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1. The ‘Shellome’ of the Crocus Clam Tridacna crocea Emphasizes Essential Components of Mollusk Shell Biomineralization

Author: Ryo Koyanagi, Laurent Plasseraud, Noriyuki Satoh, Nicolas Brosse, Frédéric Marin, Isabelle Ziegler-Devin, Takeshi Takeuchi, Cédric Broussard, Manabu Fujie, Okinawa Institute of Science and Technology Graduate University, Université de Bourgogne (UB), Institut de Chimie Moléculaire de l'Université de Bourgogne [Dijon] (ICMUB), Université de Bourgogne (UB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Etude et de Recherche sur le Matériau Bois (LERMAB), Université de Lorraine (UL), Faculté des Sciences et Technologies [Université de Lorraine] (FST ), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Study supported by internal funds from the Okinawa Institute of Science and Technology (OIST), and complementary funds obtained via annual recurrent budget of UMR CNRS Biogeosciences, Dijon., brosse, nicolas, Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-Institut de Chimie du CNRS (INC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), DNA Sequencing Section, Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB), Plateforme protéomique 3P5 [Institut Cochin] (3P5), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), and Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement
Subjects: 0301 basic medicine, [CHIM.POLY] Chemical Sciences/Polymers, [SPI.GPROC] Engineering Sciences [physics]/Chemical and Process Engineering, proteome, Tridacna crocea, JAPANESE PEARL OYSTER, QH426-470, [SPI.MAT] Engineering Sciences [physics]/Materials, [SPI.MAT]Engineering Sciences [physics]/Materials, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, 14. Life underwater, Mollusca, Genetics (clinical), Original Research, 030102 biochemistry & molecular biology, biology, [CHIM.ORGA]Chemical Sciences/Organic chemistry, fungi, biology.organism_classification, Bivalvia, biomineralization, [CHIM.ORGA] Chemical Sciences/Organic chemistry, Tridacna, Pteriomorphia, Mytilus, 030104 developmental biology, [CHIM.POLY]Chemical Sciences/Polymers, Evolutionary biology, Proteome, Molecular Medicine, shell formation, Heterodonta, transcriptome, Biomineralization
Abstract: Molluscan shells are among the most fascinating research objects because of their diverse morphologies and textures. The formation of these delicate biomineralized structures is a matrix-mediated process. A question that arises is what are the essential components required to build these exoskeletons. In order to understand the molecular mechanisms of molluscan shell formation, it is crucial to identify organic macromolecules in different shells from diverse taxa. In the case of bivalves, however, taxon sampling in previous shell proteomics studies are focused predominantly on representatives of the class Pteriomorphia such as pearl oysters, edible oysters and mussels. In this study, we have characterized the shell organic matrix from the crocus clam, Tridacna crocea, (Heterodonta) using various biochemical techniques, including SDS-PAGE, FT-IR, monosaccharide analysis, and enzyme-linked lectin assay (ELLA). Furthermore, we have identified a number of shell matrix proteins (SMPs) using a comprehensive proteomics approach combined to RNA-seq. The biochemical studies confirmed the presence of proteins, polysaccharides, and sulfates in the T. crocea shell organic matrix. Proteomics analysis revealed that the majority of the T. crocea SMPs are novel and dissimilar to known SMPs identified from the other bivalve species. Meanwhile, the SMP repertoire of the crocus clam also includes proteins with conserved functional domains such as chitin-binding domain, VWA domain, and protease inhibitor domain. We also identified BMSP (Blue Mussel Shell Protein, originally reported from Mytilus), which is widely distributed among molluscan shell matrix proteins. Tridacna SMPs also include low-complexity regions (LCRs) that are absent in the other molluscan genomes, indicating that these genes may have evolved in specific lineage. These results highlight the diversity of the organic molecules – in particular proteins – that are essential for molluscan shell formation.
Published: 2021
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2. Chromosomal Inversion Polymorphisms in Two Sympatric Ascidian Lineages

Author: Noriyuki Satoh, Yukie Mihirogi, Manabu Fujie, Mayumi Kawamitsu, Yutaka Satou, John D. D. Bishop, Kanako Hisata, Hitoyoshi Yasuo, Atsuko Sato, Kyoto University [Kyoto], Ochanomizu University, Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Marine Biological Association of the United Kingdom (MBA), Okinawa Institute of Science and Technology Graduate University, and Okinawa Institute of Science and Technology Graduate University (OIST)
Subjects: AcademicSubjects/SCI01140, 0106 biological sciences, Sympatry, Letter, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, Gene flow, 03 medical and health sciences, Genome Size, Genetic algorithm, Genetics, Animals, genome, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Local adaptation, Chromosomal inversion, [SDV.GEN]Life Sciences [q-bio]/Genetics, 0303 health sciences, Polymorphism, Genetic, AcademicSubjects/SCI01130, biology.organism_classification, chromosomal speciation, Ciona intestinalis, Ciona, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Evolutionary biology, Sympatric speciation, Chromosome Inversion, genomes
Abstract: Chromosomal rearrangements can reduce fitness of heterozygotes and can thereby prevent gene flow. Therefore, such rearrangements can play a role in local adaptation and speciation. In particular, inversions are considered to be a major potential cause for chromosomal speciation. There are two closely related, partially sympatric lineages of ascidians in the genus Ciona, which we call type-A and type-B animals in the present study. Although these invertebrate chordates are largely isolated reproductively, hybrids can be found in wild populations, suggesting incomplete prezygotic barriers. Although the genome of type-A animals has been decoded and widely used, the genome for type-B animals has not been decoded at the chromosomal level. In the present study, we sequenced the genomes of two type-B individuals from different sides of the English Channel (in the zone of sympatry with type-A individuals) and compared them at the chromosomal level with the type-A genome. Although the overall structures were well conserved between type A and type B, chromosomal alignments revealed many inversions differentiating these two types of Ciona; it is probable that the frequent inversions have contributed to separation between these two lineages. In addition, comparisons of the genomes between the two type-B individuals revealed that type B had high rates of inversion polymorphisms and nucleotide polymorphisms, and thus type B might be in the process of differentiation into multiple new types or species. Our results suggest an important role of inversions in chromosomal speciation of these broadcasting spawners.
Published: 2021
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3. Simulation of Astrocytic Calcium Dynamics in Lattice Light Sheet Microscopy Images

Author: Misa Arizono, Mathieu Ducros, Anais Badoual, Charles Kervrann, Audrey Denizot, Hugues Berry, U. Valentin Nägerl, Space-timE RePresentation, Imaging and cellular dynamics of molecular COmplexes (SERPICO), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Interdisciplinary Institute for Neuroscience [Bordeaux] (IINS), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Computational Neuroscience [Okinawa], Okinawa Institute of Science and Technology Graduate University, Bordeaux Imaging Center (BIC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut François Magendie-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Artificial Evolution and Computational Biology (BEAGLE), Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Université Lumière - Lyon 2 (UL2)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Badoual, Anaïs, Biologie Cellulaire et Cancer, Institut Curie [Paris]-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Okinawa Institute of Science and Technology Graduate University (OIST), Université de Bordeaux (UB)-Institut François Magendie-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), ANR-16-CE17-0005,GENMSMD,Dissection génétique de la Susceptibilité Mendélienne aux infections mycobactériennes chez l'homme(2016), ANR-16-CE23-0005,DALLISH,Assimilation de Données et Microscopie à Feuille de Lumière Structurée pour la Modélisation des Voies d'Endocytose et d'Exocytose en Cellule Unique(2016), CNRS UMR144, Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université Lumière - Lyon 2 (UL2)
Subjects: 0301 basic medicine, calcium signals, Computer science, chemistry.chemical_element, synthetic training datasets, Calcium, Lattice light-sheet microscopy, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Convolutional neural network, Calcium kinetics, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Calcium imaging, chemistry, image analysis, Calcium dynamics, Astrocytes, lattice light sheet microscopy, [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation, Biological system, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, 030217 neurology & neurosurgery, [SPI.SIGNAL] Engineering Sciences [physics]/Signal and Image processing
Abstract: International audience; Astrocytes regulate neuronal information processing through a variety of spatio-temporal calcium signals. Recent advances in calcium imaging have started to shine light on astrocytic activity, but the complexity and size of the recorded data strongly call for more advanced computational analysis tools. Their development is currently hindered by the lack of reliable, labeled annotations that are essential for the evaluation of algorithms and the training of learning-based methods. To solve this labeling problem, we have designed a generator of 2D/3D lattice light sheet microscopy (LLSM) sequences which realistically depict the calcium dynamics of astrocytes. By closely modeling calcium kinetics in real astrocytic ramifications, the generated datasets open the door for the deployment of convolutional neural networks in LLSM.
Published: 2021
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4. The impact of estimator choice: Disagreement in clustering solutions across K estimators for Bayesian analysis of population genetic structure across a wide range of empirical data sets

Author: Stankiewicz, Kathryn, Vasquez Kuntz, Kate, LEDOUX, Jean-Baptiste, AURELLE, D., Garrabou, Joaquim, Nakajima, Yuichi, Dahl, Mikael, Zayasu, Yuna, Jaziri, Sabri, Costantini, Federica, Baums, Iliana, Stankiewicz Kathryn H., Vasquez Kuntz Kate L., Aurelle Didier, Ledoux Jean- Baptiste, Costantini Federica, Garrabou Joaquim, Baums Iliana B., Pennsylvania State University (Penn State), Penn State System, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Ecologie Marine et BIOdiversité (EMBIO), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Okinawa Institute of Science and Technology Graduate University, The Arctic University of Norway (UiT), Okinawa Institute of Science and Technology Graduate University (OIST), Institut National des Sciences et Technologies de la Mer [Salammbô] (INSTM), Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), The Arctic University of Norway [Tromsø, Norway] (UiT), National Science Foundation (US), Pennsylvania State University, European Commission, and Agencia Estatal de Investigación (España)
Subjects: 0106 biological sciences, STRUCTURE, Genotype, Bayesian clustering methods, corals, gene flow, genotype, microsatellites, population structure, Puechmaille statistics, sampling effort, STRUCTURE, ΔK method, genotype, Bayesian probability, Posterior probability, Population, Scale (descriptive set theory), sampling effort, Biology, Population structure, 010603 evolutionary biology, 01 natural sciences, microsatellites, 03 medical and health sciences, Sampling effort, Statistics, Genetics, Range (statistics), ΔK method, Cluster Analysis, Bayesian clustering methods, Cluster analysis, education, Microsatellites, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, 0303 health sciences, education.field_of_study, Estimator, Sampling (statistics), Bayes Theorem, population structure, Gene flow, Genetics, Population, corals, Corals, Puechmaille statistics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, gene flow, Biotechnology, Microsatellite Repeats
Abstract: 14 pages, 5 figures, 2 tables, 1 appendix, supporting information https://doi.org/10.1111/1755-0998.13522.-- Data Availability Statement: All Supporting Information figures and their corresponding raw data can be accessed on Dryad (https://doi.org/10.5061/dryad.zgmsbccck), The software program STRUCTURE is one of the most cited tools for determining population structure. To infer the optimal number of clusters from STRUCTURE output, the ΔK method is often applied. However, a recent study relying on simulated microsatellite data suggested that this method has a downward bias in its estimation of K and is sensitive to uneven sampling. If this finding holds for empirical data sets, conclusions about the scale of gene flow may have to be revised for a large number of studies. To determine the impact of method choice, we applied recently described estimators of K to re-estimate genetic structure in 41 empirical microsatellite data sets; 15 from a broad range of taxa and 26 from one phylogenetic group, coral. We compared alternative estimates of K (Puechmaille statistics) with traditional (ΔK and posterior probability) estimates and found widespread disagreement of estimators across data sets. Thus, one estimator alone is insufficient for determining the optimal number of clusters; this was regardless of study organism or evenness of sampling scheme. Subsequent analysis of molecular variance (AMOVA) did not necessarily clarify which clustering solution was best. To better infer population structure, we suggest a combination of visual inspection of STRUCTURE plots and calculation of the alternative estimators at various thresholds in addition to ΔK. Disagreement between traditional and recent estimators may have important biological implications, such as previously unrecognized population structure, as was the case for many studies reanalysed here, This work was made possible by NSF grant OCE-1537959 to IBB, NIH grant T32: Computation, Bioinformatics, and Statistics (CBIOS) Training Program to KHS, a Bunton-Waller fellowship to KLVK, the strategic Funding UIDB/04423/2020 and UIDP/04423/2020 to JBL, and the Pennsylvania State University Biology Department. The project leading to this publication has received funding from European FEDER Fund under project 1166-39417 to DA. We acknowledge the funding of the Spanish government through the “Severo Ochoa Centre of Excellence” accreditation (CEX2019-000928-S)
Published: 2021
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5. Biochemical characterization of the skeletal matrix of the massive coral, Porites australiensis - The saccharide moieties and their localization

Author: Nicolas Brosse, Isabelle Ziegler-Devin, Takeshi Takeuchi, Noriyuki Satoh, Laurent Plasseraud, Chuya Shinzato, Frédéric Marin, Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Institut de Chimie Moléculaire de l'Université de Bourgogne [Dijon] (ICMUB), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-Institut de Chimie du CNRS (INC), Laboratoire d'Etude et de Recherche sur le Matériau Bois (LERMAB), Université de Lorraine (UL), Department of Marine Bioscience [Chiba], Atmosphere and Ocean Research Institute [Kashiwa-shi] (AORI), The University of Tokyo (UTokyo)-The University of Tokyo (UTokyo), Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), and Study supported by internal funds from the Okinawa Institute of Science and Technology Graduate University (OIST).
Subjects: 0106 biological sciences, 0301 basic medicine, Biomineralization, Glycan, Coral, Matrix (biology), Polysaccharide, 010603 evolutionary biology, 01 natural sciences, Calcium Carbonate, 03 medical and health sciences, Calcification, Physiologic, Saccharide, Structural Biology, Monosaccharide, Animals, 14. Life underwater, [SDV.IB.BIO]Life Sciences [q-bio]/Bioengineering/Biomaterials, Skeleton, chemistry.chemical_classification, biology, Skeletal organic matrix, Lectin, Proteins, Anthozoa, Skeleton (computer programming), Porites australiensis, Extracellular Matrix, 030104 developmental biology, Biochemistry, chemistry, biology.protein, Microscopy, Electron, Scanning, Crystallization
Abstract: 11 pages; International audience; To construct calcium carbonate skeletons of sophisticated architecture, scleractinian corals secrete an extracellular skeletal organic matrix (SOM) from aboral ectodermal cells. The SOM, which is composed of proteins, saccharides, and lipids, performs functions critical for skeleton formation. Even though polysaccharides constitute the major component of the SOM, its contribution to coral skeleton formation is poorly understood. To this end, we analyzed the SOM of the massive colonial coral, Porites australiensis, the skeleton of which has drawn great research interest because it records environmental conditions throughout the life of the colony. The coral skeleton was extensively cleaned, decalcified with acetic acid, and organic fractions were separated based on solubility. These fractions were analyzed using various techniques, including SDS-PAGE, FT-IR, in vitro crystallization, CHNS analysis, chromatography analysis of monosaccharide and enzyme-linked lectin assay (ELLA). We confirmed the acidic nature of SOM and the presence of sulphate, which is thought to initiate CaCO3 crystallization. In order to analyze glycan structures, we performed ELLA on the soluble SOM for the first time and found that it exhibits strong specificity to Datura stramonium lectin (DSL). Furthermore, using biotinylated DSL with anti-biotin antibody conjugated to nanogold, in situ localization of DSL-binding polysaccharides in the P. australiensis skeleton was performed. Signals were distributed on the surfaces of fiber-like crystals of the skeleton, suggesting that polysaccharides may modulate crystal shape. Our study emphasizes the importance of sugar moieties in biomineralization of scleractinian corals.
Published: 2018
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6. The real Nemo movie: Description of embryonic development in <scp> Amphiprion ocellaris </scp> from first division to hatching

Author: Pauline Salis, David Lecchini, Vincent Laudet, Shu‐hua Lee, Natacha Roux, Biologie intégrative des organismes marins (BIOM), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Chinese Culture University [Taipei], and Okinawa Institute of Science and Technology Graduate University
Subjects: 0301 basic medicine, Coral reef fish, Range (biology), Ecology (disciplines), Motion Pictures, Embryonic Development, timelapse video, Context (language use), Pomacentridae, developmental stages, 03 medical and health sciences, 0302 clinical medicine, time‐lapse video, Animals, pigmentation, 14. Life underwater, time-lapse video, coral reef fish, geography, geography.geographical_feature_category, biology, Coral Reefs, Fishes, Coral reef, Patterns & Phenotypes, Blastula, biology.organism_classification, Perciformes, [SDV.BDD.EO]Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, 030104 developmental biology, Evolutionary biology, Evolutionary developmental biology, embryogenesis, 030217 neurology & neurosurgery, Developmental Biology
Abstract: Background Amphiprion ocellaris is one of the rare reef fish species that can be reared in aquaria. It is increasingly used as a model species for Eco‐Evo‐Devo. Therefore, it is important to have an embryonic development table based on high quality images that will allow for standardized sampling by the scientific community. Results Here we provide high‐resolution time‐lapse videos to accompany a detailed description of embryonic development in A ocellaris. We describe a series of developmental stages and we define six broad periods of embryogenesis: zygote, cleavage, blastula, gastrula, segmentation, and organogenesis that we further subdivide into 32 stages. These periods highlight the changing spectrum of major developmental processes that occur during embryonic development. Conclusions We provide an easy system for the determination of embryonic stages, enabling the development of A ocellaris as a coral reef fish model species. This work will facilitate evolutionary development studies, in particular studies of the relationship between climate change and developmental trajectories in the context of coral reefs. Thanks to its lifestyle, complex behavior, and ecology, A ocellaris will undoubtedly become a very attractive model in a wide range of biological fields., Key Findings Six periods have been identified to describe the embryonic development of the false clown‐fish Amphiprion ocellaris.We provide a staging series organized similarly to other models allowing comparative stud‐ies of embryonic development.We provide high‐resolution time‐lapse videos to accompany a detailed description of embry‐onic development in Amphiprion ocellaris.These data provide a general framework that can be used as a tool to standardize studies and experimental procedures throughout false clownfish development.
Published: 2021
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7. Evolutionary aspects of cephalic sensory papillae of the Indo‐Pacific species of Eleotris (Teleostei: Eleotridae)

