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O'Connor LMJ, Cosentino F, Harfoot MBJ, Maiorano L, Mancino C, Pollock LJ, Thuiller W. Vulnerability of terrestrial vertebrate food webs to anthropogenic threats in Europe. Glob Chang Biol 2024; 30:e17253. [PMID: 38519878 DOI: 10.1111/gcb.17253] [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] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/07/2024] [Accepted: 02/10/2024] [Indexed: 03/25/2024]
Abstract
Vertebrate species worldwide are currently facing significant declines in many populations. Although we have gained substantial knowledge about the direct threats that affect individual species, these threats only represent a fraction of the broader vertebrate threat profile, which is also shaped by species interactions. For example, threats faced by prey species can jeopardize the survival of their predators due to food resource scarcity. Yet, indirect threats arising from species interactions have received limited investigation thus far. In this study, we investigate the indirect consequences of anthropogenic threats on biodiversity in the context of European vertebrate food webs. We integrated data on trophic interactions among over 800 terrestrial vertebrates, along with their associated human-induced threats. We quantified and mapped the vulnerability of various components of the food web, including species, interactions, and trophic groups to six major threats: pollution, agricultural intensification, climate change, direct exploitation, urbanization, and invasive alien species and diseases. Direct exploitation and agricultural intensification were two major threats for terrestrial vertebrate food webs: affecting 34% and 31% of species, respectively, they threaten 85% and 69% of interactions in Europe. By integrating network ecology with threat impact assessments, our study contributes to a better understanding of the magnitude of anthropogenic impacts on biodiversity.
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Affiliation(s)
- Louise M J O'Connor
- Laboratoire d'Écologie Alpine, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
- Biodiversity and Natural Resources Programme, International Institute of Applied Systems Analysis (IIASA), Laxenburg, Austria
| | - Francesca Cosentino
- Department of Biology and Biotechnologies "Charles Darwin", University of Rome "La Sapienza", Rome, Italy
| | - Michael B J Harfoot
- UN Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, UK
- Vizzuality, Madrid, Spain
| | - Luigi Maiorano
- Department of Biology and Biotechnologies "Charles Darwin", University of Rome "La Sapienza", Rome, Italy
| | - Chiara Mancino
- Department of Biology and Biotechnologies "Charles Darwin", University of Rome "La Sapienza", Rome, Italy
| | - Laura J Pollock
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Wilfried Thuiller
- Laboratoire d'Écologie Alpine, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
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Chopy M, Cavallini-Speisser Q, Chambrier P, Morel P, Just J, Hugouvieux V, Rodrigues Bento S, Zubieta C, Vandenbussche M, Monniaux M. Cell layer-specific expression of the homeotic MADS-box transcription factor PhDEF contributes to modular petal morphogenesis in petunia. Plant Cell 2024; 36:324-345. [PMID: 37804091 PMCID: PMC10827313 DOI: 10.1093/plcell/koad258] [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] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/31/2023] [Accepted: 09/18/2023] [Indexed: 10/08/2023]
Abstract
Floral homeotic MADS-box transcription factors ensure the correct morphogenesis of floral organs, which are organized in different cell layers deriving from distinct meristematic layers. How cells from these distinct layers acquire their respective identities and coordinate their growth to ensure normal floral organ morphogenesis is unresolved. Here, we studied petunia (Petunia × hybrida) petals that form a limb and tube through congenital fusion. We identified petunia mutants (periclinal chimeras) expressing the B-class MADS-box gene DEFICIENS in the petal epidermis or in the petal mesophyll, called wico and star, respectively. Strikingly, wico flowers form a strongly reduced tube while their limbs are almost normal, while star flowers form a normal tube but greatly reduced and unpigmented limbs, showing that petunia petal morphogenesis is highly modular. These mutants highlight the layer-specific roles of PhDEF during petal development. We explored the link between PhDEF and petal pigmentation, a well-characterized limb epidermal trait. The anthocyanin biosynthesis pathway was strongly downregulated in star petals, including its major regulator ANTHOCYANIN2 (AN2). We established that PhDEF directly binds to the AN2 terminator in vitro and in vivo, suggesting that PhDEF might regulate AN2 expression and therefore petal epidermis pigmentation. Altogether, we show that cell layer-specific homeotic activity in petunia petals differently impacts tube and limb development, revealing the relative importance of the different cell layers in the modular architecture of petunia petals.
