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2. ORTHOSKIM: In silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding applications

Author

Pouchon, Charles, Boyer, Frédéric, Roquet, Cristina, Denoeud, France, Chave, Jérome, Coissac, Eric, Alsos, Inger Greve, Lavergne, Sébastien, Smyčka, J, Boleda, M, Thuiller, W, Gielly, L, Taberlet, P, Rioux, D, Hombiat, A, Bzeznick, B, Alberti, A, Wincker, P, Orvain, C, Perrier, C, Douzet, R, Rome, M, Valay, Jg, Aubert, S, Zimmermann, N, Wüest, Ro, Latzin, S, Wipf, S, van Es, J, Garraud, L, Villaret, Jc, Abdulhak, S, Bonnet, V, Huc, S, Fort, N, Legland, T, Sanz, T, Pache, G, Mikolajczak, A, Noble, V, Michaud, H, Offerhaus, B, Pires, M, Morvant, Y, Dentant, C, Salomez, P, Bonet, R, Delahaye, T, Leccia, Mf, Perfus, M, Eggenberg, S, Möhl, A, Hurdu, B, Pușcaș, M, Slovák, M, Alsos, Ig, Merkel, F, Lammers, Y, Coissac, E, Pouchon, C, Denoeud, F, Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Université Paris Cité (UPCité), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), National Centre for Biosystematics [Oslo], Natural History Museum [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Cellule Terroirs Viticoles, Partenaires INRAE, Istituto per la Microelettronica e Microsistemi [Catania] (IMM), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université d'Angers (UA), Centre National de la Propriété Forestière (CNPF-IDF), and ANR-16-CE93-0004,Origin-Alps,Origins, assembly and conservation of plant diversity in the European Alps(2016)

Subjects
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, DNA, Chloroplast, Genomics, Sequence Analysis, DNA, Genome, Chloroplast, Transcriptome, DNA, Mitochondrial, DNA, Ribosomal, Ecology, Evolution, Behavior and Systematics, Phylogeny, Biotechnology
Abstract

Low-coverage whole genome shotgun sequencing (or genome skimming) has emerged as a cost-effective method for acquiring genomic data in nonmodel organisms. This method provides sequence information on chloroplast genome (cpDNA), mitochondrial genome (mtDNA) and nuclear ribosomal regions (rDNA), which are over-represented within cells. However, numerous bioinformatic challenges remain to accurately and rapidly obtain such data in organisms with complex genomic structures and rearrangements, in particular for mtDNA in plants or for cpDNA in some plant families. Here we introduce the pipeline ORTHOSKIM, which performs in silico capture of targeted sequences from genomic and transcriptomic libraries without assembling whole organelle genomes. ORTHOSKIM proceeds in three steps: (i) global sequence assembly, (ii) mapping against reference sequences and (iii) target sequence extraction; importantly it also includes a range of quality control tests. Different modes are implemented to capture both coding and noncoding regions of cpDNA, mtDNA and rDNA sequences, along with predefined nuclear sequences (e.g., ultraconserved elements) or collections of single-copy orthologue genes. Moreover, aligned DNA matrices are produced for phylogenetic reconstructions, by performing multiple alignments of the captured sequences. While ORTHOSKIM is suitable for any eukaryote, a case study is presented here, using 114 genome-skimming libraries and four RNA sequencing libraries obtained for two plant families, Primulaceae and Ericaceae, the latter being a well-known problematic family for cpDNA assemblies. ORTHOSKIM recovered with high success rates cpDNA, mtDNA and rDNA sequences, well suited to accurately infer evolutionary relationships within these families. ORTHOSKIM is released under a GPL-3 licence and is available at: https://github.com/cpouchon/ORTHOSKIM.

