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1. A chickpea genetic variation map based on the sequencing of 3,366 genomes

Author: Pallavi Sinha, Sushil K. Chaturvedi, Wallace Cowling, Guangyi Fan, Annapurna Chitikineni, Mohammad Yasin, Anne Céline Thuillet, Yves Vigouroux, Shiv Kumar, Aladdin Hamwieh, Eric von Wettberg, Amit Deokar, Himabindu Kudapa, Abhishek Rathore, Ben J. Hayes, Khela Ram Soren, Vikas K. Singh, Yue Wang, G. P. Dixit, Mahendar Thudi, Reka Howard, Jian Wang, Kadambot H. M. Siddique, Diego Jarquin, Prasad Bajaj, Eric Lyons, David Edwards, Aleena Francis, Trilochan Mohapatra, José Crossa, Bunyamin Tar’an, Shuai Sun, Motisagar S. Pithia, Debasis Chattopadhyay, Hari D. Upadhyaya, Narendra Singh, Vanika Garg, Aamir W. Khan, Swapan K. Datta, Manish Roorkiwal, Rajeev K. Varshney, Ramu Punna, Philippe Cubry, Xiao Du, Laurent Gentzbittel, Henry T. Nguyen, Kai P. Voss-Fels, Muneendra K. Singh, Servejeet Singh, Jeffrey L. Bennetzen, Chellapilla Bharadwaj, Xin Liu, Huanming Yang, Xun Xu, Cécile Ben, Vinod Valluri, and Lee T. Hickey
Subjects: Crops, Agricultural, Whole genome sequencing, Germplasm, Agricultural genetics, Genetic diversity, Multidisciplinary, Genetic Variation, Genomics, Sequence Analysis, DNA, Biology, Polymorphism, Single Nucleotide, Cicer, Article, Plant breeding, Natural variation in plants, Haplotypes, Evolutionary biology, Genetic variation, Structural variation, Domestication, Genome, Plant, Selection (genetic algorithm)
Abstract: Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources1. So far, few chickpea (Cicer arietinum) germplasm accessions have been characterized at the genome sequence level2. Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic diversity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic diversity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively., Whole-genome sequencing of 3,171 cultivated and 195 wild chickpea accessions is used to construct a chickpea pan-genome, providing insight into chickpea evolution and enabling breeding strategies that could improve crop productivity.
Published: 2021

2. Fish communities critically depend on forest subsidies in small neotropical streams with high biodiversity value

Author: Luc Allard, Yvan Papa, Pierre-Yves Le Bail, Anne Tréguier, Régis Vigouroux, Jean-Marc Roussel, Raphaël Covain, Écologie et santé des écosystèmes (ESE), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Museum d'Histoire Naturelle [Genève] (MHN), Laboratoire Environnement de Petit Saut, Hydreco, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and DEAL Guyane and the Parc Amazonien de Guyane for providing financial support
Subjects: 0106 biological sciences, terrestrial subsidies, Biodiversity, stable isotopes, STREAMS, 010603 evolutionary biology, 01 natural sciences, 14. Life underwater, molecular phylogeny, Ecology, Evolution, Behavior and Systematics, biology, 010604 marine biology & hydrobiology, forest streams, Subsidy, headwater streams, 15. Life on land, biology.organism_classification, French Guiana, Fishery, Geography, freshwater fish, terrestrial-aquatic linkage, Freshwater fish, %22">Fish , [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Value (mathematics)
Abstract: International audience; Trophic support of species-rich tropical fish communities remains uncertain in small forest streams where dense and constant canopy cover strongly limits the solar radiation available to aquatic producers. We sampled >1300 fish from 80 species in 14 remote headwater streams during the dry season in French Guiana. Carbon and nitrogen stable isotope analyses and mixing models were run to estimate the trophic position (TP) of each species and its dependence on terrestrial organic carbon sources. Matching patterns were found between nitrogen stable isotope ratios and the literature on diets of species at the base and top of the food web. Nearly 60% of the species fed exclusively on animal prey (mean TP >3), including piscivorous and parasitic fish species. Phylogenetic analysis revealed that TP were distributed broadly along the phylogeny and changed gradually within lineages. Carbon stable isotope ratios differed strongly between herbivores that fed on aquatic primary producers and those that fed on terrestrial plants along banksides. Terrestrial carbon was dominant in nearly 90% of species, and most of them depended more or less exclusively on terrestrial carbon. Ancestral state reconstructions indicated that only a few lineages showed local changes toward the consumption of algal carbon. We conclude that fish in neotropical headwater streams shaded by a dense tree canopy depend strongly on terrestrial subsidies. Changes in this aquatic-terrestrial linkage would have major consequences for the remarkable fish biodiversity in these streams.; La contribution majoritaire du carbone algal aux réseaux trophiques d'eau douce a été démontrée, même dans la partie amont des bassins versants où les apports de carbone terrestre sont substantiels. Ces apports terrestres proviennent principalement de lignocellulose, une source de nourriture que les consommateurs n'assimilent pas bien sous les climats tempérés, contrairement aux algues de haute qualité nutritive. La prédominance de l'apport algal reste en questionnement dans les petits cours d'eau en forêt tropicale, qui diffèrent entre autre par un couvert forestier dense et constant limitant fortement le rayonnement solaire disponible pour les producteurs aquatiques, par les essences végétales elles même, et par les caractéristiques physicochimiques du sol et de l'eau. Nous avons étudié l'écologie trophique de 80 espèces de poissons (> 1300 individus) issues de 14 ruisseaux pauvres en nutriments dans un contexte de forêt tropicale préservée en Guyane Française. Nous avons rassemblé des informations sur leur alimentation, puis combiné ces connaissances avec l'analyse des isotopes stables C et N dans leur muscle et dans une variété d'aliments potentiels, aquatiques et terrestres. Nous avons calculé leur position trophique et leur dépendance vis‐à‐vis des sources de C terrestres ou aquatiques. Nos résultats montrent des profils trophiques concomitants entre les isotopes stables de l'azote et la littérature sur les régimes alimentaires des espèces à la base et au sommet du réseau trophique, validant la pertinence d'une telle approche combinée pour ces communautés de poissons. Nous constatons qu'une majorité des espèces (60%) se nourrit de proies animales, y compris des poissons strictement piscivores. Une grande majorité (près de 90%) dépend principalement de sources alimentaires terrestres (>50% de C terrestre dans leurs tissus), et 65% en dépendrait plus ou moins exclusivement (>75% de C terrestre). Leurs niveaux trophiques sont très variables, depuis l'herbivorie (Myloplus ternetzi) jusqu’à l'ichtyoparasitisme (Ituglanis nebulosus). Seules 9 espèces sont plus fortement liées aux sources de C aquatique, et elles ont majoritairement un niveau trophique bas (Farlowella reticulata, Cyphocharax helleri, Ancistrus temminckii, Ancistrus aff. hoplogenys, Satanoperca rhynchitis and Ancistrus cf. leucostictus). Ces traits trophiques ont été utilisés dans une analyse phylogénétique pour tester leur pertinence évolutive. Ceci révèle que les positions trophiques sont largement réparties le long de la phylogénie et changent progressivement au sein des lignées. Les reconstructions d'états ancestraux indiquent toutefois que quelques lignées montrent des changements ponctuels vers la consommation de carbone algal. Nous concluons que les poissons des petits cours d'eau néotropicaux ombragés par un couvert forestier dense dépendent très fortement des apports nutritifs terrestres. Des changements dans ce lien aquatique‐terrestre auraient des conséquences majeures sur la remarquable biodiversité des poissons de ces cours d'eau. Ces connaissances aideront les gestionnaires de l'environnement à mieux appréhender les impacts potentiels des projets d'exploitation des ressources naturelles, et à proposer des solutions de remédiations plus pertinentes dans les cas de réhabilitation de sites en fin d'exploitation.
Published: 2021

3. Bilateral visual projections exist in non-teleost bony fish and predate the emergence of tetrapods

Author: Karine Duroure, Robin J. Vigouroux, Rodrigo Suárez, Juliette Vougny, Kim T. Nguyen-Ba-Charvet, Alain Chédotal, Eloisa Herrera, Shahad Albadri, Filippo Del Bene, Ingo Braasch, Peter Kozulin, Agence Nationale de la Recherche (France), National Institutes of Health (US), Institut de la Vision, Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génétique et Biologie du Développement, Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Queensland [Brisbane], Michigan State University [East Lansing], Michigan State University System, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), HAL-SU, Gestionnaire, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Instituto de Neurociencias de Alicante
Subjects: Fish Proteins, Retinal Ganglion Cells, genetic structures, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Visual system, Eye, ZIC2, Retinal ganglion, Functional Laterality, Retina, Article, [PHYS] Physics [physics], 03 medical and health sciences, 0302 clinical medicine, medicine, Animals, Humans, Visual Pathways, 14. Life underwater, Zebrafish, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, [PHYS]Physics [physics], Vision, Binocular, 0303 health sciences, Multidisciplinary, biology, Fishes, Brain, Nuclear Proteins, Cell Differentiation, Anatomy, biology.organism_classification, Biological Evolution, eye diseases, Ganglion, [SDV.BDD.EO]Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, medicine.anatomical_structure, Retinal ganglion cell, Laterality, sense organs, Binocular vision, 030217 neurology & neurosurgery, Transcription Factors
Abstract: In most vertebrates, camera-style eyes contain retinal ganglion cell neurons that project to visual centers on both sides of the brain. However, in fish, ganglion cells were thought to innervate only the contralateral side, suggesting that bilateral visual projections appeared in tetrapods. Here we show that bilateral visual projections exist in non-teleost fishes and that the appearance of ipsilateral projections does not correlate with terrestrial transition or predatory behavior. We also report that the developmental program that specifies visual system laterality differs between fishes and mammals, as the Zic2 transcription factor, which specifies ipsilateral retinal ganglion cells in tetrapods, appears to be absent from fish ganglion cells. However, overexpression of human ZIC2 induces ipsilateral visual projections in zebrafish. Therefore, the existence of bilateral visual projections likely preceded the emergence of binocular vision in tetrapods., This work was supported by Programme Investissements d’Avenir IHU FOReSIGHT (ANR-18-IAHU-01) (A.C. and F.D.B.), INSERM cross-cutting program HuDeCA 2018 (A.C.), NIH R01OD011116 (I.B.), and UQ Amplify Fellowship (R.S.)
Published: 2021

4. Adaptive introgression from maize has facilitated the establishment of teosinte as a noxious weed in Europe

Author: Yves Vigouroux, Valérie Le Corre, Mathieu Siol, Maud I. Tenaillon, Christophe Délye, Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Recherche pour le Développement (IRD), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-19-CE32-0009,DomIsol,La domestication comme un pas vers l'isolement reproducteur(2019), and ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017)
Subjects: 0106 biological sciences, Germplasm, Range (biology), [SDV]Life Sciences [q-bio], Niche, Adaptation, Biological, Plant Weeds, Introgression, rapid adaptation, Biology, Zea mays, 010603 evolutionary biology, 01 natural sciences, genetic introgression, Evolution, Molecular, 03 medical and health sciences, herbicide resistance, Genetic variation, Cultivar, plant invasion, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Multidisciplinary, Herbicides, Noxious weed, food and beverages, flowering time, Biological Sciences, 15. Life on land, Europe, Agronomy, 13. Climate action, Adaptation
Abstract: Global trade has considerably accelerated biological invasions. The annual tropical teosintes, the closest wild relatives of maize, were recently reported as new agricultural weeds in two European countries, Spain and France. Their prompt settlement under climatic conditions differing drastically from that of their native range indicates rapid genetic evolution. We performed a phenotypic comparison of French and Mexican teosintes under European conditions and showed that only the former could complete their life cycle during maize cropping season. To test the hypothesis that crop-to-wild introgression triggered such rapid adaptation, we used single nucleotide polymorphisms to characterize patterns of genetic variation in French, Spanish, and Mexican teosintes as well as in maize germplasm. We showed that both Spanish and French teosintes originated from Zea mays ssp. mexicana race “Chalco,” a weedy teosinte from the Mexican highlands. However, introduced teosintes differed markedly from their Mexican source by elevated levels of genetic introgression from the high latitude Dent maize grown in Europe. We identified a clear signature of divergent selection in a region of chromosome 8 introgressed from maize and encompassing ZCN8, a major flowering time gene associated with adaptation to high latitudes. Moreover, herbicide assays and sequencing revealed that French teosintes have acquired herbicide resistance via the introgression of a mutant herbicide-target gene (ACC1) present in herbicide-resistant maize cultivars. Altogether, our results demonstrate that adaptive crop-to-wild introgression has triggered both rapid adaptation to a new climatic niche and acquisition of herbicide resistance, thereby fostering the establishment of an emerging noxious weed.
Published: 2020

5. Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

Author: Christine Tranchant-Dubreuil, Maria Holzinger, Yves Vigouroux, Stefan Jouannic, Hélène Adam, Alain Ghesquière, Philippe Cubry, Kim Nhung Ta, Olivier François, François Sabot, Honoré Kam, Anne-Céline Thuillet, Harold Chrestin, Hélène Pidon, Laurence Albar, and Université Grenoble Alpes (UGA)
Subjects: 0106 biological sciences, Candidate gene, RYMV, Flowering time, Rice yellow mottle virus, Climate variation, Quantitative trait locus, Oryza glaberrima, lcsh:Plant culture, 01 natural sciences, Genome, 03 medical and health sciences, lcsh:SB1-1110, Domestication, 030304 developmental biology, Panicle, 2. Zero hunger, 0303 health sciences, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], biology, food and beverages, 15. Life on land, biology.organism_classification, Panicle architecture, Evolutionary biology, Original Article, Adaptation, Genome wide association study, African rice, 010606 plant biology & botany
Abstract: BackgroundAfrican rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. Since its domestication in the inner Niger delta ca. 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. However, little is known about the genetic basis of quantitative traits and adaptive variation of agricultural interest for this species.ResultsUsing a reference set of 163 fully re-sequenced accessions, we report the results of a Genome Wide Association Study carried out for African rice. We investigated a diverse panel of traits, including flowering date, panicle architecture and resistance to Rice yellow mottle virus. For this, we devised a pipeline using complementary statistical association methods. First, using flowering time as a target trait, we demonstrated that we could successfully retrieve known genes from the rice flowering pathway, and identified new genomic regions that would deserve more study. Then we applied our pipeline to panicle- and resistance-related traits, highlighting some interesting QTLs and candidate genes (including Rymv1 for resistance and SP1, Ghd7.1, APO1 and OsMADS1 for panicle architecture). Lastly, using a high-resolution climate database, we performed an association analysis based on climatic variables, searching for genomic regions that might be involved in adaptation to climatic variations.ConclusionOur results collectively provide insights into the extent to which adaptive variation is governed by sequence diversity within the O. glaberrima genome, paving the way for in-depth studies of the genetic basis of traits of interest that might be useful to the rice breeding community.
Published: 2020

6. Overlapping phenotypes between <scp>SHORT</scp> and Noonan syndromes in patients with <scp> PTPN11 </scp> pathogenic variants

Author: Charles Marques, Yline Capri, Anne Guimier, A. Micheil Innes, Jeanne Amiel, Martine Auclair, Julien Thevenon, David A. Dyment, Gilles Morin, Christel Thauvin-Robinet, Corinne Vigouroux, Emmanuelle Ranza, Michèle Mathieu-Dramard, Alain Verloes, and Laurence Faivre
Subjects: Male, musculoskeletal diseases, 0301 basic medicine, MAPK/ERK pathway, congenital, hereditary, and neonatal diseases and abnormalities, MAP Kinase Signaling System, Protein Tyrosine Phosphatase, Non-Receptor Type 11, 030105 genetics & heredity, Biology, Gene product, Phosphatidylinositol 3-Kinases, 03 medical and health sciences, Metabolic Diseases, Genetics, medicine, Humans, Missense mutation, skin and connective tissue diseases, Protein kinase B, Growth Disorders, Genetics (clinical), Genetic heterogeneity, Noonan Syndrome, Genetic Variation, medicine.disease, PTPN11, Nephrocalcinosis, Phenotype, 030104 developmental biology, SHORT syndrome, Hypercalcemia, Noonan syndrome, Female, Mitogen-Activated Protein Kinases, Signal Transduction
Abstract: Overlapping syndromes such as Noonan, Cardio-Facio-Cutaneous, Noonan syndrome (NS) with multiple lentigines and Costello syndromes are genetically heterogeneous conditions sharing a dysregulation of the RAS/mitogen-activated protein kinase (MAPK) pathway and are known collectively as the RASopathies. PTPN11 was the first disease-causing gene identified in NS and remains the more prevalent. We report seven patients from three families presenting heterozygous missense variants in PTPN11 probably responsible for a disease phenotype distinct from the classical Noonan syndrome. The clinical presentation and common features of these seven cases overlap with the SHORT syndrome. The latter is the consequence of PI3K/AKT signaling deregulation with the predominant disease-causing gene being PIK3R1. Our data suggest that the phenotypic spectrum associated with pathogenic variants of PTPN11 could be wider than previously described, and this could be due to the dual activity of SHP2 (ie, PTPN11 gene product) on the RAS/MAPK and PI3K/AKT signaling.
Published: 2020

7. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition) 1

Author: Klionsky, Daniel, Abdel-Aziz, Amal Kamal, Abdelfatah, Sara, Abdellatif, Mahmoud, Abdoli, Asghar, Abel, Steffen, Abeliovich, Hagai, Abildgaard, Marie, Abudu, Yakubu Princely, Acevedo-Arozena, Abraham, Adamopoulos, Iannis, Adeli, Khosrow, Adolph, Timon, Adornetto, Annagrazia, Aflaki, Elma, Agam, Galila, Agarwal, Anupam, Aggarwal, Bharat, Agnello, Maria, Agostinis, Patrizia, Agrewala, Javed, Agrotis, Alexander, Aguilar, Patricia, Ahmad, S Tariq, Ahmed, Zubair, Ahumada-Castro, Ulises, Aits, Sonja, Aizawa, Shu, Akkoc, Yunus, Akoumianaki, Tonia, Akpinar, Hafize Aysin, Al-Abd, Ahmed, Al-Akra, Lina, Al-Gharaibeh, Abeer, Alaoui-Jamali, Moulay, Alberti, Simon, Alcocer-Gómez, Elísabet, Alessandri, Cristiano, Ali, Muhammad, Alim Al-Bari, M Abdul, Aliwaini, Saeb, Alizadeh, Javad, Almacellas, Eugènia, Almasan, Alexandru, Alonso, Alicia, Alonso, Guillermo, Altan-Bonnet, Nihal, Altieri, Dario, Álvarez, Élida, Alves, Sara, Alves Da Costa, Cristine, Alzaharna, Mazen, Amadio, Marialaura, Amantini, Consuelo, Amaral, Cristina, Ambrosio, Susanna, Amer, Amal, Ammanathan, Veena, An, Zhenyi, Andersen, Stig, Andrabi, Shaida, Andrade-Silva, Magaiver, Andres, Allen, Angelini, Sabrina, Ann, David, Anozie, Uche, Ansari, Mohammad, Antas, Pedro, Antebi, Adam, Antón, Zuriñe, Anwar, Tahira, Apetoh, Lionel, Apostolova, Nadezda, Araki, Toshiyuki, Araki, Yasuhiro, Arasaki, Kohei, Araújo, Wagner, Araya, Jun, Arden, Catherine, Arévalo, Maria-Angeles, Arguelles, Sandro, Arias, Esperanza, Arikkath, Jyothi, Arimoto, Hirokazu, Ariosa, Aileen, Armstrong-James, Darius, Arnauné-Pelloquin, Laetitia, Aroca, Angeles, Arroyo, Daniela, Arsov, Ivica, Artero, Rubén, Asaro, Dalia Maria Lucia, Aschner, Michael, Ashrafizadeh, Milad, Ashur-Fabian, Osnat, Atanasov, Atanas, Au, Alicia, Auberger, Patrick, Auner, Holger, Aurelian, Laure, Autelli, Riccardo, Avagliano, Laura, Ávalos, Yenniffer, Aveic, Sanja, Aveleira, Célia Alexandra, Avin-Wittenberg, Tamar, Aydin, Yucel, Ayton, Scott, Ayyadevara, Srinivas, Azzopardi, Maria, Baba, Misuzu, Backer, Jonathan, Backues, Steven, Bae, Dong-Hun, Bae, Ok-Nam, Bae, Soo Han, Baehrecke, Eric, Baek, Ahruem, Baek, Seung-Hoon, Baek, Sung Hee, Bagetta, Giacinto, Bagniewska-Zadworna, Agnieszka, Bai, Hua, Bai, Jie, Bai, Xiyuan, Bai, Yidong, Bairagi, Nandadulal, Baksi, Shounak, Balbi, Teresa, Baldari, Cosima, Balduini, Walter, Ballabio, Andrea, Ballester, Maria, Balazadeh, Salma, Balzan, Rena, Bandopadhyay, Rina, Banerjee, Sreeparna, Banerjee, Sulagna, Bánréti, Ágnes, Bao, Yan, Baptista, Mauricio, Baracca, Alessandra, Barbati, Cristiana, Bargiela, Ariadna, Barilà, Daniela, Barlow, Peter, Barmada, Sami, Barreiro, Esther, Barreto, George, Bartek, Jiri, Bartel, Bonnie, Bartolome, Alberto, Barve, Gaurav, Basagoudanavar, Suresh, Bassham, Diane, Bast, Robert, Basu, Alakananda, Batoko, Henri, Batten, Isabella, Baulieu, Etienne, Baumgarner, Bradley, Bayry, Jagadeesh, Beale, Rupert, Beau, Isabelle, Beaumatin, Florian, Bechara, Luiz, Beck, George, Beers, Michael, Begun, Jakob, Behrends, Christian, Behrens, Georg, Bei, Roberto, Bejarano, Eloy, Bel, Shai, Behl, Christian, Belaid, Amine, Belgareh-Touzé, Naïma, Bellarosa, Cristina, Belleudi, Francesca, Belló Pérez, Melissa, Bello-Morales, Raquel, Beltran, Jackeline Soares de Oliveira, Beltran, Sebastián, Benbrook, Doris Mangiaracina, Bendorius, Mykolas, Benitez, Bruno, Benito-Cuesta, Irene, Bensalem, Julien, Berchtold, Martin, Berezowska, Sabina, Bergamaschi, Daniele, Bergami, Matteo, Bergmann, Andreas, Berliocchi, Laura, Berlioz-Torrent, Clarisse, Bernard, Amélie, Berthoux, Lionel, Besirli, Cagri, Besteiro, Sebastien, Betin, Virginie, Beyaert, Rudi, Bezbradica, Jelena, Bhaskar, Kiran, Bhatia-Kissova, Ingrid, Bhattacharya, Resham, Bhattacharya, Sujoy, Bhattacharyya, Shalmoli, Bhuiyan, Md Shenuarin, Bhutia, Sujit Kumar, Bi, Lanrong, Bi, Xiaolin, Biden, Trevor, Bijian, Krikor, Billes, Viktor, Binart, Nadine, Bincoletto, Claudia, Birgisdottir, Asa, Bjorkoy, Geir, Blanco, Gonzalo, Blas-Garcia, Ana, Blasiak, Janusz, Blomgran, Robert, Blomgren, Klas, Blum, Janice, Boada-Romero, Emilio, Boban, Mirta, Boesze-Battaglia, Kathleen, Boeuf, Philippe, Boland, Barry, Bomont, Pascale, Bonaldo, Paolo, Bonam, Srinivasa Reddy, Bonfili, Laura, Bonifacino, Juan, Boone, Brian, Bootman, Martin, Bordi, Matteo, Borner, Christoph, Bornhauser, Beat, Borthakur, Gautam, Bosch, Jürgen, Bose, Santanu, botana, luis, Botas, Juan, Boulanger, Chantal, Boulton, Michael, Bourdenx, Mathieu, Bourgeois, Benjamin, Bourke, Nollaig, Bousquet, Guilhem, Boya, Patricia, Bozhkov, Peter, Bozi, Luiz, Bozkurt, Tolga, Brackney, Doug, Brandts, Christian, Braun, Ralf, Braus, Gerhard, Bravo-Sagua, Roberto, Bravo-San Pedro, José, Brest, Patrick, Bringer, Marie-Agnès, Briones-Herrera, Alfredo, Broaddus, V Courtney, Brodersen, Peter, Brodsky, Jeffrey, Brody, Steven, Bronson, Paola, Bronstein, Jeff, Brown, Carolyn, Brown, Rhoderick, Brum, Patricia, Brumell, John, Brunetti-Pierri, Nicola, Bruno, Daniele, Bryson-Richardson, Robert, Bucci, Cecilia, Buchrieser, Carmen, Bueno, Marta, Buitrago-Molina, Laura Elisa, Buraschi, Simone, Buch, Shilpa, Buchan, J Ross, Buckingham, Erin, Budak, Hikmet, Budini, Mauricio, Bultynck, Geert, Burada, Florin, Burgoyne, Joseph, Burón, M Isabel, Bustos, Victor, Büttner, Sabrina, Butturini, Elena, Byrd, Aaron, Cabas, Isabel, Cabrera-Benitez, Sandra, Cadwell, Ken, Cai, Jingjing, Cai, Lu, Cai, Qian, Cairó, Montserrat, Calbet, Jose, Caldwell, Guy, Caldwell, Kim, Call, Jarrod, Calvani, Riccardo, Calvo, Ana, Calvo-Rubio Barrera, Miguel, Camara, Niels OS, Camonis, Jacques, Camougrand, Nadine, Campanella, Michelangelo, Campbell, Edward, Campbell-Valois, François-Xavier, Campello, Silvia, Campesi, Ilaria, Campos, Juliane, Camuzard, Olivier, Cancino, Jorge, Candido de Almeida, Danilo, Canesi, Laura, Caniggia, Isabella, Canonico, Barbara, Cantí, Carles, Cao, Bin, Caraglia, Michele, Caramés, Beatriz, Carchman, Evie, Cardenal-Muñoz, Elena, Cardenas, Cesar, Cardenas, Luis, Cardoso, Sandra, Carew, 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Da-Hye, Lee, Edward, Lee, Erinna, Lee, Gyun Min, Lee, He-Jin, Lee, Heung Kyu, Lee, Jae Man, Lee, Jason, Lee, Jin-A, Lee, Joo-Yong, Lee, Jun Hee, Lee, Michael, Lee, Min Goo, Lee, Min Jae, Lee, Myung-Shik, Lee, Sang Yoon, Lee, Seung-Jae, Lee, Stella, Lee, Sung Bae, Lee, Won Hee, Lee, Ying-Ray, Lee, Yong-ho, Lee, Youngil, Lefebvre, Christophe, Legouis, Renaud, Lei, Yu, Lei, Yuchen, Leikin, Sergey, Leitinger, Gerd, Lemus, Leticia, Leng, Shuilong, Lenoir, Olivia, Lenz, Guido, Lenz, Heinz Josef, Lenzi, Paola, León, Yolanda, Leopoldino, Andréia, Leschczyk, Christoph, Leskelä, Stina, Letellier, Elisabeth, Leung, Chi-Ting, Leung, Po Sing, Leventhal, Jeremy, Levine, Beth, Lewis, Patrick, Ley, Klaus, Li, Bin, Li, Da-Qiang, Li, Jianming, Li, Jing, Li, Jiong, Li, Ke, Li, Liwu, Li, Mei, Li, Min, Li, Ming, Li, Mingchuan, Li, Pin-Lan, Li, Ming-Qing, Li, Qing, Li, Sheng, Li, Tiangang, Li, Wei, Li, Wenming, Li, Xue, Li, Yi-Ping, Li, Yuan, Li, Zhiqiang, Li, Zhiyong, Li, Zhiyuan, Lian, Jiqin, Liang, Chengyu, Liang, Qiangrong, Liang, Weicheng, Liang, Yongheng, Liang, YongTian, Liao, Guanghong, Liao, Lujian, Liao, Mingzhi, Liao, Yung-Feng, Librizzi, Mariangela, Lie, Pearl, Lilly, Mary, Lim, Hyunjung, Lima, Thania, Limana, Federica, Lin, Chao, Lin, Chih-Wen, Lin, Dar-Shong, Lin, Fu-Cheng, Lin, Jiandie, Lin, Kurt, Lin, Kwang-Huei, Lin, Liang-Tzung, LIN, Pei-Hui, Lin, Qiong, Lin, Shaofeng, Lin, Su-Ju, Lin, Wenyu, Lin, Xueying, Lin, Yao-Xin, Lin, Yee-Shin, Linden, Rafael, Lindner, Paula, Ling, Shuo-Chien, Lingor, Paul, Linnemann, Amelia, Liou, Yih-Cherng, Lipinski, Marta, Lipovšek, Saška, Lira, Vitor, Lisiak, Natalia, Liton, Paloma, Liu, Chao, Liu, Ching-Hsuan, Liu, Chun-Feng, Liu, Cui Hua, Liu, Fang, Liu, Hao, Liu, Hsiao-Sheng, Liu, Hua-feng, Liu, Huifang, Liu, Jia, Liu, Jing, Liu, Julia, Liu, Leyuan, Liu, Longhua, Liu, Meilian, Liu, Qin, Liu, Wei, Liu, Wende, Liu, Xiao-Hong, Liu, Xiaodong, Liu, Xingguo, Liu, Xu, Liu, Xuedong, Liu, Yanfen, Liu, Yang, Liu, Yueyang, Liu, Yule, Livingston, J Andrew, Lizard, Gerard, Lizcano, Jose, Ljubojevic-Holzer, Senka, LLeonart, Matilde, Llobet-Navàs, David, Llorente, Alicia, Lo, Chih Hung, Lobato-Márquez, Damián, Long, Qi, Long, Yun Chau, Loos, Ben, Loos, Julia, López, Manuela, López-Doménech, Guillermo, López-Guerrero, José Antonio, López-Jiménez, Ana, López-Pérez, Óscar, López-Valero, Israel, Lorenowicz, Magdalena, Lorente, Mar, Lorincz, Peter, Lossi, Laura, Lotersztajn, Sophie, Lovat, Penny, Lovell, Jonathan, Lovy, Alenka, Lőw, Péter, Lu, Guang, Lu, Haocheng, Lu, Jia-Hong, Lu, Jin-Jian, Lu, Mengji, Lu, Shuyan, Luciani, Alessandro, Lucocq, John, Ludovico, Paula, Luftig, Micah, Luhr, Morten, Luis-Ravelo, Diego, Lum, Julian, Luna-Dulcey, Liany, Lund, Anders, Lund, Viktor, Lünemann, Jan, Lüningschrör, Patrick, Luo, Honglin, Luo, Rongcan, Luo, Shouqing, Luo, Zhi, Luparello, Claudio, Lüscher, Bernhard, Luu, Luan, Lyakhovich, Alex, Lyamzaev, Konstantin, Lystad, Alf Håkon, Lytvynchuk, Lyubomyr, Ma, Alvin, Ma, Changle, Ma, Mengxiao, Ma, Ning-Fang, Ma, Quan-Hong, Ma, Xinliang, Ma, Yueyun, Ma, Zhenyi, MacDougald, Ormond, Macian, Fernando, MacIntosh, Gustavo, MacKeigan, Jeffrey, Macleod, Kay, Maday, Sandra, Madeo, Frank, Madesh, Muniswamy, Madl, Tobias, Madrigal-Matute, Julio, Maeda, Akiko, Maejima, Yasuhiro, Magarinos, Marta, Mahavadi, Poornima, Maiani, Emiliano, Maiese, Kenneth, Maiti, Panchanan, Maiuri, Maria Chiara, Majello, Barbara, Major, Michael, Makareeva, Elena, Malik, Fayaz, Mallilankaraman, Karthik, Malorni, Walter, Maloyan, Alina, Mammadova, Najiba, Man, Gene Chi Wai, Manai, Federico, Mancias, Joseph, Mandelkow, Eva-Maria, Mandell, Michael, Manfredi, Angelo, Manjili, Masoud, Manjithaya, Ravi, Manque, Patricio, Manshian, Bella, Manzano, Raquel, Manzoni, Claudia, Mao, Kai, Marchese, Cinzia, Marchetti, Sandrine, Marconi, Anna Maria, Marcucci, Fabrizio, Mardente, Stefania, Mareninova, Olga, Margeta, Marta, Mari, Muriel, Marinelli, Sara, Marinelli, Oliviero, Mariño, Guillermo, Mariotto, Sofia, Marshall, Richard, Marten, Mark, Martens, Sascha, Martin, Alexandre, Martin, Katie, Martin, Sara, Martin, Shaun, Martín-Segura, Adrián, Martín-Acebes, Miguel, Martin-Burriel, Inmaculada, Martin-Rincon, Marcos, Martin-Sanz, Paloma, Martina, José, Martinet, Wim, Martinez, Aitor, Martinez, Ana, Martinez, Jennifer, Martinez Velazquez, Moises, Martinez-Lopez, Nuria, Martinez-Vicente, Marta, Martins, Daniel, Martins, Joilson, Martins, Waleska, Martins-Marques, Tania, Marzetti, Emanuele, Masaldan, Shashank, Masclaux-Daubresse, Celine, Mashek, Douglas, Massa, Valentina, Massieu, Lourdes, Masson, Glenn, Masuelli, Laura, Masyuk, Anatoliy, Masyuk, Tetyana, Matarrese, Paola, Matheu, Ander, Matoba, Satoaki, Matsuzaki, Sachiko, Mattar, Pamela, Matte, Alessandro, Mattoscio, Domenico, Mauriz, José, Mauthe, Mario, Mauvezin, Caroline, Maverakis, Emanual, Maycotte, Paola, Mayer, Johanna, Mazzoccoli, Gianluigi, Mazzoni, Cristina, Mazzulli, Joseph, McCarty, Nami, Mcdonald, Christine, McGill, Mitchell, McKenna, Sharon, Mclaughlin, Bethann, McLoughlin, Fionn, McNiven, Mark, McWilliams, Thomas, Mechta-Grigoriou, Fatima, Medeiros, Tania