], mental disorders, medicine, Humans, REPETITIVE BEHAVIOR, Autistic Disorder, GENOME-WIDE ASSOCIATION, Social Behavior, Association (psychology), 030304 developmental biology, SYSTEMATIZING QUOTIENT, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], MESH: Humans, Reproducibility of Results, SPECTRUM QUOTIENT AQ, medicine.disease, MESH: Male, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, lcsh:Biology (General), MESH: Genome-Wide Association Study, Autism, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], MESH: Female, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract

The core diagnostic criteria for autism comprise two symptom domains – social and communication difficulties, and unusually repetitive and restricted behaviour, interests and activities. There is some evidence to suggest that these two domains are dissociable, though this hypothesis has not yet been tested using molecular genetics. We test this using a genome-wide association study (N = 51,564) of a non-social trait related to autism, systemising, defined as the drive to analyse and build systems. We demonstrate that systemising is heritable and genetically correlated with autism. In contrast, we do not identify significant genetic correlations between social autistic traits and systemising. Supporting this, polygenic scores for systemising are significantly and positively associated with restricted and repetitive behaviour but not with social difficulties in autistic individuals. These findings strongly suggest that the two core domains of autism are genetically dissociable, and point at how to fractionate the genetics of autism., Varun Warrier et al. report a genome-wide association study of systemising, a non-social trait associated with autism. They find 3 loci associated with systemising and show that this trait has no significant genetic correlations to social phenotypic measures, demonstrating that the social and non-social aspects of autism are genetically distinct.

Published
2019
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9. Cellular Senescence: Defining a Path Forward

Author

John M. Sedivy, Paul D. Robbins, Cleo L. Bishop, Vassilis G. Gorgoulis, Konstantinos Vougas, Konstantinos Evangelou, Valery Krizhanovsky, Dorothy C. Bennett, Eiji Hara, Diana Jurk, Gerardo Ferbeyre, Judith Campisi, Masashi Narita, Laura J. Niedernhofer, Manuel Serrano, Clemens A. Schmitt, Peter D. Adams, Oliver Bischof, Andrea Alimonti, Marco Demaria, Jesús Gil, Daohong Zhou, Manuel Collado, Thomas von Zglinicki, Andrea B. Maier, João F. Passos, Institut Pasteur [Paris], National and Kapodistrian University of Athens (NKUA), University of Manchester [Manchester], Biomedical Research Foundation of the Academy of Athens (BRFAA), Institute of Cancer Sciences [Glasgow, UK] (CR-UK Beatson Institute), University of Glasgow, Sanford Burnham Prebys Medical Discovery Institute, Oncology Institute of Southern Switzerland (IOSI), Università della Svizzera italiana = University of Italian Switzerland (USI), Universita degli Studi di Padova, Veneto Institute of Molecular Medicine [Padova, Italy] (VIMM), University of London [London], Organisation Nucléaire et Oncogenèse / Nuclear Organization and Oncogenesis, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Bart's and The London School of Medicine and Dentistry, Queen Mary University of London (QMUL), Buck Institute for Research on Aging, Universidade de Santiago de Compostela [Spain] (USC ), Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CR CHUM), Centre Hospitalier de l'Université de Montréal (CHUM), Université de Montréal (UdeM)-Université de Montréal (UdeM), Université de Montréal (UdeM), MRC London Institute of Medical Sciences (LMC), Imperial College London, Research Institute for Microbial Diseases [Osaka, Japan] (RIMD), Osaka University [Osaka], Department of Molecular Cell Biology [Rehovot], Weizmann Institute of Science [Rehovot, Israël], Robert and Arlene Kogod Center on Aging [Rochester, MN, USA], Mayo Clinic, Vrije Universiteit Amsterdam [Amsterdam] (VU), University of Melbourne, University of Cambridge [UK] (CAM), University of Minnesota [Twin Cities] (UMN), University of Minnesota System, Max Delbrück Center for Molecular Medicine [Berlin] (MDC), Helmholtz-Gemeinschaft = Helmholtz Association, Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Kepler University Hospital, Brown University, Newcastle University [Newcastle], University of Florida [Gainesville] (UF), Institute for Research in Biomedicine [Barcelona, Spain] (IRB), University of Barcelona-Barcelona Institute of Science and Technology (BIST), Institució Catalana de Recerca i Estudis Avançats (ICREA), University of Groningen [Groningen], European Research Institute for the Biology of Ageing [Groningen] (ERIBA), University Medical Center Groningen [Groningen] (UMCG), M.D. is funded by the Dutch Cancer Foundation, Netherlands (grant ID 10989). V.G., K.E., and K.V. were financially supported by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grants agreement no. 722729 (SYNTRAIN), the Welfare Foundation for Social & Cultural Sciences (KIKPE), Greece, the KIKPE Foundation, Athens, Greece, Pentagon Biotechnology, UK, DeepMed IO, UK, grant no. 775 from the Hellenic Foundation for Research and Innovation (HFRI), and NKUA-SARG grants 70/3/9816, 70/3/12128, and 70/3/15603. M.S.: is funded by the IRB and by grants from the Spanish Ministry of Economy co-funded by the European Regional Development Fund (ERDF) (SAF2013-48256-R), the European Research Council (ERC-2014-AdG/669622), and 'laCaixa' Foundation., We would like to thank Nikolaos Kastrinakis, Panagiotis V.S. Vasileiou, Gkikas Magiorkinis, Eleni Fitsiou, and Michela Borghesan for their valuable support to this work. We apologize in advance that, for reason of space, we have omitted the citations of relevant papers and reviews., National and Kapodistrian University of Athens = University of Athens (NKUA | UoA), Organisation Nucléaire et Oncogenèse - Nuclear Organization and Oncogenesis, Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris], University of Santiago de Compostela [Spain] (USC), Centre de recherche du Chum [Montréal] (CRCHUM), Université de Montréal [Montréal], Research Institute for Microbial Diseases, Weizmann Institute of Science, University of Minnesota [Twin Cities], Max Delbrück Center for Molecular Medicine [Berlin], Charité - Universitätsmedizin Berlin / Charite - University Medicine Berlin, University of Florida [Gainesville], University of Barcelona, Università degli Studi di Padova = University of Padua (Unipd), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Narita, Masashi [0000-0001-7764-577X], and Apollo - University of Cambridge Repository