Author: Marion Mennesson, Philippe Keith, Ken Maeda, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), and Okinawa Institute of Science and Technology Graduate University
Subjects: [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0106 biological sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, 0303 health sciences, Teleostei, biology, Eleotris, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Zoology, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Eleotridae, Genetics, Animal Science and Zoology, 14. Life underwater, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Indo-Pacific, 030304 developmental biology
Abstract: International audience; Eleotris species (Teleostei: Eleotridae) are one of the most common fish in Indo‐Pacific estuaries and insular freshwater streams. In these rivers, they are a sit‐andwaitpredator. They have an amphidromous life cycle, that is adults grow, feed andreproduce in rivers, while larvae have a marine dispersal phase. Larvae recruit backto rivers and settle in stream habitats. Primary characters used to determine Eleotrisspecies are the presence and the disposition of cephalic sensory papillae rows on theoperculum and under the eyes as well as scale row numbers. The morphology ofthese cephalic sensory papillae is of particular importance in this predatory genusas it is generally correlated in fish to predation and feeding. In this paper, we haveestablished a molecular phylogeny of the genus based on the 12 mitochondrial protein‐coding genes to discuss the relationship between Indo‐Pacific Eleotris species.There is a well‐supported dichotomy in the molecular phylogeny, and this separationinto two main clades is also morphologically visible, as it reveals a difference in thearrangement of cephalic sensory papillae. Indeed, the phylogeny distinguishes thespecies with the “open” pattern of the operculum sensory papillae and the specieswith the “closed” one. This phylogeny thus reflects the morphology of the opercularpapillae. The evolution of this character is discussed in terms of the adaptation of theEleotris genus to life in tropical insular river systems.
Published: 2019
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8. A structural signature motif enlightens the origin and diversification of nuclear receptors

Author: Stéphane Erb, Vincent Laudet, Yassmine Chebaro, Dino Moras, Gabriel V. Markov, Alastair G. McEwen, Isabelle M. L. Billas, Brice Beinsteiner, Sarah Cianférani, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), and Okinawa Institute of Science and Technology Graduate University
Subjects: Cancer Research, [SDV]Life Sciences [q-bio], Gene regulatory network, Receptors, Cytoplasmic and Nuclear, QH426-470, Ligands, Physical Chemistry, Database and Informatics Methods, 0302 clinical medicine, Gene Regulatory Networks, Receptor, Promoter Regions, Genetic, Materials, Genetics (clinical), Data Management, Regulation of gene expression, 0303 health sciences, Crystallography, Repertoire, Physics, Monomers, Gene Expression Regulation, Developmental, Phylogenetic Analysis, Condensed Matter Physics, Phylogenetics, Chemistry, Physical Sciences, Crystal Structure, Dimerization, Sequence Analysis, Research Article, Computer and Information Sciences, Evolutionary Processes, Bioinformatics, Materials Science, Embryonic Development, Computational biology, Retinoid X receptor, Biology, Research and Analysis Methods, 03 medical and health sciences, Interaction network, Sequence Motif Analysis, Evolutionary Adaptation, Genetics, Electron Density, Solid State Physics, Humans, Evolutionary Systematics, Amino Acid Sequence, Enhancer, Dimers, Molecular Biology, Transcription factor, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Taxonomy, Evolutionary Biology, Binding Sites, Biology and Life Sciences, Exaptation, Polymer Chemistry, Retinoid X Receptors, Nuclear receptor, Hepatocyte nuclear factor 4, Chemical Properties, Evolutionary biology, Oligomers, Function (biology), 030217 neurology & neurosurgery, Transcription Factors
Abstract: Nuclear receptors are ligand-activated transcription factors that modulate gene regulatory networks from embryonic development to adult physiology and thus represent major targets for clinical interventions in many diseases. Most nuclear receptors function either as homodimers or as heterodimers. The dimerization is crucial for gene regulation by nuclear receptors, by extending the repertoire of binding sites in the promoters or the enhancers of target genes via combinatorial interactions. Here, we focused our attention on an unusual structural variation of the α-helix, called π-turn that is present in helix H7 of the ligand-binding domain of RXR and HNF4. By tracing back the complex evolutionary history of the π-turn, we demonstrate that it was present ancestrally and then independently lost in several nuclear receptor lineages. Importantly, the evolutionary history of the π-turn motif is parallel to the evolutionary diversification of the nuclear receptor dimerization ability from ancestral homodimers to derived heterodimers. We then carried out structural and biophysical analyses, in particular through point mutation studies of key RXR signature residues and showed that this motif plays a critical role in the network of interactions stabilizing homodimers. We further showed that the π-turn was instrumental in allowing a flexible heterodimeric interface of RXR in order to accommodate multiple interfaces with numerous partners and critical for the emergence of high affinity receptors. Altogether, our work allows to identify a functional role for the π-turn in oligomerization of nuclear receptors and reveals how this motif is linked to the emergence of a critical biological function. We conclude that the π-turn can be viewed as a structural exaptation that has contributed to enlarging the functional repertoire of nuclear receptors., Author summary The origin of novelties is a central topic in evolutionary biology. A fundamental question is how organisms constrained by natural selection can divert from existing schemes to set up novel structures or pathways. Among the most important strategies are exaptations, which represent pre-adaptation strategies. Many examples exist in biology, at both morphological and molecular levels, such as the one reported here that focuses on an unusual structural feature called the π-turn. It is found in the structure of the most ancestral nuclear receptors RXR and HNF4. The analyses trace back the complex evolutionary history of the π-turn to more than 500 million years ago, before the Cambrian explosion and show that this feature was essential for the heterodimerization capacity of RXR. Nuclear receptor lineages that emerged later in evolution lost the π-turn. We demonstrate here that this loss in nuclear receptors that heterodimerize with RXR was critical for the emergence of high affinity receptors, such as the vitamin D and the thyroid hormone receptors. On the other hand, the conserved π-turn in RXR allowed it to accommodate multiple heterodimer interfaces with numerous partners. This structural exaptation allowed for the remarkable diversification of nuclear receptors.
Published: 2021
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9. A star is born again: Methods for larval rearing of an emerging model organism, the False clownfish Amphiprion ocellaris

Author: David Lecchini, Vincent Laudet, Laurence Besseau, Nancy Trouillard, Natacha Roux, Rémi Pillot, Pauline Salis, Pascal Romans, Valentin Logeux, Kévin Magré, Biologie intégrative des organismes marins (BIOM), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Excellence CORAIL (LabEX CORAIL), Université des Antilles (UA)-Institut d'écologie et environnement-Université de la Nouvelle-Calédonie (UNC)-Université de la Polynésie Française (UPF)-Université de La Réunion (UR)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Université des Antilles et de la Guyane (UAG)-Institut de Recherche pour le Développement (IRD), Okinawa Institute of Science and Technology Graduate University, Academia Sinica, Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), ANR-19-CE14-0010,SENSO,Le dialogue environnement-hormones dans le contrôle du cycle de vie du poisson clown Amphiprion ocellaris.(2019), and ANR-19-CE34-0006,Manini,Effet des stress anthropogéniques sur le recrutement larvaire des poissons coralliens(2019)
Subjects: 0106 biological sciences, 0301 basic medicine, rearing methods, Coral reef fish, Ecology (disciplines), ved/biology.organism_classification_rank.species, Zoology, Captivity, anemonefishes, Biology, 010603 evolutionary biology, 01 natural sciences, Predation, 03 medical and health sciences, Laboratory Animal Science, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Genetics, Animals, Resource Article, 14. Life underwater, Animal Husbandry, Model organism, Ecology, Evolution, Behavior and Systematics, geography, Larva, coral reef fish, geography.geographical_feature_category, ved/biology, fungi, Fishes, Coral reef, eco‐evo‐devoexperimental model, 030104 developmental biology, Amphiprion ocellaris, Molecular Medicine, Animal Science and Zoology, Developmental biology, Developmental Biology
Abstract: As interest increases in ecological, evolutionary, and developmental biology (Eco‐Evo‐Devo), wild species are increasingly used as experimental models. However, we are still lacking a suitable model for marine fish species, as well as coral reef fishes that can be reared at laboratory scales. Extensive knowledge of the life cycle of anemonefishes, and the peculiarities of their biology, make them relevant marine fish models for developmental biology, ecology, and evolutionary sciences. Here, we present standard methods to maintain breeding pairs of the anemonefish Amphiprion ocellaris in captivity, obtain regular good quality spawning, and protocols to ensure larval survival throughout rearing. We provide a detailed description of the anemonefish husbandry system and life prey culturing protocols. Finally, a “low‐volume” rearing protocol useful for the pharmacological treatment of larvae is presented. Such methods are important as strict requirements for large volumes in rearing tanks often inhibit continuous treatments with expensive or rare compounds., To properly use anemonefish as a laboratory model species, it is required to have breeding pairs, husbandry with broodstock room, larval rearing tanks, and low‐volume rearing tanks for experimental purposes, and finally living prey cultures (nauplii of artemia, rotifers, and algae), Research Highlights This paper describes how to set up a rearing system for anemone fishes at the laboratory scale as this species is becoming a relevant marine fish model to tackle Eco‐Evo‐Devo questions. We detail two rearing methods, one consisting of classical rearing conditions and the other one consisting of low‐volume conditions (500 ml).
Published: 2021
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10. COVID-19 and beyond: a call for action and audacious solidarity to all the citizens and nations, it is humanity’s fight

Author: Sai-Juan Chen, Mehmet Ozturk, Michel Goldman, Denis Noble, Hiroaki Kitano, J. T. Paweska, James R. Heath, Doron Lancet, Karine Clément, Marcelo B. Soares, Mathias Uhlén, Damjana Rozman, Emiel F.M. Wouters, Christian Bréchot, Josep Roca, Ulrike Protzer, Ferran Sanz, Peter J. M. Openshaw, Olaf Wolkenhauer, Martine Laville, Antoine Magnan, Tolu Oni, Bartha Maria Knoppers, Peter J. Sterk, Ariel B. Lindner, Iruka N. Okeke, Myrna C. Bonaldo, Daria Danilenko, Alfonso Valencia, Bertrand Boutron, Rudi Balling, Samir K. Brahmachari, Andrea Gelemanovic, Sumio Sugano, Alberto Di Meglio, Edgar Morin, Jason D Goldman, Mihael H. Polymeropoulos, Christian Pristipino, Carole Goble, Sylvie van der Werf, Vincenzo Valentini, Ismail Serageldin, Laurent Nottale, Leroy Hood, Jesper Tegnér, S. Palkonen, Alfredo Cesario, Christophe Pison, Yi-Ke Guo, Andres Metspalu, Andrea Urbani, David Supple, Mark Lathrop, Laurent P. Nicod, Catherine Larue, Theresa J. Ochoa, Peter Hunter, Eran Segal, Manlio Vinciguerra, Niklas Blomberg, Lisa F. P. Ng, Helga Nowotny, Marc Santolini, Charles Auffray, Giulio Superti-Furga, Takashi Gojobori, Li Jin, Giovanni Scambia, Pulmonology, European Institute for Systems Biology and Medicine (EISBM), University of Luxembourg [Luxembourg], ELIXIR Hub [Cambridge], Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP), CSIR Institute of Genomics and Integrative Biology [New Delhi] (IGIB), Global Virus Network, University of South Florida [Tampa] (USF), Fondazione Policlinico Universitario A. Gemelli [Rome] (FPUAG), Università cattolica del Sacro Cuore = Catholic University of the Sacred Heart [Roma] (Unicatt), Shanghai Jiao Tong University School of Medicine, Nutrition et obésités: approches systémiques (UMR-S 1269) (Nutriomics), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Smorodintsev Research Institute of Influenza [Saint-Petersbourg, Russia], European Organization for Nuclear Research (CERN), Mediterranean Institute for Life Sciences [Split, Croatia] (MedILS), University of Manchester [Manchester], King Abdullah University of Science and Technology (KAUST), National Institute of Genetics [Mishima, Japan] (NIG), Providence St Joseph Health [Seattle], Université libre de Bruxelles (ULB), Imperial College London, Hong Kong Baptist University (HKBU), Institute for Systems Biology [Seattle] (ISB), University of Auckland [Auckland], Fudan University [Shanghai], The Systems Biology Institute [Tokyo] (SBI), Okinawa Institute of Science and Technology Graduate University (OIST), McGill University = Université McGill [Montréal, Canada], Weizmann Institute of Science [Rehovot, Israël], Luxembourg Institute of Health (LIH), Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL), Centre de Recherche Interdisciplinaire / Center for Research and Interdisciplinarity [Paris, France] (CRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), PHU 2 - Institut du Thorax et du Sytème Nerveux [CHU Nantes] (ITSN), Centre hospitalier universitaire de Nantes (CHU Nantes), University of Tartu, Association pour la Pensée Complexe [Montpellier], Observatoire de Paris - Site de Meudon (OBSPM), Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Universidad Peruana Cayetano Heredia (UPCH), University of Ibadan, University of Cambridge School of Clinical Medicine, University of Cape Town, Dokuz Eylül Üniversitesi = Dokuz Eylül University [Izmir] (DEÜ), Université Grenoble Alpes (UGA), Technische Universität München = Technical University of Munich (TUM), Bibliotheca Alexandrina - Library of Alexandria, University of Illinois College of Medicine, University of Illinois System, University of Amsterdam [Amsterdam] (UvA), The University of Tokyo (UTokyo), The Open University of Japan [Chiba] (OUJ), Medizinische Universität Wien = Medical University of Vienna, Karolinska University Hospital [Solna, Sweden] (KUH), Royal Institute of Technology [Stockholm] (KTH ), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Centre National de Référence des Virus des Infections Respiratoires (dont la Grippe) [Lyon] (CNR - laboratoire associé), Institut des Agents Infectieux [Lyon] (IAI), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), St. Anne’s University Hospital [Brno], University of Rostock, Maastricht University [Maastricht, Pays-Bas], Ludwig Boltzmann Institute for Lung Health [Vienna, Austria], This work was supported during its preparation phases by the State Key Laboratory of Medical Genomics, OverseasExpertise Introduction Project for Discipline Innovation [111 Project, B17029] to SJC, LH, CA, European Union grants CASyM [FP7-n°305033] to CA, RB, JR, DR, DS, JT, OW, eTRIKS (IMI-1-n°115446) to CA, RB, YG, PREPARE [FP7-n°602525] to CA, PO, SV, and initial funds in support of the deep phenotyping clinical study from philanthropic donors, Gilead, Merck and Novartis to JG, JH, LH, the Ricerca Corrente Program by the Italian Ministry of Health to AC, CPr, GS, AU, VV, the National Megaprojects of China for Infectious Diseases [2017ZX10103009-001, 2018ZX10305409-001-005], Double First-class projects from the Ministry of Education to the National Research Center for Translational Medicine Shanghai to SJC, Shanghai Municipal Science and Technology Major Project [2017SHZDZX01] to LJ., European Project: 305033,EC:FP7:HEALTH,FP7-HEALTH-2012-INNOVATION-1,CASYM(2012), and European Project: 602525,EC:FP7:HEALTH,FP7-HEALTH-2013-INNOVATION-1,PREPARE(2014)
Subjects: Civil society, Economic growth, Distancing, [SDV]Life Sciences [q-bio], viruses, Public administration, Intellectual property, Coalition, Coronavirus, Covid-19, Pandemic, Sars-cov-2, Solidarity, Systemic Crisis, Systemic Response, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Political science, 0502 economics and business, media_common.cataloged_instance, 030212 general & internal medicine, 050207 economics, European union, General Pharmacology, Toxicology and Pharmaceutics, media_common, 030304 developmental biology, Government, 0303 health sciences, 050208 finance, General Immunology and Microbiology, SARS-CoV-2, 05 social sciences, Systemic crisis, Conflict of interest, Collective intelligence, virus diseases, COVID-19, General Medicine, There is no alternative, biochemical phenomena, metabolism, and nutrition, 3. Good health, Alliance, 13. Climate action, Honorarium, Systemic response
Abstract: Background: SARS-CoV-2 belongs to a subgroup of coronaviruses rampant in bats for centuries. It has caused the COVID-19 pandemic. Most patients recover, but a minority of severe cases experience acute respiratory distress or an inflammatory storm devastating many organs that can lead to patient death. The spread of SARS-CoV-2 has been facilitated by the increasing intensity of air travel, urban congestion and human contact during the last half century. Until therapies and vaccines are available, tests for virus and exposure, confinement measures and physical distancing have helped curb the pandemic. Vision: The COVID-19 pandemic calls for safeguards and remediation measures through a systemic response. A myriad of self-organizing initiatives by scientists and citizens is developing an advanced collective intelligence response to the coronavirus crisis. Their integration forms Olympiads of Solidarity and Health. Their ability to optimize our response to COVID-19 could serve as a model to trigger a global metamorphosis of our societies with far-reaching consequences for attacking fundamental challenges facing humanity in the 21st century. Mission: For COVID-19 and these other challenges, there is no alternative but action. Meeting in Paris in 2003, we set out to "rethink research to understand life and improve health." We have now formed an international coalition of academia and industry ecosystems taking a systems medicine approach to understanding COVID-19 by thoroughly characterizing viruses, patients and populations during the pandemic, using openly shared tools. All results will be publicly available with no initial claims for intellectual property rights. This World Alliance for Health and Wellbeing will catalyze the creation of medical and health products such as diagnostic tests, drugs and vaccines that become common goods accessible to all, while seeking further alliances with civil society to bridge with socio-ecological and technological approaches that characterise urban systems, for a collective response to future health emergencies. Funding: This work was supported during its preparation phases by the State Key Laboratory of Medical Genomics, Overseas Expertise Introduction Project for Discipline Innovation (111 Project, B17029) to SJC, LH, CA; European Union grants CASyM (FP7-n°305033) to CA, RB, JR, DR, DS, JT, OW; eTRIKS (IMI-1-n°115446) to CA, RB, YG; PREPARE (FP7n°602525) to CA, PO, SV; and initial funds in support of the deep phenotyping clinical study from philanthropic donors, Gilead, Merck and Novartis to JG, JH, LH; the Ricerca Corrente Program by the Italian Ministry of Health to AC, CPr, GS, AU, VV; the National Megaprojects of China for Infectious Diseases (2017ZX10103009-001, 2018ZX10305409-001-005), Double Firstclass projects from the Ministry of Education to the National Research Center for Translational Medicine Shanghai to SJC; Shanghai Municipal Science and Technology Major Project (2017SHZDZX01) to LJ. Conflict of Interest: Rudi Balling reports being a founder/shareholder of ITTM S.A. and Megeno S.A., outside the submitted work, he is co-inventor and holder of two issued patents; James Heath reports personal fees and other from PACT Pharma, outside the submitted work; Hiroaki Kitano reports grants from Minister of Health, Welfare, and Labor of Japanese Government, grants from Okinawa Prefecture Government, outside the submitted work; Doron Lancet reports personal fees from Weizmann Institute of Science and LifeMap Science Inc., outside the submitted work; Catherine Larue reports personal fees from Genfit, outside the submitted work; Peter Openshaw reports personal fees for consultancy work with Janssen, JJ Susanna Palkonen reports grants from Aimmune, Astra Zeneca, Boehringer Ingelheim, Chiesi, DBV Technologies, GSK, Leo Pharma, Novartis, Pfizer, Regeneron Pharmaceuticals, Sanofi Genzyme, outside the submitted work, is employed by the EFA who receives unrestricted grants from corporate entities as above, represents EFA in the following advisory groups of these entities: Astra Zeneca COPD Advisory Committee, GSK Health Advisory Board and Novartis European Patient Advisory Group, receives no personal gain, honoraria, when applicable expenses are payed to her organization, is in a voluntary function the Chair of the Patient Access Partnership PACT who receives unrestricted grants from EFPIA, MedTech Europe, EUCOPE and Medicines for Europe for core operations, and project grants from individual companies, outside the submitted work; Christophe Pison reports personal fees and non-financial support from AstraZeneca, Boehringer Ingelheim, GSK, Novartis, outside the submitted work; Mihael Polymeropulos reports other from Vanda Pharmaceuticals, outside the submitted work; Ulrike Protzer reports grants from VIR Biotechnology, grants and non-financial support from Roche, grants from Alios-JJ Peter Sterk reports other from Breathomix BV, outside the submitted work; Giulio Superti-Furga reports being a shareholder of Proxygen GmbH, Haplogen GmbH and Allcyte GmbH, outside the submitted work; Vincenzo Valentini reports personal fees from Merck Serono, Betaglue, outside the submitted work; Sylvie van der Werf reports other from Sanofi Pasteur, outside the submitted work; she is the holder of four issued patents. The other authors have declared no conflict of interest.
Published: 2021
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11. A Hybrid Human-Neurorobotics Approach to Primary Intersubjectivity via Active Inference

