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Sfeir N, Kajdan M, Jalaguier S, Bonnet S, Teyssier C, Pyrdziak S, Yuan R, Bousquet E, Maraver A, Bernex F, Pirot N, Boissière-Michot F, Castet-Nicolas A, Lapierre M, Cavaillès V. RIP140 regulates transcription factor HES1 oscillatory expression and mitogenic activity in colon cancer cells. Mol Oncol 2024. [PMID: 38459621 DOI: 10.1002/1878-0261.13626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 01/17/2024] [Accepted: 02/23/2024] [Indexed: 03/10/2024] Open
Abstract
The transcription factor receptor-interacting protein 140 (RIP140) regulates intestinal homeostasis and tumorigenesis through Wnt signaling. In this study, we investigated its effect on the Notch/HES1 signaling pathway. In colorectal cancer (CRC) cell lines, RIP140 positively regulated HES1 gene expression at the transcriptional level via a recombining binding protein suppressor of hairless (RBPJ)/neurogenic locus notch homolog protein 1 (NICD)-mediated mechanism. In support of these in vitro data, RIP140 and HES1 expression significantly correlated in mouse intestine and in a cohort of CRC samples, thus supporting the positive regulation of HES1 gene expression by RIP140. Interestingly, when the Notch pathway is fully activated, RIP140 exerted a strong inhibition of HES1 gene transcription controlled by the level of HES1 itself. Moreover, RIP140 directly interacts with HES1 and reversed its mitogenic activity in human CRC cells. In line with this observation, HES1 levels were associated with a better patient survival only when tumors expressed high levels of RIP140. Our data identify RIP140 as a key regulator of the Notch/HES1 signaling pathway, with a dual effect on HES1 gene expression at the transcriptional level and a strong impact on colon cancer cell proliferation.
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Affiliation(s)
- Nour Sfeir
- IRCM, Institut de Recherche en Cancérologie de Montpellier, France
- INSERM, U1194, France
- Université de Montpellier, France
- Institut régional du Cancer de Montpellier, France
| | - Marilyn Kajdan
- IRCM, Institut de Recherche en Cancérologie de Montpellier, France
- INSERM, U1194, France
- Université de Montpellier, France
- Institut régional du Cancer de Montpellier, France
| | - Stéphan Jalaguier
- IRCM, Institut de Recherche en Cancérologie de Montpellier, France
- INSERM, U1194, France
- Université de Montpellier, France
- Institut régional du Cancer de Montpellier, France
| | - Sandrine Bonnet
- IRCM, Institut de Recherche en Cancérologie de Montpellier, France
- INSERM, U1194, France
- Université de Montpellier, France
- Institut régional du Cancer de Montpellier, France
| | - Catherine Teyssier
- IRCM, Institut de Recherche en Cancérologie de Montpellier, France
- INSERM, U1194, France
- Université de Montpellier, France
- Institut régional du Cancer de Montpellier, France
| | - Samuel Pyrdziak
- IRCM, Institut de Recherche en Cancérologie de Montpellier, France
- INSERM, U1194, France
- Université de Montpellier, France
- Institut régional du Cancer de Montpellier, France
| | - Rong Yuan
- Department of Medical Microbiology, Immunology and Cell Biology, School of Medicine, Southern Illinois University, Springfield, IL, USA
| | - Emilie Bousquet
- IRCM, Institut de Recherche en Cancérologie de Montpellier, France
- INSERM, U1194, France
- Université de Montpellier, France
- Institut régional du Cancer de Montpellier, France
| | - Antonio Maraver
- IRCM, Institut de Recherche en Cancérologie de Montpellier, France
- INSERM, U1194, France
- Université de Montpellier, France
- Institut régional du Cancer de Montpellier, France
| | - Florence Bernex
- IRCM, Institut de Recherche en Cancérologie de Montpellier, France
- INSERM, U1194, France
- Université de Montpellier, France
- Institut régional du Cancer de Montpellier, France
| | - Nelly Pirot
- IRCM, Institut de Recherche en Cancérologie de Montpellier, France
- INSERM, U1194, France
- Université de Montpellier, France
- Institut régional du Cancer de Montpellier, France
| | - Florence Boissière-Michot
- IRCM, Institut de Recherche en Cancérologie de Montpellier, France
- INSERM, U1194, France
- Université de Montpellier, France
- Institut régional du Cancer de Montpellier, France
- Translational Research Unit, Montpellier Cancer Institute Val d'Aurelle, France
| | - Audrey Castet-Nicolas
- IRCM, Institut de Recherche en Cancérologie de Montpellier, France
- INSERM, U1194, France
- Université de Montpellier, France
- Institut régional du Cancer de Montpellier, France
| | - Marion Lapierre
- IRCM, Institut de Recherche en Cancérologie de Montpellier, France
- INSERM, U1194, France
- Université de Montpellier, France
- Institut régional du Cancer de Montpellier, France
| | - Vincent Cavaillès
- IRCM, Institut de Recherche en Cancérologie de Montpellier, France
- INSERM, U1194, France
- Université de Montpellier, France
- Institut régional du Cancer de Montpellier, France
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Khalfi P, Denis Z, McKellar J, Merolla G, Chavey C, Ursic-Bedoya J, Soppa L, Szirovicza L, Hetzel U, Dufourt J, Leyrat C, Goldmann N, Goto K, Verrier E, Baumert TF, Glebe D, Courgnaud V, Gregoire D, Hepojoki J, Majzoub K. Comparative analysis of human, rodent and snake deltavirus replication. PLoS Pathog 2024; 20:e1012060. [PMID: 38442126 PMCID: PMC10942263 DOI: 10.1371/journal.ppat.1012060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 03/15/2024] [Accepted: 02/19/2024] [Indexed: 03/07/2024] Open
Abstract
The recent discovery of Hepatitis D (HDV)-like viruses across a wide range of taxa led to the establishment of the Kolmioviridae family. Recent studies suggest that kolmiovirids can be satellites of viruses other than Hepatitis B virus (HBV), challenging the strict HBV/HDV-association dogma. Studying whether kolmiovirids are able to replicate in any animal cell they enter is essential to assess their zoonotic potential. Here, we compared replication of three kolmiovirids: HDV, rodent (RDeV) and snake (SDeV) deltavirus in vitro and in vivo. We show that SDeV has the narrowest and RDeV the broadest host cell range. High resolution imaging of cells persistently replicating these viruses revealed nuclear viral hubs with a peculiar RNA-protein organization. Finally, in vivo hydrodynamic delivery of viral replicons showed that both HDV and RDeV, but not SDeV, efficiently replicate in mouse liver, forming massive nuclear viral hubs. Our comparative analysis lays the foundation for the discovery of specific host factors controlling Kolmioviridae host-shifting.