Subjects
Senescence, EXPRESSION, Aging, Cell cycle checkpoint, [SDV]Life Sciences [q-bio], Cell, DNA-DAMAGE RESPONSE, [SDV.CAN]Life Sciences [q-bio]/Cancer, Computational biology, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Mitochondrion, Biology, General Biochemistry, Genetics and Molecular Biology, CHROMATIN LANDSCAPE, 03 medical and health sciences, 0302 clinical medicine, MITOCHONDRIA, ONCOGENE-INDUCED SENESCENCE, medicine, Humans, OXIDATIVE STRESS, Senolytic, Cellular Senescence, 11 Medical and Health Sciences, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Regulation of gene expression, 0303 health sciences, P53, [SDV.MHEP.GEG]Life Sciences [q-bio]/Human health and pathology/Geriatry and gerontology, Genetic Diseases, Inborn, DARK SIDE, Cell Cycle Checkpoints, 06 Biological Sciences, CANCER, Chromatin, medicine.anatomical_structure, Gene Expression Regulation, CELLS, Developmental biology, 030217 neurology & neurosurgery, Biomarkers, Developmental Biology
Abstract

International audience; Cellular senescence is a cell state implicated in various physiological processes and a wide spectrum of age-related diseases. Recently, interest in therapeutically targeting senescence to improve healthy aging and age-related disease, otherwise known as senotherapy, has been growing rapidly. Thus, the accurate detection of senescent cells, especially in vivo, is essential. Here, we present a consensus from the International Cell Senescence Association (ICSA), defining and discussing key cellular and molecular features of senescence and offering recommendations on how to use them as biomarkers. We also present a resource tool to facilitate the identification of genes linked with senescence, SeneQuest (available at http://Senequest.net). Lastly, we propose an algorithm to accurately assess and quantify senescence, both in cultured cells and in vivo.

Published
2019
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10. Actin activates Pseudomonas aeruginosa ExoY nucleotidyl cyclase toxin and ExoY-like effector domains from MARTX toxins

Author

Undine Mechold, Abdelkader Namane, Cosmin Saveanu, Vasily Ogryzko, Alexander Belyy, Daniel Ladant, Lina Worpenberg, Souad Fellous, Dorothée Raoux-Barbot, Christien Merrifield, Elodie Assayag, Violaine David, Louis Renault, Véronique Henriot, Biochimie des Interactions Macromoléculaires / Biochemistry of Macromolecular Interactions, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Gamaleya Research Center, Génétique des Interactions Macromoléculaires, Signalisation, noyaux et innovations en cancérologie (UMR8126), Université Paris-Sud - Paris 11 (UP11)-Institut Gustave Roussy (IGR)-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), This project was funded by the Institut Pasteur under #PTR425 to U.M. and C.S. and by CNRS. A.B. was supported by a stipend from the Pasteur—Paris University (PPU) International PhD Program. We acknowledge the core facilities of Imagerie-Gif,(http://www.i2bc.paris-saclay.fr), supported by ‘France-BioImaging’ (ANR-10-INBS-04-01). This paper is dedicated to the memory of Vasily Ogryzko (1960–2016)., ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Biochimie des Interactions Macromoléculaires, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Signalisation, noyaux et innovations en cancérologie ( UMR8126 ), Université Paris-Sud - Paris 11 ( UP11 ) -Institut Gustave Roussy ( IGR ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), and ANR-10-INBS-04-01/10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée ( 2010 )