Author: Hendry Ferreira Chame, Ahmadreza Ahmadi, Jun Tani, and Okinawa Institute of Science and Technology Graduate University (OIST)
Subjects: Interaction theory, lcsh:BF1-990, [SCCO.COMP]Cognitive science/Computer science, educational technology, social cognition, 050105 experimental psychology, Human–robot interaction, neurorobotics, Phenomenology (philosophy), 03 medical and health sciences, human-robot interaction, [SCCO]Cognitive science, 0302 clinical medicine, Social cognition, Hypothesis and Theory, developmental psychology, Psychology, interaction theory, [INFO.INFO-RB]Computer Science [cs]/Robotics [cs.RO], 0501 psychology and cognitive sciences, Cognitive rehabilitation therapy, Cognitive skill, General Psychology, ComputingMilieux_MISCELLANEOUS, Cognitive science, 4. Education, 05 social sciences, Educational technology, Cognition, lcsh:Psychology, Embodied cognition, Dyadic interaction, [SCCO.PSYC]Cognitive science/Psychology, free energy principle, cognitive rehabilitation, 030217 neurology & neurosurgery, Intersubjectivity
Abstract: Interdisciplinary efforts from developmental psychology, phenomenology, and philosophy of mind, have studied the rudiments of social cognition and conceptualized distinct forms of intersubjective communication and interaction at human early life. Interaction theorists consider primary intersubjectivity a non-mentalist, pre-theoretical, non-conceptual sort of processes that ground a certain level of communication and understanding, and provide support to higher-level cognitive skills. We argue the study of human/neurorobot interaction consists in a unique opportunity to deepen understanding of underlying mechanisms in social cognition through synthetic modeling, while allowing to examine a second person experiential (2PP) access to intersubjectivity in embodied dyadic interaction. Concretely, we propose the study of primary intersubjectivity as a 2PP experience characterized by predictive engagement, where perception, cognition, and action are accounted for an hermeneutic circle in dyadic interaction. From our interpretation of the concept of active inference in free-energy principle theory, we propose an open-source methodology named neural robotics library (NRL) for experimental human/neurorobot interaction, wherein a demonstration program named virtual Cartesian robot (VCBot) provides an opportunity to experience the aforementioned embodied interaction to general audiences. Lastly, through a study case, we discuss some ways human-robot primary intersubjectivity can contribute to cognitive science research, such as to the fields of developmental psychology, educational technology, and cognitive rehabilitation.
Published: 2020
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12. Anthropogenic stressors impact fish sensory development and survival via thyroid disruption

Author: Rohan M. Brooker, William E. Feeney, David Lecchini, Marc Besson, Marc Metian, Loïc François, Natacha Roux, Vincent Laudet, Guillaume Holzer, Isadora Moniz, Besson, Marc [0000-0003-3381-322X], Feeney, William E [0000-0002-7475-4724], François, Loïc [0000-0001-9962-2675], Brooker, Rohan M [0000-0001-8739-6914], Holzer, Guillaume [0000-0002-5778-8500], Metian, Marc [0000-0003-1485-5029], Laudet, Vincent [0000-0003-4022-4175], Apollo - University of Cambridge Repository, Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Centre for Marine Science, School of Biological Sciences, University of Queensland, University of Queensland [Brisbane], Centre for Integrative Ecology, School of Life and Environmental Sciences, University of Delaware [Newark], Inflammasome NLRP3 – NLRP3 Inflammasome, Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), International Atomic Energy Agency - Environment Laboratories Monaco (IAEA-EL), Biologie intégrative des organismes marins (BIOM), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Okinawa Institute of Science and Technology Graduate University (OIST), Laboratoire d'Excellence CORAIL (LabEX CORAIL), Université des Antilles (UA)-Institut d'écologie et environnement-Université de la Nouvelle-Calédonie (UNC)-Université de la Polynésie Française (UPF)-Université de La Réunion (UR)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Université des Antilles et de la Guyane (UAG)-Institut de Recherche pour le Développement (IRD), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), ANR-19-CE34-0006,Manini,Effet des stress anthropogéniques sur le recrutement larvaire des poissons coralliens(2019), Feeney, William E. [0000-0002-7475-4724], and Brooker, Rohan M. [0000-0001-8739-6914]
Subjects: 0301 basic medicine, 010504 meteorology & atmospheric sciences, Behavioural ecology, Ecophysiology, Thyroid Gland, General Physics and Astronomy, 01 natural sciences, Predation, Environmental impact, lcsh:Science, media_common, Marine biology, Multidisciplinary, biology, Ecology, Thyroid, Fishes, Metamorphosis, Biological, 704/829/826, Acanthurus triostegus, 631/158/856, medicine.anatomical_structure, Larva, Chlorpyrifos, psychological phenomena and processes, endocrine system, Thyroid Hormones, Science, media_common.quotation_subject, Affect (psychology), behavioral disciplines and activities, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Stress, Physiological, 704/172/4081, medicine, Animals, Metamorphosis, Pesticides, 0105 earth and related environmental sciences, Mechanism (biology), Stressor, General Chemistry, 631/158/2455, biology.organism_classification, 030104 developmental biology, lcsh:Q, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Environmental Pollution, Water Pollutants, Chemical
Abstract: Larval metamorphosis and recruitment represent critical life-history transitions for most teleost fishes. While the detrimental effects of anthropogenic stressors on the behavior and survival of recruiting fishes are well-documented, the physiological mechanisms that underpin these patterns remain unclear. Here, we use pharmacological treatments to highlight the role that thyroid hormones (TH) play in sensory development and determining anti-predator responses in metamorphosing convict surgeonfish, Acanthurus triostegus. We then show that high doses of a physical stressor (increased temperature of +3 °C) and a chemical stressor (the pesticide chlorpyrifos at 30 µg L−1) induced similar defects by decreasing fish TH levels and affecting their sensory development. Stressor-exposed fish experienced higher predation; however, their ability to avoid predation improved when they received supplemental TH. Our results highlight that two different anthropogenic stressors can affect critical developmental and ecological transitions via the same physiological pathway. This finding provides a unifying mechanism to explain past results and underlines the profound threat anthropogenic stressors pose to fish communities., Anthropogenic stressors affect many aspects of marine organismal health. Here, the authors expose surgeonfish to temperature and pesticide stressors and show that the stressors, separately and in combination, have adverse effects on thyroid signaling, which disrupts several sensory systems and important predation defenses.
Published: 2020
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13. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

Author: Reinhard Schneider, Jan Hasenauer, Egon Willighagen, Francesco Messina, Hiroaki Kitano, Charles Auffray, Marc Gillespie, Joaquín Dopazo, Emmanuel Barillot, Andreas Dräger, Akira Funahashi, Alexander R. Pico, Anna Niarakis, Aurelio Orta-Resendiz, Alfonso Valencia, Henning Hermjakob, Falk Schreiber, Chris T. Evelo, Rudi Balling, Laura I. Furlong, Inna Kuperstein, Olaf Wolkenhauer, Emek Demir, Alexander Mazein, Marek Ostaszewski, Bioinformatica, RS: NUTRIM - R1 - Obesity, diabetes and cardiovascular health, RS: FHML MaCSBio, [Ostaszewski,M, Mazein,A, Balling,R, Schneider,R] Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg. [Gillespie,ME] Ontario Institute for Cancer Research, Toronto, Canada. [Gillespie,ME] College of Pharmacy and Health Sciences, St. John's University, Queens, NY, USA. [Kuperstein,I, Barillot,E] Institut Curie, PSL Research University, Mines Paris Tech, Inserm, Paris, France. [Niarakis,A] Department of Biology, Univ. Évry, University of Paris-Saclay, Genopole, 91025, Évry, France. [Hermjakob,H] European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK. [Pico,AR] Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, United States. [Willighagen,EL, and Evelo,CT] Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands. [Evelo,CT] Maastricht Centre for Systems Biology, Maastricht University, Maastricht, The Netherlands. [Hasenauer,J] Helmholtz Zentrum München, Institute of Computational Biology, Neuherberg, Germany. [Hasenauer,J] Center for Mathematics, Technische Universität München, Garching, Germany. [Hasenauer,J] Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany. [Schreiber,F] University of Konstanz, Department of Computer and Information Science, Konstanz, Germany. [Schreiber,F] Monash University, Faculty of Information Technology, Melbourne, Australia. [Dräger,A] Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076, Tübingen, Germany. [Dräger,A] Department of Computer Science, University of Tübingen, 72076, Tübingen, Germany. [Dräger,A] German Center for Infection Research (DZIF), partner site, Tübingen, Germany. [Demir,E] Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, USA. [Wolkenhauer,O] Department of Systems Biology & Bioinformatics, University of Rostock, Rostock, Germany. [Wolkenhauer,O] Stellenbosch Institute of Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, 7602, Stellenbosch, South Africa. [Furlong,LI] Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain. [Dopazo,J] Clinical Bioinformatics Area, Fundación Progreso y Salud. Hosp. Virgen del Rocío, Sevilla, Spain. [Dopazo,J] Bioinformatics in Rare Diseases. Centro de Investigación Biomédica en Red de Enfermedades Raras, Fundación Progreso y Salud, Hosp. Virgen del Rocío, Sevilla, Spain. [Dopazo,J] INB-ELIXIR-es, FPS, Hospital Virgen del Rocío, Sevilla, 42013, Spain. [Dopazo,J] Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Sevilla, Spain. [Orta-Resendiz,A] HIV, Inflammation and Persistence Unit, Virology Department, Institut Pasteur, Paris, France. [Orta-Resendiz,A] Bio Sorbonne Paris Cité, Université de Paris, Paris, France. [Messina,F] Dipartimento di Epidemiologia Ricerca Pre-Clinica e Diagnostica Avanzata, National Institute for Infectious Diseases 'Lazzaro Spallanzani' I.R.C.C.S., Rome, Italy. [Messina,F] COVID 19 INMI Network Medicine for IDs Study Group, National Institute for Infectious Diseases 'Lazzaro Spallanzani' I.R.C.C.S., Rome, Italy. [Valencia,A] Barcelona Supercomputer Center (BSC), Barcelona, Spain. [Valencia,A] Institucio Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain. [Funahashi,A] Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan. [Kitano,H] The Systems Biology Institute, Shinagawa, Tokyo, Japan. [Kitano,H] Okinawa Institute of Science and Technology Graduate University, Kunigami, Okinawa, Japan. [Kitano,H] Sony Computer Science Laboratories, Inc., Tokyo, Japan. [Auffray,C] European Institute for Systems Biology and Medicine (EISBM), Vourles, France.
Subjects: Databases, Factual, 010504 meteorology & atmospheric sciences, Computer science, International Cooperation, Disease, 01 natural sciences, Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::Humans [Medical Subject Headings], Multidisciplinaire, généralités & autres [C99] [Ingénierie, informatique & technologie], Pandemic, Modelos biológicos, Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Models, Theoretical::Models, Biological [Medical Subject Headings], Molècules, lcsh:Science, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), 0303 health sciences, Multidisciplinary, general & others [C99] [Engineering, computing & technology], Humanos, Computer Science Applications, Pademia, Disciplines and Occupations::Natural Science Disciplines::Biological Science Disciplines::Biology::Computational Biology [Medical Subject Headings], Host-Pathogen Interactions, Biología computacional, Bases de datos factuales, Statistics, Probability and Uncertainty, Diseases::Respiratory Tract Diseases::Respiratory Tract Infections::Pneumonia::Pneumonia, Viral [Medical Subject Headings], Coronavirus Infections, Information Systems, Statistics and Probability, 2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), Phenomena and Processes::Microbiological Phenomena::Microbiological Processes::Host-Pathogen Interactions [Medical Subject Headings], Infecciones por coronavirus, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Pneumonia, Viral, Computational biology, Library and Information Sciences, Virus-host interaction, Models, Biological, Education, Betacoronavirus, 03 medical and health sciences, Cooperación internacional, Information Science::Information Science::Medical Informatics::Medical Informatics Applications::Information Systems::Databases as Topic::Databases, Factual [Medical Subject Headings], Humans, Interacciones huésped-patógeno, Anthropology, Education, Sociology and Social Phenomena::Social Sciences::Internationality::International Cooperation [Medical Subject Headings], Pandemics, Viral immunology, 030304 developmental biology, 0105 earth and related environmental sciences, Host Microbial Interactions, SARS-CoV-2, Health Care::Environment and Public Health::Public Health::Disease Outbreaks::Epidemics::Pandemics [Medical Subject Headings], Computational Biology, COVID-19, Diseases::Virus Diseases::RNA Virus Infections::Nidovirales Infections::Coronaviridae Infections::Coronavirus Infections [Medical Subject Headings], Coronavirus, Neumonía viral, lcsh:Q, ddc:004, COVID-19 -- Malaltia
Abstract: Researchers around the world join forces to reconstruct the molecular processes of the virus-host interactions aiming to combat the cause of the ongoing pandemic.
Published: 2020

14. Varroa destructor: A Complex Parasite, Crippling Honey Bees Worldwide

Author: Panuwan Chantawannakul, Kirsten S. Traynor, Vienna Kowallik, Melissa A. Y. Oddie, Alison McAfee, Joachim R. de Miranda, Fanny Mondet, Maéva Angélique Techer, Arizona State University [Tempe] (ASU), Abeilles et Environnement (AE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Swedish University of Agricultural Sciences (SLU), Okinawa Institute of Science and Technology Graduate University, Chiang Mai University (CMU), North Carolina State University [Raleigh] (NC State), and University of North Carolina System (UNC)
Subjects: 0301 basic medicine, Beekeeping, Pollination, [SDV]Life Sciences [q-bio], Varroidae, 030231 tropical medicine, Population, Drug Resistance, Zoology, virus, entomology, Host-Parasite Interactions, 03 medical and health sciences, 0302 clinical medicine, Mite, honey bee, Animals, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, education, Apis cerana, Acaricides, education.field_of_study, biology, Host–parasite, [SDV.BA]Life Sciences [q-bio]/Animal biology, fungi, food and beverages, Honey bee, Bees, biology.organism_classification, 030104 developmental biology, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, mite control, Varroa destructor, behavior and behavior mechanisms, Parasitology, Varroa, varroa
Abstract: The parasitic mite, Varroa destructor, has shaken the beekeeping and pollination industries since its spread from its native host, the Asian honey bee (Apis cerana), to the naïve European honey bee (A. mellifera) used commercially for pollination and honey production around the globe. Varroa is the greatest threat to honey bee health. Worrying observations include increasing acaricide resistance in the varroa population and sinking economic treatment thresholds, suggesting that the mites or their vectored viruses are becoming more virulent. Highly infested weak colonies facilitate mite dispersal and disease transmission to stronger and healthier colonies. Here, we review recent developments in the biology, pathology and management of varroa, and integrate older knowledge that is less well known.
Published: 2020
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15. Organelle inheritance and genome architecture variation in isogamous brown algae