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Affiliation(s)
- Pierre Khalfi
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Zoé Denis
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Joe McKellar
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Giovanni Merolla
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Carine Chavey
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - José Ursic-Bedoya
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- Department of hepato-gastroenterology, Hepatology and Liver Transplantation Unit, Saint Eloi University Hospital, Montpellier, France
| | - Lena Soppa
- Institute of Medical Virology, National Reference Centre for Hepatitis B Viruses and Hepatitis D Viruses, German Center for Infection Research (DZIF, Partner Site Giessen-Marburg-Langen), Justus Liebig University Giessen, Giessen, Germany
| | - Leonora Szirovicza
- Medicum, Department of Virology, University of Helsinki, Helsinki, Finland
| | - Udo Hetzel
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
| | - Jeremy Dufourt
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR9004, Montpellier, France
| | - Cedric Leyrat
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Nora Goldmann
- Institute of Medical Virology, National Reference Centre for Hepatitis B Viruses and Hepatitis D Viruses, German Center for Infection Research (DZIF, Partner Site Giessen-Marburg-Langen), Justus Liebig University Giessen, Giessen, Germany
| | - Kaku Goto
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, Strasbourg, France
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France
| | - Eloi Verrier
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, Strasbourg, France
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France
| | - Thomas F. Baumert
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, Strasbourg, France
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France
| | - Dieter Glebe
- Institute of Medical Virology, National Reference Centre for Hepatitis B Viruses and Hepatitis D Viruses, German Center for Infection Research (DZIF, Partner Site Giessen-Marburg-Langen), Justus Liebig University Giessen, Giessen, Germany
| | - Valérie Courgnaud
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Damien Gregoire
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Jussi Hepojoki
- Medicum, Department of Virology, University of Helsinki, Helsinki, Finland
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
| | - Karim Majzoub
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
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3
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Quiroga-Artigas G, Moriel-Carretero M. Storage cell proliferation during somatic growth establishes that tardigrades are not eutelic organisms. Biol Open 2024; 13:bio060299. [PMID: 38411464 PMCID: PMC10924213 DOI: 10.1242/bio.060299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 01/22/2024] [Indexed: 02/28/2024] Open
Abstract
Tardigrades, microscopic ecdysozoans known for extreme environment resilience, were traditionally believed to maintain a constant cell number after completing embryonic development, a phenomenon termed eutely. However, sporadic reports of dividing cells have raised questions about this assumption. In this study, we explored tardigrade post-embryonic cell proliferation using the model species Hypsibius exemplaris. Comparing hatchlings to adults, we observed an increase in the number of storage cells, responsible for nutrient storage. We monitored cell proliferation via 5-ethynyl-2'-deoxyuridine (EdU) incorporation, revealing large numbers of EdU+ storage cells during growth, which starvation halted. EdU incorporation associated with molting, a vital post-embryonic development process involving cuticle renewal for further growth. Notably, DNA replication inhibition strongly reduced EdU+ cell numbers and caused molting-related fatalities. Our study is the first to demonstrate using molecular approaches that storage cells actively proliferate during tardigrade post-embryonic development, providing a comprehensive insight into replication events throughout their somatic growth. Additionally, our data underscore the significance of proper DNA replication in tardigrade molting and survival. This work definitely establishes that tardigrades are not eutelic, and offers insights into cell cycle regulation, replication stress, and DNA damage management in these remarkable creatures as genetic manipulation techniques emerge within the field.
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Affiliation(s)
- Gonzalo Quiroga-Artigas
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier CEDEX 05, France
| | - María Moriel-Carretero
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier CEDEX 05, France
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4
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Desroys du Roure P, Lajoie L, Mallavialle A, Alcaraz LB, Mansouri H, Fenou L, Garambois V, Rubio L, David T, Coenon L, Boissière-Michot F, Chateau MC, Ngo G, Jarlier M, Villalba M, Martineau P, Laurent-Matha V, Roger P, Guiu S, Chardès T, Gros L, Liaudet-Coopman E. A novel Fc-engineered cathepsin D-targeting antibody enhances ADCC, triggers tumor-infiltrating NK cell recruitment, and improves treatment with paclitaxel and enzalutamide in triple-negative breast cancer. J Immunother Cancer 2024; 12:e007135. [PMID: 38290768 PMCID: PMC10828871 DOI: 10.1136/jitc-2023-007135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2023] [Indexed: 02/01/2024] Open
Abstract
INTRODUCTION Triple-negative breast cancer (TNBC) prognosis is poor. Immunotherapies to enhance the antibody-induced natural killer (NK) cell antitumor activity are emerging for TNBC that is frequently immunogenic. The aspartic protease cathepsin D (cath-D), a tumor cell-associated extracellular protein with protumor activity and a poor prognosis marker in TNBC, is a prime target for antibody-based therapy to induce NK cell-mediated antibody-dependent cellular cytotoxicity (ADCC). This study investigated whether Fc-engineered anti-cath-D antibodies trigger ADCC, their impact on antitumor efficacy and tumor-infiltrating NK cells, and their relevance for combinatory therapy in TNBC. METHODS Cath-D expression and localization in TNBC samples were evaluated by western blotting, immunofluorescence, and immunohistochemistry. The binding of human anti-cath-D F1M1 and Fc-engineered antibody variants, which enhance (F1M1-Fc+) or prevent (F1M1-Fc-) affinity for CD16a, to secreted human and murine cath-D was analyzed by ELISA, and to CD16a by surface plasmon resonance and flow cytometry. NK cell activation was investigated by flow cytometry, and ADCC by lactate dehydrogenase release. The antitumor efficacy of F1M1 Fc-variants was investigated using TNBC cell xenografts in nude mice. NK cell recruitment, activation, and cytotoxic activity were analyzed in MDA-MB-231 cell xenografts by immunophenotyping and RT-qPCR. NK cells were depleted using an anti-asialo GM1 antibody. F1M1-Fc+ antitumor effect was assessed in TNBC patient-derived xenografts (PDXs) and TNBC SUM159 cell xenografts, and in combination with paclitaxel or enzalutamide. RESULTS Cath-D expression on the TNBC cell surface could be exploited to induce ADCC. F1M1 Fc-variants recognized human and mouse cath-D. F1M1-Fc+ activated NK cells in vitro and induced ADCC against TNBC cells and cancer-associated fibroblasts more efficiently than F1M1. F1M1-Fc- was ineffective. In the MDA-MB-231 cell xenograft model, F1M1-Fc+ displayed higher antitumor activity than F1M1, whereas F1M1-Fc- was less effective, reflecting the importance of Fc-dependent mechanisms in vivo. F1M1-Fc+ triggered tumor-infiltrating NK cell recruitment, activation and cytotoxic activity in MDA-MB-231 cell xenografts. NK cell depletion impaired F1M1-Fc+ antitumor activity, demonstrating their key role. F1M1-Fc+ inhibited growth of SUM159 cell xenografts and two TNBC PDXs. In combination therapy, F1M1-Fc+ improved paclitaxel and enzalutamide therapeutic efficacy without toxicity. CONCLUSIONS F1M1-Fc+ is a promising immunotherapy for TNBC that could be combined with conventional regimens, including chemotherapy or antiandrogens.