Subjects
0301 basic medicine, Science, Bacterial Toxins, General Physics and Astronomy, macromolecular substances, Saccharomyces cerevisiae, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Filamentous actin, Cyclase, Article, General Biochemistry, Genetics and Molecular Biology, Type three secretion system, Adenylyl cyclase, 03 medical and health sciences, Cyclic nucleotide, chemistry.chemical_compound, Bacterial Proteins, ExoY, Type III Secretion Systems, Adenylate cyclase, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Actin, Multidisciplinary, Virulence, Mass spectrometry, [ SDV.BC ] Life Sciences [q-bio]/Cellular Biology, Chemistry, Effector, General Chemistry, Transfection, Guanylate cyclase, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Actins, 3. Good health, Cell biology, 030104 developmental biology, Glucosyltransferases, Mutation, Pseudomonas aeruginosa, Protein Binding
Abstract

The nucleotidyl cyclase toxin ExoY is one of the virulence factors injected by the Pseudomonas aeruginosa type III secretion system into host cells. Inside cells, it is activated by an unknown eukaryotic cofactor to synthesize various cyclic nucleotide monophosphates. ExoY-like adenylate cyclases are also found in Multifunctional-Autoprocessing Repeats-in-ToXin (MARTX) toxins produced by various Gram-negative pathogens. Here we demonstrate that filamentous actin (F-actin) is the hitherto unknown cofactor of ExoY. Association with F-actin stimulates ExoY activity more than 10,000 fold in vitro and results in stabilization of actin filaments. ExoY is recruited to actin filaments in transfected cells and alters F-actin turnover. Actin also activates an ExoY-like adenylate cyclase MARTX effector domain from Vibrio nigripulchritudo. Finally, using a yeast genetic screen, we identify actin mutants that no longer activate ExoY. Our results thus reveal a new sub-group within the class II adenylyl cyclase family, namely actin-activated nucleotidyl cyclase (AA-NC) toxins., The ExoY toxin is injected by Pseudomonas aeruginosa into host cells, where it is activated by an unknown host factor. Here the authors identify such factor as filamentous actin.

Published
2016

11. Microarray-based Identification of Individual HERV Loci Expression: Application to Biomarker Discovery in Prostate Cancer

Author

Claire Rodriguez-Lafrasse, Myriam Decaussin-Petrucci, Philippe Pérot, Valérie Cheynet, Alain Ruffion, François Mallet, Guy Oriol, Nathalie Mugnier, BIOMERIEUX, Hospices Civils de Lyon (HCL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, This work was supported by bioMérieux SA, the Hospices Civils de Lyon and the French public agency OSEO (Advanced Diagnostics for New Therapeutic Approaches, a French government-funded program dedicated to personalized medicine). PP, VC, GO, NM, and FM are employees of bioMérieux SA. PP, NM and FM have submitted patent applications covering the findings of this paper, and We thank Cecile Montgiraud, Juliette Gimenez, Magali Jaillard and Bertrand Bonnaud for their contribution to the initial development and optimization of the HERV-V2 protocol. We also wish to thank Hader Haidous for his guidance on ethical considerations.

Subjects
Male, General Chemical Engineering, Endogenous retrovirus, Gene Expression, Genome, Transcriptome, 0302 clinical medicine, Affymetrix, Diagnosis, RNA, Neoplasm, Tumor Markers, Cancer Biology, Oligonucleotide Array Sequence Analysis, MESH: Aged, Genetics, 0303 health sciences, MESH: Middle Aged, General Neuroscience, Prostate, Middle Aged, prostate cancer, 3. Good health, MESH: DNA, Single-Stranded, 030220 oncology & carcinogenesis, Medicine, MESH: Biomarkers, Tumor, microarray, MESH: Endogenous Retroviruses, PCA3, DNA, Complementary, Human Endogenous Retroviruses, NcRNA transcription, DNA, Single-Stranded, [SDV.CAN]Life Sciences [q-bio]/Cancer, Biology, ENCODE, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.MHEP.AHA]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], Biomarkers, Tumor, Humans, Molecular Biology, 030304 developmental biology, Aged, Prostatectomy, MESH: Humans, General Immunology and Microbiology, Microarray analysis techniques, Pharmacological, Endogenous Retroviruses, Prostatic Neoplasms, MESH: DNA, Complementary, MESH: RNA, Neoplasm, Biological, Microarray Analysis, MESH: Male, Retroviridae, MESH: Prostatic Neoplasms, MESH: Oligonucleotide Array Sequence Analysis, Human genome, Issue 81, HERV, Biomarkers
Abstract