Catarina, Medina, Diego, Megeney, Lynn, Megyeri, Klara, Mehrpour, Maryam, Mehta, Jawahar, Meijer, Alfred, Meijer, Annemarie, Mejlvang, Jakob, Meléndez, Alicia, Melk, Annette, Memisoglu, Gonen, Mendes, Alexandrina, Meng, Delong, Meng, Fei, Meng, Tian, Menna-Barreto, Rubem, Menon, Manoj, Mercer, Carol, Mercier, Anne, MERGNY, Jean-Louis, Merighi, Adalberto, Merkley, Seth, Merla, Giuseppe, Meske, Volker, Mestre, Ana Cecilia, Metur, Shree Padma, Meyer, Christian, Meyer, Hemmo, Mi, Wenyi, Mialet-Perez, Jeanne, Miao, Junying, Micale, Lucia, Miki, Yasuo, Milan, Enrico, Milczarek, Małgorzata, Miller, Dana, Miller, Samuel, Miller, Silke, Millward, Steven, Milosevic, Ira, Minina, Elena, Mirzaei, Hamed, Mirzaei, Hamid Reza, Mirzaei, Mehdi, Mishra, Amit, Mishra, Nandita, Mishra, Paras Kumar, Misirkic Marjanovic, Maja, Misasi, Roberta, Misra, Amit, Misso, Gabriella, Mitchell, Claire, Mitou, Geraldine, Miura, Tetsuji, Miyamoto, Shigeki, MIYAZAKI, Makoto, Miyazaki, Mitsunori, Miyazaki, Taiga, Miyazawa, Keisuke, Mizushima, Noboru, Mogensen, Trine, Mograbi, Baharia, Mohammadinejad, Reza, Mohamud, Yasir, Mohanty, Abhishek, Mohapatra, Sipra, Möhlmann, Torsten, Mohmmed, Asif, Moles, Anna, Moley, Kelle, Molinari, Maurizio, Mollace, Vincenzo, Møller, Andreas Buch, Mollereau, Bertrand, Mollinedo, Faustino, Montagna, Costanza, Monteiro, Mervyn, Montella, Andrea, Montes, L Ruth, Montico, Barbara, Mony, Vinod, Monzio Compagnoni, Giacomo, Moore, Michael, Moosavi, Mohammad, Mora, Ana, Mora, Marina, Morales-Alamo, David, Moratalla, Rosario, Moreira, Paula, Morelli, Elena, Moreno, Sandra, Moreno-Blas, Daniel, Moresi, Viviana, Morga, Benjamin, Morgan, Alwena, Morin, Fabrice, Morishita, Hideaki, Moritz, Orson, Moriyama, Mariko, Moriyasu, Yuji, Morleo, Manuela, Morselli, Eugenia, Moruno-Manchon, Jose, Moscat, Jorge, Mostowy, Serge, Motori, Elisa, Moura, Andrea 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Ney, Paul, Nezis, Ioannis, Ng, Charlene, Ng, Tzi Bun, Nguyen, Hang, Nguyen, Long, Ni, Hong-Min, Ní Cheallaigh, Clíona, Ni, Zhenhong, Nicolao, M Celeste, Nicoli, Francesco, Nieto-Diaz, Manuel, Nilsson, Per, Ning, Shunbin, Niranjan, Rituraj, Nishimune, Hiroshi, Niso-Santano, Mireia, Nixon, Ralph, Nobili, Annalisa, Nobrega, Clevio, Noda, Takeshi, Nogueira-Recalde, Uxía, Nolan, Trevor, Nombela, Ivan, Novak, Ivana, Novoa, Beatriz, Nozawa, Takashi, Nukina, Nobuyuki, Nussbaum-Krammer, Carmen, Nylandsted, Jesper, O'Donovan, Tracey, O'Leary, Seónadh, O'Rourke, Eyleen, O'Sullivan, Mary, O'Sullivan, Timothy, Oddo, Salvatore, Oehme, Ina, Ogawa, Michinaga, Ogier-Denis, Eric, Ogmundsdottir, Margret, Ogretmen, Besim, Oh, Goo Taeg, Oh, Seon-Hee, Oh, Young, Ohama, Takashi, Ohashi, Yohei, Ohmuraya, Masaki, Oikonomou, Vasileios, Ojha, Rani, Okamoto, Koji, Okazawa, Hitoshi, Oku, Masahide, Oliván, Sara, Oliveira, Jorge, Ollmann, Michael, Olzmann, James, Omari, Shakib, Omary, M Bishr, Önal, Gizem, Ondrej, 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Andrei, Smith, Matthew, Soenen, Stefaan, Sohn, Eun Jung, Sok, Sophia, Solaini, Giancarlo, Soldati, Thierry, Soleimanpour, Scott, Soler, Rosa, Solovchenko, Alexei, Somarelli, Jason, Sonawane, Avinash, Song, Fuyong, Song, Hyun Kyu, Song, Ju-Xian, Song, Kunhua, Song, Zhiyin, Soria, Leandro, Sorice, Maurizio, Soukas, Alexander, Soukup, Sandra-Fausia, Sousa, Diana, Sousa, Nadia, Spagnuolo, Paul, Spector, Stephen, Srinivas Bharath, M., St Clair, Daret, Stagni, Venturina, Staiano, Leopoldo, Stalnecker, Clint, Stankov, Metodi, Stathopulos, Peter, Stefan, Katja, Stefan, Sven Marcel, Stefanis, Leonidas, Steffan, Joan, Steinkasserer, Alexander, Stenmark, Harald, Sterneckert, Jared, Stevens, Craig, Stoka, Veronika, Storch, Stephan, Stork, Björn, Strappazzon, Flavie, Strohecker, Anne Marie, Stupack, Dwayne, Su, Huanxing, Su, Ling-Yan, Su, Longxiang, Suarez-Fontes, Ana, Subauste, Carlos, Subbian, Selvakumar, Subirada, Paula, Sudhandiran, Ganapasam, Sue, Carolyn, Sui, Xinbing, Summers, Corey, Sun, Guangchao, Sun, Jun, SUN, Kang, Sun, Meng-xiang, Sun, Qiming, Sun, Yi, Sun, Zhongjie, Sunahara, Karen, Sundberg, Eva, Susztak, Katalin, Sutovsky, Peter, Suzuki, Hidekazu, Sweeney, Gary, Symons, J David, Sze, Stephen Cho Wing, Szewczyk, Nathaniel, Tabęcka-Łonczynska, Anna, Tabolacci, Claudio, Tacke, Frank, Taegtmeyer, Heinrich, Tafani, Marco, Tagaya, Mitsuo, Tai, Haoran, Tait, Stephen, Takahashi, Yoshinori, Takats, Szabolcs, Talwar, Priti, Tam, Chit, Tam, Shing Yau, Tampellini, Davide, Tamura, Atsushi, Tan, Chong Teik, Tan, Eng-King, Tan, Ya-Qin, Tanaka, Masaki, Tanaka, Motomasa, Tang, Daolin, Tang, Jingfeng, Tang, Tie-Shan, Tanida, Isei, Tao, Zhipeng, Taouis, Mohammed, Tatenhorst, Lars, Tavernarakis, Nektarios, Taylor, Allen, Taylor, Gregory, Taylor, Joan, Tchetina, Elena, Tee, Andrew, Tegeder, Irmgard, Teis, David, Teixeira, Natercia, Teixeira-Clerc, Fatima, Tekirdag, Kumsal, Tencomnao, Tewin, Tenreiro, Sandra, Tepikin, Alexei, Testillano, Pilar, Tettamanti, Gianluca, Tharaux, Pierre-Louis, Thedieck, Kathrin, Thekkinghat, Arvind, Thellung, Stefano, Thinwa, Josephine, Thirumalaikumar, V.P., Thomas, Sufi Mary, Thomes, Paul, Thorburn, Andrew, Thukral, Lipi, Thum, Thomas, Thumm, Michael, Tian, Ling, Tichy, Ales, Till, Andreas, Timmerman, Vincent, Titorenko, Vladimir, Todi, Sokol, Todorova, Krassimira, Toivonen, Janne, Tomaipitinca, Luana, Tomar, Dhanendra, Tomas-Zapico, Cristina, Tomić, Sergej, Tong, Benjamin Chun-Kit, Tong, Chao, Tong, Xin, Tooze, Sharon, Torgersen, Maria, Torii, Satoru, Torres-López, Liliana, Torriglia, Alicia, Towers, Christina, Towns, Roberto, Toyokuni, Shinya, Trajkovic, Vladimir, Tramontano, Donatella, Tran, Quynh-Giao, Travassos, Leonardo, Trelford, Charles, Tremel, Shirley, Trougakos, Ioannis, Tsao, Betty, Tschan, Mario, Tse, Hung-Fat, Tse, Tak Fu, Tsugawa, Hitoshi, Tsvetkov, Andrey, Tumbarello, David, Tumtas, Yasin, Tuñón, María, Turcotte, Sandra, Turk, Boris, Turk, Vito, Turner, Bradley, Tuxworth, Richard, Tyler, Jessica, Tyutereva, Elena, Uchiyama, Yasuo, Ugun-Klusek, Aslihan, Uhlig, Holm, Ułamek-Kozioł, Marzena, Ulasov, Ilya, Umekawa, Midori, Ungermann, Christian, Unno, Rei, Urbe, Sylvie, Uribe-Carretero, Elisabet, Üstün, Suayib, Uversky, Vladimir, Vaccari, Thomas, Vaccaro, Maria, Vahsen, Björn, Vakifahmetoglu-Norberg, Helin, Valdor, Rut, Valente, Maria, Valko, Ayelén, Vallee, Richard, Valverde, Angela, Van Den Berghe, Greet, van der Veen, Stijn, Van Kaer, Luc, van Loosdregt, Jorg, van Wijk, Sjoerd, Vandenberghe, Wim, Vanhorebeek, Ilse, Vannier-Santos, Marcos, Vannini, Nicola, Vanrell, M Cristina, Vantaggiato, Chiara, Varano, Gabriele, Varela-Nieto, Isabel, Varga, Máté, Vasconcelos, M Helena, Vats, Somya, Vavvas, Demetrios, Vega-Naredo, Ignacio, Vega-Rubin-de-Celis, Silvia, Velasco, Guillermo, Velázquez, Ariadna, Vellai, Tibor, Vellenga, Edo, Velotti, Francesca, Verdier, Mireille, Verginis, Panayotis, Vergne, Isabelle, Verkade, Paul, Verma, Manish, Verstreken, Patrik, Vervliet, Tim, Vervoorts, Jörg, Vessoni, Alexandre, Victor, Victor, Vidal, Michel, Vidoni, Chiara, Vieira, Otilia, Vierstra, Richard, Viganó, Sonia, Vihinen, Helena, Vijayan, Vinoy, Vila, Miquel, Vilar, Marçal, Villalba, José, Villalobo, Antonio, Villarejo-Zori, Beatriz, Villarroya, Francesc, Villarroya, Joan, Vincent, Olivier, Vindis, Cecile, Viret, Christophe, Viscomi, Maria Teresa, Visnjic, Dora, Vitale, Ilio, Vocadlo, David, Voitsekhovskaja, Olga, Volonté, Cinzia, Volta, Mattia, Vomero, Marta, Von Haefen, Clarissa, Vooijs, Marc, Voos, Wolfgang, Vucicevic, Ljubica, Wade-Martins, Richard, Waguri, Satoshi, Waite, Kenrick, Wakatsuki, Shuji, Walker, David, Walker, Mark, Walker, Simon, Walter, Jochen, Wandosell, Francisco, Wang, Bo, Wang, Chao-Yung, Wang, Chen, Wang, Chenran, Wang, Chenwei, Wang, Cun-Yu, Wang, Dong, Wang, Fangyang, Wang, Feng, Wang, Fengming, Wang, Guansong, Wang, Han, Wang, Hao, Wang, Hexiang, Wang, Hong-Gang, Wang, Jianrong, Wang, Jigang, Wang, Jiou, Wang, Jundong, Wang, Kui, Wang, Lianrong, Wang, Liming, Wang, Maggie Haitian, Wang, Meiqing, Wang, Nanbu, Wang, PengWei, Wang, PeiPei, Wang, Ping, Wang, Qing Jun, Wang, Qing, Wang, Qing Kenneth, Wang, Qiong, Wang, Wen-Tao, Wang, Wuyang, Wang, Xinnan, Wang, Xuejun, Wang, Yan, Wang, Yanchang, Wang, Yanzhuang, Wang, Yen-Yun, Wang, Yihua, Wang, Yipeng, Wang, Yu, wang, yuqi, Wang, Zhe, Wang, Zhenyu, Wang, Zhouguang, Warnes, Gary, Warnsmann, Verena, Watada, Hirotaka, Watanabe, Eizo, Watchon, Maxinne, Wawrzyńska, Anna, Weaver, Timothy, Wegrzyn, Grzegorz, Wehman, Ann, Wei, Huafeng, Wei, Lei, Wei, Taotao, Wei, Yongjie, Weiergräber, Oliver, Weihl, Conrad, Weindl, Günther, Weiskirchen, Ralf, Wells, Alan, Wen, Runxia, Wen, Xin, Werner, Antonia, Weykopf, Beatrice, Wheatley, Sally, Whitton, J Lindsay, Whitworth, Alexander, Wiktorska, Katarzyna, Wildenberg, Manon, Wileman, Tom, Wilkinson, Simon, Willbold, Dieter, Williams, Brett, Williams, Robin, Williams, Roger, Williamson, Peter, Wilson, Richard, Winner, Beate, Winsor, Nathaniel, Witkin, Steven, Wodrich, Harald, Woehlbier, Ute, Wollert, Thomas, Wong, Esther, Wong, Jack Ho, Wong, Richard, Wong, Vincent Kam Wai, Wong, W Wei-Lynn, Wu, An-Guo, Wu, Chengbiao, Wu, Jian, Wu, Junfang, Wu, Kenneth, Wu, Min, Wu, Shan-Ying, Wu, Shengzhou, Wu, Shu-Yan, Wu, Shufang, Wu, William, Wu, Xiaohong, Wu, Xiaoqing, Wu, Yao-Wen, Wu, Yihua, Xavier, Ramnik, Xia, Hongguang, Xia, Lixin, Xia, Zhengyuan, Xiang, Ge, Xiang, Jin, Xiang, Mingliang, Xiang, Wei, Xiao, Bin, Xiao, Guozhi, Xiao, Hengyi, Xiao, Hong-tao, Xiao, Jian, Xiao, Lan, Xiao, Shi, Xiao, Yin, Xie, Baoming, Xie, Chuan-Ming, Xie, Min, Xie, Yuxiang, Xie, Zhiping, Xie, Zhonglin, Xilouri, Maria, Xu, Congfeng, Xu, En, Xu, Haoxing, Xu, Jing, Xu, Jinrong, Xu, Liang, Xu, Wen Wen, Xu, Xiulong, Xue, Yu, Yakhine-Diop, Sokhna, Yamaguchi, Masamitsu, Yamaguchi, Osamu, Yamamoto, Ai, Yamashina, Shunhei, Yan, Shengmin, Yan, Shian-Jang, Yan, Zhen, Yanagi, Yasuo, Yang, Chuanbin, Yang, Dun-Sheng, Yang, Huan, Yang, Huang-Tian, Yang, Hui, Yang, Jin-Ming, Yang, Jing, Yang, Jingyu, Yang, Ling, Yang, Liu, Yang, Ming, Yang, Pei-Ming, Yang, Qian, Yang, Seungwon, Yang, Shu, Yang, Shun-Fa, Yang, Wannian, Yang, Wei Yuan, Yang, Xiaoyong, Yang, Xuesong, Yang, Yi, Yang, Ying, Yao, Honghong, Yao, Shenggen, Yao, Xiaoqiang, Yao, Yong-Gang, Yao, Yong-Ming, Yasui, Takahiro, Yazdankhah, Meysam, Yen, Paul, Yi, Cong, Yin, Xiao-Ming, Yin, Yanhai, Yin, Zhangyuan, Yin, Ziyi, Ying, Meidan, Ying, Zheng, Yip, Calvin, Yiu, Stephanie Pei Tung, Yoo, Young, Yoshida, Kiyotsugu, Yoshii, Saori, Yoshimori, Tamotsu, Yousefi, Bahman, Yu, Boxuan, Yu, Haiyang, Yu, Jun, Yu, Li, Yu, Ming-Lung, Yu, Seong-Woon, Yu, Victor, Yu, W