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Affiliation(s)
| | - Laurie Lajoie
- Université de Tours - INRAE, UMR1282, Infectiologie et Santé Publique (ISP), équipe BioMédicaments Anti-Parasitaires (BioMAP), Tours, France
| | - Aude Mallavialle
- IRCM, INSERM U1194, University of Montpellier, ICM, Montpellier, France
| | - Lindsay B Alcaraz
- IRCM, INSERM U1194, University of Montpellier, ICM, Montpellier, France
| | - Hanane Mansouri
- IRCM, INSERM U1194, University of Montpellier, ICM, Montpellier, France
- RHEM, IRCM, Montpellier, France
| | - Lise Fenou
- IRCM, INSERM U1194, University of Montpellier, ICM, Montpellier, France
| | | | - Lucie Rubio
- IRCM, INSERM U1194, University of Montpellier, ICM, Montpellier, France
| | - Timothée David
- IRCM, INSERM U1194, University of Montpellier, ICM, Montpellier, France
| | - Loïs Coenon
- IRMB, University of Montpellier, INSERM, CNRS, CHU Montpellier, Montpellier, France
| | | | | | - Giang Ngo
- IRCM, INSERM U1194, University of Montpellier, ICM, Montpellier, France
| | | | - Martin Villalba
- IRMB, University of Montpellier, INSERM, CNRS, CHU Montpellier, Montpellier, France
- Institut du Cancer Avignon-Provence Sainte Catherine, Avignon, France
| | - Pierre Martineau
- IRCM, INSERM U1194, University of Montpellier, ICM, Montpellier, France
| | | | - Pascal Roger
- IRCM, INSERM U1194, University of Montpellier, ICM, Montpellier, France
- Department of Pathology, CHU Nîmes, Nimes, France
| | - Séverine Guiu
- IRCM, INSERM U1194, University of Montpellier, ICM, Montpellier, France
- Department of Medical Oncology, ICM, Montpellier, France
| | - Thierry Chardès
- IRCM, INSERM U1194, University of Montpellier, ICM, Montpellier, France
- CNRS, Centre national de la recherche Scientifique, Paris, F-75016, France
| | - Laurent Gros
- IRCM, INSERM U1194, University of Montpellier, ICM, Montpellier, France
- CNRS, Centre national de la recherche Scientifique, Paris, F-75016, France
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5
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Bonnamy M, Brousse A, Pirolles E, Michalakis Y, Blanc S. The genome formula of a multipartite virus is regulated both at the individual segment and the segment group levels. PLoS Pathog 2024; 20:e1011973. [PMID: 38271470 PMCID: PMC10846721 DOI: 10.1371/journal.ppat.1011973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/06/2024] [Accepted: 01/14/2024] [Indexed: 01/27/2024] Open
Abstract
Differential accumulation of the distinct genome segments is a common feature of viruses with segmented genomes. The reproducible and specific pattern of genome segment accumulation within the host is referred to as the "genome formula". There is speculation and some experimental support for a functional role of the genome formula by modulating gene expression through copy number variations. However, the mechanisms of genome formula regulation have not yet been identified. In this study, we investigated whether the genome formula of the octopartite nanovirus faba bean necrotic stunt virus (FBNSV) is regulated by processes acting at the individual segment vs. viral population levels. We used a leaf infiltration system to show that the two most accumulated genome segments of the FBNSV possess a greater intrinsic accumulation capacity in Vicia faba tissues than the other segments. Nevertheless, processes acting at the individual segment level are insufficient to generate the genome formula, suggesting the involvement of additional mechanisms acting at the supra-segment level. Indeed, the absence of segments with important functions during systemic infection strongly modifies the relative frequency of the others, indicating that the genome formula is a property of the segment group. Together, these results demonstrate that the FBNSV genome formula is shaped by a complex process acting at both the individual segment and the segment group levels.
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Affiliation(s)
- Mélia Bonnamy
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- MIVEGEC, CNRS, IRD, Univ Montpellier, Montpellier, France
| | - Andy Brousse
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- MIVEGEC, CNRS, IRD, Univ Montpellier, Montpellier, France
| | - Elodie Pirolles
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | - Stéphane Blanc
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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6
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Moneuse R, Bourgeois D, Le Goff X, Lehn JM, Meyer D. Behavior of a Dynamic Covalent Library Driven by Combined Pd(II) and Biphasic Effectors for Metal Transport between Phases. Chemistry 2023; 29:e202302188. [PMID: 37566451 DOI: 10.1002/chem.202302188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023]
Abstract
This work reports the effect of Pd(II) as chemical effector on an acylhydrazone-based dynamic covalent library (DCL) in biphasic systems (water/chloroform). The constituents of the DCL are self-built and distributed in the two phases, two of them are lipophilic enough to play the role of a carrier agent that may transfer Pd(II) from the aqueous phase to the organic phase. Upon addition of Pd(II), the DCL of components exhibits a strong amplification of the constituent that is the most adapted to stabilize Pd(II) in chloroform as well as its agonist in water. This evolution is driven by the combination of the interaction of the DCL with Pd(II) and the presence of the two phases. This study paves the way to a novel approach for liquid/liquid extraction and metal recovery by means of adaptive extractant species generated in situ by a DCL.
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Affiliation(s)
- Raphaël Moneuse
- Institut de Chimie Séparative de Marcoule (ICSM) UMR 5257, Université de Montpellier, CEA, CNRS, ENSCM, Site de Marcoule, Bâtiment 426, BP 17171, 30207, Bagnols-sur-Cèze, France
| | - Damien Bourgeois
- Institut de Chimie Séparative de Marcoule (ICSM) UMR 5257, Université de Montpellier, CEA, CNRS, ENSCM, Site de Marcoule, Bâtiment 426, BP 17171, 30207, Bagnols-sur-Cèze, France
| | - Xavier Le Goff
- Institut de Chimie Séparative de Marcoule (ICSM) UMR 5257, Université de Montpellier, CEA, CNRS, ENSCM, Site de Marcoule, Bâtiment 426, BP 17171, 30207, Bagnols-sur-Cèze, France
| | - Jean-Marie Lehn
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), UMR 7006, 8 Allée Gaspard Monge, BP 70028, 67083, Strasbourg, France
| | - Daniel Meyer
- Institut de Chimie Séparative de Marcoule (ICSM) UMR 5257, Université de Montpellier, CEA, CNRS, ENSCM, Site de Marcoule, Bâtiment 426, BP 17171, 30207, Bagnols-sur-Cèze, France
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7
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Douaihy M, Topno R, Lagha M, Bertrand E, Radulescu O. BurstDECONV: a signal deconvolution method to uncover mechanisms of transcriptional bursting in live cells. Nucleic Acids Res 2023; 51:e88. [PMID: 37522372 PMCID: PMC10484743 DOI: 10.1093/nar/gkad629] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 06/23/2023] [Accepted: 07/17/2023] [Indexed: 08/01/2023] Open
Abstract
Monitoring transcription in living cells gives access to the dynamics of this complex fundamental process. It reveals that transcription is discontinuous, whereby active periods (bursts) are separated by one or several types of inactive periods of distinct lifetimes. However, decoding temporal fluctuations arising from live imaging and inferring the distinct transcriptional steps eliciting them is a challenge. We present BurstDECONV, a novel statistical inference method that deconvolves signal traces into individual transcription initiation events. We use the distribution of waiting times between successive polymerase initiation events to identify mechanistic features of transcription such as the number of rate-limiting steps and their kinetics. Comparison of our method to alternative methods emphasizes its advantages in terms of precision and flexibility. Unique features such as the direct determination of the number of promoter states and the simultaneous analysis of several potential transcription models make BurstDECONV an ideal analytic framework for live cell transcription imaging experiments. Using simulated realistic data, we found that our method is robust with regards to noise or suboptimal experimental designs. To show its generality, we applied it to different biological contexts such as Drosophila embryos or human cells.