International audience; The prostate-specific antigen (PSA) is the main diagnostic biomarker for prostate cancer in clinical use, but it lacks specificity and sensitivity, particularly in low dosage values 1. 'How to use PSA' remains a current issue, either for diagnosis as a gray zone corresponding to a concentration in serum of 2.5-10 ng/ml which does not allow a clear differentiation to be made between cancer and noncancer 2 or for patient follow-up as analysis of post-operative PSA kinetic parameters can pose considerable challenges for their practical application 3,4. Alternatively, noncoding RNAs (ncRNAs) are emerging as key molecules in human cancer, with the potential to serve as novel markers of disease, e.g. PCA3 in prostate cancer 5,6 and to reveal uncharacterized aspects of tumor biology. Moreover, data from the ENCODE project published in 2012 showed that different RNA types cover about 62% of the genome. It also appears that the amount of transcriptional regulatory motifs is at least 4.5x higher than the one corresponding to protein-coding exons. Thus, long terminal repeats (LTRs) of human endogenous retroviruses (HERVs) constitute a wide range of putative/candidate transcriptional regulatory sequences, as it is their primary function in infectious retroviruses. HERVs, which are spread throughout the human genome, originate from ancestral and independent infections within the germ line, followed by copy-paste propagation processes and leading to multicopy families occupying 8% of the human genome (note that exons span 2% of our genome). Some HERV loci still express proteins that have been associated with several pathologies including cancer 7-10. We have designed a high-density microarray, in Affymetrix format, aiming to optimally characterize individual HERV loci expression, in order to better understand whether they can be active, if they drive ncRNA transcription or modulate coding gene expression. This tool has been applied in the prostate cancer field (Figure 1).

Published
2013

12. Constitutive expression of stromal derived factor-1 by mucosal epithelia and its role in HIV transmission and propagation

Author

Mariagrazia Uguccioni, Bernhard Moser, X Y Li, Fernando Arenzana-Seisdedos, Christina M. Parker, Ellen C. Ebert, Jan Marsal, Ali Amara, William W. Agace, José L. Pablos, Thierry Delaunay, Arthur I. Roberts, Sylvia Thelen, Génomique, développement et pouvoir pathogène (GD2P), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Brigham and Women’s Hospital [Boston, MA], Harvard Medical School [Boston] (HMS), Immunologie Virale, Institut Pasteur [Paris] (IP), Robert Wood Johnson Medical School [Piscataway, NJ] (RWJMS), Hospital Universitario 12 de Octubre [Madrid], Universität Bern [Bern] (UNIBE), Institut National de la Recherche Agronomique (INRA), and This work was supported by grants from the Swedish Foundation for International Cooperation in Research and Higher Education (STINT) and the Swedish Medical Research Council (MFR 3131) to W.W.A., grants from the NIH to C.M.P. (DK52978) and to E.C.E. (DK42166), a grant from the Agence Nationale de Recherche sur le SIDA (ANRS) to A.A., grant 438+/050291 from the Swiss National Science Foundation to B.M., and grant 98/0356 from the Fondo de Investigaciones Sanitarias, Ministerio de Sanidad y Consumo (FIS) to J.L.P. One of the authors of this paper, C.M.P., had a financial interest in Millennium Pharmaceuticals Inc.

Subjects
Receptors, CXCR4, Chemokine, Stromal cell, Receptors, CCR5, Chemokine receptor CCR5, [SDV]Life Sciences [q-bio], CXCR4, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Chemokine receptor, 0302 clinical medicine, Viral entry, Humans, Intestinal Mucosa, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, biology, Agricultural and Biological Sciences(all), Biochemistry, Genetics and Molecular Biology(all), virus diseases, HIV, Virology, Chemokine CXCL12, 3. Good health, VIROLOGIE, CCL20, Immunology, biology.protein, General Agricultural and Biological Sciences, Chemokines, CXC, Ex vivo, 030215 immunology
Abstract

International audience; HIV particles that use the chemokine receptor CXCR4 as a coreceptor for entry into cells (X4-HIV) inefficiently transmit infection across mucosal surfaces [1], despite their presence in seminal fluid and mucosal secretions from infected individuals 2, 3, 4. In addition, although intestinal lymphocytes are susceptible to infection with either X4-HIV particles or particles that use the chemokine receptor CCR5 for viral entry (R5-HIV) during ex vivo culture [5], only systemic inoculation of R5-chimeric simian-HIV (S-HIV) results in a rapid loss of CD4+ intestinal lymphocytes in macaques [6]. The mechanisms underlying the inefficient capacity of X4-HIV to transmit infection across mucosal surfaces and to infect intestinal lymphocytes in vivo have remained elusive. The CCR5 ligands RANTES, MIP-1α and MIP-1β suppress infection by R5-HIV-1 particles via induction of CCR5 internalization, and individuals whose peripheral blood lymphocytes produce high levels of these chemokines are relatively resistant to infection 7, 8, 9. Here, we show that the CXCR4 ligand stromal derived factor-1 (SDF-1) is constitutively expressed by mucosal epithelial cells at sites of HIV transmission and propagation. Furthermore, CXCR4 is selectively downmodulated on intestinal lymphocytes within the setting of prominent SDF-1 expression. We postulate that mucosally derived SDF-1 continuously downmodulates CXCR4 on resident HIV target cells, thereby reducing the transmission and propagation of X4 HIV at mucosal sites. Moreover, such a mechanism could contribute to the delayed emergence of X4 isolates, which predominantly occurs during the later stages of the HIV infection.