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Affiliation(s)
- Mathilde Chopy
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
| | - Quentin Cavallini-Speisser
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
| | - Pierre Chambrier
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
| | - Patrice Morel
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
| | - Jérémy Just
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
| | - Véronique Hugouvieux
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, Grenoble 38000, France
| | - Suzanne Rodrigues Bento
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
| | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, Grenoble 38000, France
| | - Michiel Vandenbussche
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
| | - Marie Monniaux
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69007, France
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Nivet C, Custovic I, Avoscan L, Bikker FJ, Bonnotte A, Bourillot E, Briand L, Brignot H, Heydel JM, Herrmann N, Lelièvre M, Lesniewska E, Neiers F, Piétrement O, Schwartz M, Belloir C, Canon F. Development of New Models of Oral Mucosa to Investigate the Impact of the Structure of Transmembrane Mucin-1 on the Mucosal Pellicle Formation and Its Physicochemical Properties. Biomedicines 2024; 12:139. [PMID: 38255244 PMCID: PMC10812975 DOI: 10.3390/biomedicines12010139] [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: 08/03/2023] [Revised: 12/21/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
The mucosal pellicle (MP) is a biological film protecting the oral mucosa. It is composed of bounded salivary proteins and transmembrane mucin MUC1 expressed by oral epithelial cells. Previous research indicates that MUC1 expression enhances the binding of the main salivary protein forming the MP, MUC5B. This study investigated the influence of MUC1 structure on MP formation. A TR146 cell line, which does not express MUC1 natively, was stably transfected with genes coding for three MUC1 isoforms differing in the structure of the two main extracellular domains: the VNTR domain, exhibiting a variable number of tandem repeats, and the SEA domain, maintaining the two bound subunits of MUC1. Semi-quantification of MUC1 using dot blot chemiluminescence showed comparable expression levels in all transfected cell lines. Semi-quantification of MUC5B by immunostaining after incubation with saliva revealed that MUC1 expression significantly increased MUC5B adsorption. Neither the VNTR domain nor the SEA domain was influenced MUC5B anchoring, suggesting the key role of the MUC1 N-terminal domain. AFM-IR nanospectroscopy revealed discernible shifts indicative of changes in the chemical properties at the cell surface due to the expression of the MUC1 isoform. Furthermore, the observed chemical shifts suggest the involvement of hydrophobic effects in the interaction between MUC1 and salivary proteins.
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Affiliation(s)
- Clément Nivet
- Center for Taste and Feeding Behaviour (CSGA), UMR1324 INRAE, Institut Agro Dijon, Université de Bourgogne, UMR6265 CNRS, 21000 Dijon, France; (C.N.); (L.B.); (H.B.); (J.-M.H.); (N.H.); (M.L.); (F.N.); (M.S.); (C.B.)
| | - Irma Custovic
- Institut Carnot de Bourgogne (ICB), UMR CNRS 6303, University of Bourgogne, 21000 Dijon, France; (I.C.); (E.B.); (E.L.); (O.P.)
| | - Laure Avoscan
- Agroécologie, UMR1347 INRAE, ERL CNRS 6300, DimaCell Platform, Center of Microscopy INRAE, University of Bourgogne, 21000 Dijon, France; (L.A.); (A.B.)
| | - Floris J. Bikker
- Department of Oral Biochemistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, 1081 LA Amsterdam, The Netherlands;
| | - Aline Bonnotte
- Agroécologie, UMR1347 INRAE, ERL CNRS 6300, DimaCell Platform, Center of Microscopy INRAE, University of Bourgogne, 21000 Dijon, France; (L.A.); (A.B.)
| | - Eric Bourillot
- Institut Carnot de Bourgogne (ICB), UMR CNRS 6303, University of Bourgogne, 21000 Dijon, France; (I.C.); (E.B.); (E.L.); (O.P.)
| | - Loïc Briand
- Center for Taste and Feeding Behaviour (CSGA), UMR1324 INRAE, Institut Agro Dijon, Université de Bourgogne, UMR6265 CNRS, 21000 Dijon, France; (C.N.); (L.B.); (H.B.); (J.-M.H.); (N.H.); (M.L.); (F.N.); (M.S.); (C.B.)