Haung, Yu, Zhengping, Yu, Zhou, Yuan, Junying, Yuan, Ling-Qing, Yuan, Shilin, Yuan, Shyng-Shiou, Yuan, Yanggang, Yuan, Zengqiang, Yue, Jianbo, Yue, Zhenyu, Yun, Jeanho, Yung, Raymond, Zacks, David, Zaffagnini, Gabriele, Zambelli, Vanessa, Zanella, Isabella, Zang, Qun, Zanivan, Sara, Zappavigna, Silvia, Zaragoza, Pilar, Zarbalis, Konstantinos, Zarebkohan, Amir, Zarrouk, Amira, Zeitlin, Scott, Zeng, Jialiu, Zeng, Ju-deng, Žerovnik, Eva, Zhan, Lixuan, Zhang, Bin, Zhang, Donna, Zhang, Hanlin, Zhang, Hong, Zhang, Honghe, Zhang, Huafeng, Zhang, Huaye, Zhang, Hui, Zhang, Hui-Ling, Zhang, Jianbin, Zhang, Jianhua, Zhang, Jing-Pu, Zhang, Kalin, Zhang, Leshuai, Zhang, Lin, Zhang, Lisheng, Zhang, Lu, Zhang, Luoying, Zhang, Menghuan, Zhang, Peng, Zhang, Sheng, Zhang, Wei, Zhang, Xiangnan, Zhang, Xiao-Wei, Zhang, Xiaolei, Zhang, Xiaoyan, Zhang, Xin, Zhang, Xinxin, Zhang, Xu Dong, Zhang, Yang, Zhang, Yanjin, Zhang, Yi, Zhang, Ying-Dong, Zhang, Yingmei, Zhang, Yuan-Yuan, Zhang, Yuchen, Zhang, Zhe, Zhang, Zhengguang, Zhang, Zhibing, Zhang, Zhihai, Zhang, Zhiyong, Zhang, Zili, Zhao, Haobin, Zhao, Lei, Zhao, Shuang, Zhao, Tongbiao, Zhao, Xiao-Fan, Zhao, Ying, Zhao, Yongchao, Zhao, Yongliang, Zhao, Yuting, Zheng, Guoping, Zheng, Kai, Zheng, Ling, Zheng, Shizhong, Zheng, Xi-Long, Zheng, Yi, Zheng, Zu-Guo, Zhivotovsky, Boris, Zhong, Qing, Zhou, Ao, Zhou, Ben, Zhou, Cefan, ZHOU, Gang, Zhou, Hao, Zhou, Hong, Zhou, Hongbo, Zhou, Jie, Zhou, Jing, Zhou, Jiyong, Zhou, Kailiang, Zhou, Rongjia, Zhou, Xu-jie, Zhou, Yanshuang, Zhou, Yinghong, Zhou, Yubin, Zhou, Zheng-Yu, Zhou, Zhou, Zhu, Binglin, Zhu, Changlian, Zhu, Guo-Qing, Zhu, Haining, Zhu, Hongxin, Zhu, Hua, Zhu, Wei-Guo, Zhu, Yanping, Zhu, Yushan, Zhuang, Haixia, Zhuang, Xiaohong, Zientara-Rytter, Katarzyna, Zimmermann, Christine, Ziviani, Elena, Zoladek, Teresa, Zong, Wei-Xing, Zorov, Dmitry, Zorzano, Antonio, Zou, Weiping, Zou, Zhen, Zou, Zhengzhi, Zuryn, Steven, Zwerschke, Werner, Brand-Saberi, Beate, Dong, X Charlie, Kenchappa, Chandra Shekar, Li, Zuguo, Lin, Yong, Oshima, Shigeru, Rong, Yueguang, Sluimer, Judith, Stallings, Christina, Tong, Chun-Kit, Ahmad, S. Tariq, Alim Al-Bari, M. Abdul, Bechara, Luiz R.G., Behrens, Georg M.N., Bhuiyan, Md. Shenuarin, Broaddus, V. Courtney, Buchan, J. Ross, Burón, M. Isabel, Carter, A. Brent, Chan, Matthew T.V., Choi, Augustine M.K., D’Adamo, Stefania, D’Amelio, Marcello, D’Arcangelo, Daniela, D’Lugos, Andrew, D’Orazi, Gabriella, De Meyer, Guido R.Y., Delpino, M. Victoria, Distler, Jörg H.W., Dixon, Ian M.C., Dobson, Renwick C.J., 2nd Dorn, Gerald, Eissa, N. Tony, Engelsen, Agnete S.T., Fairlie, W. Douglas, Ferreira, Julio C.B., H.B., Ranjitha, Hanson, Phyllis I., Hejtmancik, J. Fielding, Ho, Idy H.T., Hobbs, G. Aaron, Hoet, Peter H.M., Huang, Michael L.H., Iyer, Anand Krishnan V., Johnson, Gail V.W., Joosten, Leo A.B., Karim, Md. Razaul, Kaufmann, Stefan H.E., Ko, Ben C.B., Leck, Lionel Y.W., Lima, Thania R.R., Livingston, J. Andrew, Martin, Alexandre P.J., Montes, L. Ruth, Murphy, J. Patrick, Ng, Charlene C.W., Nicolao, M. Celeste, O’Donovan, Tracey, O’Leary, Seónadh, O’Rourke, Eyleen, O’Sullivan, Mary, O’Sullivan, Timothy, Omary, M. Bishr, Pereira, Gustavo J.S., Ratnayaka, J. Arjuna, Riazuddin, S. Amer, Rouschop, Kasper M.A., Sanderson, J. Thomas, Scaglione, K. Matthew, Schapira, Anthony H.V., Scovassi, A. Ivana, St. Clair, Daret, Sunahara, Karen K.S., Symons, J. David, Triola, Gemma, van Wijk, Sjoerd J.L., Vanrell, M. Cristina, Vasconcelos, M. Helena, Whitton, J. Lindsay, Williams, Robin S.B., Wong, W. Wei-Lynn, Wu, William K.K., Yakhine-Diop, Sokhna M.S., Yu, W. Haung, Zhang, Kalin Y.B., Dong, X. Charlie, Ain Shams University [ASU], Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University [JGU], Medical University Graz, Centre de Recherche des Cordeliers [CRC (UMR_S_1138 / U1138)], Institut Pasteur d'Iran, Leibniz Institute of Plant Biochemistry [IPB], The University of Texas M.D. Anderson Cancer Center [Houston], Institut de pharmacologie moléculaire et cellulaire [IPMC], Lipides - Nutrition - Cancer [Dijon - U1231] [LNC], Centre méditerranéen de médecine moléculaire [C3M], Institut de Biologie Valrose [IBV], Petites Molécules de neuroprotection, neurorégénération et remyélinisation, Signalisation Hormonale, Physiopathologie Endocrinienne et Métabolique, Institut Cochin [IC UM3 (UMR 8104 / U1016)], Institut NeuroMyoGène [INMG], Paris-Centre de Recherche Cardiovasculaire [PARCC (UMR_S 970/ U970)], Marqueurs cardiovasculaires en situation de stress [MASCOT (UMR_S_942 / U942)], Institut de Recherche sur le Cancer et le Vieillissement [IRCAN], Centre de Recherche en Cancérologie de Marseille [CRCM], Centre for Integrative Biology - CBI [Inserm U964 - CNRS UMR7104 - IGBMC], Oncogenesis, Stress, Signaling [OSS], Institut Necker Enfants-Malades [INEM - UM 111 (UMR 8253 / U1151)], Institut de Biologie Intégrative de la Cellule [I2BC], Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte [M2iSH], Centre de Recherches en Cancérologie de Toulouse [CRCT], Physiopathologie et traitement des maladies du foie, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 [CIIL], Institut de Génétique et de Biologie Moléculaire et Cellulaire [IGBMC], Laboratoire Bio-PeroxIL. Biochimie du peroxysome, inflammation et métabolisme lipidique [Dijon] [BIO-PEROXIL], Centre de recherche sur l'Inflammation [CRI (UMR_S_1149 / ERL_8252 / U1149)], Unité de génétique et biologie des cancers [U830], Laboratoire d'Optique et Biosciences [LOB], Institut des Maladies Métaboliques et Casdiovasculaires [UPS/Inserm U1297 - I2MC], Différenciation et communication neuronale et neuroendocrine [DC2N], Institut de Recherche en Cancérologie de Montpellier [IRCM - U1194 Inserm - UM], Centre d'Immunologie de Marseille - Luminy [CIML], Physiopathologie et imagerie des troubles neurologiques [PhIND], Laboratory of Fundamental and Applied Bioenergetics = Laboratoire de bioénergétique fondamentale et appliquée [LBFA], Imagine - Institut des maladies génétiques (IHU) [Imagine - U1163], Institut Mondor de Recherche Biomédicale [IMRB], Franco-czech Laboratory for clinical research on obesity, University of Michigan [Ann Arbor], University of Michigan System, Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Université Côte d'Azur (UCA), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Centre méditerranéen de médecine moléculaire (C3M), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), Institut de Biologie Valrose (IBV), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Sud - Paris 11 (UP11), Centre de Recherche des Cordeliers (CRC (UMR_S_1138 / U1138)), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université de Paris (UP), Université Paris-Sud - Paris 11 (UP11)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Nutrition, Métabolisme, Aquaculture (NuMéA), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Institut NeuroMyoGène (INMG), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Paris-Centre de Recherche Cardiovasculaire (PARCC - UMR-S U970), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre de Recherche en Cancérologie de Marseille (CRCM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Aix Marseille Université (AMU), Centre for Integrative Biology - CBI (Inserm U964 - CNRS UMR7104 - IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institute of genetics and molecular and cellular biology-Centre National de la Recherche Scientifique (CNRS), Chemistry, Oncogenesis, Stress and Signaling (COSS), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-CRLCC Eugène Marquis (CRLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Unité de Nutrition Humaine (UNH), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Institut des Maladies Neurodégénératives [Bordeaux] (IMN), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), 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), Centre de Recherches en Cancérologie de Toulouse (CRCT), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Laboratoire Bio-PeroxIL. Biochimie du peroxysome, inflammation et métabolisme lipidique [Dijon] (BIO-PEROXIL), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre de recherche sur l'Inflammation (CRI (UMR_S_1149 / ERL_8252 / U1149)), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de génétique et biologie des cancers (U830), Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Différenciation et communication neuronale et neuroendocrine (DC2N), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche en Cancérologie de Montpellier (IRCM - U1194 Inserm - UM), CRLCC Val d'Aurelle - Paul Lamarque-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Centre d'Immunologie de Marseille - Luminy (CIML), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Physiopathologie et imagerie des troubles neurologiques (PhIND), Université de Caen Normandie (UNICAEN), Laboratory of Fundamental and Applied Bioenergetics = Laboratoire de bioénergétique fondamentale et appliquée (LBFA), Université Grenoble Alpes (UGA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Epithelial biology and disease - Liliane Bettencourt Chair of Developmental Biology (Equipe Inserm U1163), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Biomécanique cellulaire et respiratoire (BCR), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Charles University [Prague]-Institut National de la Santé et de la Recherche Médicale (INSERM), This work was supported by the National Institute of General Medical Sciences [GM131919]., Université Paris-Sud - Paris 11 (UP11)-Institut National de la Santé et de la Recherche Médicale (INSERM), Marqueurs cardiovasculaires en situation de stress (MASCOT (UMR_S_942 / U942)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Université Sorbonne Paris Nord, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Physiopathologie des Adaptations Nutritionnelles (PhAN), Université de Nantes (UN)-Institut National de la Recherche Agronomique (INRA), Département Plateforme (PF I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut Gustave Roussy (IGR), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Chinese Academy of Medical Sciences [Suzhou, Chine] (CAMS), Karolinska Institutet [Stockholm], Karolinska University Hospital [Stockholm], Department of Women's and Children's Health [Stockholm, Sweden], Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Université de Strasbourg (UNISTRA)-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 National de la Santé et de la Recherche Médicale (INSERM)-École polytechnique (X), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, FHU OncoAge - Pathologies liées à l’âge [CHU Nice] (OncoAge), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Institut de Pharmacologie Moléculaire et Cellulaire [UNIV Côte d'Azur] (UPMC), Institut Universitaire du Cancer de Toulouse - Oncopole (IUCT Oncopole - UMR 1037), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM), Life Sciences Institute [Ann Arbor, MI, USA], University of Michigan System-University of Michigan System, European Institute of Oncology IRCCS [Milan, Italy] (EIO), Ain Shams University (ASU), Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris Cité (UPCité), Réseau International des Instituts Pasteur (RIIP), Leibniz Institute of Plant Biochemistry (IPB), Hebrew University of Jerusalem, Université Nice Sophia Antipolis (1965 - 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 Côte d'Azur (UCA), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Paris-Centre de Recherche Cardiovasculaire (PARCC (UMR_S 970/ U970)), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Oncogenesis, Stress, Signaling (OSS), Institut des Maladies Métaboliques et Casdiovasculaires (UPS/Inserm U1297 - I2MC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Charles University [Prague] (CU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Klionsky, D. J., Abdel-Aziz, A. K., Abdelfatah, S., Abdellatif, M., Abdoli, A., Abel, S., Abeliovich, H., Abildgaard, M. H., Abudu, Y. P., Acevedo-Arozena, A., Adamopoulos, I. E., Adeli, K., Adolph, T. E., Adornetto, A., Aflaki, E., Agam, G., Agarwal, A., Aggarwal, B. B., Agnello, M., Agostinis, P., Agrewala, J. N., Agrotis, A., Aguilar, P. V., Ahmad, S. T., Ahmed, Z. M., Ahumada-Castro, U., Aits, S., Aizawa, S., Akkoc, Y., Akoumianaki, T., Akpinar, H. A., Al-Abd, A. M., Al-Akra, L., Al-Gharaibeh, A., Alaoui-Jamali, M. A., Alberti, S., Alcocer-Gomez, E., Alessandri, C., Ali, M., Alim Al-Bari, M. A., Aliwaini, S., Alizadeh, J., Almacellas, E., Almasan, A., Alonso, A., Alonso, G. D., Altan-Bonnet, N., Altieri, D. C., Alvarez, E. M. C., Alves, S., Alves da Costa, C., Alzaharna, M. M., Amadio, M., Amantini, C., Amaral, C., Ambrosio, S., Amer, A. O., Ammanathan, V., An, Z., Andersen, S. U., Andrabi, S. A., Andrade-Silva, M., Andres, A. M., Angelini, S., Ann, D., Anozie, U. C., Ansari, M. 