Published
2000
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13. β-lactam antibiotics promote bacterial mutagenesis via an RpoS-mediated reduction in replication fidelity

Author

Jörg Vogel, Ivan Matic, S. Crussard, Jesús Blázquez, Luisa Laureti, Zeynep Baharoglu, Didier Mazel, F. Darfeuille, Alexandro Rodríguez-Rojas, Arnaud Gutierrez, Heni Abida, Robustesse et évolvabilité de la vie (U1001), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología [Madrid] (CNB-CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Plasticité du Génome Bactérien - Bacterial Genome Plasticity (PGB), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Régulations Naturelles et Artificielles (ARNA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bordeaux Ségalen [Bordeaux 2], Julius-Maximilians-Universität Würzburg (JMU), This work was supported by the FP7-HEALTH-F3-2010-241476 and ANR-09-BLAN-0251 grants. A.G. was supported by a fellowship from the French Ministry of Science and Education. D.M. was supported by the Institut Pasteur, Centre National de la Recherche Scientifique (CNRS-UMR 3525), the French National Research Agency (ANR-08-MIE-016), LABEX IBEID and the European Union Seventh Framework Programme EvoTAR. Z.B. was supported by a postdoctoral fellowship from the DIM Malinf. J.B. was supported by grants PI10/00105 (FIS) and REIPI (RD06/0008), both from Ministerio de Ciencia e Innovacion, Instituto de Salud Carlos III., We thank Dan Andersson’s lab (Uppsala University, Sweden) for providing the anti-DinB antibody, Marie Francoise Norel (Pasteur Institute, Paris) for providing the anti-RpoS antibody and Paul Modrich’s lab for providing the anti-MutS antibody., I.M., A.G., D.M., J.B., F.D. and J.V. designed the research and wrote the paper. A.G., L.L., H.A. and S.C. performed experiments with E. coli. Z.B. performed experiments and analysed data with V. cholerae. A.R.R. performed experiments and analysed data with P. aeruginosa. F.D. and J.V. performed in vitro experiments with SdsR and analysed data., ANR-09-BLAN-0251,bactadapt(2009), ANR-08-MIEN-0016,IIRE,Integrase d'integron recombinaison et expression(2008), European Project: 241476,EC:FP7:HEALTH,FP7-HEALTH-2009-single-stage,PAR(2010), European Project: 282004,EC:FP7:HEALTH,FP7-HEALTH-2011-single-stage,EVOTAR(2011), HOFFMANN, Isabelle, Blanc - - bactadapt2009 - ANR-09-BLAN-0251 - Blanc - VALID, Maladies Infectieuses et environnement - Integrase d'integron recombinaison et expression - - IIRE2008 - ANR-08-MIEN-0016 - MIE - VALID, Predicting antibiotic resistance - PAR - - EC:FP7:HEALTH2010-04-01 - 2013-03-31 - 241476 - VALID, Evolution and Transfer of Antibiotic Resistance - EVOTAR - - EC:FP7:HEALTH2011-10-01 - 2015-09-30 - 282004 - VALID, Centro Nacional de Biotecnologia, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU)

Subjects
DNA Replication, medicine.drug_class, [SDV]Life Sciences [q-bio], Antibiotics, General Physics and Astronomy, Sigma Factor, MESH: DNA Replication, Biology, beta-Lactams, medicine.disease_cause, General Biochemistry, Genetics and Molecular Biology, Microbiology, 03 medical and health sciences, Antibiotic resistance, Bacterial Proteins, MESH: beta-Lactams, MESH: Anti-Bacterial Agents, Escherichia coli, medicine, Vibrio cholerae, MESH: Bacterial Proteins, 030304 developmental biology, MESH: Mutagenesis, 0303 health sciences, Multidisciplinary, Bacteria, 030306 microbiology, Pseudomonas aeruginosa, MESH: Escherichia coli, Mutagenesis, MESH: Reactive Oxygen Species, MESH: Sigma Factor, General Chemistry, biochemical phenomena, metabolism, and nutrition, Anti-Bacterial Agents, 3. Good health, [SDV] Life Sciences [q-bio], MESH: Bacteria, Regulon, MESH: Pseudomonas aeruginosa, bacteria, Reactive Oxygen Species, rpoS, MESH: Vibrio cholerae
Abstract

Antimicrobials: mismatch excels when ampicillin runs low. [Nat Rev Microbiol. 2013]; International audience; Regardless of their targets and modes of action, subinhibitory concentrations of antibiotics can have an impact on cell physiology and trigger a large variety of cellular responses in different bacterial species. Subinhibitory concentrations of β-lactam antibiotics cause reactive oxygen species production and induce PolIV-dependent mutagenesis in Escherichia coli. Here we show that subinhibitory concentrations of β-lactam antibiotics induce the RpoS regulon. RpoS regulon induction is required for PolIV-dependent mutagenesis because it diminishes the control of DNA-replication fidelity by depleting MutS in E. coli, Vibrio cholerae and Pseudomonas aeruginosa. We also show that in E. coli, the reduction in mismatch-repair activity is mediated by SdsR, the RpoS-controlled small RNA. In summary, we show that mutagenesis induced by subinhibitory concentrations of antibiotics is a genetically controlled process. Because this mutagenesis can generate mutations conferring antibiotic resistance, it should be taken into consideration for the development of more efficient antimicrobial therapeutic strategies.