Published
2022
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4. Ecosystems changes in a context of hominins presence in the SW of Turkey. First results

Author

Andrieu-Ponel, Valérie, Rochette, P., Vialet, A., Rambeau, C, Alçiçek, H, Boulbes, N., Demory, F., Helvaci, C, Lebatard, Ae, Mayda, S, Michaud, H., Moigne, Am, Perrin, Mireille, Ponel, P., Nomade, S., Alçiçek, Cm, Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Collège de France (CdF (institution))-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Histoire naturelle de l'Homme préhistorique (HNHP), Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Archéologie des Sociétés Méditerranéennes (ASM), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Avignon Université (AU), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD), Université Paul-Valéry - Montpellier 3 (UM3)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Matériaux, ingénierie et science [Villeurbanne] (MATEIS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Paul-Valéry - Montpellier 3 (UM3)-Ministère de la Culture et de la Communication (MCC), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Perpignan Via Domitia (UPVD), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDE]Environmental Sciences, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

5. Non Pollen Palynomorphs and pollen of the long lacustrine sequence of Acigöl (Anatolia, Turkey): preliminary results

Author

Andrieu-Ponel, Valérie, Rochette, P., Vialet, A., Rambeau, C, Alçiçek, H, Boulbes, N., Demory, F., Helvacı, C, Lebatard, AE, Mayda, S, MICHAUD, H., Moigne, AM, Perrin, Mireille, Ponel, P., Nomade, S., Alçiçek, MC, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Histoire naturelle de l'Homme préhistorique (HNHP), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD), Archéologie des Sociétés Méditerranéennes (ASM), Université Paul-Valéry - Montpellier 3 (UM3)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Paul-Valéry - Montpellier 3 (UM3)-Ministère de la Culture et de la Communication (MCC), Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Collège de France (CdF (institution))-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Perpignan Via Domitia (UPVD), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), and Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDE]Environmental Sciences, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2017

6. Bilan stationnel de Cerastium siculum Guss

Author

Traclet, S., Pires, M., Michaud, H., Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), and Beaussier, Catherine

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; no abstract

Published
2016

7. Astragalus echinatus Murray dans le département des Bouches-du-Rhône

Author

Abadie, J., Georges, N., MICHAUD, H., Pavon, Daniel, Pires, Mathias, Animaux modèles pour la recherche en oncologie comparée (AMaROC), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Conservatoire Botanique National Méditerranéen de Porquerolles, Conservatoire National Botanique, Beaussier, Catherine, Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), AMaROC - Oniris Nantes, Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU)

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; no abstract

Published
2016

8. Tactile Prosthetics in WiseSkin

Author

Farserotu, J., primary, Decotignie, J-D., additional, Baborowski, J., additional, Volpe, P-N, additional, Quirós, C.R., additional, Kopta, V., additional, Enz, C., additional, Lacour, S., additional, Michaud, H., additional, Martuzzi, R., additional, Koch, V., additional, Li, T., additional, and Antfolk, C., additional

Published
2015
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9. Tactile prosthetics in WiseSkin.

Author

Farserotu, J., Decotignie, J-D., Baborowski, J., Volpe, P-N, Quiros, C R., Kopta, V., Koch, V., Huang, H., Li, T., Enz, C., Lacour, S., Michaud, H., Martuzzi, R., and Antfolk, C.

Published
2015

10. Quantifying the topographical structure of rocky and coral seabeds.

Author

Sous D, Meulé S, Dealbera S, Michaud H, Gassier G, Pezerat M, and Bouchette F

Subjects
Animals, Geologic Sediments, Ecosystem, Anthozoa anatomy & histology
Abstract

Describing the structural complexity of seabeds is of primary importance for a number of geomorphological, hydrodynamical and ecological issues. Aiming to bring a decisive insight on the long-term development of a unified view, the present study reports on a comparative multi-site analysis of high resolution topography surveys in rough nearshore environments. The nine study sites have been selected to cover a wide variety of topographical features, including rocky and coral seabeds. The topography data has been processed to separate roughness and bathymetry-related terrain features, allowing to perform a comprehensive spectral and statistical analysis of each site. A series of roughness metrics have been tested to identify the most relevant estimators of the bottom roughness at each site. The spectral analysis highlights the systematic presence of a self-affine range of variable extension and spectral slope. The standard deviation of the seabed elevation varies from 0.04 to 0.77 m. The statistical and multi-scale analysis performed on the whole set of roughness metrics allows to identify connection between metrics and therefore to propose a reduced set of relevant roughness estimators. A more general emphasis is placed on the need to properly define a unified framework when reconstructing roughness statistics and bathymetry from fine seabed topographical data., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Sous et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Published
2024
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11. All taxa biodiversity inventory of the Bois de Bouis estate (Var, France): a 10-year public-private partnership.