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T., Balduini, W., Ballabio, A., Ballester, M., Balazadeh, S., Balzan, R., Bandopadhyay, R., Banerjee, S., Banreti, A., Bao, Y., Baptista, M. S., Baracca, A., Barbati, C., Bargiela, A., Barila, D., Barlow, P. G., Barmada, S. J., Barreiro, E., Barreto, G. E., Bartek, J., Bartel, B., Bartolome, A., Barve, G. R., Basagoudanavar, S. H., Bassham, D. C., Bast, R. C., Basu, A., Batoko, H., Batten, I., Baulieu, E. E., Baumgarner, B. L., Bayry, J., Beale, R., Beau, I., Beaumatin, F., Bechara, L. R. G., Beck, G. R., Beers, M. F., Begun, J., Behrends, C., Behrens, G. M. N., Bei, R., Bejarano, E., Bel, S., Behl, C., Belaid, A., Belgareh-Touze, N., Bellarosa, C., Belleudi, F., Bello Perez, M., Bello-Morales, R., Beltran, J. S. D. O., Beltran, S., Benbrook, D. M., Bendorius, M., Benitez, B. A., Benito-Cuesta, I., Bensalem, J., Berchtold, M. W., Berezowska, S., Bergamaschi, D., Bergami, M., Bergmann, A., Berliocchi, L., Berlioz-Torrent, C., Bernard, A., Berthoux, L., Besirli, C. G., Besteiro, S., Betin, V. M., Beyaert, R., Bezbradica, J. S., Bhaskar, K., Bhatia-Kissova, I., Bhattacharya, R., Bhattacharya, S., Bhattacharyya, S., Bhuiyan, M. S., Bhutia, S. K., Bi, L., Bi, X., Biden, T. J., Bijian, K., Billes, V. A., Binart, N., Bincoletto, C., Birgisdottir, A. B., Bjorkoy, G., Blanco, G., Blas-Garcia, A., Blasiak, J., Blomgran, R., Blomgren, K., Blum, J. S., Boada-Romero, E., Boban, M., Boesze-Battaglia, K., Boeuf, P., Boland, B., Bomont, P., Bonaldo, P., Bonam, S. R., Bonfili, L., Bonifacino, J. S., Boone, B. A., Bootman, M. D., Bordi, M., Borner, C., Bornhauser, B. C., Borthakur, G., Bosch, J., Bose, S., Botana, L. M., Botas, J., Boulanger, C. M., Boulton, M. E., Bourdenx, M., Bourgeois, B., Bourke, N. M., Bousquet, G., Boya, P., Bozhkov, P. V., Bozi, L. H. M., Bozkurt, T. O., Brackney, D. E., Brandts, C. H., Braun, R. J., Braus, G. H., Bravo-Sagua, R., Bravo-San Pedro, J. M., Brest, P., Bringer, M. -A., Briones-Herrera, A., Broaddus, V. C., Brodersen, P., Brodsky, J. L., Brody, S. L., Bronson, P. G., Bronstein, J. M., Brown, C. N., Brown, R. E., Brum, P. C., Brumell, J. H., Brunetti-Pierri, N., Bruno, D., Bryson-Richardson, R. J., Bucci, C., Buchrieser, C., Bueno, M., Buitrago-Molina, L. E., Buraschi, S., Buch, S., Buchan, J. R., Buckingham, E. M., Budak, H., Budini, M., Bultynck, G., Burada, F., Burgoyne, J. R., Buron, M. I., Bustos, V., Buttner, S., Butturini, E., Byrd, A., Cabas, I., Cabrera-Benitez, S., Cadwell, K., Cai, J., Cai, L., Cai, Q., Cairo, M., Calbet, J. A., Caldwell, G. A., Caldwell, K. A., Call, J. A., Calvani, R., Calvo, A. C., Calvo-Rubio Barrera, M., Camara, N. O. S., Camonis, J. H., Camougrand, N., Campanella, M., Campbell, E. M., Campbell-Valois, F. -X., Campello, S., Campesi, I., Campos, J. C., Camuzard, O., Cancino, J., Candido de Almeida, D., Canesi, L., Caniggia, I., Canonico, B., Canti, C., Cao, B., Caraglia, M., Carames, B., Carchman, E. H., Cardenal-Munoz, E., Cardenas, C., Cardenas, L., Cardoso, S. M., Carew, J. S., Carle, G. F., Carleton, G., Carloni, S., Carmona-Gutierrez, D., Carneiro, L. A., Carnevali, O., Carosi, J. M., Carra, S., Carrier, A., Carrier, L., Carroll, B., Carter, A. B., Carvalho, A. N., Casanova, M., Casas, C., Casas, J., Cassioli, C., Castillo, E. F., Castillo, K., Castillo-Lluva, S., Castoldi, F., Castori, M., Castro, A. F., Castro-Caldas, M., Castro-Hernandez, J., Castro-Obregon, S., Catz, S. D., Cavadas, C., Cavaliere, F., Cavallini, G., Cavinato, M., Cayuela, M. L., Cebollada Rica, P., Cecarini, V., Cecconi, F., Cechowska-Pasko, M., Cenci, S., Ceperuelo-Mallafre, V., Cerqueira, J. J., Cerutti, J. M., Cervia, D., Cetintas, V. B., Cetrullo, S., Chae, H. -J., Chagin, A. S., Chai, C. -Y., Chakrabarti, G., Chakrabarti, O., Chakraborty, T., Chami, M., Chamilos, G., Chan, D. W., Chan, E. Y. W., Chan, E. D., Chan, H. Y. E., Chan, H. H., Chan, H., Chan, M. T. V., Chan, Y. S., Chandra, P. K., Chang, C. -P., Chang, C., Chang, H. -C., Chang, K., Chao, J., Chapman, T., Charlet-Berguerand, N., Chatterjee, S., Chaube, S. K., Chaudhary, A., Chauhan, S., Chaum, E., Checler, F., Cheetham, M. E., Chen, C. -S., Chen, G. -C., Chen, J. -F., Chen, L. L., Chen, L., Chen, M., Chen, M. -K., Chen, N., Chen, Q., Chen, R. -H., Chen, S., Chen, W., Chen, X. -M., Chen, X. -W., Chen, X., Chen, Y., Chen, Y. -G., Chen, Y. -J., Chen, Y. -Q., Chen, Z. S., Chen, Z., Chen, Z. -H., Chen, Z. J., Cheng, H., Cheng, J., Cheng, S. -Y., Cheng, W., Cheng, X., Cheng, X. -T., Cheng, Y., Cheng, Z., Cheong, H., Cheong, J. K., Chernyak, B. V., Cherry, S., Cheung, C. F. R., Cheung, C. H. A., Cheung, K. -H., Chevet, E., Chi, R. J., Chiang, A. K. S., Chiaradonna, F., Chiarelli, R., Chiariello, M., Chica, N., Chiocca, S., Chiong, M., Chiou, S. -H., Chiramel, A. I., Chiurchiu, V., Cho, D. -H., Choe, S. -K., Choi, A. M. K., Choi, M. E., Choudhury, K. R., Chow, N. S., Chu, C. T., Chua, J. P., Chua, J. J. E., Chung, H., Chung, K. P., Chung, S., Chung, S. -H., Chung, Y. -L., Cianfanelli, V., Ciechomska, I. A., Cifuentes, M., Cinque, L., Cirak, S., Cirone, M., Clague, M. J., Clarke, R., Clementi, E., Coccia, E. M., Codogno, P., Cohen, E., Cohen, M. M., Colasanti, T., Colasuonno, F., Colbert, R. A., Colell, A., Colic, M., Coll, N. S., Collins, M. O., Colombo, M. I., Colon-Ramos, D. A., Combaret, L., Comincini, S., Cominetti, M. R., Consiglio, A., Conte, A., Conti, F., Contu, V. R., Cookson, M. R., Coombs, K. M., Coppens, I., Corasaniti, M. T., Corkery, D. P., Cordes, N., Cortese, K., Costa, M. D. C., Costantino, S., Costelli, P., Coto-Montes, A., Crack, P. J., Crespo, J. L., Criollo, A., Crippa, V., Cristofani, R., Csizmadia, T., Cuadrado, A., Cui, B., Cui, J., Cui, Y., Culetto, E., Cumino, A. C., Cybulsky, A. V., Czaja, M. J., Czuczwar, S. J., D'Adamo, S., D'Amelio, M., D'Arcangelo, D., D'Lugos, A. C., D'Orazi, G., da Silva, J. A., Dafsari, H. S., Dagda, R. K., Dagdas, Y., Daglia, M., Dai, X., Dai, Y., Dal Col, J., Dalhaimer, P., Dalla Valle, L., Dallenga, T., Dalmasso, G., Damme, M., Dando, I., Dantuma, N. P., Darling, A. L., Das, H., Dasarathy, S., Dasari, S. K., Dash, S., Daumke, O., Dauphinee, A. N., Davies, J. S., Davila, V. A., Davis, R. J., Davis, T., Dayalan Naidu, S., De Amicis, F., De Bosscher, K., De Felice, F., De Franceschi, L., De Leonibus, C., de Mattos Barbosa, M. G., De Meyer, G. R. Y., De Milito, A., De Nunzio, C., De Palma, C., De Santi, M., De Virgilio, C., De Zio, D., Debnath, J., Debosch, B. J., Decuypere, J. -P., Deehan, M. A., Deflorian, G., Degregori, J., Dehay, B., Del Rio, G., Delaney, J. R., Delbridge, L. M. D., Delorme-Axford, E., Delpino, M. V., Demarchi, F., Dembitz, V., Demers, N. D., Deng, H., Deng, Z., Dengjel, J., Dent, P., Denton, D., Depamphilis, M. L., Der, C. 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A., Ebrahimi-Fakhari, D., Eckhart, L., Edelstein, C. L., Efferth, T., Eftekharpour, E., Eichinger, L., Eid, N., Eisenberg, T., Eissa, N. T., Eissa, S., Ejarque, M., El Andaloussi, A., El-Hage, N., El-Naggar, S., Eleuteri, A. M., El-Shafey, E. S., Elgendy, M., Eliopoulos, A. G., Elizalde, M. M., Elks, P. M., Elsasser, H. -P., Elsherbiny, E. S., Emerling, B. M., Emre, N. C. T., Eng, C. H., Engedal, N., Engelbrecht, A. -M., Engelsen, A. S. T., Enserink, J. M., Escalante, R., Esclatine, A., Escobar-Henriques, M., Eskelinen, E. -L., Espert, L., Eusebio, M. -O., Fabrias, G., Fabrizi, C., Facchiano, A., Facchiano, F., Fadeel, B., Fader, C., Faesen, A. C., Fairlie, W. D., Falco, A., Falkenburger, B. H., Fan, D., Fan, J., Fan, Y., Fang, E. F., Fang, Y., Fanto, M., Farfel-Becker, T., Faure, M., Fazeli, G., Fedele, A. O., Feldman, A. M., Feng, D., Feng, J., Feng, L., Feng, Y., Feng, W., Fenz Araujo, T., Ferguson, T. A., Fernandez, A. F., Fernandez-Checa, J. C., Fernandez-Veledo, S., Fernie, A. 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D., Zhang, H., Zhang, H. -L., Zhang, J., Zhang, J. -P., Zhang, K. Y. B., Zhang, L. W., Zhang, L., Zhang, M., Zhang, P., Zhang, S., Zhang, W., Zhang, X., Zhang, X. -W., Zhang, X. D., Zhang, Y., Zhang, Y. -D., Zhang, Y. -Y., Zhang, Z., Zhao, H., Zhao, L., Zhao, S., Zhao, T., Zhao, X. -F., Zhao, Y., Zheng, G., Zheng, K., Zheng, L., Zheng, S., Zheng, X. -L., Zheng, Y., Zheng, Z. -G., Zhivotovsky, B., Zhong, Q., Zhou, A., Zhou, B., Zhou, C., Zhou, G., Zhou, H., Zhou, J., Zhou, K., Zhou, R., Zhou, X. -J., Zhou, Y., Zhou, Z. -Y., Zhou, Z., Zhu, B., Zhu, C., Zhu, G. -Q., Zhu, H., Zhu, W. -G., Zhu, Y., Zhuang, H., Zhuang, X., Zientara-Rytter, K., Zimmermann, C. M., Ziviani, E., Zoladek, T., Zong, W. -X., Zorov, D. B., Zorzano, A., Zou, W., Zou, Z., Zuryn, S., Zwerschke, W., Brand-Saberi, B., Dong, X. C., Kenchappa, C. S., Lin, Y., Oshima, S., Rong, Y., Sluimer, J. C., Stallings, C. L., Tong, C. -K., and Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Programmed cell death, Settore BIO/06, Autophagosome, Autolysosome, [SDV]Life Sciences [q-bio], lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Autophagy-Related Proteins, Review, Computational biology, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Settore MED/04, 03 medical and health sciences, stress, Chaperone-mediated autophagy, ddc:570, Autophagy, LC3, Animals, Humans, cancer, Settore BIO/10, flux, lysosome, macroautophagy, neurodegeneration, phagophore, vacuole, Set (psychology), Molecular Biology, 030102 biochemistry & molecular biology, business.industry, Interpretation (philosophy), Autophagosomes, Cell Biology, Multicellular organism, 030104 developmental biology, Knowledge base, Biological Assay, Lysosomes, business, Biomarkers, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: Contains fulltext : 232759.pdf (Publisher’s version ) (Closed access) In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.
Published: 2021