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Affiliation(s)
- Maria Douaihy
- LPHI, University of Montpellier and CNRS, Place Eugène Bataillon, Montpellier 34095, France
- IGMM, University of Montpellier and CNRS, 1919 Rte de Mende, Montpellier 34090, France
| | - Rachel Topno
- LPHI, University of Montpellier and CNRS, Place Eugène Bataillon, Montpellier 34095, France
- IGH, University of Montpellier and CNRS, 141 Rue de la Cardonille, Montpellier 34094, France
| | - Mounia Lagha
- IGMM, University of Montpellier and CNRS, 1919 Rte de Mende, Montpellier 34090, France
| | - Edouard Bertrand
- IGH, University of Montpellier and CNRS, 141 Rue de la Cardonille, Montpellier 34094, France
| | - Ovidiu Radulescu
- LPHI, University of Montpellier and CNRS, Place Eugène Bataillon, Montpellier 34095, France
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8
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Jarne P, Pinay G. Towards closer integration between ecology and evolution. Ecol Lett 2023; 26 Suppl 1:S5-S10. [PMID: 37840023 DOI: 10.1111/ele.14298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 10/17/2023]
Affiliation(s)
- Philippe Jarne
- CEFE, UMR 5175, CNRS-Université de Montpellier-IRD-EPHE, Montpellier Cedex 5, France
| | - Gilles Pinay
- Environnement, Ville & Société (EVS), UMR 5600, CNRS-, Lyon Cedex 08, France
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9
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Félix G, Sene S, Kulakova A, Bilyachenko AN, Khrustalev VN, Shubina ES, Guari Y, Larionova J. Tetranuclear lanthanide-based silsesquioxanes: towards a combination of a slow relaxation of the magnetization and a luminescent thermometry. RSC Adv 2023; 13:26302-26312. [PMID: 37670999 PMCID: PMC10476019 DOI: 10.1039/d3ra04901a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/28/2023] [Indexed: 09/07/2023] Open
Abstract
Lanthanide-based silsesquioxanes constitute an emerging family of cage-like metallasilsesquioxanes with exciting optical and magnetic properties. We report here the synthesis, structures and luminescence properties of a series of tetranuclear lanthanide-silsesquioxane compounds of general formula [NEt4]2[(Ph4Si4O8)2(Ln/Ln')4(NO3)6(EtOH)2(MeCN)2]·4(MeCN) with different lanthanide ions (where Ln/Ln' = Dy3+/Eu3+ (1), Dy3+/Tb3+ (2) and Eu3+/Tb3+/Y3+ (3)) and investigate the impact of the lanthanide ions combination on magnetic and photo-luminescent properties. Compound 1 behaves as a field-induced Single Molecule Magnet (SMM) and presents temperature-dependent luminescence characteristics of Eu3+ making it an emissive thermometer working in the temperature range 293-373 K with the maximum relative sensitivity of 1.15% K-1 achieved at 293 K. Compounds 2 and 3 are paramagnets, which demonstrate a characteristic photoluminescence with Dy3+ to Tb3+ and Tb3+ to Eu3+ energy transfers, respectively.
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Affiliation(s)
- Gautier Félix
- ICGM, Univ. Montpellier, CNRS, ENSCM Montpellier France
| | - Saad Sene
- ICGM, Univ. Montpellier, CNRS, ENSCM Montpellier France
| | - Alena Kulakova
- ICGM, Univ. Montpellier, CNRS, ENSCM Montpellier France
- A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences 28 Vavilova Str. 119334 Moscow Russia
- Peoples' Friendship University of Russia, (RUDN University) Miklukho-Maklay Str., 6 117198 Moscow Russia
| | - Alexey N Bilyachenko
- A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences 28 Vavilova Str. 119334 Moscow Russia
- Peoples' Friendship University of Russia, (RUDN University) Miklukho-Maklay Str., 6 117198 Moscow Russia
| | - Victor N Khrustalev
- Peoples' Friendship University of Russia, (RUDN University) Miklukho-Maklay Str., 6 117198 Moscow Russia
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences Leninsky Prospect 47 Moscow 119991 Russia
| | - Elena S Shubina
- A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences 28 Vavilova Str. 119334 Moscow Russia
| | - Yannick Guari
- ICGM, Univ. Montpellier, CNRS, ENSCM Montpellier France
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10
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Zanella S, Aragon-Alberti M, Brite CDS, Salles F, Carlos LD, Long J. Luminescent Single-Molecule Magnets as Dual Magneto-Optical Molecular Thermometers. Angew Chem Int Ed Engl 2023; 62:e202306970. [PMID: 37418512 DOI: 10.1002/anie.202306970] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023]
Abstract
Luminescent thermometry allows the remote detection of the temperature and holds great potential in future technological applications in which conventional systems could not operate. Complementary approaches to measuring the temperature aiming to enhance the thermal sensitivity would however represent a decisive step forward. For the first time, we demonstrate the proof-of-concept that luminescence thermometry could be associated with a complementary temperature readout related to a different property. Namely, we propose to take advantage of the temperature dependence of both magnetic (canonical susceptibility and relaxation time) and luminescence features (emission intensity) found in Single-Molecule Magnets (SMM) to develop original dual magneto-optical molecular thermometers to conciliate high-performance SMM and Boltzmann-type luminescence thermometry. We highlight this integrative approach to concurrent luminescent and magnetic thermometry using an air-stable benchmark SMM [Dy(bbpen)Cl] (H2 bbpen=N,N'-bis(2-hydroxybenzyl)-N,N'-bis(2-methylpyridyl)ethyl-enediamine)) exhibiting Dy3+ luminescence. The synergy between multiparametric magneto-optical readouts and multiple linear regression makes possible a 10-fold improvement in the relative thermal sensitivity of the thermometer over the whole temperature range, compared with the values obtained with the single optical or magnetic devices.