Author: Akira F. Peters, Louis Graf, Chikako Nagasato, Koki Nishitsuji, J. Mark Cock, Ji Won Choi, Eiichi Shoguchi, Hwan Su Yoon, Asuka Arimoto, Chang Geun Choi, Sungkyunkwan University [Suwon] (SKKU), Bezhin Rosko, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Okinawa Institute of Science and Technology Graduate University, Institute of Algological Research [Muroran], Hokkaido University [Sapporo, Japan], and Pukyong National University
Subjects: 0106 biological sciences, 0301 basic medicine, Mitochondrial DNA, Isogamy, [SDV]Life Sciences [q-bio], Genome, Plastid, Inheritance Patterns, lcsh:Medicine, Biology, Phaeophyta, DNA, Mitochondrial, 01 natural sciences, Genome, Article, Oogamy, Evolution, Molecular, 03 medical and health sciences, Plastids, 14. Life underwater, lcsh:Science, Gene Rearrangement, Multidisciplinary, Evolutionary theory, lcsh:R, food and beverages, Genomics, Sequence Analysis, DNA, Gene rearrangement, biology.organism_classification, Phylogenetics, 030104 developmental biology, Evolutionary biology, Genome, Mitochondrial, Molecular evolution, lcsh:Q, Ectocarpales, Organelle inheritance, 010606 plant biology & botany
Abstract: International audience; Among the brown algal lineages, ectocarpales species have isogamous fertilization in which male and female gametes are morphologically similar. in contrast, female gametes are much larger than male gametes in the oogamous species found in many other brown algal lineages. it has been reported that the plastids of isogamous species are biparentally inherited whereas the plastids of oogamous species are maternally inherited. in contrast, in both isogamous and oogamous species, the mitochondria are usually inherited maternally. to investigate whether there is any relationship between the modes of inheritance and organellar genome architecture, we sequenced six plastid genomes (ptDnA) and two mitochondrial genomes (mtDnA) of isogamous species from the ectocarpales and compared them with previously sequenced organellar genomes. We found that the biparentally inherited ptDnAs of isogamous species presented distinctive structural rearrangements whereas maternally inherited ptDnAs of oogamous species showed no rearrangements. our analysis permits the hypothesis that structural rearrangements in ptDnAs may be a consequence of the mode of inheritance. The brown algae (Phaeophyceae) are a group of photosynthetic heterokonts (=stramenopiles), a secondary endosymbiotic lineage containing red algal-derived plastids 1. The four brown algal orders analyzed in this study, Ectocarpales, Fucales, Laminariales, and Dictyotales, have macroscopic thalli and are distributed worldwide in low-to-mid latitudes where they play important roles in marine ecosystems. Also, they have great potential for commercial uses such as food or in other seaweed industries. From a taxonomic point of view, the orders Ectocarpales, Fucales and Laminariales are grouped into the subclass Fucophycidae, which is defined as a lineage derived from the brown algal crown radiation (BACR), whereas Dictyotales is classified into the Dictyotophycidae 2 (Fig. S1). The life cycles of most brown algae, including species of the Laminariales and Ectocarpales, are characterized by an alternation between a diploid sporophyte and a haploid gametophyte (i.e., a diploid-haploid life cycle). In contrast, in the Fucales meiosis occurs in the parental diploid plants and they directly produce gametes (i.e., a diplontic life cycle) 3,4. Three fertilization types can be defined based on the morphologies and flagella of gametes, independent of whether they are produced via a gametophyte stage or not: the isogamous type in which flagel-lated gametes are morphologically similar; the anisogamous type where one flagellated gamete is larger than the other; and the oogamous type in which one gamete is a non-motile cell called the egg cell (or oocyte) and the other is a smaller, flagellated sperm cell 5. Most brown algae, including the Laminariales and most species of the Fucales, are oogamous. Anisogamy is only observed in a few lineages such as the Onslowiales, Asterocladales, Nemodermatales, and in some Fucales, Sphacelariales and Ectocarpales species. With the exception of the orders Ectocarpales and Sphacelariales, isogamy is observed only in some species-poor orders such as the Ralfsiales, Scytothamnales, Ascoseirales, Syringodermatales and Ishigeales. Most of the 750 Ectocarpales species are considered to be isogamous 1,6 , although some of these species exhibit a very low level of anisogamy, for example the
Published: 2020
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16. SBML Level 3: an extensible format for the exchange and reuse of biological models

Author: Edda Klipp, Marco Antoniotti, Frank Bergmann, James C. Schaff, Peter D. Karp, Daniel Lucio, Kedar Nath Natarajan, Thomas M. Hamm, Leandro Watanabe, Henning Hermjakob, David Tolnay, John Wagner, Joerg Stelling, Alida Palmisano, Falk Schreiber, Yukiko Matsuoka, Harold F. Gómez, Huaiyu Mi, Carole J. Proctor, Ulrike Wittig, Neil Swainston, Jan Červený, Denis Thieffry, Piero Dalle Pezze, Julio Saez-Rodriguez, Maciej J. Swat, Bin Hu, Martina Kutmon, Thomas Pfau, Bas Teusink, Sarah M. Keating, Fedor A. Kolpakov, Andreas Dräger, Pedro Mendes, Martin Scharm, Emek Demir, Ioannis Xenarios, Christoph Flamm, Axel von Kamp, Darren J. Wilkinson, Nick Juty, Fengkai Zhang, Leonard A. Harris, Michael Schubert, Dagmar Waltemath, Lucian P. Smith, Steffen Klamt, Herbert M. Sauro, Ali Ebrahim, Wolfram Liebermeister, Christian Knüpfer, Nicolas Rodriguez, Tramy Nguyen, Naoki Tanimura, Christopher Cox, Stuart C. Sealfon, Nicholas Alexander Allen, Clemens Wrzodek, Bastian R. Angermann, Martin Meier-Schellersheim, Anna Zhukova, Jean-Baptiste Pettit, Hovakim Grabski, Devin P. Sullivan, Claudine Chaouiya, Michael L. Blinov, John Doyle, Ilya Kiselev, Roman Schulte, Alex Gutteridge, Mélanie Courtot, Eric Mjolsness, Finja Wrzodek, Rahuman S Malik-Sheriff, Ronan M. T. Fleming, Bruce E. Shapiro, Kimberly Begley, Leslie M. Loew, Colin S. Gillespie, Ibrahim Vazirabad, Michael Hucka, Akira Funahashi, Bernhard O. Palsson, Hamid Bolouri, Tomáš Helikar, Camille Laibe, William S. Denney, Chris T. Evelo, Florian Mittag, William S. Hlavacek, Ron Henkel, Harish Dharuri, Julien Dorier, Karthik Raman, Martina Fröhlich, Conor Lawless, Rainer Machné, Falko Krause, Damon Hachmeister, Matthias König, Clifford A. Shaffer, Benjamin D. Heavner, Douglas B. Kell, Jonathan R. Karr, Mihai Glont, Lukas Endler, Melanie I. Stefan, Robert Phair, Lu Li, Henning Schmidt, Dirk Drasdo, Johan Elf, Allyson L. Lister, Hiroaki Kitano, Richard R. Adams, Oliver A. Ruebenacker, Roland Keller, Sven Sahle, Ion I. Moraru, Gary D. Bader, Poul M. F. Nielsen, Johann M. Rohwer, Johannes Eichner, Daniel R. Hyduke, James R. Faeder, Stefan Hoops, Emanuel Gonçalves, Yuichiro Inagaki, Aurélien Naldi, Koichi Takahashi, Sylvain Soliman, Brett G. Olivier, Kieran Smallbone, Stuart L. Moodie, Pedro T. Monteiro, Chris J. Myers, Martin Golebiewski, Tomas Radivoyevitch, Jeremy Zucker, Hidde de Jong, Andrew Finney, Keating, S, Waltemath, D, König, M, Zhang, F, Dräger, A, Chaouiya, C, Bergmann, F, Finney, A, Gillespie, C, Helikar, T, Hoops, S, Malik-Sheriff, R, Moodie, S, Moraru, I, Myers, C, Naldi, A, Olivier, B, Sahle, S, Schaff, J, Smith, L, Swat, M, Thieffry, D, Watanabe, L, Wilkinson, D, Blinov, M, Begley, K, Faeder, J, Gómez, H, Hamm, T, Inagaki, Y, Liebermeister, W, Lister, A, Lucio, D, Mjolsness, E, Proctor, C, Raman, K, Rodriguez, N, Shaffer, C, Shapiro, B, Stelling, J, Swainston, N, Tanimura, N, Wagner, J, Meier-Schellersheim, M, Sauro, H, Palsson, B, Bolouri, H, Kitano, H, Funahashi, A, Hermjakob, H, Doyle, J, Hucka, M, Adams, R, Allen, N, Angermann, B, Antoniotti, M, Bader, G, Červený, J, Courtot, M, Cox, C, Dalle Pezze, P, Demir, E, Denney, W, Dharuri, H, Dorier, J, Drasdo, D, Ebrahim, A, Eichner, J, Elf, J, Endler, L, Evelo, C, Flamm, C, Fleming, R, Fröhlich, M, Glont, M, Gonçalves, E, Golebiewski, M, Grabski, H, Gutteridge, A, Hachmeister, D, Harris, L, Heavner, B, Henkel, R, Hlavacek, W, Hu, B, Hyduke, D, Jong, H, Juty, N, Karp, P, Karr, J, Kell, D, Keller, R, Kiselev, I, Klamt, S, Klipp, E, Knüpfer, C, Kolpakov, F, Krause, F, Kutmon, M, Laibe, C, Lawless, C, Li, L, Loew, L, Machne, R, Matsuoka, Y, Mendes, P, Mi, H, Mittag, F, Monteiro, P, Natarajan, K, Nielsen, P, Nguyen, T, Palmisano, A, Jean-Baptiste, P, Pfau, T, Phair, R, Radivoyevitch, T, Rohwer, J, Ruebenacker, O, Saez-Rodriguez, J, Scharm, M, Schmidt, H, Schreiber, F, Schubert, M, Schulte, R, Sealfon, S, Smallbone, K, Soliman, S, Stefan, M, Sullivan, D, Takahashi, K, Teusink, B, Tolnay, D, Vazirabad, I, Kamp, A, Wittig, U, Wrzodek, C, Wrzodek, F, Xenarios, I, Zhukova, A, Zucker, J, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Heidelberg University Hospital [Heidelberg], Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), European Molecular Biology Laboratory (EMBL), University of Connecticut (UCONN), National Institutes of Health [Bethesda] (NIH), Chercheur indépendant, Amazon Web Services [Seattle] (AWS), Università degli Studi di Milano-Bicocca = University of Milano-Bicocca (UNIMIB), University of Toronto, Masaryk University [Brno] (MUNI), Terry Fox Laboratory, BC Cancer Agency (BCCRC)-British Columbia Cancer Agency Research Centre, The University of Tennessee [Knoxville], The Babraham Institute [Cambridge, UK], Oregon Health and Science University [Portland] (OHSU), Human Predictions LLC, Illumina, Swiss-Prot Group, Swiss Institute of Bioinformatics [Genève] (SIB), Modelling and Analysis for Medical and Biological Applications (MAMBA), Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jacques-Louis Lions (LJLL (UMR_7598)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), University of California [San Diego] (UC San Diego), University of California (UC), Center for Bioinformatics (ZBIT), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Uppsala University, Institut für Populationsgenetik [Vienna], Veterinärmedizinische Universität Wien, Maastricht University [Maastricht], Alpen-Adria-Universität Klagenfurt [Klagenfurt, Austria], Medizinische Universität Wien = Medical University of Vienna, German Cancer Research Center - Deutsches Krebsforschungszentrum [Heidelberg] (DKFZ), Heidelberg Institute for Theoretical Studies (HITS ), Russian-Armenian University (RAU), GlaxoSmithKline [Stevenage, UK] (GSK), GlaxoSmithKline [Headquarters, London, UK] (GSK), Microsoft Technology Licensing (MTL), Microsoft Corporation [Redmond, Wash.], Vanderbilt University School of Medicine [Nashville], University of Washington [Seattle], University of Rostock, Los Alamos National Laboratory (LANL), Lorentz Institute, Universiteit Leiden, Tegmine Therapeutics, Modeling, simulation, measurement, and control of bacterial regulatory networks (IBIS), Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] (LAPM), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut Jean Roget, SRI International [Menlo Park] (SRI), Icahn School of Medicine at Mount Sinai [New York] (MSSM), University of Liverpool, Universitätsklinikum Tübingen - University Hospital of Tübingen, Institute of Information and Computational Technologies (IICT), Max Planck Institute for Dynamics of Complex Technical Systems, Max-Planck-Gesellschaft, Max-Planck-Institut für Molekulare Genetik (MPIMG), Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Humboldt University Of Berlin, Newcastle University [Newcastle], École polytechnique (X), Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], The Systems Biology Institute [Tokyo] (SBI), Centro de Quimica Estrutural (CQE), Instituto Superior Técnico, Universidade Técnica de Lisboa (IST), University of Southern California (USC), Instituto Gulbenkian de Ciência [Oeiras] (IGC), Fundação Calouste Gulbenkian, University of Southern Denmark (SDU), University of Auckland [Auckland], University of Utah, Virginia Tech [Blacksburg], University of Luxembourg [Luxembourg], Integrative Bioinformatics Inc [Mountain View], Cleveland Clinic, Stellenbosch University, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Universität Heidelberg [Heidelberg] = Heidelberg University, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Mount Sinai School of Medicine, Department of Psychiatry-Icahn School of Medicine at Mount Sinai [New York] (MSSM), University of Manchester [Manchester], Computational systems biology and optimization (Lifeware), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), California Institute of Technology (CALTECH), Encodia Inc [San Diego], Shinshu University [Nagano], University of Amsterdam [Amsterdam] (UvA), Versiti Blood Center of Wisconsin, Greifswald University Hospital, Bioinformatique évolutive - Evolutionary Bioinformatics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Pacific Northwest National Laboratory (PNNL), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), Department of Bioengineering, University of California (UC)-University of California (UC), ANSYS, Virginia Polytechnic Institute and State University [Blacksburg], Eight Pillars Ltd, Center for Integrative Genomics - Institute of Bioinformatics, Génopode (CIG), Université de Lausanne = University of Lausanne (UNIL)-Université de Lausanne = University of Lausanne (UNIL), Universität Heidelberg, Bioquant, Applied Biomathematics [New York], SimCYP Ltd, Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Utah School of Medicine [Salt Lake City], University of Pittsburgh School of Medicine, Pennsylvania Commonwealth System of Higher Education (PCSHE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Mizuho Information and Research Institute, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Oxford, Computer Science (North Carolina State University), North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), University of California [Irvine] (UC Irvine), Indian Institute of Technology Madras (IIT Madras), California State University [Northridge] (CSUN), Biotechnology and Biological Sciences Research Council (BBSRC), IBM Research [Melbourne], Benaroya Research Institute [Seattle] (BRI), Okinawa Institute of Science and Technology Graduate University, Keio University, Department of Computing and Mathematical sciences, members, SBML Level 3 Community, Université de Lausanne (UNIL), Università degli Studi di Milano-Bicocca [Milano] (UNIMIB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), University of California, Universiteit Leiden [Leiden], Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Inria Grenoble - Rhône-Alpes, Humboldt University of Berlin, Universität Heidelberg [Heidelberg], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Humboldt-Universität zu Berlin, University of California-University of California, Université de Lausanne (UNIL)-Université de Lausanne (UNIL), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Oxford [Oxford], University of California [Irvine] (UCI), Biotechnology and Biological Sciences Research Council, Computer Science, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)
Subjects: computational modeling, Medicine (General), Markup language, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, INFORMATION, Interoperability, interoperability, Review, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], ANNOTATION, 0302 clinical medicine, Software, file forma, Models, Biology (General), 0303 health sciences, Computational model, Applied Mathematics, Systems Biology, systems biology, File format, 3. Good health, Networking and Information Technology R&D, Networking and Information Technology R&D (NITRD), Computational Theory and Mathematics, SIMULATION, General Agricultural and Biological Sciences, STANDARDS, REPOSITORY, Information Systems, QH301-705.5, Bioinformatics, Systems biology, Software ecosystem, Reviews, Bioengineering, Methods & Resources, Biology, MARKUP LANGUAGE, Models, Biological, SBML Level 3 Community members, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, R5-920, Animals, Humans, SBML, reproducibility, 030304 developmental biology, ENVIRONMENT, General Immunology and Microbiology, file format, business.industry, Computational Biology, Biological, ONTOLOGY, Metabolism, Logistic Models, Biochemistry and Cell Biology, Other Biological Sciences, Software engineering, business, 030217 neurology & neurosurgery
Abstract: Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction‐based models and packages that extend the core with features suited to other model types including constraint‐based models, reaction‐diffusion models, logical network models, and rule‐based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single‐cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution., Over the past two decades, scientists from different fields have been developing SBML, a standard format for encoding computational models in biology and medicine. This article summarizes recent progress and gives perspectives on emerging challenges.
Published: 2020
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17. The loss of flight in ant workers enabled an evolutionary redesign of the thorax for ground labour

Author: Alexander Blanke, Evan P. Economo, Christian Peeters, Roberto A. Keller, Georg Fischer, Adam Khalife, Julian Katzke, Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universidade de Lisboa (ULISBOA), Centre for Ecology - Evolution and Environmental Changes (cE3c), Okinawa Institute of Science and Technology Graduate University, University of Cologne, Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Universidade de Lisboa = University of Lisbon (ULISBOA)
Subjects: 0106 biological sciences, 0301 basic medicine, Micro-CT, Foraging, Petiole (insect anatomy), 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, ddc:570, lcsh:Zoology, Muscle attachment, Thorax (insect anatomy), Endoskeleton, lcsh:QL1-991, Mutillidae, Formicidae, Ecology, Evolution, Behavior and Systematics, Core (anatomy), Wing, biology, Research, Muscles, Central place foraging, biology.organism_classification, Ponerinae, body regions, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, 030104 developmental biology, Evolutionary biology, Animal Science and Zoology, Queen
Abstract: Background Explanations for the ecological dominance of ants generally focus on the benefits of division of labour and cooperation during foraging. However, the principal innovation of ants relative to their wasp ancestors was the evolution of a new phenotype: a wingless worker caste optimized for ground labour. Ant workers are famous for their ability to lift and carry heavy loads, but we know surprisingly little about the morphological basis of their strength. Here we examine the consequences of the universal loss of flight in ant workers on skeletomuscular adaptations in the thorax for enhanced foraging on six legs. Results Using X-ray microcomputed tomography and 3D segmentation, we compared winged queens and wingless workers in Euponera sikorae (subfamily Ponerinae) and Cataglyphis savignyi (subfamily Formicinae). Workers are characterized by five major changes to their thorax: i) fusion of the articulated flight thorax (queens) into a rigid box optimized to support the muscles that operate the head, legs and abdomen, ii) redesign of internal cuticular structures for better bracing and muscle attachment, iii) substantial enlargement of the neck muscles for suspending and moving the head, iv) lengthening of the external trochanter muscles, predominant for the leg actions that lift the body off the ground, v) modified angle of the petiole muscles that are key for flexion of the abdomen. We measured volumes and pennation angles for a few key muscles to assess their increased efficacy. Our comparisons of additional workers across five genera in subfamilies Dorylinae and Myrmicinae show these modifications in the wingless thorax to be consistent. In contrast, a mutillid wasp showed a different pattern of muscle adaptations resulting from the lack of wing muscles. Conclusions Rather than simply a subtraction of costly flight muscles, we propose the ant worker thorax evolved into a power core underlying stronger mandibles, legs, and sting. This contrasts with solitary flightless insects where the lack of central place foraging generated distinct selective pressures for rearranging the thorax. Stronger emphasis is needed on morphological innovations of social insects to further our understanding of the evolution of social behaviours.
Published: 2020
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18. Nanoscale dynamics of peptidoglycan assembly during the cell cycle of Streptococcus pneumoniae