| | - Hélène Brignot
- Center for Taste and Feeding Behaviour (CSGA), UMR1324 INRAE, Institut Agro Dijon, Université de Bourgogne, UMR6265 CNRS, 21000 Dijon, France; (C.N.); (L.B.); (H.B.); (J.-M.H.); (N.H.); (M.L.); (F.N.); (M.S.); (C.B.)
| | - Jean-Marie Heydel
- Center for Taste and Feeding Behaviour (CSGA), UMR1324 INRAE, Institut Agro Dijon, Université de Bourgogne, UMR6265 CNRS, 21000 Dijon, France; (C.N.); (L.B.); (H.B.); (J.-M.H.); (N.H.); (M.L.); (F.N.); (M.S.); (C.B.)
| | - Noémie Herrmann
- Center for Taste and Feeding Behaviour (CSGA), UMR1324 INRAE, Institut Agro Dijon, Université de Bourgogne, UMR6265 CNRS, 21000 Dijon, France; (C.N.); (L.B.); (H.B.); (J.-M.H.); (N.H.); (M.L.); (F.N.); (M.S.); (C.B.)
| | - Mélanie Lelièvre
- Center for Taste and Feeding Behaviour (CSGA), UMR1324 INRAE, Institut Agro Dijon, Université de Bourgogne, UMR6265 CNRS, 21000 Dijon, France; (C.N.); (L.B.); (H.B.); (J.-M.H.); (N.H.); (M.L.); (F.N.); (M.S.); (C.B.)
| | - Eric Lesniewska
- Institut Carnot de Bourgogne (ICB), UMR CNRS 6303, University of Bourgogne, 21000 Dijon, France; (I.C.); (E.B.); (E.L.); (O.P.)
| | - Fabrice Neiers
- Center for Taste and Feeding Behaviour (CSGA), UMR1324 INRAE, Institut Agro Dijon, Université de Bourgogne, UMR6265 CNRS, 21000 Dijon, France; (C.N.); (L.B.); (H.B.); (J.-M.H.); (N.H.); (M.L.); (F.N.); (M.S.); (C.B.)
| | - Olivier Piétrement
- Institut Carnot de Bourgogne (ICB), UMR CNRS 6303, University of Bourgogne, 21000 Dijon, France; (I.C.); (E.B.); (E.L.); (O.P.)
| | - Mathieu Schwartz
- Center for Taste and Feeding Behaviour (CSGA), UMR1324 INRAE, Institut Agro Dijon, Université de Bourgogne, UMR6265 CNRS, 21000 Dijon, France; (C.N.); (L.B.); (H.B.); (J.-M.H.); (N.H.); (M.L.); (F.N.); (M.S.); (C.B.)
| | - Christine Belloir
- Center for Taste and Feeding Behaviour (CSGA), UMR1324 INRAE, Institut Agro Dijon, Université de Bourgogne, UMR6265 CNRS, 21000 Dijon, France; (C.N.); (L.B.); (H.B.); (J.-M.H.); (N.H.); (M.L.); (F.N.); (M.S.); (C.B.)
| | - Francis Canon
- Center for Taste and Feeding Behaviour (CSGA), UMR1324 INRAE, Institut Agro Dijon, Université de Bourgogne, UMR6265 CNRS, 21000 Dijon, France; (C.N.); (L.B.); (H.B.); (J.-M.H.); (N.H.); (M.L.); (F.N.); (M.S.); (C.B.)
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Bourdais A, Dehapiot B, Halet G. MRCK activates mouse oocyte myosin II for spindle rotation and male pronucleus centration. J Cell Biol 2023; 222:e202211029. [PMID: 37651121 PMCID: PMC10470461 DOI: 10.1083/jcb.202211029] [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: 11/08/2022] [Revised: 06/24/2023] [Accepted: 08/09/2023] [Indexed: 09/01/2023] Open
Abstract
Asymmetric meiotic divisions in oocytes rely on spindle positioning in close vicinity to the cortex. In metaphase II mouse oocytes, eccentric spindle positioning triggers cortical polarization, including the build-up of an actin cap surrounded by a ring of activated myosin II. While the role of the actin cap in promoting polar body formation is established, ring myosin II activation mechanisms and functions have remained elusive. Here, we show that ring myosin II activation requires myotonic dystrophy kinase-related Cdc42-binding kinase (MRCK), downstream of polarized Cdc42. MRCK inhibition resulted in spindle rotation defects during anaphase II, precluding polar body extrusion. Remarkably, disengagement of segregated chromatids from the anaphase spindle could rescue rotation. We further show that the MRCK/myosin II pathway is activated in the fertilization cone and is required for male pronucleus migration toward the center of the zygote. These findings provide novel insights into the mechanism of myosin II activation in oocytes and its role in orchestrating asymmetric division and pronucleus centration.