Published
2013

14. Evidence for carry-over effects of predator exposure on pathogen transmission potential

Author

Thierry Lefèvre, Koudraogo B. Yameogo, Kounbobr Roch Dabiré, Frédéric Simard, Olivier Roux, Abdoulaye Diabaté, Benjamin Roche, Amélie Vantaux, Institut de Recherche en Sciences de la Santé (IRSS), CNRST, Diversity, ecology, evolution & Adaptation of arthropod vectors (MIVEGEC-DEEVA), Evolution des Systèmes Vectoriels (ESV), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD [France-Nord])-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Sorbonne Université (SU), Transmission-Interactions-Adaptations hôtes/vecteurs/pathogènes (MIVEGEC-TRIAD), O.R. received financial support through a post-doctoral fellowship from the IRD. Experimental infections were supported by the ANR grant no. 11-PDOC-006-01., and We thank the Associate Editor Dr Pejman Rohani and two anonymous reviewers for their valuable comments that greatly improved the manuscript. We thank Boubacar Nikiema for the RFLP-PCR, Jean Bazié and Raymond Hien for technical help with dissections and Andrea Yockey-Dejean for proofreading the paper.

Subjects
Male, life history, [SDV]Life Sciences [q-bio], Predation, Food chain, MESH: Malaria, Falciparum/transmission, MESH: Animals, Malaria, Falciparum, Life history, Predator, Pathogen, Research Articles, General Environmental Science, media_common, Ecology, Transmission potential, Longevity, General Medicine, Anopheles coluzzii, 3. Good health, carry-over effects, MESH: Larva/growth & development, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Anopheles/physiology, MESH: Longevity, Larva, Female, General Agricultural and Biological Sciences, Food Chain, media_common.quotation_subject, Plasmodium falciparum, MESH: Insect Vectors, Biology, General Biochemistry, Genetics and Molecular Biology, Competition (biology), MESH: Predatory Behavior, Heteroptera, MESH: Plasmodium falciparum/growth & development, Anopheles, parasitic diseases, Animals, Humans, MESH: Food Chain, host-parasite and predator-prey, MESH: Humans, General Immunology and Microbiology, fungi, MESH: Anopheles/growth & development, MESH: Heteroptera/physiology, MESH: Fertility, interactions, host–parasite and predator–prey interactions, MESH: Male, Insect Vectors, non-consumptive effects, MESH: Larva/physiology, Fertility, Predatory Behavior, MESH: Female
Abstract

Accumulating evidence indicates that species interactions such as competition and predation can indirectly alter interactions with other community members, including parasites. For example, presence of predators can induce behavioural defences in the prey, resulting in a change in susceptibility to parasites. Such predator-induced phenotypic changes may be especially pervasive in prey with discrete larval and adult stages, for which exposure to predators during larval development can have strong carry-over effects on adult phenotypes. To the best of our knowledge, no study to date has examined possible carry-over effects of predator exposure on pathogen transmission. We addressed this question using a natural food web consisting of the human malaria parasite Plasmodium falciparum , the mosquito vector Anopheles coluzzii and a backswimmer, an aquatic predator of mosquito larvae. Although predator exposure did not significantly alter mosquito susceptibility to P. falciparum , it incurred strong fitness costs on other key mosquito life-history traits, including larval development, adult size, fecundity and longevity. Using an epidemiological model, we show that larval predator exposure should overall significantly decrease malaria transmission. These results highlight the importance of taking into account the effect of environmental stressors on disease ecology and epidemiology.

Published
2015

15. PGC-1β: A Regulator of Mitochondrial Function with Subtle Roles in Energy Metabolism

Author

Adrienn Kis, Mark Campbell, Mohammad Bohlooly-Y, Keira Curtis, Barbara Cannon, Matej Orešič, E. Dale Abel, Vlad G. Zaha, Gema Medina-Gomez, Sheldon E. Litwin, Mercedes Jimenez-Linan, Antonio Vidal-Puig, Sihem Boudina, Kimberly T Fountain, Leonard H Storlien, Miguel López, Margaret Blount, Ping Hu, Helena M. Feldmann, Christopher J. Lelliott, Mikael Bjursell, Natasa Petrovic, Dongfang Zhang, Nadeene Parker, Maria Strömstedt, Aline Meirhaeghe, Michael Snaith, Autard, Delphine, Department of Clinical Biochemistry, University of Cambridge [UK] (CAM), AstraZeneca, The Wenner-Gren Institute, Stockholm University, Division of Cardiology, University of Utah, Division of Endocrinology, Metabolism, and Diabetes, Epidémiologie des maladies chroniques : impact des interactions gène environnement sur la santé des populations, Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille, Droit et Santé, Technical Research Centre of Finland, VTT Technical Research Centre of Finland (VTT), The work presented in this paper was supported by grants from the British Heart Foundation, Wellcome Trust Integrative Physiology, and Diabetes Wellness Research Foundation (to AVP lab), and NIH grants RO1HL73167 and UO1HL70525 from the National Institutes of Health and the Ben and Iris Margolis Foundation (to EDA - Established Investigator of the American Heart Association). Support was from the European Union (DLARFID), the Swedish Research Council, and the Swedish Cancer Society (to BC lab).