Author: Dominique Bourgeois, Bill Söderström, Cécile Morlot, Yung-Sing Wong, Anne Marie Di Guilmi, Christophe Grangeasse, Anais Pelletier, Christopher Arthaud, Jennyfer Trouve, Claire Durmort, André Zapun, Groupe Pneumocoque (IBS-PG), Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), iThree Institute, University of Technology Sydney (UTS), Okinawa Institute of Science and Technology Graduate University (OIST), Microbiologie moléculaire et biochimie structurale / Molecular Microbiology and Structural Biochemistry (MMSB), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Groupe Imagerie intégrée de la réponse au stress / Integrated Imaging of Stress Response Group (IBS-I2SR), Département de pharmacochimie moléculaire (DPM), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), ANR-16-CE11-0016,DIVinHD,Imagerie super-résolue de la division bactérienne(2016), and ANR-19-CE15-0011,LookingForPegase,A la recherche de protéines régulant des enzymes responsables de la synthèse du peptidoglycane(2019)
Subjects: 0301 basic medicine, Cell division, Cell, Morphogenesis, Peptidoglycan, Biology, Cleavage (embryo), General Biochemistry, Genetics and Molecular Biology, Cell wall, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Bacterial Proteins, Cell Wall, medicine, Bacteria, Cell morphogenesis, Cell Cycle, Cell cycle, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Cell biology, Streptococcus pneumoniae, 030104 developmental biology, medicine.anatomical_structure, chemistry, 06 Biological Sciences, 11 Medical and Health Sciences, 17 Psychology and Cognitive Sciences, General Agricultural and Biological Sciences, Cell Division, 030217 neurology & neurosurgery, Developmental Biology
Abstract: International audience; Dynamics of cell elongation and septation are key determinants of bacterial morphogenesis. These processes are intimately linked to peptidoglycan synthesis performed by macromolecular complexes called the elongasome and the divisome. In rod-shaped bacteria, cell elongation and septation, which are dissociated in time and space, have been well described. By contrast, in ovoid-shaped bacteria, the dynamics and relationships between these processes remain poorly understood because they are concomitant and confined to a nanometer-scale annular region at midcell. Here, we set up a metabolic peptidoglycan labeling approach using click chemistry to image peptidoglycan synthesis by single-molecule localization micro- scopy in the ovoid bacterium Streptococcus pneumoniae. Our nanoscale-resolution data reveal spatiotemporal features of peptidoglycan assembly and fate along the cell cycle and provide geometrical parameters that we used to construct a morphogenesis model of the ovoid cell. These analyses show that septal and peripheral peptidoglycan syntheses first occur within a single annular region that later separates in two concentric regions and that elongation persists after septation is completed. In addition, our data reveal that freshly synthesized peptidoglycan is remodeled all along the cell cycle. Altogether, our work provides evidence that septal peptidoglycan is synthesized from the beginning of the cell cycle and is constantly remodeled through cleavage and insertion of material at its periphery. The ovoid-cell morphogenesis would thus rely on the relative dynamics between peptidoglycan synthesis and cleavage rather than on the existence of two distinct successive phases of peripheral and septal synthesis.
Published: 2021
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19. A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals

Author: Nori Satoh, Paul Simion, Alexander V. Ereskovsky, Hervé Philippe, Nicole King, Erwan Corre, Frédéric Delsuc, Pascal Lapébie, Béatrice Roure, Michaël Manuel, Denis Baurain, Gert Wörheide, Muriel Jager, Daniel J. Richter, Arnaud Di Franco, Eric Quéinnec, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Université de Montréal (UdeM), Integrative Biological Sciences (InBioS), Université de Liège, Evolution Paris Seine, Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Department of Molecular & Cell Biology [Berkeley], University of California [Berkeley], University of California-University of California, Howard Hughes Medical Institute (HHMI), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Okinawa Institute of Science and Technology Graduate University, 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), Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Ludwig-Maximilians-Universität München (LMU), SNMB-Bayerische Staatssammlung für Paläontologie und Geologie, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC), and Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU)
Subjects: 0301 basic medicine, metazoanervous system, Lineage (evolution), Zoology, phylogeny, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Phylogenomics, evolution, Animals, long branch attraction, animal, Bilateria, Long branch attraction, Genome, biology, Ctenophora, phylogenomics, Genomics, biology.organism_classification, Biological Evolution, Invertebrates, Eumetazoa, Porifera, 030104 developmental biology, Sister group, Evolutionary biology, Vertebrates, Placozoa, General Agricultural and Biological Sciences
Abstract: International audience; Resolving the early diversification of animal lineages has proven difficult, even using genome-scale datasets. Several phylogenomic studies have supported the classical scenario in which sponges (Porifera) are the sister group to all other animals (''Porifera-sister''3 hypothesis), consistent with a single origin of the gut, nerve cells, and muscle cells in the stem lineage of eumetazoans (bilaterians + ctenophores + cnidarians). In contrast, several other studies have recovered an alternative topology in which ctenophores are the sister group to all other animals (including sponges). The ``Ctenophora-sister'' hypothesis implies that eumetazoan-specific traits, such as neurons and muscle cells, either evolved once along the metazoan stem lineage and were then lost in sponges and placozoans or evolved at least twice independently in Ctenophora and in Cnidaria + Bilateria. Here, we report on our reconstruction of deep metazoan relationships using a 1,719-gene dataset with dense taxonomic sampling of non-bilaterian animals that was assembled using a semi-automated procedure, designed to reduce known error sources. Our dataset outperforms previous metazoan gene superalignments in terms of data quality and quantity. Analyses with a best-fitting site-heterogeneous evolutionary model provide strong statistical support for placing sponges as the sister-group to all other metazoans, with ctenophores emerging as the second-earliest branching animal lineage. Only those methodological settings that exacerbated long-branch attraction artifacts yielded Ctenophora-sister. These results show that methodological issues must be carefully addressed to tackle difficult phylogenetic questions and pave the road to a better understanding of how fundamental features of animal body plans have emerged.
Published: 2017
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20. Bystander effectors of chondrosarcoma cells irradiated at different LET impair proliferation of chondrocytes

Author: Yannick Saintigny, Mihaela Temelie, Guillaume Vares, François Chevalier, Marion Boulanger, Diana Savu, Christophe Hirtz, Emilie Brotin, Charlotte Lepleux, Tetsuo Nakajima, Aurélie Marie-Brasset, Mary B. Goldring, Laboratoire d'Accueil et de Recherche avec les Ions Accélérés (LARIA), 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), Centre de recherche sur les Ions, les MAtériaux et la Photonique (CIMAP - UMR 6252), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU), Horia Hulubei National Institute of Physics and Nuclear Engineering (NIPNE), IFIN-HH, ImpedanCELL, Interactions Cellules Organismes Environnement (ICORE), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN)-Tumorothèque de Caen Basse-Normandie (TCBN)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN)-Tumorothèque de Caen Basse-Normandie (TCBN), Axe BioTICLA, Unité de recherche interdisciplinaire pour la prévention et le traitement des cancers (ANTICIPE), Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN)-Tumorothèque de Caen Basse-Normandie (TCBN)-Centre Régional de Lutte contre le Cancer François Baclesse [Caen] (UNICANCER/CRLC), UNICANCER-Tumorothèque de Caen Basse-Normandie (TCBN)-Normandie Université (NU)-UNICANCER-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Caen Normandie (UNICAEN), UNICANCER-Tumorothèque de Caen Basse-Normandie (TCBN)-Normandie Université (NU)-UNICANCER-Institut National de la Santé et de la Recherche Médicale (INSERM), Weill Medical College of Cornell University [New York], Cellules Souches, Plasticité Cellulaire, Médecine Régénératrice et Immunothérapies (IRMB), Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Okinawa Institute of Science and Technology Graduate University (OIST), Chiba University, This work was also supported by 'Agence Nationale de la Recherche', in the frame of the 'Investments for the Future' under the references France HADRON (ANR-11-INBS-0007) and Equipex Rec-Hadron (ANR-10-EQPX-1401), French Institute of Romania, French Ministry of Foreign Affairs – Partenariat Hubert Curien Sakura (35973SB)., ANR-10-EQPX-0014,REC-HADRON,RECherche fondamentale en HADRONthérapie(2010), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche sur les Matériaux Avancés (IRMA), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU)-UNICANCER-Tumorothèque de Caen Basse-Normandie (TCBN)-UNICANCER-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-UNICANCER-Tumorothèque de Caen Basse-Normandie (TCBN)-UNICANCER-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Bodescot, Myriam, and Equipements d'excellence - RECherche fondamentale en HADRONthérapie - - REC-HADRON2010 - ANR-10-EQPX-0014 - EQPX - VALID
Subjects: 0301 basic medicine, Cell type, Chondrosarcoma, Linear energy transfer, [SDV.CAN]Life Sciences [q-bio]/Cancer, [SDV.IB.MN]Life Sciences [q-bio]/Bioengineering/Nuclear medicine, Biochemistry, Chondrocyte, [SDV.IB.MN] Life Sciences [q-bio]/Bioengineering/Nuclear medicine, 03 medical and health sciences, 0302 clinical medicine, [SDV.CAN] Life Sciences [q-bio]/Cancer, medicine, Bystander effect, Clonogenic assay, Molecular Biology, Effector, Chemistry, Low-dose irradiation, Cell Biology, medicine.disease, 030104 developmental biology, medicine.anatomical_structure, 030220 oncology & carcinogenesis, Micronucleus test, Radiation-induced bystander effect, Cancer research, Research Article, High-LET
Abstract: While the dose-response relationship of radiation-induced bystander effect (RIBE) is controversial at low and high linear energy transfer (LET), mechanisms and effectors of cell-to-cell communication stay unclear and highly dependent of cell type. In the present study, we investigated the capacity of chondrocytes in responding to bystander factors released by chondrosarcoma cells irradiated at different doses (0.05 to 8 Gy) with X-rays and C-ions. Following a medium transfer protocol, cell survival, proliferation and DNA damages were quantified in bystander chondrocytes. The bystander factors secreted by chondrosarcoma cells were characterized. A significant and major RIBE response was observed in chondrocyte cells (T/C-28a2) receiving conditioned medium from chondrosarcoma cells (SW1353) irradiated with 0.1 Gy of X-rays and 0.05 Gy of C-ions, resulting in cell survivals of 36% and 62%, respectively. Micronuclei induction in bystander cells was observed from the same low doses. The cell survival results obtained by clonogenic assays were confirmed using impedancemetry. The bystander activity was vanished after a heat treatment or a dilution of the conditioned media. The cytokines which are well known as bystander factors, TNF-α and IL-6, were increased as a function of doses and LET according to an ELISA multiplex analysis. Together, the results demonstrate that irradiated chondrosarcoma cells can communicate stress factors to non-irradiated chondrocytes, inducing a wide and specific bystander response related to both doses and LET. Electronic supplementary material The online version of this article (10.1007/s12079-019-00515-9) contains supplementary material, which is available to authorized users.
Published: 2019
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21. Developmental and comparative transcriptomic identification of iridophore contribution to white barring in clownfish

Author: Laurence Besseau, Carine Rey, Marie-Line Escande, Marie Sémon, David M. Parichy, Natacha Roux, Vincent Laudet, Thibault Lorin, Jean-Nicolas Volff, Pauline Salis, Nicolas Salamin, Victor M Lewis, Anna Marcionetti, Biologie intégrative des organismes marins (BIOM), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire de biologie et modélisation de la cellule (LBMC UMR 5239), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Lausanne = University of Lausanne (UNIL), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Department of Biology, Department of Cell Biology, University of Virginia, Charlottesville, Virgi, Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Biology, University of Washington, Seattle, Washington, Swiss Institute of Bioinformatics [Lausanne] (SIB), Okinawa Institute of Science and Technology, and Okinawa Institute of Science and Technology Graduate University (OIST)
Subjects: 0301 basic medicine, Fish Proteins, Cell type, genetic structures, leucophore, [SDV]Life Sciences [q-bio], Dermatology, Biology, iridophore, Genome, General Biochemistry, Genetics and Molecular Biology, Article, Transcriptome, 03 medical and health sciences, Pigment, 0302 clinical medicine, Amphiprion, Animals, Chromatophores, Gene, Zebrafish, coral reef fish, Pigmentation, Fishes, clownfish, Gene Expression Regulation, Developmental, transcriptomic, biology.organism_classification, Chromatophore, White (mutation), 030104 developmental biology, Oncology, Evolutionary biology, 030220 oncology & carcinogenesis, visual_art, visual_art.visual_art_medium
Abstract: International audience; Actinopterygian fishes harbor at least eight distinct pigment cell types, leading to a fascinating diversity of colors. Among this diversity, the cellular origin of the white color appears to be linked to several pigment cell types such as iridophores or leuco‐phores. We used the clownfish Amphiprion ocellaris, which has a color pattern con‐sisting of white bars over a darker body, to characterize the pigment cells that underlie the white hue. We observe by electron microscopy that cells in white bars are similar to iridophores. In addition, the transcriptomic signature of clownfish white bars ex‐hibits similarities with that of zebrafish iridophores. We further show by pharmaco‐logical treatments that these cells are necessary for the white color. Among the top differentially expressed genes in white skin, we identified several genes (fhl2a, fhl2b, saiyan, gpnmb, and apoD1a) and show that three of them are expressed in iridophores. Finally, we show by CRISPR/Cas9 mutagenesis that these genes are critical for irido‐phore development in zebrafish. Our analyses provide clues to the genomic under‐pinning of color diversity and allow identification of new iridophore genes in fish
Published: 2019
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22. Mitigating anticipated effects of systematic errors supports sister-group relationship between Xenacoelomorpha and Ambulacraria

Author: Albert J. Poustka, Richard R. Copley, Katharina J. Hoff, Steven Müller, Heiner Kuhl, Bernd Timmermann, Tomoe Hikosaka-Katayama, Pedro Martinez, Philipp H. Schiffer, Christophe Dessimoz, Florian Mertes, Bartlomiej Tomiczek, Morgane Thomas-Chollier, Daryl Domman, Matthias Horn, Andreas Wallberg, Maximilian J. Telford, Thomas Hankeln, Noriyuki Satoh, Marta Chiodin, Hiroaki Nakano, Hervé Philippe, Matthew L. Rowe, Maurice R. Elphick, Jonathan P. Rast, Canadian Institute for Advanced Research (CIFAR), Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Max Planck Institute for Molecular Genetics (MPIMG), Max-Planck-Gesellschaft, Dahlem Center for Complex Quantum Systems & Fachbereich Physik, Freie Universität Berlin, Universitat de Barcelona (UB), New York University School of Medicine, NYU System (NYU), Universität Greifswald - University of Greifswald, University College of London [London] (UCL), Department of Computer Science (Queen Mary University of London), Queen Mary University of London (QMUL), Université de Lausanne (UNIL), Medical University of Gdańsk, The Wellcome Trust Sanger Institute [Cambridge], University of Vienna [Vienna], Los Alamos National Laboratory (LANL), Max-Planck-Institut für Informatik (MPII), Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Hiroshima City University, Université de Tsukuba = University of Tsukuba, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), GENterprise Genomics, University Medical Center [Mainz], Helmholtz-Zentrum München (HZM), Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Emory University School of Medicine, Emory University [Atlanta, GA], Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institució Catalana de Recerca i Estudis Avançats (ICREA), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Université de Lausanne = University of Lausanne (UNIL), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Helmholtz Zentrum München = German Research Center for Environmental Health, and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Xenoturbella, Ambulacraria, media_common.quotation_subject, Acoelomorpha, Metazoa, Nephrozoa, Phylogenomics, Phylogeny, Systematic Error, Context (language use), phylogeny, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, General Biochemistry, Genetics and Molecular Biology, systematic error, 03 medical and health sciences, 0302 clinical medicine, Animals, Simplicity, Chordata, media_common, Long branch attraction, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], phylogenomics, biology.organism_classification, Biological Evolution, Invertebrates, Xenacoelomorpha, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, 030104 developmental biology, Sister group, Evolutionary biology, Outgroup, General Agricultural and Biological Sciences, 030217 neurology & neurosurgery, Echinodermata
Abstract: International audience; Xenoturbella and the acoelomorph worms (Xenacoelomorpha) are simple marine animals with controversial affinities. They have been placed as the sister group of all other bilaterian animals (Nephrozoa hypothesis), implying their simplicity is an ancient characteristic ]; alternatively, they have been linked to the complex Ambulacraria (echinoderms and hemichordates) in a clade called the Xenambulacraria , suggesting their simplicity evolved by reduction from a complex ancestor. The difficulty resolving this problem implies the phylogenetic signal supporting the correct solution is weak and affected by inadequate modeling, creating a misleading non-phylogenetic signal. The idea that the Nephrozoa hypothesis might be an artifact is prompted by the faster molecular evolutionary rate observed within the Acoelomorpha. Unequal rates of evolution are known to result in the systematic artifact of long branch attraction, which would be predicted to result in an attraction between long-branch acoelomorphs and the outgroup, pulling them toward the root . Other biases inadequately accommodated by the models used can also have strong effects, exacerbated in the context of short internal branches and long terminal branches . We have assembled a large and informative dataset to address this problem. Analyses designed to reduce or to emphasize misleading signals show the Nephrozoa hypothesis is supported under conditions expected to exacerbate errors, and the Xenambulacraria hypothesis is preferred in conditions designed to reduce errors. Our reanalyses of two other recently published datasets produce the same result. We conclude that the Xenacoelomorpha are simplified relatives of the Ambulacraria.
Published: 2019
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23. Cognitive and motor compliance in intentional human-robot interaction

Author: Hendry Ferreira Chame, Jun Tani, and Okinawa Institute of Science and Technology Graduate University (OIST)
Subjects: FOS: Computer and information sciences, Computer Science - Human-Computer Interaction, [SCCO.COMP]Cognitive science/Computer science, Inference, 050105 experimental psychology, Human–robot interaction, Compliance (psychology), Human-Computer Interaction (cs.HC), 92B20, 68T40, 93B52, [SCCO]Cognitive science, Computer Science - Robotics, 03 medical and health sciences, Nonverbal communication, 0302 clinical medicine, [INFO.INFO-RB]Computer Science [cs]/Robotics [cs.RO], 0501 psychology and cognitive sciences, Neural and Evolutionary Computing (cs.NE), ComputingMilieux_MISCELLANEOUS, business.industry, 05 social sciences, Perspective (graphical), Computer Science - Neural and Evolutionary Computing, Robotics, Cognition, [SCCO.PSYC]Cognitive science/Psychology, Artificial intelligence, business, Psychology, Robotics (cs.RO), 030217 neurology & neurosurgery, Neurorobotics, Cognitive psychology
Abstract: Embodiment and subjective experience in human-robot interaction are important aspects to consider when studying both natural cognition and adaptive robotics to human environments. Although several researches have focused on nonverbal communication and collaboration, the study of autonomous physical interaction has obtained less attention. From the perspective of neurorobotics, we investigate the relation between intentionality, motor compliance, cognitive compliance, and behavior emergence. We propose a variational model inspired by the principles of predictive coding and active inference to study intentionality and cognitive compliance, and an intermittent control concept for motor deliberation and compliance based on torque feed-back. Our experiments with the humanoid Torobo portrait interesting perspectives for the bio-inspired study of developmental and social processes., Comment: "\c{opyright} 20XX IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works."
Published: 2019
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24. ZP4 Is Present in Murine Zona Pellucida and Is Not Responsible for the Specific Gamete Interaction