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Affiliation(s)
- Sofia Zanella
- Phantom-g, CICECO-Aveiro Institute of Materials, Physics Department, University of Aveiro, 3810-193, Aveiro, Portugal
| | | | - Carlos D S Brite
- Phantom-g, CICECO-Aveiro Institute of Materials, Physics Department, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Fabrice Salles
- ICGM, Univ. Montpellier, CNRS, ENSCM, Montpellier, France
| | - Luís D Carlos
- Phantom-g, CICECO-Aveiro Institute of Materials, Physics Department, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Jérôme Long
- ICGM, Univ. Montpellier, CNRS, ENSCM, Montpellier, France
- Institut Universitaire de France, (IUF), 1 rue Descartes, 75231, Paris Cedex 05, France
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11
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Ribot C, Soler C, Chartier A, Al Hayek S, Naït-Saïdi R, Barbezier N, Coux O, Simonelig M. Activation of the ubiquitin-proteasome system contributes to oculopharyngeal muscular dystrophy through muscle atrophy. PLoS Genet 2022; 18:e1010015. [PMID: 35025870 PMCID: PMC8791501 DOI: 10.1371/journal.pgen.1010015] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 01/26/2022] [Accepted: 01/01/2022] [Indexed: 12/05/2022] Open
Abstract
Oculopharyngeal muscular dystrophy (OPMD) is a late-onset disorder characterized by progressive weakness and degeneration of specific muscles. OPMD is due to extension of a polyalanine tract in poly(A) binding protein nuclear 1 (PABPN1). Aggregation of the mutant protein in muscle nuclei is a hallmark of the disease. Previous transcriptomic analyses revealed the consistent deregulation of the ubiquitin-proteasome system (UPS) in OPMD animal models and patients, suggesting a role of this deregulation in OPMD pathogenesis. Subsequent studies proposed that UPS contribution to OPMD involved PABPN1 aggregation. Here, we use a Drosophila model of OPMD to address the functional importance of UPS deregulation in OPMD. Through genome-wide and targeted genetic screens we identify a large number of UPS components that are involved in OPMD. Half dosage of UPS genes reduces OPMD muscle defects suggesting a pathological increase of UPS activity in the disease. Quantification of proteasome activity confirms stronger activity in OPMD muscles, associated with degradation of myofibrillar proteins. Importantly, improvement of muscle structure and function in the presence of UPS mutants does not correlate with the levels of PABPN1 aggregation, but is linked to decreased degradation of muscle proteins. Oral treatment with the proteasome inhibitor MG132 is beneficial to the OPMD Drosophila model, improving muscle function although PABPN1 aggregation is enhanced. This functional study reveals the importance of increased UPS activity that underlies muscle atrophy in OPMD. It also provides a proof-of-concept that inhibitors of proteasome activity might be an attractive pharmacological approach for OPMD. Oculopharyngeal muscular dystrophy (OPMD) is a genetic disease characterized by progressive weakness of specific muscles, leading to swallowing difficulties (dysphagia), eyelid drooping (ptosis) and walking difficulties at later stages. No drug treatments are currently available. OPMD is due to mutations in a nuclear protein called poly(A) binding protein nuclear 1 (PABPN1) that is involved in processing of different classes of RNAs in the nucleus. We have used an animal model of OPMD that we have developed in the fly Drosophila to investigate the role in OPMD of the ubiquitin-proteasome system, a pathway specialized in protein degradation. We report an increased activity of the ubiquitin-proteasome system that is associated with degradation of muscular proteins in the OPMD Drosophila model. We propose that higher activity of the ubiquitin-proteasome system leads to muscle atrophy in OPMD. Importantly, oral treatment of this OPMD animal model with an inhibitor of proteasome activity reduces muscle defects. A number of proteasome inhibitors are approved drugs used in clinic against cancers, therefore our results provide a proof-of-concept that inhibitors of proteasome might be of interest in future treatments of OPMD.
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Affiliation(s)
- Cécile Ribot
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-Univ Montpellier, Montpellier, France
| | - Cédric Soler
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-Univ Montpellier, Montpellier, France
| | - Aymeric Chartier
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-Univ Montpellier, Montpellier, France
| | - Sandy Al Hayek
- GReD Laboratory, Clermont-Auvergne University, INSERM U1103, CNRS UMR6293, Clermont-Ferrand, France
| | - Rima Naït-Saïdi
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-Univ Montpellier, Montpellier, France
| | - Nicolas Barbezier
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-Univ Montpellier, Montpellier, France
| | - Olivier Coux
- Ubiquitin-proteasome system and cell cycle control, Montpellier Cell Biology Research Center, UMR5237 CNRS-Univ Montpellier, Montpellier, France
| | - Martine Simonelig
- mRNA Regulation and Development, Institute of Human Genetics, UMR9002 CNRS-Univ Montpellier, Montpellier, France
- * E-mail:
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12
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Lorenzi C, Barriere S, Arnold K, Luco RF, Oldfield AJ, Ritchie W. IRFinder-S: a comprehensive suite to discover and explore intron retention. Genome Biol 2021; 22:307. [PMID: 34749764 PMCID: PMC8573998 DOI: 10.1186/s13059-021-02515-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022] Open
Abstract
Accurate quantification and detection of intron retention levels require specialized software. Building on our previous software, we create a suite of tools called IRFinder-S, to analyze and explore intron retention events in multiple samples. Specifically, IRFinder-S allows a better identification of true intron retention events using a convolutional neural network, allows the sharing of intron retention results between labs, integrates a dynamic database to explore and contrast available samples, and provides a tested method to detect differential levels of intron retention.
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Affiliation(s)
- Claudio Lorenzi
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France
| | - Sylvain Barriere
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France
| | - Katharina Arnold
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France
| | - Reini F Luco
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France
| | - Andrew J Oldfield
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France
| | - William Ritchie
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France.
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13
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Bonnet E, Daures JP, Landais P. Determination of thresholds of risk in women at average risk of breast cancer to personalize the organized screening program. Sci Rep 2021; 11:19104. [PMID: 34580360 PMCID: PMC8476568 DOI: 10.1038/s41598-021-98604-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 09/06/2021] [Indexed: 11/08/2022] Open
Abstract
In France, more than 10 million women at "average" risk of breast cancer (BC), are included in the organized BC screening. Existing predictive models of BC risk are not adapted to the French population. Thus, we set up a new score in the French Hérault region and looked for subgroups at a graded level of risk in women at "average" risk. We recruited a retrospective cohort of women, aged 50 to 60, who underwent the organized BC screening, and included 2241 non-cancer women and 527 who developed a BC during a 12-year follow-up period (2006-2018). The risk factors identified were high breast density (ACR BI-RADS grading)(B vs A: HR = 1.41, 95%CI [1.05; 1.9], p = 0.023; C vs A: HR = 1.65 [1.2; 2.27], p = 0.02 ; D vs A: HR = 2.11 [1.25;3.58], p = 0.006), a history of maternal breast cancer (HR = 1.61 [1.24; 2.09], p < 0.001), and socioeconomic difficulties (HR 1.23 [1.09; 1.55], p = 0.003). While early menopause (HR = 0.36 [0.13; 0.99], p = 0.003) and an age at menarche after 12 years (HR = 0.77 [0.63; 0.95], p = 0.047) were protective factors. We identified 3 groups at risk: lower, average, and higher, respectively. A low threshold was characterized at 1.9% of 12-year risk and a high threshold at 4.5% 12-year risk. Mean 12-year risks in the 3 groups of risk were 1.37%, 2.68%, and 5.84%, respectively. Thus, 12% of women presented a level of risk different from the average risk group, corresponding to 600,000 women involved in the French organized BC screening, enabling to propose a new strategy to personalize the national BC screening. On one hand, for women at lower risk, we proposed to reduce the frequency of mammograms and on the other hand, for women at higher risk, we suggested intensifying surveillance.