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Affiliation(s)
- Anne Bourdais
- University of Rennes, CNRS - UMR 6290, Institute of Genetics and Development of Rennes, Rennes, France
| | - Benoit Dehapiot
- University of Rennes, CNRS - UMR 6290, Institute of Genetics and Development of Rennes, Rennes, France
| | - Guillaume Halet
- University of Rennes, CNRS - UMR 6290, Institute of Genetics and Development of Rennes, Rennes, France
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Hadjerci J, Billet A, Kessler P, Mourier G, Ghazarian M, Gonzalez A, Wunder C, Mabrouk N, Tartour E, Servent D, Johannes L. Engineered Synthetic STxB for Enhanced Cytosolic Delivery. Cells 2023; 12:cells12091291. [PMID: 37174690 PMCID: PMC10177378 DOI: 10.3390/cells12091291] [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: 01/13/2023] [Revised: 04/12/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Many molecular targets for cancer therapy are located in the cytosol. Therapeutic macromolecules are generally not able to spontaneously translocate across membranes to reach these cytosolic targets. Therefore a strong need exists for tools that enhance cytosolic delivery. Shiga toxin B-subunit (STxB) is used to deliver therapeutic principles to disease-relevant cells that express its receptor, the glycolipid Gb3. Based on its naturally existing membrane translocation capacity, STxB delivers antigens to the cytosol of Gb3-positive dendritic cells, leading to the induction of CD8+ T cells. Here, we have explored the possibility of further increasing the membrane translocation of STxB to enable other therapeutic applications. For this, our capacity to synthesize STxB chemically was exploited to introduce unnatural amino acids at different positions of the protein. These were then functionalized with hydrophobic entities to locally destabilize endosomal membranes. Intracellular trafficking of these functionalized STxB was measured by confocal microscopy and their cytosolic arrival with a recently developed highly robust, sensitive, and quantitative translocation assay. From different types of hydrophobic moieties that were linked to STxB, the most efficient configuration was determined. STxB translocation was increased by a factor of 2.5, paving the path for new biomedical opportunities.
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Affiliation(s)
- Justine Hadjerci
- Cellular and Chemical Biology Unit, Institut Curie, Université PSL, U1143 INSERM, UMR3666 CNRS, 26 Rue d'Ulm, CEDEX 05, 75248 Paris, France
| | - Anne Billet
- Cellular and Chemical Biology Unit, Institut Curie, Université PSL, U1143 INSERM, UMR3666 CNRS, 26 Rue d'Ulm, CEDEX 05, 75248 Paris, France
- Université de Paris, 85 Boulevard Saint-Germain, 75006 Paris, France
| | - Pascal Kessler
- DMTS/SIMoS, CEA, Université Paris Saclay, 91191 Gif sur Yvette, France
| | - Gilles Mourier
- DMTS/SIMoS, CEA, Université Paris Saclay, 91191 Gif sur Yvette, France
| | - Marine Ghazarian
- DMTS/SIMoS, CEA, Université Paris Saclay, 91191 Gif sur Yvette, France
| | - Anthony Gonzalez
- DMTS/SIMoS, CEA, Université Paris Saclay, 91191 Gif sur Yvette, France
| | - Christian Wunder
- Cellular and Chemical Biology Unit, Institut Curie, Université PSL, U1143 INSERM, UMR3666 CNRS, 26 Rue d'Ulm, CEDEX 05, 75248 Paris, France
| | | | - Eric Tartour
- PARCC, INSERM, Université Paris Cité, 75015 Paris, France
- Department of Immunology, Hôpital Européen Georges-Pompidou, AP-HP, CEDEX 15, 75908 Paris, France
| | - Denis Servent
- DMTS/SIMoS, CEA, Université Paris Saclay, 91191 Gif sur Yvette, France
| | - Ludger Johannes
- Cellular and Chemical Biology Unit, Institut Curie, Université PSL, U1143 INSERM, UMR3666 CNRS, 26 Rue d'Ulm, CEDEX 05, 75248 Paris, France
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Yeh SC, Strilets T, Tan WL, Castillo D, Medkour H, Rey-Cadilhac F, Serrato-Pomar IM, Rachenne F, Chowdhury A, Chuo V, Azar SR, Singh MK, Hamel R, Missé D, Kini RM, Kenney LJ, Vasilakis N, Marti-Renom MA, Nir G, Pompon J, Garcia-Blanco MA. The anti-immune dengue subgenomic flaviviral RNA is present in vesicles in mosquito saliva and is associated with increased infectivity. PLoS Pathog 2023; 19:e1011224. [PMID: 36996041 PMCID: PMC10062553 DOI: 10.1371/journal.ppat.1011224] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 02/20/2023] [Indexed: 03/31/2023] Open
Abstract