8. Genetic control of rhizosheath formation in pearl millet

Author: Ndour Pms, Barrachina C, Wafa Achouak, Assigbetse K, Sixtine Passot, Pascal Gantet, Debieu M, Ndjido Ardo Kane, Thierry Heulin, de la Fuente Canto C, Laurent Laplaze, Pratlong M, Abadala Gamby Diédhiou, Alexandre Grondin, Laurent Cournac, Antony Champion, Philippe Cubry, Diouf Mn, and Yves Vigouroux
Subjects: Crop, Rhizosphere, Candidate gene, education.field_of_study, Nutrient, Symbiosis, Agronomy, Inbred strain, Population, food and beverages, Root hair, Biology, education
Abstract: The rhizosheath, the layer of soil that adheres strongly to roots, influences water and nutrients acquisition. Pearl millet is a cereal crop that plays a major role for food security in arid regions of sub Saharan Africa and India. We previously showed that root-adhering soil mass is a heritable trait in pearl millet and that it correlates with changes in rhizosphere microbiota structure and functions. Here, we studied the correlation between root-adhering soil mass and root hair development, root architecture, and symbiosis with arbuscular mycorrhizal fungi and we analysed the genetic control of this trait using genome wide association (GWAS) combined with bulk segregant analysis and gene expression studies. Root-adhering soil mass was weakly correlated only to root hairs traits in pearl millet. Twelve QTLs for rhizosheath formation were identified by GWAS. Bulk segregant analysis on a biparental population validated five of these QTLs. Combining genetics with a comparison of global gene expression in the root tip of contrasted inbred lines revealed candidate genes that might control rhizosheath formation in pearl millet. Our study indicates that rhizosheath formation is under complex genetic control in pearl millet and suggests that it is mainly regulated by root exudation.HighlightFormation of the rhizosheath, a layer of soil adhering to the root, is under complex genetic control in pearl millet and is mainly regulated by root exudation.
Published: 2021

9. MYC dosage compensation is mediated by miRNA-transcription factor interactions in aneuploid cancer

Author: Yendry Oses-Vargas, Francisco Siles-Canales, Jorge L. Arias-Arias, Guillermo Oviedo, Rodrigo Mora-Rodriguez, Andrés Segura-Castillo, Diana Bravo-Estupiñan, Gloriana Vásquez-Vargas, Jorge Torres-Calvo, ManSai Acón, Pedro Mendes, Baez Edwin, Luis A. Rojas-Matey, Jose Guevara-Coto, Carsten Geiß, Anne Régnier-Vigouroux, and Steve Quirós-Barrantes
Subjects: Candidate gene, Multidisciplinary, Dosage compensation, Colorectal cancer, Bioinformatics, Science, Cancer, Myc, Biology, medicine.disease, Article, Downregulation and upregulation, Cancer cell, microRNA, Transcription factors, medicine, Cancer research, cancer, aneuploidy, Mathematical biosciences, Systems biology, Transcription factor, miRNA
Abstract: Summary We hypothesize that dosage compensation of critical genes arises from systems-level properties for cancer cells to withstand the negative effects of aneuploidy. We identified several candidate genes in cancer multiomics data and developed a biocomputational platform to construct a mathematical model of their interaction network with micro-RNAs and transcription factors, where the property of dosage compensation emerged for MYC and was dependent on the kinetic parameters of its feedback interactions with three micro-RNAs. These circuits were experimentally validated using a genetic tug-of-war technique to overexpress an exogenous MYC, leading to overexpression of the three microRNAs involved and downregulation of endogenous MYC. In addition, MYC overexpression or inhibition of its compensating miRNAs led to dosage-dependent cytotoxicity in MYC-amplified colon cancer cells. Finally, we identified negative correlation of MYC dosage compensation with patient survival in TCGA breast cancer patients, highlighting the potential of this mechanism to prevent aneuploid cancer progression., Graphical abstract, Highlights • BioNetUCR is a platform to model large miRNA-transcription factor networks • Compensated genes have low variation in expression despite high copy number variation • Gene dosage compensation depends on circuit kinetic parameters to emerge in silico • A genetic tug-of-war technique validates transcriptional gene dosage compensation, Bioinformatics; Mathematical biosciences; Systems biology
Published: 2021

10. Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach

Author: Tony Dejean, Jean-Baptiste Decotte, Régis Vigouroux, Jérôme Murienne, Isabel Cantera, Sébastien Brosse, and Alice Valentini
Subjects: Distance decay, geography.geographical_feature_category, Community, Ecology, Range (biology), Fauna, Species distribution, Drainage basin, Biodiversity, Fishes, Biology, DNA, Environmental, Geography, Rivers, Genetics, Spatial ecology, Animals, DNA Barcoding, Taxonomic, Environmental DNA, Ecology, Evolution, Behavior and Systematics, Ecosystem, Biotechnology, Environmental Monitoring
Abstract: Environmental DNA (eDNA) is gaining a growing popularity among scientists but its applicability to biodiversity research and management remains limited in river systems by the lack of knowledge about the spatial extent of the downstream transport of eDNA.Here, we assessed the ability of eDNA inventories to retrieve spatial patterns of fish assemblages along two large and species rich Neotropical rivers. We first examined overall community variation with distance through the distance decay of similarity and compared this pattern to capture-based samples. We then considered previous knowledge on individual species distributions, and compared it to the eDNA inventories for a set of 53 species.eDNA collected from 28 sites in the Maroni and 25 sites in the Oyapock rivers permitted to retrieve a decline of species similarity with distance between sites. The distance decay of similarity derived from eDNA was similar, and even more pronounced, than that obtained with capture-based methods (gil-nets). In addition, the species upstream-downstream distribution range derived from eDNA matched to the known distribution of most species.Our results demonstrate that environmental DNA does not represent an integrative measure of biodiversity across the whole upstream river basin but provide a relevant picture of local fish assemblages. Importantly, the spatial signal gathered from eDNA was therefore comparable to that gathered with local capture based methods, which describes fish fauna over a few hundred metres.
Published: 2021

11. Lipodystrophic syndromes due toLMNAmutations: recent developments on biomolecular aspects, pathophysiological hypotheses and therapeutic perspectives

Author: Caroline Le Dour, Corinne Vigouroux, Pauline Afonso, Véronique Béréziat, Guillaume Bidault, Olivier Lascols, Anne-Claire Guenantin, Camille Vatier, Jacqueline Capeau, Isabelle Jéru, Emilie Capel, Nolwenn Briand, Centre de Recherche Saint-Antoine (UMRS893), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Laboratoire commun de biologie et génétique moléculaires [CHU Saint-Antoine], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), The Wellcome Trust Sanger Institute [Cambridge], Metabolic Research Laboratories [Cambridge, UK] (University of Cambridge), Wellcome Trust - MRC Cambridge-Addenbrooke’s Hospital [Cambridge, UK], Department of Molecular Medicine [Oslo], Institute of Basic Medical Sciences [Oslo], Faculty of Medicine [Oslo], University of Oslo (UiO)-University of Oslo (UiO)-Faculty of Medicine [Oslo], University of Oslo (UiO)-University of Oslo (UiO), The authors thank Sorbonne Université, former Université Pierre and Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM), Institute of Cardio Metabolism (ICAN), ANRS (France REcherche Nord&Sud Sidahiv Hépatites), Région Ile-de-France STEM-Pole, Association Française d’Etude et de Recherche sur l’Obésité (AFERO), Fondation de France, Fondation pour la Recherche Médicale, Société Francophone du Diabète (SFD), for the financial support to our research team at Saint Antoine Research Centre, Paris, France., and Vigouroux, Corinne
Subjects: 0301 basic medicine, Senescence, lipodystrophy, senescence, induced pluripotent stem cells, extracellular matrix, Adipose tissue, Biology, Bioinformatics, LMNA, 03 medical and health sciences, Metreleptin, chemistry.chemical_compound, 0302 clinical medicine, medicine, Humans, Epigenetics, [SDV.MHEP.EM] Life Sciences [q-bio]/Human health and pathology/Endocrinology and metabolism, Lamin A/C, epigenetics, integumentary system, Laminopathies, differentiation, Cell Biology, [SDV.MHEP.EM]Life Sciences [q-bio]/Human health and pathology/Endocrinology and metabolism, Lamin Type A, medicine.disease, adipose tissue, 3. Good health, 030104 developmental biology, chemistry, metreleptin, 030220 oncology & carcinogenesis, Mutation, Anticipation (genetics), anticipation, Lipodystrophy, Lamin
Abstract: International audience; Mutations in LMNA, encoding A-type lamins, are responsible for laminopathies including musculardystrophies, lipodystrophies, and premature ageing syndromes. LMNA mutations have been shownto alter nuclear structure and stiffness, binding to partners at the nuclear envelope or within thenucleoplasm, gene expression and/or prelamin A maturation. LMNA-associated lipodystrophicfeatures, combining generalized or partial fat atrophy and metabolic alterations associated withinsulin resistance, could result from altered adipocyte differentiation or from altered fat structure.Recent studies shed some light on how pathogenic A-type lamin variants could triggerlipodystrophy, metabolic complications, and precocious cardiovascular events. Alterations inadipose tissue extracellular matrix and TGF-beta signaling could initiate metabolic inflexibility.Premature senescence of vascular cells could contribute to cardiovascular complications. Inaffected families, metabolic alterations occur at an earlier age across generations, which couldresult from epigenetic deregulation induced by LMNA mutations. Novel cellular modelsrecapitulating adipogenic developmental pathways provide scalable tools for disease modelingand therapeutic screening.
Published: 2018

12. Direct measurement of near‐nano‐Newton forces developed by self‐organizing actomyosin fibers bound α‐catenin

Author: Guillaume Romet-Lemonne, René-Marc Mège, Surabhi Sonam, Clémence Vigouroux, Benoit Ladoux, Antoine Jégou, Christophe Le Clainche, Institut Jacques Monod (IJM (UMR_7592)), Université de Paris (UP)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), and ANR-17-CE13-0013,POLCAM,Rôles de l'adhésion et des forces mécaniques dans la polarisation cellulaire et tissulaire(2017)
Subjects: [SDV]Life Sciences [q-bio], macromolecular substances, Biology, 010402 general chemistry, Mechanotransduction, Cellular, 01 natural sciences, mechanical force, 03 medical and health sciences, Cell Adhesion, α-catenin, Mechanotransduction, Cell adhesion, Cytoskeleton, 030304 developmental biology, 0303 health sciences, Cadherin, actomyosin, Cell Biology, General Medicine, Adhesion, Cadherins, Actin cytoskeleton, Actins, 0104 chemical sciences, Actin Cytoskeleton, cell-cell adhesion, Catenin, Biophysics, micro force sensing arrays, alpha Catenin, Micropatterning
Abstract: International audience; Background Information: Actin cytoskeleton contractility plays a critical role in morphogenetic processes by generating forces that are then transmitted to cell-cell and cell-ECM adhesion complexes. In turn, mechanical properties of the environment are sensed and transmitted to the cytoskeleton at cell adhesion sites, influencing cellular processes such as cell migration, differentiation and survival. Anchoring of the actomyosin cytoskeleton to adhesion sites is mediated by adaptor proteins such as talin or α-catenin that link F-actin to transmembrane cell adhesion receptors, thereby allowing mechanical coupling between the intracellular and extracellular compartments. Thus, a key issue is to be able to measure the forces generated by actomyosin and transmitted to the adhesion complexes. Approaches developed in cells and those probing single molecule mechanical properties of α-catenin molecules allowed to identify α-catenin, an F-actin binding protein which binds to the cadherin complexes as a major player in cadherin-based mechanotransduction. However, it is still very difficult to bridge intercellular forces measured at cellular levels and those measured at the single-molecule level. Results: Here, we applied an intermediate approach allowing reconstruction of the actomyosin-α-catenin complex in acellular conditions to probe directly the transmitted forces. For this, we combined micropatterning of purified α-catenin and spontaneous actomyosin network assembly in the presence of G-actin and Myosin II with microforce sensor arrays used so far to measure cell-generated forces. Conclusions: Using this method, we show that self-organizing actomyosin bundles bound to micrometric α-catenin patches can apply near-nano-Newton forces. Significance: Our results pave the way for future studies on molecular/cellular mechanotransduction and mechanosensing.
Published: 2021