Author: Mª José Izquierdo-Rico, Carla Moros-Nicolás, Míriam Pérez-Crespo, Ricardo Laguna-Barraza, Alfonso Gutiérrez-Adán, Frédéric Veyrunes, José Ballesta, Vincent Laudet, Pascale Chevret, Manuel Avilés, Ministerio de Ciencia e Innovación (España), European Commission, Fundación Séneca, Izquierdo-Rico, Mª José [0000-0001-9438-6933], Moros-Nicolás, Carla [0000-0003-0926-7804], Pérez-Crespo, Míriam [0000-0001-7166-5112], Gutiérrez-Adán, Alfonso [0000-0001-9893-9179], Veyrunes, Frédéric [0000-0002-1706-9915], Ballesta, José [0000-0001-7965-5277], Laudet, Vincent [0000-0003-4022-4175], Chevret, Pascale [0000-0002-4186-875X], Avilés, Manuel [0000-0003-4396-4718], Izquierdo-Rico, Mª José, Moros-Nicolás, Carla, Pérez-Crespo, Míriam, Gutiérrez-Adán, Alfonso, Veyrunes, Frédéric, Ballesta, José, Laudet, Vincent, Chevret, Pascale, Avilés, Manuel, Universidad de Murcia, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Okinawa Institute of Science and Technology Graduate University (OIST), Ecologie et évolution des populations, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226
Subjects: 0106 biological sciences, 0301 basic medicine, Oocyte, Pseudogene, zona pellucida, Acrosome reaction, pseudogene, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, sperm, Cell and Developmental Biology, 03 medical and health sciences, medicine, Mus musculus, Zona pellucida, oocyte, lcsh:QH301-705.5, Murine phylogeny, ComputingMilieux_MISCELLANEOUS, Original Research, chemistry.chemical_classification, murine phylogeny, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, Embryo, Cell Biology, Sperm, 3. Good health, Cell biology, ZP4, 030104 developmental biology, medicine.anatomical_structure, chemistry, lcsh:Biology (General), Gamete, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Glycoprotein, Developmental Biology
Abstract: Departamento de Reproducción Animal (INIA), Mammalian eggs are surrounded by an extracellular matrix called the zona pellucida (ZP). This envelope participates in processes such as acrosome reaction induction, sperm binding, protection of the oviductal embryo, and may be involved in speciation. In eutherian mammals, this coat is formed of three or four glycoproteins (ZP1-ZP4). While Mus musculus has been used as a model to study the ZP for more than 35 years, surprisingly, it is the only eutherian species in which the ZP is formed of three glycoproteins Zp1, Zp2, and Zp3, Zp4 being a pseudogene. Zp4 was lost in the Mus lineage after it diverged from Rattus, although it is not known when precisely this loss occurred. In this work, the status of Zp4 in several murine rodents was tested by phylogenetic, molecular, and proteomic analyses. Additionally, assays of cross in vitro fertilization between three and four ZP rodents were performed to test the effect of the presence of Zp4 in murine ZP and its possible involvement in reproductive isolation. Our results showed that Zp4 pseudogenization is restricted to the subgenus Mus, which diverged around 6 MYA. Heterologous in vitro fertilization assays demonstrate that a ZP formed of four glycoproteins is not a barrier for the spermatozoa of species with a ZP formed of three glycoproteins. This study identifies the existence of several mouse species with four ZPs that can be considered suitable for use as an experimental animal model to understand the structural and functional roles of the four ZP proteins in other species, including human., This work was supported by Ministerio de Ciencia e Innovación Español (AGL2012-40180-C03-02, AGL2015-7159, and PGC2018-094781-B-I00), The European Commission, The European Regional Development Fund, and Fundación Séneca (0452/GERM/06)., 18 Pág.
Published: 2021
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25. Amphioxus functional genomics and the origins of vertebrate gene regulation

Author: Patrick Wincker, Pierre Pontarotti, Elisa de la Calle-Mustienes, Zbynek Kozmik, Malcolm Perry, José Luis Gómez-Skarmeta, Cristian Cañestro, Stéphanie Bertrand, Yamile Marquez, Èlia Benito-Gutiérrez, Juan J. Tena, Hector Escriva, Alexandra Louis, Anthony Leon, Matthew T. Weirauch, Juan Ramón Martínez-Morales, Panos N. Firbas, Peter W. H. Holland, Iryna Kozmikova, Daniel Aldea, Sandra Jiménez-Gancedo, Jordi Garcia-Fernàndez, Jean-Marc Aury, Michael Schubert, Paul Edward Duckett, Beatriz Albuixech-Crespo, Simon J. van Heeringen, Boris Lenhard, Piero Carninci, Carlos Herrera-Úbeda, Olivier Mirabeau, Demian Burguera, Lorena Buono, Tokiharu Takahashi, Rafael D. Acemel, Silvia Naranjo, Ryan Lister, Sophie Mangenot, Lucie Subirana, Ksenia Skvortsova, Jr-Kai Yu, Hugues Roest Crollius, Ildiko M. L. Somorjai, Vincent Laudet, Piotr J. Balwierz, Gabriel A. B. Marais, Ignacio Maeso, Anlong Xu, Christopher D. R. Wyatt, Shengfeng Huang, Ozren Bogdanovic, David E. K. Ferrier, Ferdinand Marlétaz, Salvatore D'Aniello, Jon Permanyer, Filipe Castro, Manuel Irimia, Ricard Albalat, Yann Le Petillon, Ensieh Farahani, Hervé Seitz, Okinawa Institute of Science and Technology Graduate University (OIST), Department of Zoology [Oxford], University of Oxford, Centro Andaluz de Biología del Desarrollo, Universidad Pablo Olavide, University of New South Wales [Sydney] (UNSW), The University of Western Australia (UWA), Imperial College London, Universitat Pompeu Fabra [Barcelona] (UPF), Biologie intégrative des organismes marins (BIOM), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Barcelona Institute of Science and Technology (BIST), Universidad Pablo de Olavide [Sevilla] (UPO), Radboud University [Nijmegen], University of Barcelona, Garvan Institute of medical research, Institute of Molecular Genetics of the Czech Academy of Sciences (IMG / CAS), Czech Academy of Sciences [Prague] (CAS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), 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), Department of Genetics and IrBio, University of Cambridge [UK] (CAM), Universidade do Porto = University of Porto, Stazione Zoologica Anton Dohrn (SZN), University of St Andrews [Scotland], Sun Yat-Sen University [Guangzhou] (SYSU), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), University of Manchester [Manchester], Université Paris sciences et lettres (PSL), Academia Sinica, RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), University of Cincinnati (UC), University of Bergen (UiB), ANR-16-CE12-0008,CHORELAND,Détermination de la conservation du landscape génomique de régulation au cours de l'embryogenèse des chordés(2016), European Project: 637591,H2020,ERC-2014-STG,NEURAL AS(2015), European Project: 658521,H2020,H2020-MSCA-IF-2014,EVOREL(2016), European Project: 268513,EC:FP7:ERC,ERC-2010-AdG_20100317,GENEVA(2011), European Commission, The Leverhulme Trust, University of St Andrews. School of Biology, University of St Andrews. Marine Alliance for Science & Technology Scotland, University of St Andrews. Scottish Oceans Institute, University of St Andrews. Biomedical Sciences Research Complex, University of Oxford [Oxford], Radboud university [Nijmegen], Garvan Institute of Medical Research, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Universidade do Porto, Commission of the European Communities, Biotechnology and Biological Sciences Research Council (BBSRC), Wellcome Trust, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Departament de Genetica, Facultat de Biologia, Universitat de Barcelona (UB), Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas, Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Max F. Perutz Laboratories, University of Vienna [Vienna], DYnamique et Organisation des GENomes - Equipe de l'IBENS (DYOGEN), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-IFR140-Centre National de la Recherche Scientifique (CNRS), Stress, Immunité, Pathogènes (SIMPA), Université de Lorraine (UL), Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Génomique d'Evry (IG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Departament de Genètica, Universitat Autònoma de Barcelona [Barcelona] (UAB), Texas A&M University [College Station], Sun Yat-Sen University (SYSU), Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Sexe et évolution, Département PEGASE [LBBE] (PEGASE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup (VAS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Analyse, Topologie, Probabilités (LATP), Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Centre National de la Recherche Scientifique (CNRS), Unité de génétique et biologie des cancers (U830), Université Paris Descartes - Paris 5 (UPD5)-Institut Curie-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Medical Sciences / Beijing, Institute of Cellular and Organismic Biology, Ctr Life Sci Technol, Div Gen Technol, Tsurumi Ku, RIKEN, Centre of Excellence in Plant Energy Biology (ARC), Australian National University (ANU)-School of Biochemistry and Molecular Biology, SARS International Centre for Marine Molecular Biology, Modèles en biologie cellulaire et évolutive (MBCE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), European Research Council, Ministerio de Economía y Competitividad (España), Australian Research Council, Maeso, Ignacio [0000-0002-6440-8457], Tena, Juan J [0000-0001-8165-7984], Perry, Malcolm [0000-0001-5228-3434], Wyatt, Christopher DR [0000-0001-8033-2213], de la Calle-Mustienes, Elisa [0000-0002-8975-6503], Bertrand, Stephanie [0000-0002-0689-0126], Naranjo, Silvia [0000-0002-4529-3332], Jimenez-Gancedo, Sandra [0000-0002-2247-1319], Aldea, Daniel [0000-0001-5101-0194], Buono, Lorena [0000-0002-5457-4515], Louis, Alexandra [0000-0001-7032-5650], Balwierz, Piotr J [0000-0002-1548-4605], Aury, Jean-Marc [0000-0003-1718-3010], Albalat, Ricard [0000-0003-0282-9595], Benito-Gutiérrez, Èlia [0000-0003-2435-0948], Cañestro, Cristian [0000-0003-4623-8105], Castro, Filipe [0000-0001-7697-386X], Ferrier, David EK [0000-0003-3247-6233], Schubert, Michael [0000-0002-2341-712X], Seitz, Hervé [0000-0001-8172-5393], Somorjai, Ildiko [0000-0001-5243-6664], Takahashi, Tokiharu [0000-0002-5785-8660], Yu, Jr-Kai [0000-0001-8591-0529], Carninci, Piero [0000-0001-7202-7243], Martinez-Morales, Juan Ramon [0000-0002-4650-4293], Garcia-Fernàndez, Jordi [0000-0001-5677-5970], Lister, Ryan [0000-0001-6637-7239], Escriva, Hector [0000-0001-7577-5028], Irimia, Manuel [0000-0002-2179-2567], Apollo - University of Cambridge Repository, CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, COMBE, Isabelle, Détermination de la conservation du landscape génomique de régulation au cours de l'embryogenèse des chordés - - CHORELAND2016 - ANR-16-CE12-0008 - AAPG2016 - VALID, Functions and evolutionary impact of transcriptomic novelties in the vertebrate brain - NEURAL AS - - H20202015-04-01 - 2020-03-31 - 637591 - VALID, Evolution of Regulatory Landscapes in Chordates - EVOREL - - H20202016-01-01 - 2017-12-31 - 658521 - VALID, Genome Evolution in the Animal Kingdom - GENEVA - - EC:FP7:ERC2011-06-01 - 2016-05-31 - 268513 - VALID, Institute of Molecular Genetics of the Czech Academy of Sciences, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA) - Grenoble, Laboratoire de Biologie Moléculaire de la Cellule (LBMC), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Mathématiques de Marseille (I2M), Centre National de la Recherche Scientifique (CNRS)-Ecole Centrale de Marseille (ECM)-Aix Marseille Université (AMU), Riken Omics Science Center, Riken Yokohama Institute, Cincinnati Children's Hospital Medical Center, and Computational Regulatory Genomics
Subjects: Epigenomics, Branchiostoma, genetic analysis, animal cell, transcriptomics, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, vertebrate, zebra fish, histone modification, Branchiostoma lanceolatum, ComputingMilieux_MISCELLANEOUS, comparative study, Lancelets, Regulation of gene expression, DDC model, DNA methylation, adult, Vertebrate, Genomics, priority journal, Science & Technology - Other Topics, Molecular Developmental Biology, LANDSCAPES, whole genome duplication, Functional genomics, chordate evolution, CONSERVATION, embryo, gene sequence, PLURIPOTENCY, Article, animal tissue, 03 medical and health sciences, regulatory genomics, biology.animal, genomics, Humans, genome, mouse, Science & Technology, Molecular Sequence Annotation, TRANSGENESIS, DNA Methylation, Ancestral expression, developmental stage, 030104 developmental biology, hourglass model, Amfiox, Evolutionary biology, molecular genetics, chromatin, Subfunctionalization, transcriptome, 030217 neurology & neurosurgery, CHROMATIN, 0301 basic medicine, Branchiostoma Lanceolatum, Genome, specialization, Gene duplication, Vertebrats, Promoter Regions, Genetic, Whole-genome Duplication (WGD), Multidisciplinary, gene control, BRANCHIOSTOMA-LANCEOLATUM, innovation, Multidisciplinary Sciences, female, SEQ, Vertebrates, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Phylotypic Period, General Science & Technology, invertebrate, QH426 Genetics, Biology, DNA DEMETHYLATION, male, evolution, Animals, controlled study, gene, QH426, multigene family, Body Patterning, Vertebrata, nonhuman, Amphioxus, ZEBRAFISH, gene duplication, embryo development, DAS, biology.organism_classification, EVOLUTION, [SDV.BDD.EO]Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, Gene Expression Regulation, gene expression, Molecular evolution, Transcriptome
Abstract: Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. Here we sequence the genome of the Mediterranean amphioxus (Branchiostoma lanceolatum) and characterize DNA methylation, chromatin accessibility, histone modifications and transcriptomes across multiple developmental stages and adult tissues to investigate the evolution of the regulation of the chordate genome. Comparisons with vertebrates identify an intermediate stage in the evolution of differentially methylated enhancers, and a high conservation of gene expression and its cis-regulatory logic between amphioxus and vertebrates that occurs maximally at an earlier mid-embryonic phylotypic period. We analyse regulatory evolution after whole-genome duplications, and find that—in vertebrates—over 80% of broadly expressed gene families with multiple paralogues derived from whole-genome duplications have members that restricted their ancestral expression, and underwent specialization rather than subfunctionalization. Counter-intuitively, paralogues that restricted their expression increased the complexity of their regulatory landscapes. These data pave the way for a better understanding of the regulatory principles that underlie key vertebrate innovations., This research was funded primarily by the European Research Council (ERC) under the European Union’s Horizon 2020 and Seventh Framework Program FP7 research and innovation programs (ERC-AdG-LS8-740041 to J.L.G.-S., ERC-StG-LS2-637591 to M.I., a Marie Sklodowska-Curie Grant (658521) to I.M. and a FP7/2007-2013-ERC-268513 to P.W.H.H.), the Spanish Ministerio de Economía y Competitividad (BFU2016-74961-P to J.L.G.-S., RYC-2016-20089 to I.M., BFU2014-55076-P and BFU2017-89201-P to M.I. and BFU2014-55738-REDT to J.L.G.-S, M.I. and J.R.M.-M), the ‘Centro de Excelencia Severo Ochoa 2013-2017’(SEV-2012-0208), the ‘Unidad de Excelencia María de Maetzu 2017-2021’(MDM-2016-0687), the People Program (Marie Curie Actions) of the European Union’s Seventh Framework Program FP7 under REA grant agreement number 607142 (DevCom) to J.L.G.-S., and the CNRS and the ANR (ANR16-CE12-0008-01) to H.E. O.B. was supported by an Australian Research Council Discovery Early Career Researcher Award (DECRA; DE140101962).
Published: 2018
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26. Genomics of the origin and evolution of Citrus

Author: Manuel Talon, Joaquín Dopazo, Francisco R. Tadeo, Concha Domingo, Dongliang Du, Estela Pérez-Román, Victoria Ibanez, Guohong Albert Wu, José Carbonell-Caballero, Carles Borredá, Patrick Ollitrault, Daniel S. Rokhsar, Javier Terol, Antonio López-García, Roberto Alonso, Mikeal L. Roose, Frederick G. Gmitter, Franck Curk, Wu, Guohong Albert, Rokhsar, Daniel S., Talon, Manuel, United States Department of Energy, Centro de Genómica - Centre de Genòmica [IVIA], Instituto Valenciano de Investigaciones Agrarias - Institut Valencià d'Investigacions Agraries - Valencian Institute for agricultural Research (IVIA), Centro de Investigación Príncipe Felipe (CIPF), Amélioration Génétique et Adaptation des Plantes méditerranéennes et Tropicales Corse - Antenne Corse (AGAP-Corse), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), University of South Florida [Tampa] (USF), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Department of Botany and Plant Sciences, University of California, Spanish National Bioinformatics Institute (INB), University of Florida [Gainesville] (UF), IFAS, Unite de recherche migrations et sociétés (URMIS), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), University of California [Berkeley], Technology Graduate University, and Okinawa Institute of Science and Technology Graduate University (OIST)
Subjects: 0301 basic medicine, Citrus, Phylogénie, [SDV]Life Sciences [q-bio], Plant genetics, Biodiversity, Évolution, F30 - Génétique et amélioration des plantes, Génétique des populations, Asia, Southeastern, History, Ancient, Phylogeny, Multidisciplinary, Domestication des plantes, food and beverages, Genomics, F70 - Taxonomie végétale et phytogéographie, Crop Production, Provenance, Genome, Plant, Citrus hybrids, Heterozygote, Genetic Speciation, Human Migration, Introgression, Biology, Southeast asian, génomique, Evolution, Molecular, 03 medical and health sciences, Variation génétique, Phylogenetics, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Domestication, Hybrid, Génome, 15. Life on land, biology.organism_classification, 030104 developmental biology, Haplotypes, Hybridization, Genetic
Abstract: The genus Citrus, comprising some of the most widely cultivated fruit crops worldwide, includes an uncertain number of species. Here we describe ten natural citrus species, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms, and propose that citrus diversified during the late Miocene epoch through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons. A second radiation enabled by migration across the Wallace line gave rise to the Australian limes in the early Pliocene epoch. Further identification and analyses of hybrids and admixed genomes provides insights into the genealogy of major commercial cultivars of citrus. Among mandarins and sweet orange, we find an extensive network of relatedness that illuminates the domestication of these groups. Widespread pummelo admixture among these mandarins and its correlation with fruit size and acidity suggests a plausible role of pummelo introgression in the selection of palatable mandarins. This work provides a new evolutionary framework for the genus Citrus. The origin, evolution and domestication of Citrus and the genealogy of the most important wild and cultivated citrus varieties. Citrus fruits are one of the most cultivated crops worldwide, yet the evolutionary relationships among citrus species remain uncertain. Daniel Rokhsar, Manuel Talon and colleagues analyse the genomes of 60 accessions that represent a diverse range of citrus species, including 30 newly sequenced citrus genomes. They characterize the diversity and evolution of citrus at the species level and identify interspecific citrus hybrids and admixtures—genetic mixing between previously isolated populations—that could be the result of human activities such as migration and agriculture. The authors identify 10 progenitor species and suggest that citrus originated in southeast Asia, diversifying during the late Miocene epoch through a rapid southeast Asian radiation that correlated with a changing climate, including the weakening of the monsoons. They also find extensive relatedness among mandarins and sweet oranges, showing a complex history of admixture during the domestication of these groups.
Published: 2018
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27. NR3E receptors in cnidarians: A new family of steroid receptor relatives extends the possible mechanisms for ligand binding