Mosquito transmission of dengue viruses to humans starts with infection of skin resident cells at the biting site. There is great interest in identifying transmission-enhancing factors in mosquito saliva in order to counteract them. Here we report the discovery of high levels of the anti-immune subgenomic flaviviral RNA (sfRNA) in dengue virus 2-infected mosquito saliva. We established that sfRNA is present in saliva using three different methods: northern blot, RT-qPCR and RNA sequencing. We next show that salivary sfRNA is protected in detergent-sensitive compartments, likely extracellular vesicles. In support of this hypothesis, we visualized viral RNAs in vesicles in mosquito saliva and noted a marked enrichment of signal from 3'UTR sequences, which is consistent with the presence of sfRNA. Furthermore, we show that incubation with mosquito saliva containing higher sfRNA levels results in higher virus infectivity in a human hepatoma cell line and human primary dermal fibroblasts. Transfection of 3'UTR RNA prior to DENV2 infection inhibited type I and III interferon induction and signaling, and enhanced viral replication. Therefore, we posit that sfRNA present in salivary extracellular vesicles is delivered to cells at the biting site to inhibit innate immunity and enhance dengue virus transmission.
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Affiliation(s)
- Shih-Chia Yeh
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Tania Strilets
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Wei-Lian Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - David Castillo
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Hacène Medkour
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
| | | | | | | | - Avisha Chowdhury
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Vanessa Chuo
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Sasha R. Azar
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Moirangthem Kiran Singh
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Rodolphe Hamel
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
| | - Dorothée Missé
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
| | - R. Manjunatha Kini
- Department of Biological Sciences, National University of Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Linda J. Kenney
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Tropical Diseases, University of University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Vector-Borne and Zoonotic Diseases, University of University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Preventive Medicine and Population Health, University of University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center for Emerging Viruses and Arboviruses, University of University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Marc A. Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Guy Nir
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Julien Pompon
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
| | - Mariano A. Garcia-Blanco
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, United States of America
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7
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Allioux M, Yvenou S, Merkel A, Cozannet M, Aubé J, Pommellec J, Le Romancer M, Lavastre V, Guillaume D, Alain K. A metagenomic insight into the microbiomes of geothermal springs in the Subantarctic Kerguelen Islands. Sci Rep 2022; 12:22243. [PMID: 36564496 PMCID: PMC9789041 DOI: 10.1038/s41598-022-26299-4] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
The Kerguelen Islands, located in the southern part of the Indian Ocean, are very isolated geographically. The microbial diversity and communities present on the island, especially associated to geothermal springs, have never been analyzed with high-throughput sequencing methods. In this article, we performed the first metagenomics analysis of microorganisms present in Kerguelen hot springs. From four hot springs, we assembled metagenomes and recovered 42 metagenome-assembled genomes, mostly associated with new putative taxa based on phylogenomic analyses and overall genome relatedness indices. The 42 MAGs were studied in detail and showed putative affiliations to 13 new genomic species and 6 new genera of Bacteria or Archaea according to GTDB. Functional potential of MAGs suggests the presence of thermophiles and hyperthermophiles, as well as heterotrophs and primary producers possibly involved in the sulfur cycle, notably in the oxidation of sulfur compounds. This paper focused on only four of the dozens of hot springs in the Kerguelen Islands and should be considered as a preliminary study of the microorganisms inhabiting the hot springs of these isolated islands. These results show that more efforts should be made towards characterization of Kerguelen Islands ecosystems, as they represent a reservoir of unknown microbial lineages.