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Affiliation(s)
- Emmanuel Bonnet
- Montpellier University, EA2415, Institut Universitaire de recherche clinique, 34093, Montpellier Cedex 5, France.
- Languedoc Mutualité, Nouvelles Technologies, AESIO, Montpellier, France.
| | - Jean-Pierre Daures
- Montpellier University, EA2415, Institut Universitaire de recherche clinique, 34093, Montpellier Cedex 5, France
- Languedoc Mutualité, Nouvelles Technologies, AESIO, Montpellier, France
| | - Paul Landais
- Montpellier University, EA2415, Institut Universitaire de recherche clinique, 34093, Montpellier Cedex 5, France
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14
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Robira B, Benhamou S, Masi S, Llaurens V, Riotte-Lambert L. Foraging efficiency in temporally predictable environments: is a long-term temporal memory really advantageous? R Soc Open Sci 2021; 8:210809. [PMID: 34567589 PMCID: PMC8456140 DOI: 10.1098/rsos.210809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Cognitive abilities enabling animals that feed on ephemeral but yearly renewable resources to infer when resources are available may have been favoured by natural selection, but the magnitude of the benefits brought by these abilities remains poorly known. Using computer simulations, we compared the efficiencies of three main types of foragers with different abilities to process temporal information, in spatially and/or temporally homogeneous or heterogeneous environments. One was endowed with a sampling memory, which stores recent experience about the availability of the different food types. The other two were endowed with a chronological or associative memory, which stores long-term temporal information about absolute times of these availabilities or delays between them, respectively. To determine the range of possible efficiencies, we also simulated a forager without temporal cognition but which simply targeted the closest and possibly empty food sources, and a perfectly prescient forager, able to know at any time which food source was effectively providing food. The sampling, associative and chronological foragers were far more efficient than the forager without temporal cognition in temporally predictable environments, and interestingly, their efficiencies increased with the level of temporal heterogeneity. The use of a long-term temporal memory results in a foraging efficiency up to 1.16 times better (chronological memory) or 1.14 times worse (associative memory) than the use of a simple sampling memory. Our results thus show that, for everyday foraging, a long-term temporal memory did not provide a clear benefit over a simple short-term memory that keeps track of the current resource availability. Long-term temporal memories may therefore have emerged in contexts where short-term temporal cognition is useless, i.e. when the anticipation of future environmental changes is strongly needed.
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Affiliation(s)
- Benjamin Robira
- Centre d'Ecologie Fonctionnelle et Evolutive, Université de Montpellier and CNRS, Montpellier, France
| | - Simon Benhamou
- Centre d'Ecologie Fonctionnelle et Evolutive, Université de Montpellier and CNRS, Montpellier, France
| | - Shelly Masi
- Eco-anthropologie, Muséum National d'Histoire Naturelle, CNRS, Université de Paris, Paris, France
| | - Violaine Llaurens
- Institut de Systématique, Evolution, Biodiversité, CNRS-École Pratique des Hautes Études, Muséum National d'Histoire Naturelle, Université Pierre-et-Marie-Curie, Paris, France
| | - Louise Riotte-Lambert
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
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15
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Gleizes A, Triki M, Bonnet S, Baccari N, Jimenez-Dominguez G, Covinhes A, Pirot N, Blache P, Yuan R, Győrffy B, Cavaillès V, Lapierre M. RIP140 Represses Intestinal Paneth Cell Differentiation and Interplays with SOX9 Signaling in Colorectal Cancer. Cancers (Basel) 2021; 13:3192. [PMID: 34206767 PMCID: PMC8268705 DOI: 10.3390/cancers13133192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/03/2021] [Accepted: 06/21/2021] [Indexed: 11/23/2022] Open
Abstract
RIP140 is a major transcriptional coregulator of gut homeostasis and tumorigenesis through the regulation of Wnt/APC signaling. Here, we investigated the effect of RIP140 on Paneth cell differentiation and its interplay with the transcription factor SOX9. Using loss of function mouse models, human colon cancer cells, and tumor microarray data sets we evaluated the role of RIP140 in SOX9 expression and activity using RT-qPCR, immunohistochemistry, luciferase reporter assays, and GST-pull down. We first evidence that RIP140 strongly represses the Paneth cell lineage in the intestinal epithelium cells by inhibiting Sox9 expression. We then demonstrate that RIP140 interacts with SOX9 and inhibits its transcriptional activity. Our results reveal that the Wnt signaling pathway exerts an opposite regulation on SOX9 and RIP140. Finally, the levels of expression of RIP140 and SOX9 exhibit a reverse response and prognosis value in human colorectal cancer biopsies. This work highlights an intimate transcriptional cross-talk between RIP140 and SOX9 in intestinal physiopathology.
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Affiliation(s)
- Antoine Gleizes
- IRCM—Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, CNRS, 208 rue des Apothicaires, F-34298 Montpellier, France; (A.G.); (M.T.); (S.B.); (N.B.); (G.J.-D.); (P.B.); (V.C.)
| | - Mouna Triki
- IRCM—Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, CNRS, 208 rue des Apothicaires, F-34298 Montpellier, France; (A.G.); (M.T.); (S.B.); (N.B.); (G.J.-D.); (P.B.); (V.C.)
| | - Sandrine Bonnet
- IRCM—Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, CNRS, 208 rue des Apothicaires, F-34298 Montpellier, France; (A.G.); (M.T.); (S.B.); (N.B.); (G.J.-D.); (P.B.); (V.C.)
| | - Naomi Baccari
- IRCM—Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, CNRS, 208 rue des Apothicaires, F-34298 Montpellier, France; (A.G.); (M.T.); (S.B.); (N.B.); (G.J.-D.); (P.B.); (V.C.)
| | - Gabriel Jimenez-Dominguez
- IRCM—Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, CNRS, 208 rue des Apothicaires, F-34298 Montpellier, France; (A.G.); (M.T.); (S.B.); (N.B.); (G.J.-D.); (P.B.); (V.C.)
| | - Aurélie Covinhes
- BioCampus, RHEM, Université de Montpellier, CNRS, INSERM, F-34093 Montpellier, France; (A.C.); (N.P.)
| | - Nelly Pirot
- BioCampus, RHEM, Université de Montpellier, CNRS, INSERM, F-34093 Montpellier, France; (A.C.); (N.P.)
| | - Philippe Blache
- IRCM—Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, CNRS, 208 rue des Apothicaires, F-34298 Montpellier, France; (A.G.); (M.T.); (S.B.); (N.B.); (G.J.-D.); (P.B.); (V.C.)
| | - Rong Yuan
- Department of Medical Microbiology, Immunology and Cell Biology, School of Medicine, Southern Illinois University, Springfield, IL 62794-9628, USA;
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, 1094 Budapest, Hungary;
- Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Vincent Cavaillès
- IRCM—Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, CNRS, 208 rue des Apothicaires, F-34298 Montpellier, France; (A.G.); (M.T.); (S.B.); (N.B.); (G.J.-D.); (P.B.); (V.C.)
| | - Marion Lapierre
- IRCM—Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, CNRS, 208 rue des Apothicaires, F-34298 Montpellier, France; (A.G.); (M.T.); (S.B.); (N.B.); (G.J.-D.); (P.B.); (V.C.)