Author: Yassmine Chebaro, Gabriel V. Markov, Adam M. Reitzel, Konstantin Khalturin, Vincent Laudet, Isabelle M. L. Billas, Ann M. Tarrant, Okinawa Institute of Science and Technology Graduate University (OIST), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of North Carolina [Charlotte] (UNC), University of North Carolina System (UNC), Woods Hole Oceanographic Institution (WHOI), Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Receptors, Steroid, Hydra, Endocrinology, Diabetes and Metabolism, medicine.medical_treatment, Clinical Biochemistry, Biology, Ligands, Biochemistry, Article, Steroid, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Endocrinology, biology.animal, medicine, Animals, Humans, Receptor, cnidarian, Molecular Biology, Binding Sites, Estrogen Receptor alpha, Vertebrate, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell Biology, steroid receptor, biology.organism_classification, Ligand (biochemistry), A-ring aromatic steroid, Cell biology, Molecular Docking Simulation, Steroid hormone, 030104 developmental biology, Nuclear receptor, Hydra vulgaris, aromatization, Molecular Medicine, Lernaean Hydra, 030217 neurology & neurosurgery, Signal Transduction
Abstract: International audience; Steroid hormone receptors are important regulators of development and physiology in bilaterian animals, but the role of steroid signaling in cnidarians has been contentious. Cnidarians produce steroids, including A-ring aromatic steroids with a side-chain, but these are probably made through pathways different than the one used by vertebrates to make their A-ring aromatic steroids. Here we present comparative genomic analyses indicating the presence of a previously undescribed nuclear receptor family within medusozoan cnidarians, that we propose to call NR3E. This family predates the diversification of ERR/ER/SR in bilaterians, indicating that the first NR3 evolved in the common ancestor of the placozoan and cnidarian-bilaterian with lineage-specific loss in the anthozoans, even though multiple species in this lineage have been shown to produce aromatic steroids, whose function remain unclear. We discovered serendipitously that a cytoplasmic factor within epidermal cells of transgenic Hydra vulgaris can trigger the nuclear translocation of heterologously expressed human ERα. This led us to hypothesize that aromatic steroids may also be present in the medusozoan cnidarian lineage, which includes Hydra, and may explain the translocation of human ERα. Docking experiments with paraestrol A, a cnidarian A-ring aromatic steroid, into the ligand-binding pocket of Hydra NR3E indicates that, if an aromatic steroid is indeed the true ligand, which remains to be demonstrated, it would bind to the pocket through a partially distinct mechanism from the manner in which estradiol binds to vertebrate ER.
Published: 2018
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28. Skeletal organic matrices in molluscs: origin, evolution, diagenesis

Author: Christophe Durlet, Frédéric Marin, Takeshi Takeuchi, Elias Samankassou, Davorin Medakovic, Aurélien Chmiel, Irina Bundeleva, Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Department of Earth Sciences [Geneva], University of Geneva [Switzerland], Center for Marine Research Rovinj, Rudjer Boskovic Institute [Zagreb], Work supported by NEWFELPRO programme, by funds from OIST, by EC2CO project and by annual funds from UMR Biogeosciences., K. Endo, T. Kogure, and H. Nagasawa
Subjects: 0301 basic medicine, Proteomics, Subfossil, Protein, Biology, Functional domains, biology.organism_classification, Fossilization, Sequences, Tridacna, Diagenesis, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Order (biology), Evolutionary biology, Mollusc shell, Shell, Identification (biology), 14. Life underwater, Mollusc, 030217 neurology & neurosurgery
Abstract: 8 pages; International audience; The mollusc shell comprises a small amount of organic macromolecules, mostly proteins and polysaccharides, which, all together, constitute the skeletal organic matrix (SOM). In the recent years, the study of the SOM of about two dozens of mollusc species via transcriptomics and/or proteomics has led to the identification of hundreds of shell-associated proteins. This rapidly growing set of data allows several comparisons, shedding light on similarities and differences at the primary structure level and on some peculiar evolutionary mechanisms that may have affected SOM proteins. In addition, it constitutes a prerequisite for investigating the SOM repertoires of sub-fossils or fossil specimens, closely related to known extant species, in order to revisit diagenetic processes, i.e. how SOM proteins degrade during fossilization. These two aspects are briefly exemplified here: on the one hand, Aplysia californica, the sea hare, exhibits a vestigial internal shell that has kept a proteomic signature similar to that found in fully functional external shells. On the other hand, subfossil specimens of the giant clam Tridacna, collected in French Polynesia, precisely dated and analysed by proteomics for their SOM content, comprise several preserved proteins that can still be identified by their peptide signature, in spite of information losses likely due to diagenetic transformations.
Published: 2017
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29. Dispersal strategies in the highly polygynous ant crematogaster (orthocrema) pygmaea forel (formicidae: Myrmicinae)

Author: Yves Quinet, Rachid Hamidi, Glauco Bezerra Martins Segundo, Matheus Torres Marinho Bezerril M.T.M.B. Fontenelle, Jean Christophe de Biseau, Thomas Bourguignon, Institut d'écologie et des sciences de l'environnement de Paris (iEES), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA), Evolutio nary Biology and Ecology, Université libre de Bruxelles (ULB), Technology Graduate University, Okinawa Institute of Science and Technology Graduate University (OIST), School of Life and Environm ental Sciences, University of Sydney, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague (CZU), Laboratorio de Entomolo gia Instituto Superior de Ciências Biomedicas, Universidade Estadual do Ceará (UECE), Fond National de la Recherche Scientifique (FNRS), Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq) [473939/2004-5], Fundagao Cearense de Apoio ao Desenvolvimento Cientifico e Tecnologico (FUNCAP), Institut d'écologie et des sciences de l'environnement de Paris (IEES), Université Libre de Bruxelles [Bruxelles] (ULB), Okinawa Institute of Science and Technology (OIST), Czech University of Life Sciences, and Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Life Cycles, Multiple-Queen Colonies, Physiology, Success, [SDV]Life Sciences [q-bio], Psychologie appliquée, lcsh:Medicine, Imported Fire Ant, 01 natural sciences, Larvae, Medicine and Health Sciences, Foraging, lcsh:Science, Polygyny, Workers, reproductive and urinary physiology, Multidisciplinary, biology, Animal Behavior, Number, Thorax, Sciences bio-médicales et agricoles, Insects, Laboratory Equipment, Physiological Parameters, Engineering and Technology, Seasons, Anatomy, Biologie, Research Article, Honeydew, Crematogaster, Hymenoptera-Formicidae, Arthropoda, Evolution, Solenopsis-Invicta, Population-Structure, Storage Proteins, Zoology, Equipment, 010603 evolutionary biology, 03 medical and health sciences, Propagule, Nectar, Animals, Behavior, Ants, lcsh:R, Body Weight, Organisms, Biology and Life Sciences, Laboratory Glassware, Pupae, biology.organism_classification, Invertebrates, Hymenoptera, Brood, 030104 developmental biology, Earth Sciences, Biological dispersal, lcsh:Q, Developmental Biology
Abstract: In ants, dispersal strategies and morphology of female sexuals are generally linked to the mode of colony founding. In species using long-range dispersal tactics, queen/worker dimorphism is generally high and young queens are able to initiate new colonies by themselves, using their metabolic reserves. By contrast, in species using short-range dispersal strategies, queen/worker dimorphism is generally low and, due to their limited metabolic reserves, queens have lost the capacity to raise their brood alone and to found their colony independently. Moreover, polygyny is also often associated with short-range dispersal strategies, although the relationship between the number of queens and the dispersal strategy in ants is not clear-cut. Here, dispersal strategies were investigated in C. pygmaea, a highly polygynous and polydomous ant species from northeastern Brazil. Field observations and laboratory experiments show that this ant exhibits a suite of traits that are more commonly associated with long-range dispersal and independent colony foundation: functional wings in both males and females, high queen/worker dimorphism, strong weight loss in mature queens, nuptial flights and, in the lab, ability of young queens to found new colonies in haplometrotic conditions. On the other hand, this species shows a high degree of polygyny with a strong seasonal component, and, at least under laboratory conditions, mature queens seem able to develop propagules if they are accompanied by at least 10 workers. These features strongly suggest that (1) some of the gynes do not engage in a long-range dispersal but become new queens in their mother colony and (2) that budding events are possible in this species. We therefore speculate that C. pygmaea has a dual dispersal strategy probably related to environmental conditions: some gynes engage in long-range dispersal followed by independent colony foundation at the beginning of rainy season, while others mate in the parental colony and are re-Adopted leading to high polygyny. During the rainy season, budding events can lead to colony extension and increased polydomy. Polydomy is commonly thought to improve resource discovery and exploitation through decentralized foraging behavior, a significant advantage during the rainy season when food ressources (mainly floral/ extrafloral nectaries and hemipteran honeydew) are more abundant and when colony needs for food supplies are highest., SCOPUS: ar.j, info:eu-repo/semantics/published
Published: 2017
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30. Organic matrices in metazoan calcium carbonate skeletons: composition, functions, evolution

Author: Frédéric Marin, Françoise Immel, Takeshi Takeuchi, Davorin Medakovic, Irina Bundeleva, Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Laboratoire de biogenèse membranaire (LBM), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Center for Marine Research Rovinj, Rudjer Boskovic Institute [Zagreb], Work financially supported by a FABER grant (N° 2014-9201AAO047S04458, Conseil Régional de Bourgogne), two grants from OSU-Theta (SRO 2014) and from INTERRVIE (call 2014), an OIST (Okinawa Institute of Sciences and Technologies) post-doctoral grant, within the framework of collaboration between this institution and UBFC (Université de Bourgogne Franche-Comté), a three-year NEWFELPRO grant (Marsupial, Oct 2014-Sept 2017), within the framework of a Marie Curie Action, between UBFC and the Ruder Boskovic Institute (Croatia)., Biogéosciences [Dijon] ( BGS ), AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Okinawa Institute of Science and Technology, Laboratoire de biogenèse membranaire ( LBM ), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique ( CNRS ), and Ruder Boskovic Institute
Subjects: 0301 basic medicine, Biomineralization, Proteomics, Computational biology, Biology, Skeletal tissue, Calcium Carbonate, biomineralization, metazoan, calcification, skeleton, skeletal matrix, proteomics, Calcification, Evolution, Molecular, 03 medical and health sciences, chemistry.chemical_compound, Matrix (mathematics), Calcification, Physiologic, Metazoan, Structural Biology, [SDV.IB.BIO]Life Sciences [q-bio]/Bioengineering/Biomaterials, Skeleton, [ SDV.IB.BIO ] Life Sciences [q-bio]/Bioengineering/Biomaterials, Rapid identification, Skeletal matrix, 030104 developmental biology, Calcium carbonate, chemistry, Biochemistry
Abstract: 9 pages; International audience; Calcium carbonate skeletal tissues in metazoans comprise a small quantity of occluded organic macromolecules, mostly proteins and polysaccharides that constitute the skeletal matrix. Because its functions in modulating the biomineralization process are well known, the skeletal matrix has been extensively studied, successively via classical biochemical approaches, via molecular biology and, in recent years, via transcriptomics and proteomics. The optimistic view that the deposition of calcium carbonate minerals requires a limited number of macromolecules has been challenged, in the last decade, by high-throughput approaches. Such approaches have made possible the rapid identification of large sets of mineral-associated proteins, i.e., ‘skeletal repertoires’ or ‘skeletomes’, in several calcifying animal models, ranging from sponges to echinoderms. One of the consequences of this expanding set of data is that a simple definition of the skeletal matrix is no longer possible. This increase in available data, however, makes it easier to compare skeletal repertoires, shedding light on the fundamental evolutionary mechanisms affecting matrix components.
Published: 2016
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31. Multiple I-Type Lysozymes in the Hydrothermal Vent Mussel Bathymodiolus azoricus and Their Role in Symbiotic Plasticity

Author: Eiichi Shoguchi, François H. Lallier, Camille Detree, Jean Yves Mary, Nori Satoh, Arnaud Tanguy, Apolline Chabenat, Adaptation et Biologie des Invertébrés en Conditions Extrêmes (ABICE), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Okinawa Institute of Science and Technology, and Okinawa Institute of Science and Technology Graduate University (OIST)
Subjects: 0106 biological sciences, 0301 basic medicine, Gills, lcsh:Medicine, Gene Expression, Marine and Aquatic Sciences, Artificial Gene Amplification and Extension, 01 natural sciences, Polymerase Chain Reaction, Biochemistry, Chlorobi, Mussels, Post-Translational Modification, lcsh:Science, Phylogeny, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Multidisciplinary, biology, Endosymbiosis, Ecology, Isoenzymes, Methylococcaceae, Marine Geology, Signal Peptides, Hydrothermal vent, Symbiotic bacteria, Research Article, Bivalves, Gram-negative bacteria, animal structures, Molecular Sequence Data, Zoology, Research and Analysis Methods, 010603 evolutionary biology, 03 medical and health sciences, Hydrothermal Vents, Extraction techniques, Symbiosis, Bacterial Proteins, Gram-Negative Bacteria, Genetics, Animals, 14. Life underwater, Amino Acid Sequence, Molecular Biology Techniques, Molecular Biology, Ecosystem, lcsh:R, fungi, Organisms, Biology and Life Sciences, Proteins, Mussel, Gene Expression Regulation, Bacterial, Molluscs, Bivalvia, biology.organism_classification, Invertebrates, RNA extraction, Species Interactions, 030104 developmental biology, Earth Sciences, lcsh:Q, Muramidase, Sequence Alignment, Bacteria
Abstract: International audience; The aim of this study was first to identify lysozymes paralogs in the deep sea mussel Bathy-modiolus azoricus then to measure their relative expression or activity in different tissue or conditions. B. azoricus is a bivalve that lives close to hydrothermal chimney in the Mid-Atlantic Ridge (MAR). They harbour in specialized gill cells two types of endosymbiont (gram— bacteria): sulphide oxidizing bacteria (SOX) and methanotrophic bacteria (MOX). This association is thought to be ruled by specific mechanism or actors of regulation to deal with the presence of symbiont but these mechanisms are still poorly understood. Here, we focused on the implication of lysozyme, a bactericidal enzyme, in this endosymbiosis. The relative expression of Ba-lysozymes paralogs and the global anti-microbial activity, were measured in natural population (Lucky Strike-1700m, Mid-Atlantic Ridge), and in in situ experimental conditions. B. azoricus individuals were moved away from the hydrothermal fluid to induce a loss of symbiont. Then after 6 days some mussels were brought back to the mussel bed to induce a re-acquisition of symbiotic bacteria. Results show the presence of 6 paralogs in B. azoricus. In absence of symbionts, 3 paralogs are up-regulated while others are not differentially expressed. Moreover the global activity of lysozyme is increasing with the loss of symbiont. All together these results suggest that lysozyme may play a crucial role in symbiont regulation.
Published: 2016
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32. A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation

Author: Daniel Aldea, Elisa de la Calle-Mustienes, Ignacio Maeso, Stéphanie Bertrand, Peter W. H. Holland, Ferdinand Marlétaz, Jean-Marc Aury, Carlos Gómez-Marín, Damien P. Devos, Sergio G Diaz, Sophie Mangenot, Juan J. Tena, Hector Escriva, Rafael D. Acemel, José Luis Gómez-Skarmeta, Ibai Irastorza-Azcarate, European Molecular Biology Laboratory, European Commission, European Research Council, Junta de Andalucía, Comisión Nacional de Investigación Científica y Tecnológica (Chile), Ministerio de Economía y Competitividad (España), Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas, Max Delbrück Center for Molecular Medicine [Berlin] (MDC), Helmholtz-Gemeinschaft = Helmholtz Association, Okinawa Institute of Science and Technology Graduate University (OIST), Department of Zoology [Oxford], University of Oxford, Biologie intégrative des organismes marins (BIOM), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-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), Centro Andaluz de Biología del Desarrollo, and Universidad Pablo Olavide
Subjects: 0301 basic medicine, animal structures, Chordate, Conserved sequence, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Phylogenetics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], biology.animal, Genetics, Animals, Hox gene, Conserved Sequence, Phylogeny, Epigenomics, Body Patterning, Lancelets, Regulation of gene expression, Homeodomain Proteins, Amphioxus, biology, Vertebrate, Gene Expression Regulation, Developmental, Extremities, TAD, Anatomy, Hox, biology.organism_classification, Chromatin, 030104 developmental biology, Evolutionary biology, Multigene Family, Vertebrates, embryonic structures, 030217 neurology & neurosurgery
Abstract: Acemel, Rafael D. et al., The HoxA and HoxD gene clusters of jawed vertebrates are organized into bipartite three-dimensional chromatin structures that separate long-range regulatory inputs coming from the anterior and posterior Hox-neighboring regions. This architecture is instrumental in allowing vertebrate Hox genes to pattern disparate parts of the body, including limbs. Almost nothing is known about how these three-dimensional topologies originated. Here we perform extensive 4C-seq profiling of the Hox cluster in embryos of amphioxus, an invertebrate chordate. We find that, in contrast to the architecture in vertebrates, the amphioxus Hox cluster is organized into a single chromatin interaction domain that includes long-range contacts mostly from the anterior side, bringing distant cis-regulatory elements into contact with Hox genes. We infer that the vertebrate Hox bipartite regulatory system is an evolutionary novelty generated by combining ancient long-range regulatory contacts from DNA in the anterior Hox neighborhood with new regulatory inputs from the posterior side., Work was funded by grants from the Ministerio de Economía y Competitividad (BFU2013-41322-P to J.L.G.-S.; Juan de la Cierva postdoctoral contract to I.M.; BFU2014-58449-JIN to J.J.T.); the Andalusian government (BIO-396 to J.L.G.-S.; C2A (EE: 2013/2506) to D.P.D. and I.I.-A.); the European Research Council (ERC; grant 268513) to P.W.H.H. and F.M.; a European Molecular Biology Organization (EMBO) short fellowship to I.M.; the Universidad Pablo de Olavide to J.J.T.; and Conicyt 'Becas Chile' to D.A.
Published: 2016
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33. Chitin-based barrier immunity and its loss predated mucus-colonization by indigenous gut microbiota