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Affiliation(s)
- Maxime Allioux
- Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, Unité Biologie et Ecologie des Ecosystèmes Marins Profonds BEEP, IUEM, Rue Dumont d'Urville, 29280, Plouzané, France
| | - Stéven Yvenou
- Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, Unité Biologie et Ecologie des Ecosystèmes Marins Profonds BEEP, IUEM, Rue Dumont d'Urville, 29280, Plouzané, France
| | - Alexander Merkel
- , Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Marc Cozannet
- Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, Unité Biologie et Ecologie des Ecosystèmes Marins Profonds BEEP, IUEM, Rue Dumont d'Urville, 29280, Plouzané, France
| | - Johanne Aubé
- Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, Unité Biologie et Ecologie des Ecosystèmes Marins Profonds BEEP, IUEM, Rue Dumont d'Urville, 29280, Plouzané, France
| | - Jolann Pommellec
- Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, Unité Biologie et Ecologie des Ecosystèmes Marins Profonds BEEP, IUEM, Rue Dumont d'Urville, 29280, Plouzané, France
| | - Marc Le Romancer
- UBO, UFR Sciences et Techniques, UR 7462, Laboratoire Géoarchitecture, Territoires, Urbanisation, Biodiversité, Environnement, Rennes, France
| | | | | | - Karine Alain
- Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, Unité Biologie et Ecologie des Ecosystèmes Marins Profonds BEEP, IUEM, Rue Dumont d'Urville, 29280, Plouzané, France.
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8
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Cozannet M, Borrel G, Roussel E, Moalic Y, Allioux M, Sanvoisin A, Toffin L, Alain K. New Insights into the Ecology and Physiology of Methanomassiliicoccales from Terrestrial and Aquatic Environments. Microorganisms 2020; 9:E30. [PMID: 33374130 PMCID: PMC7824343 DOI: 10.3390/microorganisms9010030] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 12/01/2020] [Revised: 12/19/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
Members of the archaeal order Methanomassiliicoccales are methanogens mainly associated with animal digestive tracts. However, environmental members remain poorly characterized as no representatives not associated with a host have been cultivated so far. In this study, metabarcoding screening combined with quantitative PCR analyses on a collection of diverse non-host-associated environmental samples revealed that Methanomassiliicoccales were very scarce in most terrestrial and aquatic ecosystems. Relative abundance of Methanomassiliicoccales and substrates/products of methanogenesis were monitored during incubation of environmental slurries. A sediment slurry enriched in Methanomassiliicoccales was obtained from a freshwater sample. It allowed the reconstruction of a high-quality metagenome-assembled genome (MAG) corresponding to a new candidate species, for which we propose the name of Candidatus 'Methanomassiliicoccus armoricus MXMAG1'. Comparison of the annotated genome of MXMAG1 with the published genomes and MAGs from Methanomassiliicoccales belonging to the 2 known clades ('free-living'/non-host-associated environmental clade and 'host-associated'/digestive clade) allowed us to explore the putative physiological traits of Candidatus 'M. armoricus MXMAG1'. As expected, Ca. 'Methanomassiliicoccus armoricus MXMAG1' had the genetic potential to produce methane by reduction of methyl compounds and dihydrogen oxidation. This MAG encodes for several putative physiological and stress response adaptations, including biosynthesis of trehalose (osmotic and temperature regulations), agmatine production (pH regulation), and arsenic detoxication, by reduction and excretion of arsenite, a mechanism that was only present in the 'free-living' clade. An analysis of co-occurrence networks carried out on environmental samples and slurries also showed that Methanomassiliicoccales detected in terrestrial and aquatic ecosystems were strongly associated with acetate and dihydrogen producing bacteria commonly found in digestive habitats and which have been reported to form syntrophic relationships with methanogens.