Author

Lacoeuilhe A, Percevault L, Ichter J, Gourdain P, Herard K, Michaud H, Poncet L, Ramage T, Roquinarc'h O, and Withers P

Abstract

Background: This data paper describes the results of a 10-year scientific investigation of a biodiversity-rich private golf estate in south-eastern France in partnership with PatriNat (Office français de la biodiversité/Centre national de la recherche scientifique/Muséum national d'Histoire naturelle, Institut de Recherche pour le Développement). In total, 3,160 species and subspecies, including 1,796 arthropods and 1,049 flora, were inventoried and 65 habitat types were surveyed and mapped. This project is the first All taxa biodiversity inventory (ATBI) in a private property in France with all information available in open data., New Information: The 20 datasets of fauna, flora, lichens and habitat types from the Bois de Bouis estate are now publicly available. Between 2012 and 2022, more than 22,000 occurrences were recorded, checked and published in the INPN information system. All this information is available in open access in the French portal OpenObs, operated by PatriNat and in the Global Biodiversity Information Facility (GBIF). This data paper provides an overview of the project, its main results and its contribution to the French National Inventory of Natural Heritage (INPN).This data paper presents a list eight species never previously recorded to France; three Hymenoptera: Charitopesleucobasis Townes, 1983 (Ichneumonidae), Dryinustussaci Olmi, 1989 (Dryinidae) and Sparasionmunitus Kozlov & Kononova, 1990 (Sparasionidae) and five Diptera: Clusiodesapicalis (Zetterstedt, 1848) (Clusiidae), Dicraeusvagans (Meigen, 1838) (Chloropidae), Stilponintermedius Raffone, 1994, Stilponsubnubilus Chvala, 1988 and Tachydromiaundulata (Strobl, 1906) (Hybotidae).It also includes a table comparing the project to 18 All-taxa biodiversity inventories in France and Belgium and published for the first time., (Aurélie Lacoeuilhe, Louise Percevault, Jean Ichter, Philippe Gourdain, Katia Herard, Henri Michaud, Laurent Poncet, Thibault Ramage, Océane Roquinarc'h, Phil Withers.)

Published
2023
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13. IL-2 and IL-15 drive intrathymic development of distinct periphery-seeding CD4 + Foxp3 + regulatory T lymphocytes.

Author

Apert C, Galindo-Albarrán AO, Castan S, Detraves C, Michaud H, McJannett N, Haegeman B, Fillatreau S, Malissen B, Holländer G, Žuklys S, Santamaria JC, Joffre OP, Romagnoli P, and van Meerwijk JPM

Subjects
Animals, Cytokines, Forkhead Transcription Factors genetics, Mice, Receptors, Antigen, T-Cell, Interleukin-2, T-Lymphocytes, Regulatory
Abstract

Development of Foxp3-expressing regulatory T-lymphocytes (Treg) in the thymus is controlled by signals delivered in T-cell precursors via the TCR, co-stimulatory receptors, and cytokine receptors. In absence of IL-2, IL-15 or their receptors, fewer Treg apparently develop in the thymus. However, it was recently shown that a substantial part of thymic Treg are cells that had recirculated from the periphery back to the thymus, troubling interpretation of these results. We therefore reassessed the involvement of IL-2 and IL-15 in the development of Treg, taking into account Treg-recirculation. At the age of three weeks, when in wt and IL-15-deficient (but not in IL-2-deficient) mice substantial amounts of recirculating Treg are present in the thymus, we found similarly reduced proportions of newly developed Treg in absence of IL-2 or IL-15, and in absence of both cytokines even less Treg developed. In neonates, when practically no recirculating Treg were found in the thymus, the absence of IL-2 led to substantially more reduced Treg-development than deficiency in IL-15. IL-2 but not IL-15 modulated the CD25, GITR, OX40, and CD73-phenotypes of the thymus-egress-competent and periphery-seeding Treg-population. Interestingly, IL-2 and IL-15 also modulated the TCR-repertoire expressed by developing Treg. Upon transfer into Treg-less Foxp3 sf mice, newly developed Treg from IL-2- (and to a much lesser extent IL-15-) deficient mice suppressed immunopathology less efficiently than wt Treg. Taken together, our results firmly establish important non-redundant quantitative and qualitative roles for IL-2 and, to a lesser extent, IL-15 in intrathymic Treg-development., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Apert, Galindo-Albarrán, Castan, Detraves, Michaud, McJannett, Haegeman, Fillatreau, Malissen, Holländer, Žuklys, Santamaria, Joffre, Romagnoli and van Meerwijk.)