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16
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Lyonnais S, Hénaut M, Neyret A, Merida P, Cazevieille C, Gros N, Chable-Bessia C, Muriaux D. Atomic force microscopy analysis of native infectious and inactivated SARS-CoV-2 virions. Sci Rep 2021; 11:11885. [PMID: 34088957 PMCID: PMC8178396 DOI: 10.1038/s41598-021-91371-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/26/2021] [Indexed: 12/14/2022] Open
Abstract
SARS-CoV-2 is an enveloped virus responsible for the Coronavirus Disease 2019 (COVID-19) pandemic. Here, single viruses were analyzed by atomic force microscopy (AFM) operating directly in a level 3 biosafety (BSL3) facility, which appeared as a fast and powerful method to assess at the nanoscale level and in 3D infectious virus morphology in its native conformation, or upon inactivation treatments. AFM imaging reveals structurally intact infectious and inactivated SARS-CoV-2 upon low concentration of formaldehyde treatment. This protocol combining AFM and plaque assays allows the preparation of intact inactivated SARS-CoV-2 particles for safe use of samples out of level 3 laboratory to accelerate researches against the COVID-19 pandemic. Overall, we illustrate how adapted BSL3-AFM is a remarkable toolbox for rapid and direct virus analysis based on nanoscale morphology.
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Affiliation(s)
| | - Mathilde Hénaut
- CEMIPAI, University of Montpellier, UAR3725 CNRS, Montpellier, France
| | - Aymeric Neyret
- CEMIPAI, University of Montpellier, UAR3725 CNRS, Montpellier, France
| | - Peggy Merida
- Institute of Research in Infectiology of Montpellier (IRIM), University of Montpellier, UMR9004 CNRS, Montpellier, France
| | - Chantal Cazevieille
- Institut des Neurosciences de Montpellier (INM), Université de Montpellier, Montpellier, France
| | - Nathalie Gros
- CEMIPAI, University of Montpellier, UAR3725 CNRS, Montpellier, France
| | | | - Delphine Muriaux
- CEMIPAI, University of Montpellier, UAR3725 CNRS, Montpellier, France.
- Institute of Research in Infectiology of Montpellier (IRIM), University of Montpellier, UMR9004 CNRS, Montpellier, France.
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17
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Deshaies S, Cazals G, Enjalbal C, Constantin T, Garcia F, Mouls L, Saucier C. Red Wine Oxidation: Accelerated Ageing Tests, Possible Reaction Mechanisms and Application to Syrah Red Wines. Antioxidants (Basel) 2020; 9:E663. [PMID: 32722307 PMCID: PMC7464692 DOI: 10.3390/antiox9080663] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 11/16/2022] Open
Abstract
Wine oxidation and ageing involve many complex chemical pathways and reaction mechanisms. The purpose of this study is to set up new and reproducible accelerated red wine ageing tests and identify chemical oxidation or ageing molecular markers. Three accelerated and reproducible ageing tests were developed: a heat test (60 °C); an enzymatic test (laccase test; a chemical test (hydrogen peroxide test). Depending on the test, oxygen consumption was significantly different. For a young wine (2018), the oxygen consumption rate moved from 2.40 ppm.h-1 for the heat test to 3.33 ppm.h-1 for the enzymatic test and 2.86 ppm.h-1 for the chemical test. Once applied to two other vintages (2010 and 2014) from the same winery, the tests revealed different comportments corresponding to wine natural evolution. High resolution UPLC-MS was performed on forced ageing samples and compared to naturally aged red wines. Specific oxidation or ageing ion markers were found with significant differences between tests, revealing the specificity of each test and different possible molecular pathways involved. The hydrogen peroxide test seems to be closer to natural oxidation with an important decrease in absorbance at 520 nm and similar molecular ion variations for [M+H]+ = 291, 331, 347, 493, 535, 581, 639 Da.
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Affiliation(s)
- Stacy Deshaies
- SPO, Université de Montpellier, INRAE, Institut Agro, 34000 Montpellier, France; (S.D.); (F.G.); (L.M.)
| | - Guillaume Cazals
- IBMM, Université de Montpellier, 34093 Montpellier, France; (G.C.); (C.E.)
| | - Christine Enjalbal
- IBMM, Université de Montpellier, 34093 Montpellier, France; (G.C.); (C.E.)
| | - Thibaut Constantin
- Laboratoire d’Œnologie, UFR Pharmacie, Université de Montpellier, 34000 Montpellier, France;
| | - François Garcia
- SPO, Université de Montpellier, INRAE, Institut Agro, 34000 Montpellier, France; (S.D.); (F.G.); (L.M.)
| | - Laetitia Mouls
- SPO, Université de Montpellier, INRAE, Institut Agro, 34000 Montpellier, France; (S.D.); (F.G.); (L.M.)
| | - Cédric Saucier
- SPO, Université de Montpellier, INRAE, Institut Agro, 34000 Montpellier, France; (S.D.); (F.G.); (L.M.)
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Orsucci M, Audiot P, Nidelet S, Dorkeld F, Pommier A, Vabre M, Severac D, Rohmer M, Gschloessl B, Streiff R. Transcriptomic response of female adult moths to host and non-host plants in two closely related species. BMC Evol Biol 2018; 18:145. [PMID: 30236059 PMCID: PMC6148789 DOI: 10.1186/s12862-018-1257-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 08/30/2018] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Divergent selection has been shown to promote speciation in many taxa and especially in phytophagous insects. In the Ostrinia species complex, the European corn borer (ECB) and adzuki bean borer (ABB) are two sibling species specialized to different host plants. The first is a well-known maize pest, whereas the second is a polyphagous species associated with various dicotyledons. Their specialization to host plants is driven by morphological, behavioral and physiological adaptations. In particular, previous studies have shown that ECB and ABB display marked behavior with regard to plant choice during oviposition, involving specific preference and avoidance mechanisms. In this study, our goal was to identify the mechanisms underlying this host-plant specialization in adult females through an analysis of their gene expression. We assembled and annotated a de novo reference transcriptome and measured differences in gene expression between ECB and ABB females, and between environments. We related differentially expressed genes to host preference behavior, and highlighted the functional categories involved. We also conducted a specific analysis of chemosensory genes, which are considered to be good candidates for host recognition before oviposition. RESULTS We recorded more differentially expressed genes in ECB than in ABB samples, and noticed that the majority of genes potentially involved in the host preference were different between the two species. At the functional level, the response to plant environment in adult females involved many processes, including the metabolism of carbohydrates, lipids, proteins, and amino acids; detoxification mechanisms and immunity; and the chemosensory repertoire (as expected). Until now, most of the olfactory receptors described in Ostrinia spp. had been tested for their putative role in pheromone recognition by males. Here we observed that one specific olfactory receptor was clearly associated with ECB's discrimination between maize and mugwort conditions, highlighting a potential new candidate involved in plant odor discrimination in adult females. CONCLUSIONS Our results are a first step toward the identification of candidate genes and functions involved in chemosensory processes, carbohydrate metabolism, and virus and retrovirus dynamics. These candidates provide new avenues for research into understanding the role of divergent selection between different environments in species diversification.