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Affiliation(s)
- Marc Cozannet
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Guillaume Borrel
- Unit Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institute Pasteur, 75015 Paris, France;
| | - Erwan Roussel
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Yann Moalic
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Maxime Allioux
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Amandine Sanvoisin
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Laurent Toffin
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Karine Alain
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
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Métras R, Fournié G, Dommergues L, Camacho A, Cavalerie L, Mérot P, Keeling MJ, Cêtre-Sossah C, Cardinale E, Edmunds WJ. Drivers for Rift Valley fever emergence in Mayotte: A Bayesian modelling approach. PLoS Negl Trop Dis 2017; 11:e0005767. [PMID: 28732006 PMCID: PMC5540619 DOI: 10.1371/journal.pntd.0005767] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 03/02/2017] [Revised: 08/02/2017] [Accepted: 06/30/2017] [Indexed: 11/28/2022] Open
Abstract
Rift Valley fever (RVF) is a major zoonotic and arboviral hemorrhagic fever. The conditions leading to RVF epidemics are still unclear, and the relative role of climatic and anthropogenic factors may vary between ecosystems. Here, we estimate the most likely scenario that led to RVF emergence on the island of Mayotte, following the 2006-2007 African epidemic. We developed the first mathematical model for RVF that accounts for climate, animal imports and livestock susceptibility, which is fitted to a 12-years dataset. RVF emergence was found to be triggered by the import of infectious animals, whilst transmissibility was approximated as a linear or exponential function of vegetation density. Model forecasts indicated a very low probability of virus endemicity in 2017, and therefore of re-emergence in a closed system (i.e. without import of infected animals). However, the very high proportion of naive animals reached in 2016 implies that the island remains vulnerable to the import of infectious animals. We recommend reinforcing surveillance in livestock, should RVF be reported is neighbouring territories. Our model should be tested elsewhere, with ecosystem-specific data.
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Affiliation(s)
- Raphaëlle Métras
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Guillaume Fournié
- Veterinary Epidemiology, Economics and Public Health group, Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
| | - Laure Dommergues
- GDS Mayotte-Coopérative Agricole des Eleveurs Mahorais, Coconi, Mayotte, France
| | - Anton Camacho
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Epicentre, Paris, France
| | - Lisa Cavalerie
- Centre de coopération internationale en recherche agronomique pour le développement (CIRAD) UMR ASTRE, Cyroi platform, Sainte Clotilde, La Réunion, France
- Institut National de Recherche Agronomique (INRA) UMR 1309 ASTRE, Montpellier, France
- Bureau de la Santé Animale, Direction Générale de l’Alimentation, Paris, France
- Université de La Réunion, Saint Denis, France
| | - Philippe Mérot
- Direction de l’Alimentation, de l’Agriculture et de la Forêt de Mayotte, Mamoudzou, France
| | - Matt J. Keeling
- WIDER, Warwick University, Coventry, United Kingdom
- Life Sciences, Warwick University, Coventry, United Kingdom
- Mathematics Institute, Warwick University, Coventry, United Kingdom
| | - Catherine Cêtre-Sossah
- Centre de coopération internationale en recherche agronomique pour le développement (CIRAD) UMR ASTRE, Cyroi platform, Sainte Clotilde, La Réunion, France
- Institut National de Recherche Agronomique (INRA) UMR 1309 ASTRE, Montpellier, France
| | - Eric Cardinale
- Centre de coopération internationale en recherche agronomique pour le développement (CIRAD) UMR ASTRE, Cyroi platform, Sainte Clotilde, La Réunion, France
- Institut National de Recherche Agronomique (INRA) UMR 1309 ASTRE, Montpellier, France
| | - W. John Edmunds
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
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Balaguier R, Madeleine P, Vuillerme N. Is One Trial Sufficient to Obtain Excellent Pressure Pain Threshold Reliability in the Low Back of Asymptomatic Individuals? A Test-Retest Study. PLoS One 2016; 11:e0160866. [PMID: 27513474 PMCID: PMC4981327 DOI: 10.1371/journal.pone.0160866] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [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: 12/15/2015] [Accepted: 07/26/2016] [Indexed: 02/06/2023] Open
Abstract