Subjects
Male, MESH: Cold Temperature, Adipose tissue, White adipose tissue, Mitochondrion, MESH: Mice, Knockout, Mitochondria, Heart, chemistry.chemical_compound, Mice, Norepinephrine, 0302 clinical medicine, Adipose Tissue, Brown, Heart Rate, Brown adipose tissue, Body Fat Distribution, Diabetes/Endocrinology/Metabolism, MESH: Thermogenesis, MESH: Animals, Biology (General), MESH: Heart Rate, Mice, Knockout, Mammals, 0303 health sciences, MESH: Muscle, Skeletal, General Neuroscience, MESH: Energy Metabolism, Heart, Thermogenesis, Mus (Mouse), Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha, MESH: Gene Expression Regulation, Mitochondria, Cold Temperature, medicine.anatomical_structure, Liver, MESH: Adipose Tissue, White, Synopsis, Female, MESH: Mitochondria, Heart, General Agricultural and Biological Sciences, Metabolic Networks and Pathways, Research Article, MESH: Electron Transport Chain Complex Proteins, medicine.medical_specialty, QH301-705.5, MESH: Mitochondria, MESH: Trans-Activators, Adipose Tissue, White, Biology, MESH: Diet, Atherogenic, MESH: Adipose Tissue, Brown, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Adrenergic Agents, Internal medicine, MESH: Norepinephrine, medicine, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Animals, MESH: Body Fat Distribution, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Muscle, Skeletal, MESH: Mice, 030304 developmental biology, Soleus muscle, General Immunology and Microbiology, Triglyceride, Body Weight, medicine.disease, MESH: Adrenergic Agents, MESH: Male, MESH: Body Weight, MESH: Heart, Endocrinology, chemistry, Electron Transport Chain Complex Proteins, Gene Expression Regulation, MESH: Metabolic Networks and Pathways, Trans-Activators, Diet, Atherogenic, Steatosis, Energy Metabolism, MESH: Female, 030217 neurology & neurosurgery, Transcription Factors, MESH: Liver
Abstract

The transcriptional coactivator peroxisome proliferator-activated receptor-gamma coactivator-1β (PGC-1β) has been implicated in important metabolic processes. A mouse lacking PGC-1β (PGC1βKO) was generated and phenotyped using physiological, molecular, and bioinformatic approaches. PGC1βKO mice are generally viable and metabolically healthy. Using systems biology, we identified a general defect in the expression of genes involved in mitochondrial function and, specifically, the electron transport chain. This defect correlated with reduced mitochondrial volume fraction in soleus muscle and heart, but not brown adipose tissue (BAT). Under ambient temperature conditions, PGC-1β ablation was partially compensated by up-regulation of PGC-1α in BAT and white adipose tissue (WAT) that lead to increased thermogenesis, reduced body weight, and reduced fat mass. Despite their decreased fat mass, PGC1βKO mice had hypertrophic adipocytes in WAT. The thermogenic role of PGC-1β was identified in thermoneutral and cold-adapted conditions by inadequate responses to norepinephrine injection. Furthermore, PGC1βKO hearts showed a blunted chronotropic response to dobutamine stimulation, and isolated soleus muscle fibres from PGC1βKO mice have impaired mitochondrial function. Lack of PGC-1β also impaired hepatic lipid metabolism in response to acute high fat dietary loads, resulting in hepatic steatosis and reduced lipoprotein-associated triglyceride and cholesterol content. Altogether, our data suggest that PGC-1β plays a general role in controlling basal mitochondrial function and also participates in tissue-specific adaptive responses during metabolic stress., The authors conduct an in-depth analysis of a PGC-1β knockout mouse; these animals posses specific defects in basal mitochondrial function and adaptation to metabolic stress.