Published
2022
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15. Continuous presence of proto-cereals in Anatolia since 2.3 Ma, and their possible co-evolution with large herbivores and hominins.

Author

Andrieu-Ponel V, Rochette P, Demory F, Alçiçek H, Boulbes N, Bourlès D, Helvacı C, Lebatard AE, Mayda S, Michaud H, Moigne AM, Nomade S, Perrin M, Ponel P, Rambeau C, Vialet A, Gambin B, and Alçiçek MC

Subjects
Animals, History, Ancient, Humans, Biological Evolution, Domestication, Edible Grain history, Herbivory, Hominidae
Abstract

Cereals are a central resource for the human diet and are traditionally assumed to have evolved from wild grasses at the onset of the Neolithic under the pressure of agriculture. Here we demonstrate that cereals may have a significantly longer and more diverse lineage, based on the study of a 0-2.3 Ma, 601 m long sedimentary core from Lake Acıgöl (South-West Anatolia). Pollen characteristic of cereals is abundant throughout the sedimentary sequence. The presence of large lakes within this arid bioclimatic zone led to the concentration of large herbivore herds, as indicated by the continuous occurrence of coprophilous fungi spores in the record. Our hypothesis is that the effects of overgrazing on soils and herbaceous stratum, during this long period, led to genetic modifications of the Poaceae taxa and to the appearance of proto-cereals. The simultaneous presence of hominins is attested as early as about 1.4 Ma in the lake vicinity, and 1.8 Ma in Georgia and Levant. These ancient hominins probably benefited from the availability of these proto-cereals, rich in nutrients, as well as various other edible plants, opening the way, in this region of the Middle East, to a process of domestication, which reached its full development during the Neolithic.

Published
2021
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16. [Predictive assays for responses of tumors and normal tissues in radiation oncology].

Author

Riou O, Bourgier C, Brengues M, Bonnefoi N, Michaud HA, Castan F, Gourgou S, Draghici R, Farcy-Jacquet MP, Bons F, Fenoglietto P, Ozsahin M, and Azria D

Subjects
Biomarkers, Tumor, Blood Cells radiation effects, DNA Repair genetics, Humans, Neoplasms genetics, Organ Specificity, Prognosis, Proteomics, Radiation Injuries etiology, Radiotherapy Dosage, Sensitivity and Specificity, Treatment Outcome, Neoplasms radiotherapy, Organs at Risk radiation effects, Radiation Tolerance
Abstract

The impact of curative radiotherapy depends mainly on the total dose delivered homogenously in the target volume. Tumor sensitivity to radiotherapy may be particularly inconstant depending on location, histology, somatic genetic parameters and the capacity of the immune system to infiltrate the tumor. In addition, the dose delivered to the surrounding healthy tissues may reduce the therapeutic ratio of many radiation treatments. In a same population treated in one center with the same technique, it appears that individual radiosensitivity clearly exists, namely in terms of late side effects that are in principle non-reversible. This review details the different radiobiological approaches that have been developed to better predict the tumor response but also the radiation-induced late effects., (Copyright © 2019 Société française de radiothérapie oncologique (SFRO). Published by Elsevier Masson SAS. All rights reserved.)

Published
2019
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