The assessment of pressure pain threshold (PPT) provides a quantitative value related to the mechanical sensitivity to pain of deep structures. Although excellent reliability of PPT has been reported in numerous anatomical locations, its absolute and relative reliability in the lower back region remains to be determined. Because of the high prevalence of low back pain in the general population and because low back pain is one of the leading causes of disability in industrialized countries, assessing pressure pain thresholds over the low back is particularly of interest. The purpose of this study study was (1) to evaluate the intra- and inter- absolute and relative reliability of PPT within 14 locations covering the low back region of asymptomatic individuals and (2) to determine the number of trial required to ensure reliable PPT measurements. Fifteen asymptomatic subjects were included in this study. PPTs were assessed among 14 anatomical locations in the low back region over two sessions separated by one hour interval. For the two sessions, three PPT assessments were performed on each location. Reliability was assessed computing intraclass correlation coefficients (ICC), standard error of measurement (SEM) and minimum detectable change (MDC) for all possible combinations between trials and sessions. Bland-Altman plots were also generated to assess potential bias in the dataset. Relative reliability for both intra- and inter- session was almost perfect with ICC ranged from 0.85 to 0.99. With respect to the intra-session, no statistical difference was reported for ICCs and SEM regardless of the conducted comparisons between trials. Conversely, for inter-session, ICCs and SEM values were significantly larger when two consecutive PPT measurements were used for data analysis. No significant difference was observed for the comparison between two consecutive measurements and three measurements. Excellent relative and absolute reliabilities were reported for both intra- and inter-session. Reliable measurements can be equally achieved when using the mean of two or three consecutive PPT measurements, as usually proposed in the literature, or with only the first one. Although reliability was almost perfect regardless of the conducted comparison between PPT assessments, our results suggest using two consecutive measurements to obtain higher short term absolute reliability.
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Affiliation(s)
- Romain Balaguier
- Univ. Grenoble-Alpes, EA AGEIS, Grenoble, France
- Physical Activity and Human Performance group—SMI, Dept. of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Pascal Madeleine
- Physical Activity and Human Performance group—SMI, Dept. of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Nicolas Vuillerme
- Univ. Grenoble-Alpes, EA AGEIS, Grenoble, France
- Physical Activity and Human Performance group—SMI, Dept. of Health Science and Technology, Aalborg University, Aalborg, Denmark
- Institut Universitaire de France, Paris, France
- * E-mail:
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Masson F, Zaidman-Rémy A, Heddi A. Antimicrobial peptides and cell processes tracking endosymbiont dynamics. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150298. [PMID: 27160600 PMCID: PMC4874395 DOI: 10.1098/rstb.2015.0298] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [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: 01/04/2016] [Indexed: 11/12/2022] Open
Abstract
Many insects sustain long-term relationships with intracellular symbiotic bacteria that provide them with essential nutrients. Such endosymbiotic relationships likely emerged from ancestral infections of the host by free-living bacteria, the genomes of which experience drastic gene losses and rearrangements during the host-symbiont coevolution. While it is well documented that endosymbiont genome shrinkage results in the loss of bacterial virulence genes, whether and how the host immune system evolves towards the tolerance and control of bacterial partners remains elusive. Remarkably, many insects rely on a 'compartmentalization strategy' that consists in secluding endosymbionts within specialized host cells, the bacteriocytes, thus preventing direct symbiont contact with the host systemic immune system. In this review, we compile recent advances in the understanding of the bacteriocyte immune and cellular regulators involved in endosymbiont maintenance and control. We focus on the cereal weevils Sitophilus spp., in which bacteriocytes form bacteriome organs that strikingly evolve in structure and number according to insect development and physiological needs. We discuss how weevils track endosymbiont dynamics through at least two mechanisms: (i) a bacteriome local antimicrobial peptide synthesis that regulates endosymbiont cell cytokinesis and helps to maintain a homeostatic state within bacteriocytes and (ii) some cellular processes such as apoptosis and autophagy which adjust endosymbiont load to the host developmental requirements, hence ensuring a fine-tuned integration of symbiosis costs and benefits.This article is part of the themed issue 'Evolutionary ecology of arthropod antimicrobial peptides'.
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Affiliation(s)
- Florent Masson
- Université de Lyon, INSA-Lyon, INRA, BF2I, UMR0203, 69621 Villeurbanne, France
| | - Anna Zaidman-Rémy
- Université de Lyon, INSA-Lyon, INRA, BF2I, UMR0203, 69621 Villeurbanne, France
| | - Abdelaziz Heddi
- Université de Lyon, INSA-Lyon, INRA, BF2I, UMR0203, 69621 Villeurbanne, France
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