Published
2006

16. Coordinated recruitment of Spir actin nucleators and myosin V motors to Rab11 vesicle membranes

Author

Andreas T. Grasskamp, Martin Kollmar, Janine Tittel, Margaret A. Titus, Petra Schwille, Eugen Kerkhoff, Florian Chardon, Bruno Goud, Thomas Weidemann, Gilles Malherbe, Olena Pylypenko, Annette Samol-Wolf, Bruno Baron, Patrick England, Carina Ida Luise Michel, Sabine Weiss, Alistair N. Hume, Anne Houdusse, Tobias Welz, Biologie Cellulaire et Cancer, Institut Curie [Paris]-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University Hospital Regensburg, Max-Planck-Institut für Biochemie = Max Planck Institute of Biochemistry (MPIB), Max-Planck-Gesellschaft, Max-Planck-Institut für Biophysikalische Chemie - Max Planck Institute for Biophysical Chemistry [Göttingen], Motilité structurale, Compartimentation et dynamique cellulaires (CDC), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS), University of Nottingham, UK (UON), Biophysique des macromolécules et leurs interactions, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), University of Minnesota [Twin Cities] (UMN), University of Minnesota System, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS), This paper was supported by the following grants:Centre National de la Recherche Scientifique to Anne Houdusse, Olena Pylypenko., Deutsche Forschungsgemeinschaft SPP 1464: KO 2251/13-1 to Martin Kollmar., Bayerische Forschungsstiftung WFKMS Nr. F2 - 5121.4.3.1 ‐10c (BayGene) to Eugen Kerkhoff., Fondation de la Recherche Medicale ING20140129255 to Anne Houdusse., Agence Nationale de la Recherche ANR-13-BSV8-0019-01 to Anne Houdusse., National Science Foundation MCB-1244235 to Margaret A Titus., University of Minnesota Medical School Award, E-0915-04 to Margaret A Titus., Deutsche Forschungsgemeinschaft SPP 1464: SCHW 716/11-1, -2 to Petra Schwille., Ligue Contre le Cancer RS16/75-67 to Anne Houdusse., Fondation ARC pour la Recherche sur le Cancer SFI20121205398 to Anne Houdusse., Deutsche Forschungsgemeinschaft SPP 1464: KE 447/10-1, -2 to Eugen Kerkhoff., We acknowledge SOLEIL for provision of synchrotron radiation facilities (proposal 20141015) and we would like to thank Pierre Legrand and Beatriz Guimares for assistance in using beamline PX1. We thank Sandra Lemke, Carsten Grashoff, Yilmaz Niyaz (Zeiss) and Volker Buschmann (Picoquant) for their generous support in FLIM. We thank Mitsuo Ikebe for providing a MyoVb cDNA. We acknowledge Wikayatou Attanda and Charles Gauquelin for support in recombinant protein production. We also acknowledge Damarys Loew and Vanessa Masson (Curie Institute Protein Mass Spectrometry Platform) for the peptide fingerprint analysis of Spir-2 constructs. BG, AHo, OP, GM, FC are part of the Labex CelTisPhyBio 11-LBX-0038, which is part of the IDEX PSL (ANR-10-IDEX-0001-02 PSL)., Max Planck Institute of Biochemistry (MPIB), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], and Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC)

Subjects
0301 basic medicine, Models, Molecular, Protein Conformation, none, [SDV]Life Sciences [q-bio], Arp2/3 complex, Microfilament, Crystallography, X-Ray, vesicle transport, Myosin head, Mice, 0302 clinical medicine, MESH: Protein Conformation, biophysics, Myosin, cell biology, structural biology, MESH: Animals, Biology (General), Actin nucleation, MESH: Protein Multimerization, General Neuroscience, Microfilament Proteins, General Medicine, Biophysics and Structural Biology, MESH: rab GTP-Binding Proteins/chemistry, Cell biology, MESH: rab GTP-Binding Proteins/metabolism, Medicine, MESH: Cytoplasmic Vesicles/metabolism, MESH: Membranes/metabolism, MESH: Models, Molecular, Research Article, Protein Binding, Myosin light-chain kinase, QH301-705.5, Science, Myosin Type V, MESH: Microfilament Proteins/chemistry, MESH: Microfilament Proteins/metabolism, macromolecular substances, Biology, General Biochemistry, Genetics and Molecular Biology, actin motor proteins, 03 medical and health sciences, MESH: Myosin Type V/metabolism, Animals, MESH: Protein Binding, Actin-binding protein, MESH: Mice, MESH: Myosin Type V/chemistry, Membranes, Spire, General Immunology and Microbiology, Cytoplasmic Vesicles, myosin V, Actin remodeling, MESH: Crystallography, X-Ray, 030104 developmental biology, rab GTP-Binding Proteins, Rab11, biology.protein, Protein Multimerization, actin nucleation, 030217 neurology & neurosurgery
Abstract

There is growing evidence for a coupling of actin assembly and myosin motor activity in cells. However, mechanisms for recruitment of actin nucleators and motors on specific membrane compartments remain unclear. Here we report how Spir actin nucleators and myosin V motors coordinate their specific membrane recruitment. The myosin V globular tail domain (MyoV-GTD) interacts directly with an evolutionarily conserved Spir sequence motif. We determined crystal structures of MyoVa-GTD bound either to the Spir-2 motif or to Rab11 and show that a Spir-2:MyoVa:Rab11 complex can form. The ternary complex architecture explains how Rab11 vesicles support coordinated F-actin nucleation and myosin force generation for vesicle transport and tethering. New insights are also provided into how myosin activation can be coupled with the generation of actin tracks. Since MyoV binds several Rab GTPases, synchronized nucleator and motor targeting could provide a common mechanism to control force generation and motility in different cellular processes. DOI: http://dx.doi.org/10.7554/eLife.17523.001