Author: Lixy Yamada, Che-Huang Tung, Toyoji Kaneko, Tsai-Ming Lu, Keisuke Nakashima, Sakura Kikuchi, Yu Ogawa, Noriyuki Satoh, Satoshi Kimura, Satoshi Soma, Soichi Watanabe, Jr-Kai Yu, Hitoshi Sawada, Alejandro Villar-Briones, Centre de Recherches sur les Macromolécules Végétales (CERMAV ), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Nagoya (NAGOYA), Nagoya University, Institute of Cellular and Organismic Biology, Academia Sinica, Marine Genomics Unit, and Okinawa Institute of Science and Technology Graduate University (OIST)
Subjects: 0301 basic medicine, Male, Applied Microbiology, Nanofibers, General Physics and Astronomy, Chitin, Gut flora, co-evolution, chemistry.chemical_compound, Mice, 0302 clinical medicine, Colonization, Intestinal Mucosa, Axenic, lcsh:Science, Chordata, ComputingMilieux_MISCELLANEOUS, Multidisciplinary, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Fishes, Gut Epithelium, [SDV.IMM]Life Sciences [q-bio]/Immunology, gut, Science, macromolecular substances, digestive system, Microbiology, General Biochemistry, Genetics and Molecular Biology, mucus layer, 03 medical and health sciences, Immune system, Immunity, Genetics, microbiota, Animals, Molecular Biology, fungi, General Chemistry, biology.organism_classification, Mucus, Gastrointestinal Microbiome, carbohydrates (lipids), Mice, Inbred C57BL, [CHIM.POLY]Chemical Sciences/Polymers, 030104 developmental biology, chemistry, mucosal immunity, lcsh:Q, chordates, Ciona, 030217 neurology & neurosurgery
Abstract: Mammalian gut microbiota are integral to host health. However, how this association began remains unclear. We show that in basal chordates the gut space is radially compartmentalized into a luminal part where food microbes pass and an almost axenic peripheral part, defined by membranous delamination of the gut epithelium. While this membrane, framed with chitin nanofibers, structurally resembles invertebrate peritrophic membranes, proteome supports its affinity to mammalian mucus layers, where gut microbiota colonize. In ray-finned fish, intestines harbor indigenous microbes, but chitinous membranes segregate these luminal microbes from the surrounding mucus layer. These data suggest that chitin-based barrier immunity is an ancient system, the loss of which, at least in mammals, provided mucus layers as a novel niche for microbial colonization. These findings provide a missing link for intestinal immune systems in animals, revealing disparate mucosal environment in model organisms and highlighting the loss of a proven system as innovation.
Published: 2015
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34. Genome-wide negative feedback drives transgenerational DNA methylation dynamics in Arabidopsis

Author: Hidetoshi Saze, Yoshiaki Tarutani, Atsushi Toyoda, Vincent Colot, Taiko Kim To, Evelyne Duvernois-Berthet, Tetsuji Kakutani, Mohamed Kassam, Kazuya Takashima, Sandra Cortijo, Tasuku Ito, Asao Fujiyama, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Department of Integrated Genetics, National Institute of Genetics, Mishima, Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Okinawa Institute of Science and Technology Graduate University, Center for Information Biology, National Institute of Genetics, Yata, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Duvernois-Berthet, Evelyne
Subjects: 0106 biological sciences, Cancer Research, lcsh:QH426-470, [SDV]Life Sciences [q-bio], Arabidopsis, Biology, 01 natural sciences, Epigenesis, Genetic, Cytosine, 03 medical and health sciences, Epigenetics of physical exercise, Gene Expression Regulation, Plant, Histone methylation, Genetics, Epigenetics, Molecular Biology, RNA-Directed DNA Methylation, Genetics (clinical), Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Epigenomics, Feedback, Physiological, 0303 health sciences, Arabidopsis Proteins, Methylation, DNA Methylation, Chromatin Assembly and Disassembly, Chromatin, DNA-Binding Proteins, [SDV] Life Sciences [q-bio], lcsh:Genetics, Mutation, DNA methylation, DNA Transposable Elements, Genome, Plant, Research Article, Transcription Factors, 010606 plant biology & botany
Abstract: Epigenetic variations of phenotypes, especially those associated with DNA methylation, are often inherited over multiple generations in plants. The active and inactive chromatin states are heritable and can be maintained or even be amplified by positive feedback in a transgenerational manner. However, mechanisms controlling the transgenerational DNA methylation dynamics are largely unknown. As an approach to understand the transgenerational dynamics, we examined long-term effect of impaired DNA methylation in Arabidopsis mutants of the chromatin remodeler gene DDM1 (Decrease in DNA Methylation 1) through whole genome DNA methylation sequencing. The ddm1 mutation induces a drastic decrease in DNA methylation of transposable elements (TEs) and repeats in the initial generation, while also inducing ectopic DNA methylation at hundreds of loci. Unexpectedly, this ectopic methylation can only be seen after repeated self-pollination. The ectopic cytosine methylation is found primarily in the non-CG context and starts from 3’ regions within transcription units and spreads upstream. Remarkably, when chromosomes with reduced DNA methylation were introduced from a ddm1 mutant into a DDM1 wild-type background, the ddm1-derived chromosomes also induced analogous de novo accumulation of DNA methylation in trans. These results lead us to propose a model to explain the transgenerational DNA methylation redistribution by genome-wide negative feedback. The global negative feedback, together with local positive feedback, would ensure robust and balanced differentiation of chromatin states within the genome., Author Summary DNA methylation is important for controlling activity of transposable elements and genes. An intriguing feature of DNA methylation in plants is that its pattern can be inherited over multiple generations at high fidelity in a Mendelian manner. However, mechanisms controlling the trans-generational DNA methylation dynamics are largely unknown. Arabidopsis mutants of a chromatin remodeler gene DDM1 (Decrease in DNA Methylation 1) show drastic reduction of DNA methylation in transposons and repeats, and also show progressive changes in developmental phenotypes during propagation through self-pollination. We now show using whole genome DNA methylation sequencing that upon repeated selfing, the ddm1 mutation induces an ectopic accumulation of DNA methylation at hundreds of loci. Remarkably, even in the wild type background, the analogous de novo increase of DNA methylation can be induced in trans by chromosomes with reduced DNA methylation. Collectively, our findings support a model to explain the transgenerational DNA methylation redistribution by genome-wide negative feedback, which should be important for balanced differentiation of DNA methylation states within the genome.
Published: 2015
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35. Bmcc1s, a novel brain-isoform of Bmcc1, affects cell morphology by regulating MAP6/STOP functions

Author: Edwige Amigou, Christian Delphin, Christophe Bosc, Laure Wingertsmann, Jessica Arama, Martine Cohen-Salmon, Anne-Cécile Boulay, Laurent Guillaud, Philippe Rostaing, Damarys Loew, Christian Giaume, Annie Andrieux, Pascal Ezan, Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Pierre et Marie Curie - Paris 6 (UPMC), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution)), INSERM U836, équipe 1, Physiopathologie du cytosquelette, Grenoble Institut des Neurosciences (GIN), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie [Paris], Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Cell and Molecular Synaptic Function Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Groupe Physiopathologie du Cytosquelette (GPC), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Grenoble Institut des Neurosciences (GIN), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Joseph Fourier - Grenoble 1 (UJF), cancéropole Institut National du Cancer, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL), Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Grenoble Institut des Neurosciences (GIN), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), and Andrieux, Annie
Subjects: Central Nervous System, Anatomy and Physiology, Mouse, MESH: Cold Temperature, MESH: Neurons, lcsh:Medicine, Gene Expression, MESH: Amino Acid Sequence, MESH: Protein Isoforms, Cell morphology, Microtubules, Mice, 0302 clinical medicine, Molecular Cell Biology, Protein Isoforms, MESH: Animals, MAP6, MESH: Nerve Tissue Proteins, Cytoskeleton, Intermediate filament, lcsh:Science, ComputingMilieux_MISCELLANEOUS, Neurons, 0303 health sciences, Multidisciplinary, MESH: Microtubules, Brain, Animal Models, Cellular Structures, Cell biology, Neoplasm Proteins, Cold Temperature, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Cellular Types, Microtubule-Associated Proteins, Research Article, Gene isoform, Neurite, Microtubule-associated protein, Molecular Sequence Data, Nerve Tissue Proteins, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Neurological System, Molecular Genetics, 03 medical and health sciences, MESH: Brain, Model Organisms, Microtubule, Genetics, Animals, Humans, Gene Regulation, [SDV.NEU] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Amino Acid Sequence, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, MESH: Mice, 030304 developmental biology, MESH: Molecular Sequence Data, MESH: Humans, lcsh:R, MESH: Astrocytes, MESH: Microtubule-Associated Proteins, Astrocytes, MESH: HeLa Cells, Nervous System Components, lcsh:Q, 030217 neurology & neurosurgery, HeLa Cells
Abstract: The BCH (BNIP2 and Cdc42GAP Homology) domain-containing protein Bmcc1/Prune2 is highly enriched in the brain and is involved in the regulation of cytoskeleton dynamics and cell survival. However, the molecular mechanisms accounting for these functions are poorly defined. Here, we have identified Bmcc1s, a novel isoform of Bmcc1 predominantly expressed in the mouse brain. In primary cultures of astrocytes and neurons, Bmcc1s localized on intermediate filaments and microtubules and interacted directly with MAP6/STOP, a microtubule-binding protein responsible for microtubule cold stability. Bmcc1s overexpression inhibited MAP6-induced microtubule cold stability by displacing MAP6 away from microtubules. It also resulted in the formation of membrane protrusions for which MAP6 was a necessary cofactor of Bmcc1s. This study identifies Bmcc1s as a new MAP6 interacting protein able to modulate MAP6-induced microtubule cold stability. Moreover, it illustrates a novel mechanism by which Bmcc1 regulates cell morphology.
Published: 2012
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36. Atorvastatin prevents Plasmodium falciparum cytoadherence and endothelial damage

Author: Paco Pino, Angelita Rebollo, Serge B. Assi, Zacharie Taoufiq, Issam Arrouss, Dominique Mazier, Florent Soubrier, Nadine N'dilimabaka, Immunité et Infection, Université Pierre et Marie Curie - Paris 6 (UPMC)-IFR113-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Okinawa Institute of Science and Technology, Okinawa Institute of Science and Technology Graduate University (OIST), Department of Microbiology and Molecular Medicine, Université de Genève = University of Geneva (UNIGE), Institut Pierre Richet (IPR), Génétique épidémiologique et moléculaire des pathologies cardiovasculaires, Université Pierre et Marie Curie - Paris 6 (UPMC)-IFR14-Institut National de la Santé et de la Recherche Médicale (INSERM), ZT was financially supported by the Ministère de l'Education Nationale, de la Recherche et de la Technologie.and by la Fondation pour la Recherche Médicale (FRM)., Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), University of Geneva [Switzerland], Service de parasitologie - mycologie [CHU Pitié-Salpétrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), BMC, Ed., Service de Parasitologie - Mycologie [CHU Pitié-Salpétrière], and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)
Subjects: Atorvastatin, Pharmacology, medicine.disease_cause, chemistry.chemical_compound, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Endothelial Cells, Cells, Cultured, MESH: Plasmodium falciparum, 0303 health sciences, biology, Cell adhesion molecule, Pathophysiology, 3. Good health, Infectious Diseases, medicine.anatomical_structure, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Pyrroles, medicine.drug, MESH: Cells, Cultured, lcsh:Arctic medicine. Tropical medicine, lcsh:RC955-962, MESH: Heptanoic Acids, Plasmodium falciparum, 030231 tropical medicine, lcsh:Infectious and parasitic diseases, MESH: Cell Adhesion, MESH: Coculture Techniques, Antimalarials, 03 medical and health sciences, Cell Adhesion, medicine, Humans, Pyrroles, lcsh:RC109-216, 030304 developmental biology, MESH: Humans, Cholesterol, Research, Endothelial Cells, biology.organism_classification, MESH: Antimalarials, Coculture Techniques, Red blood cell, chemistry, Heptanoic Acids, Apoptosis, Immunology, Parasitology, Oxidative stress
Abstract: Background The adhesion of Plasmodium falciparum parasitized red blood cell (PRBC) to human endothelial cells (EC) induces inflammatory processes, coagulation cascades, oxidative stress and apoptosis. These pathological processes are suspected to be responsible for the blood-brain-barrier and other organs' endothelial dysfunctions observed in fatal cases of malaria. Atorvastatin, a drug that belongs to the lowering cholesterol molecule family of statins, has been shown to ameliorate endothelial functions and is widely used in patients with cardiovascular disorders. Methods The effect of this compound on PRBC induced endothelial impairments was assessed using endothelial co-culture models. Results Atorvastatin pre-treatment of EC was found to reduce the expression of adhesion molecules and P. falciparum cytoadherence, to protect cells against PRBC-induced apoptosis and to enhance endothelial monolayer integrity during co-incubation with parasites. Conclusions These results might suggest a potential interest use of atorvastatin as a protective treatment to interfere with the pathophysiological cascades leading to severe malaria.
Published: 2011
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37. The amphioxus genome illuminates vertebrate origins and cephalochordate biology

Author: Kazutoyo Osoegawa, Finn Hallböök, Kazuyoshi Hosomichi, Hidetoshi Inoko, Naohito Takatori, Masanobu Satake, Jeremy J. Gibson-Brown, Christian M. Zmasek, Yasunori Sasakura, Yutaka Satou, Kaoru Azumi, Linda Z. Holland, Anlong Xu, Peter W. H. Holland, Zeev Pancer, Masaru Nonaka, Dan Hirose, Noriyuki Satoh, Carmela Gissi, Adam Godzik, Alice C. McHardy, Takashi Shiina, Masanori Kasahara, Takeshi Kawashima, Zbynek Kozmik, Graeme J. Roch, Larry J. Dishaw, Simona Candiani, Nancy M. Sherwood, Jordi Garcia-Fernàndez, Jun Kasamatsu, Len A. Pennacchio, Mario Pestarino, Qing Zhang, Nicholas H. Putnam, Marianne Bronner-Fraser, Shuichi Wada, Fumiko Yoshizaki, Isidore Rigoutsos, Daniel S. Rokhsar, Frédéric Brunet, Hidetoshi Saiga, Keita Yoshida, Robert Piotr Olinski, Marc Robinson-Rechavi, Èlia Benito-Gutiérrez, Masaaki Kobayashi, Thomas Butts, Kaoru Kubokawa, David E. K. Ferrier, Ayuko Kimura, Daniel Meulemans, Gary W. Litman, Tetsuro Ikuta, Ricard Albalat, Jonathan P. Rast, Vincent Laudet, Michael Schubert, Matthew J. Blow, Pavel Vopalensky, Yuzhen Ye, Pieter J. de Jong, Jr-Kai Yu, Javier Tello, Marine Biology Research Division, University of California [San Diego] (UC San Diego), University of California-University of California-Scripps Institution of Oceanography, University of Barcelona, Hokkaido University [Sapporo, Japan], United States Department of Energy, California Institute of Technology (CALTECH), Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Department of Zoology, University of Cambridge [UK] (CAM), Dipartimento di Biologia, Universita degli studi di Genova, H. Lee Moffitt Cancer Center and Research Institute, All Children’s Hospital, University of St Andrews [Scotland], Department of Biology, Washington University in Saint Louis (WUSTL), Institute for Evolutionary Discovery, Partenaires INRAE, Università degli studi di Milano [Milano], Sanford Burnham Prebys Medical Discovery Institute, Uppsala University, Tokyo Metropolitan University, Tokai University School of Medicine, Hokkaido University Graduate School of Medicine, University Graduate School of Medicine, University of California [Berkeley], University of California, Okinawa Institute of Science and Technology Graduate University (OIST), The University of Tokyo, Institute of Molecular Genetics of the Czech Academy of Sciences (IMG / CAS), Czech Academy of Sciences [Prague] (CAS), University of South Florida (USF), IBM Thomas J. Watson Research Center, Max Planck Institute for Computer Science, University of Maryland Biotechnology Institute, University of Toronto, Université de Lausanne (UNIL), Northern Arizona University [Flagstaff], Shimoda Marine Research Center, University of Tsukuba, Tohoku University [Sendai], Kyoto University [Kyoto], Osaka University, Nagahama Institute of Bio-Science and Technology, Sun Yat-Sen University [Guangzhou] (SYSU), Juntendo University, and Children's Hospital Oakland Research Institute
Subjects: Branchiostoma, Letter, animal structures, [SDV]Life Sciences [q-bio], 2R hypothesis, Chordate, Mice, Transgenic, Genome, Evolution, Molecular, 03 medical and health sciences, Mice, 0302 clinical medicine, Chordata, Nonvertebrate, Branchiostoma floridae, Genetics, Gene family, Animals, Humans, [INFO]Computer Science [cs], Hox gene, Genetics (clinical), Phylogeny, 030304 developmental biology, Cephalochordate, 0303 health sciences, biology, Genes, Homeobox, biology.organism_classification, Vertebrates, 030217 neurology & neurosurgery
Abstract: Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cephalochordate Branchiostoma floridae, commonly called amphioxus or lancelets. Special attention was given to homeobox genes, opsin genes, genes involved in neural crest development, nuclear receptor genes, genes encoding components of the endocrine and immune systems, and conserved cis-regulatory enhancers. The amphioxus genome contains a basic set of chordate genes involved in development and cell signaling, including a fifteenth Hox gene. This set includes many genes that were co-opted in vertebrates for new roles in neural crest development and adaptive immunity. However, where amphioxus has a single gene, vertebrates often have two, three, or four paralogs derived from two whole-genome duplication events. In addition, several transcriptional enhancers are conserved between amphioxus and vertebrates—a very wide phylogenetic distance. In contrast, urochordate genomes have lost many genes, including a diversity of homeobox families and genes involved in steroid hormone function. The amphioxus genome also exhibits derived features, including duplications of opsins and genes proposed to function in innate immunity and endocrine systems. Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates.
Published: 2008
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