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Affiliation(s)
- M. Orsucci
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
- DGIMI, INRA, Univ Montpellier, Montpellier, France
- Present address: Department of Ecology and Genetics, EBC, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - P. Audiot
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - S. Nidelet
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - F. Dorkeld
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - A. Pommier
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | | | - D. Severac
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 34094 Montpellier Cedex 5, France
| | - M. Rohmer
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 34094 Montpellier Cedex 5, France
| | - B. Gschloessl
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - R. Streiff
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
- DGIMI, INRA, Univ Montpellier, Montpellier, France
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Baroukh C, Turon V, Bernard O. Dynamic metabolic modeling of heterotrophic and mixotrophic microalgal growth on fermentative wastes. PLoS Comput Biol 2017; 13:e1005590. [PMID: 28582469 PMCID: PMC5476291 DOI: 10.1371/journal.pcbi.1005590] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/19/2017] [Accepted: 05/24/2017] [Indexed: 11/21/2022] Open
Abstract
Microalgae are promising microorganisms for the production of numerous molecules of interest, such as pigments, proteins or triglycerides that can be turned into biofuels. Heterotrophic or mixotrophic growth on fermentative wastes represents an interesting approach to achieving higher biomass concentrations, while reducing cost and improving the environmental footprint. Fermentative wastes generally consist of a blend of diverse molecules and it is thus crucial to understand microalgal metabolism in such conditions, where switching between substrates might occur. Metabolic modeling has proven to be an efficient tool for understanding metabolism and guiding the optimization of biomass or target molecule production. Here, we focused on the metabolism of Chlorella sorokiniana growing heterotrophically and mixotrophically on acetate and butyrate. The metabolism was represented by 172 metabolic reactions. The DRUM modeling framework with a mildly relaxed quasi-steady-state assumption was used to account for the switching between substrates and the presence of light. Nine experiments were used to calibrate the model and nine experiments for the validation. The model efficiently predicted the experimental data, including the transient behavior during heterotrophic, autotrophic, mixotrophic and diauxic growth. It shows that an accurate model of metabolism can now be constructed, even in dynamic conditions, with the presence of several carbon substrates. It also opens new perspectives for the heterotrophic and mixotrophic use of microalgae, especially for biofuel production from wastes.
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Affiliation(s)
- Caroline Baroukh
- INRA, UR0050 Laboratoire de Biotechnologie de l'Environnement, Narbonne, France
- INRIA, BIOCORE, Sophia-Antipolis, FRANCE
| | - Violette Turon
- INRA, UR0050 Laboratoire de Biotechnologie de l'Environnement, Narbonne, France
| | - Olivier Bernard
- INRIA, BIOCORE, Sophia-Antipolis, FRANCE
- UPMC, LOV, CNRS UMR 7093, Station Zoologique, Villefranche-sur-mer, FRANCE
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Leboulanger C, Agogué H, Bernard C, Bouvy M, Carré C, Cellamare M, Duval C, Fouilland E, Got P, Intertaglia L, Lavergne C, Le Floc’h E, Roques C, Sarazin G. Microbial Diversity and Cyanobacterial Production in Dziani Dzaha Crater Lake, a Unique Tropical Thalassohaline Environment. PLoS One 2017; 12:e0168879. [PMID: 28045976 PMCID: PMC5207672 DOI: 10.1371/journal.pone.0168879] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 12/07/2016] [Indexed: 11/18/2022] Open
Abstract
This study describes, for the first time, the water chemistry and microbial diversity in Dziani Dzaha, a tropical crater lake located on Mayotte Island (Comoros archipelago, Western Indian Ocean). The lake water had a high level of dissolved matter and high alkalinity (10.6-14.5 g L-1 eq. CO32-, i.e. 160-220 mM compare to around 2-2.5 in seawater), with salinity up to 52 psu, 1.5 higher than seawater. Hierarchical clustering discriminated Dziani Dzaha water from other alkaline, saline lakes, highlighting its thalassohaline nature. The phytoplankton biomass was very high, with a total chlorophyll a concentration of 524 to 875 μg chl a L-1 depending on the survey, homogeneously distributed from surface to bottom (4 m). Throughout the whole water column the photosynthetic biomass was dominated (>97% of total biovolume) by the filamentous cyanobacteria Arthrospira sp. with a straight morphotype. In situ daily photosynthetic oxygen production ranged from 17.3 to 22.2 g O2 m-2 d-1, consistent with experimental production / irradiance measurements and modeling. Heterotrophic bacterioplankton was extremely abundant, with cell densities up to 1.5 108 cells mL-1 in the whole water column. Isolation and culture of 59 Eubacteria strains revealed the prevalence of alkaliphilic and halophilic organisms together with taxa unknown to date, based on 16S rRNA gene analysis. A single cloning-sequencing approach using archaeal 16S rDNA gene primers unveiled the presence of diverse extremophilic Euryarchaeota. The water chemistry of Dziani Dzaha Lake supports the hypothesis that it was derived from seawater and strongly modified by geological conditions and microbial activities that increased the alkalinity. Dziani Dzaha has a unique consortium of cyanobacteria, phytoplankton, heterotrophic Eubacteria and Archaea, with very few unicellular protozoa, that will deserve further deep analysis to unravel its uncommon diversity. A single taxon, belonging to the genus Arthrospira, was found responsible for almost all photosynthetic primary production.
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Affiliation(s)
| | - Hélène Agogué
- UMR LIENSs, Centre National de la Recherche Scientifique, La Rochelle, France
| | - Cécile Bernard
- UMR MCAM, Muséum National d’Histoire Naturelle, Paris, France
| | - Marc Bouvy
- UMR MARBEC, Institut de Recherche pour le Développement, Sète-Montpellier, France
| | - Claire Carré
- UMR MARBEC, Institut de Recherche pour le Développement, Sète-Montpellier, France
| | - Maria Cellamare
- UMR MCAM, Muséum National d’Histoire Naturelle, Paris, France
| | - Charlotte Duval
- UMR MCAM, Muséum National d’Histoire Naturelle, Paris, France
| | - Eric Fouilland
- UMR MARBEC, Centre National de la Recherche Scientifique, Sète-Montpellier, France
| | - Patrice Got
- UMR MARBEC, Centre National de la Recherche Scientifique, Sète-Montpellier, France
| | - Laurent Intertaglia
- Observatoire Océanologique de Banyuls-sur-Mer, Université Pierre et Marie Curie, Banyuls-sur-Mer, France
| | - Céline Lavergne
- UMR LIENSs, Centre National de la Recherche Scientifique, La Rochelle, France
| | - Emilie Le Floc’h
- UMR MARBEC, Centre National de la Recherche Scientifique, Sète-Montpellier, France
| | - Cécile Roques
- UMR MARBEC, Centre National de la Recherche Scientifique, Sète-Montpellier, France
| | - Gérard Sarazin
- UMR7154 Institut de Physique du Globe de Paris, Université Paris Diderot, Paris, France
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