13. The Reference Genome Sequence of Scutellaria baicalensis Provides Insights into the Evolution of Wogonin Biosynthesis

Author: Meng-Ying Cui, Zhicheng Xu, Cathie Martin, Xiao-Ya Chen, Yonghong Hu, Jie Liu, Burkhard Steuernagel, Marielle Vigouroux, Tomáš Pluskal, Mengxiao Yan, Yumin Fang, Reheman Yidiresi, Yu-Kun Wei, Huiwen Shang, Jing-Ke Weng, Jun Yang, Qing Zhao, Lei Yang, and Wen-Qing Qiu
Subjects: 0106 biological sciences, 0301 basic medicine, Plant Science, Computational biology, Plant Roots, 01 natural sciences, Genome, 03 medical and health sciences, chemistry.chemical_compound, Wogonin, food, Gene duplication, Mint family, Medicine, Chinese Traditional, Molecular Biology, Gene, Flavonoids, Plants, Medicinal, Whole Genome Sequencing, biology, Plant Extracts, biology.organism_classification, food.food, Biosynthetic Pathways, 030104 developmental biology, chemistry, Flavanones, Scutellaria, Scutellaria baicalensis, Genome, Plant, 010606 plant biology & botany, Reference genome
Abstract: Scutellaria baicalensis Georgi is important in Chinese traditional medicine where preparations of dried roots, “Huang Qin,” are used for liver and lung complaints and as complementary cancer treatments. We report a high-quality reference genome sequence for S. baicalensis where 93% of the 408.14-Mb genome has been assembled into nine pseudochromosomes with a super-N50 of 33.2 Mb. Comparison of this sequence with those of closely related species in the order Lamiales, Sesamum indicum and Salvia splendens, revealed that a specialized metabolic pathway for the synthesis of 4′-deoxyflavone bioactives evolved in the genus Scutellaria. We found that the gene encoding a specific cinnamate coenzyme A ligase likely obtained its new function following recent mutations, and that four genes encoding enzymes in the 4′-deoxyflavone pathway are present as tandem repeats in the genome of S. baicalensis. Further analyses revealed that gene duplications, segmental duplication, gene amplification, and point mutations coupled to gene neo- and subfunctionalizations were involved in the evolution of 4′-deoxyflavone synthesis in the genus Scutellaria. Our study not only provides significant insight into the evolution of specific flavone biosynthetic pathways in the mint family, Lamiaceae, but also will facilitate the development of tools for enhancing bioactive productivity by metabolic engineering in microbes or by molecular breeding in plants. The reference genome of S. baicalensis is also useful for improving the genome assemblies for other members of the mint family and offers an important foundation for decoding the synthetic pathways of bioactive compounds in medicinal plants.
Published: 2019

14. MYC dosage compensation is mediated by miRNA-transcription factor interactions in aneuploid cancer

Author: ManSai Acón, Carsten Geiß, Jorge Torres-Calvo, Diana Bravo-Estupiñan, Guillermo Oviedo, Jorge L Arias-Arias, Luis A Rojas-Matey, Edwin Baez, Gloriana Vásquez-Vargas, Yendry Oses-Vargas, José Guevara-Coto, Andrés Segura-Castillo, Francisco Siles-Canales, Steve Quirós-Barrantes, Anne Régnier-Vigouroux, Pedro Mendes, and Rodrigo Mora-Rodríguez
Subjects: Genome instability, Dosage compensation, Colorectal cancer, microRNA, Cancer cell, medicine, Cancer research, Cancer, Biology, medicine.disease, Gene dosage, Transcription factor
Abstract: SummaryWe hypothesize that dosage compensation of critical genes arises from systems-level properties for cancer cells to withstand the negative effects of aneuploidy. We identified several candidate genes in cancer multi-omics data and developed a biocomputational platform to construct a mathematical model of their interaction network with miRNAs and transcription factors, where the property of dosage compensation emerged for MYC and was dependent on the kinetic parameters of its feedback interactions with three micro-RNAs. These circuits were experimentally validated with a novel genetic tug-of-war technique by overexpressing an exogenous MYC leading to over-expression of the three microRNAs involved and down-regulation of endogenous MYC. In addition, MYC overexpression or inhibition of its compensating miRNAs led to dosage-dependent cytotoxicity in MYC-amplified colon cancer cells. Finally, we identified negative correlation of MYC dosage compensation with patient survival in TCGA breast cancer patients, highlighting the potential of this mechanism to prevent aneuploid cancer progression.HighlightsThe systems-level property of gene dosage-compensation emerges in silico in miRNA-transcription factor networks depending on the kinetic parameters of its interactions.We established a criterion to identify compensated candidate genes with low variation in expression despite high copy number variation.BioNetUCR is a novel biocomputational platform to model miRNA-transcription factor interactionsWe present a novel genetic tug-of-war technique to experimentally validate gene dosage compensation at the transcriptional level.Abstract Figure
Published: 2021

15. Autoimmune hypoglycemia expands the biological spectrum of HHV8(+) multicentric Castleman disease

Author: David Boutboul, Eric Oksenhendler, Claire Fieschi, Pierre Arnautou, Lionel Galicier, Jehane Fadlallah, Djaouida Bengoufa, Nicolas Blin, Soraya Fellahi, Corinne Vigouroux, Elias Barrak, Viviane Queyrel-Moranne, Martine Auclair, Laurence Gérard, Lucy Chaillous, Clara Bouché, Marion Malphettes, and Rémi Bertinchamp
Subjects: biology, business.industry, Castleman Disease, Autoantibody, nutritional and metabolic diseases, Hematology, Autoimmune hypoglycemia, Stimulus Report, Hypoglycemia, Insulin receptor, Insulin signal transduction pathway and regulation of blood glucose, Immunology, Herpesvirus 8, Human, biology.protein, Effective treatment, Medicine, Humans, Rituximab, Multicentric Castleman Disease, Complication, business, medicine.drug
Abstract: Key Points Autoimmune hypoglycemia belongs to the clinical spectrum of HHV8+ MCD and rituximab is an effective treatment of this condition. This rare complication is related to autoantibodies directed toward the insulin receptor and activating the insulin signaling pathway.
Published: 2021

16. Glycogen Synthase Kinase 3 regulates the genesis of the rare displaced ganglion cell retinal subtype

Author: Alain Chédotal, Elena Kisseleff, Sopie Lourdel, Catherine Hottin, Jerome E. Roger, Muriel Perron, Parth Shah, Anand Swaroop, and Robin J. Vigouroux
Subjects: Retina, Cell type, Retinal, Biology, Cell biology, chemistry.chemical_compound, medicine.anatomical_structure, Retinal ganglion cell, chemistry, GSK-3, medicine, Optomotor response, sense organs, Signal transduction, Neural development
Abstract: Glycogen Synthase Kinase 3 (GSK) proteins (GSK3α and GSK3β) are key mediators of signaling pathways, with crucial roles in coordinating fundamental biological processes during neural development. Here we show that the complete loss of GSK3 signaling in mouse retinal progenitors leads to microphthalmia with broad morphological defects. Both proliferation of retinal progenitors and neuronal differentiation are impaired and result in enhanced cell death. A single wild-type allele of either Gsk3α or Gsk3β is able to rescue these phenotypes. In this genetic context, all cell types are present with a functional retina. However, we unexpectedly detect a large number of cells in the inner nuclear layer expressing retinal ganglion cell (RGC)-specific markers (called displaced RGCs, dRGCs) when at least one allele of Gsk3α is expressed. Excess dRGCs lead to increased number of axons projecting into the ipsilateral medial terminal nucleus, an area of the brain belonging to the non-image-forming visual circuit and poorly targeted by RGCs in wild-type retina. Transcriptome analysis and optomotor response assay suggest that at least a subset of dRGCs in Gsk3 mutant mice are direction-selective RGCs. Our study thus uncovers a unique role of GSK3 in controlling the genesis of dRGCs, a rare and poorly characterized retinal cell type.
Published: 2021

17. Comparative analysis of the course of infection and the immune response in rainbow trout (Oncorhynchus mykiss) infected with the 5 genotypes of infectious hematopoietic necrosis virus

Author: Thierry Morin, Joëlle Cabon, Lénaïg Louboutin, Morgane Danion, Estelle Vigouroux, Laboratoire de Ploufragan-Plouzané-Niort [ANSES], and Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)
Subjects: Infectious hematopoietic necrosis virus, Genotype, [SDV]Life Sciences [q-bio], Virulence, Biology, Host Specificity, Virus, Cell Line, 03 medical and health sciences, Immune system, Neutralization Tests, Virology, Animals, Mortality, Pathogen, 030304 developmental biology, 0303 health sciences, 030302 biochemistry & molecular biology, Immunity, Viral Load, biology.organism_classification, 3. Good health, Viral replication, Oncorhynchus mykiss, Rainbow trout, Viral load
Abstract: Infectious hematopoietic necrosis virus (IHNV) is a pathogen of importance for salmonid aquaculture. In this study, we aimed to characterize virus behavior and defense mechanisms developed in rainbow trout (RT, Oncorhynchus mykiss) experimentally infected with isolates belonging to the five described genotypes of IHNV, i.e. L, U, M, E and J. Mortality was monitored for two months, and blood and target organs were sampled at different times post-infection to assess viral load and cellular and humoral immune responses. Profiles of virulence were highly linked to precocious viral replication but also to the innate and specific immunity elicited in the host. Seroneutralization test (SNT) used for specific antibodies detection exhibited reliable results, with efficient cross-neutralization observed in heterologous systems except for the Asian representative. These data bring new insights about IHNV/RT interaction and reinforce the interest of SNT as preventive and epidemiological tool.
Published: 2021

18. Trees and their seed networks: The social dynamics of urban fruit trees and implications for genetic diversity

Author: Yves Vigouroux, Stéphanie M. Carrière, Vincent Johnson, Marie-Louise Avana, Jérôme Duminil, Alexis Gakwavu, Aurore Rimlinger, A. Awono, Taïna Lemoine, Barbara Vinceti, Lison Marie, Armel Chakocha, Franca Mboujda, Diversité, adaptation, développement des plantes (UMR DIADE), 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 [France-Sud])-Université de Montpellier (UM), University of Dschang, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-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)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Savoirs, ENvironnement et Sociétés (SENS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut de Recherche pour le Développement (IRD)
Subjects: Tree planting, Plant Science, Plant Genetics, Ecosystem services, Cameroon, Data Management, Principal Component Analysis, Ecology, biology, Agroforestry, Plant Anatomy, Eukaryota, Phylogenetic Analysis, Agriculture, Plants, Phylogenetics, Social dynamics, Geography, Dacryodes edulis, Seeds, Medicine, Planting, Burseraceae, Research Article, Computer and Information Sciences, Ecological Metrics, Science, Context (language use), Horticulture, Indigenous, Fruits, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Genetics, Evolutionary Systematics, Social Factors, Taxonomy, Crop Genetics, Evolutionary Biology, Genetic diversity, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Population Biology, Ecology and Environmental Sciences, Organisms, Biology and Life Sciences, Genetic Variation, Species Diversity, Bayes Theorem, biology.organism_classification, [SDE.ES]Environmental Sciences/Environmental and Society, Agronomy, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Population Genetics, Fruit tree, Microsatellite Repeats
Abstract: Trees are a traditional component of urban spaces where they provide ecosystem services critical to urban wellbeing. In the Tropics, urban trees’ seed origins have rarely been characterized. Yet, understanding the social dynamics linked to tree planting is critical given their influence on the distribution of associated genetic diversity. This study examines elements of these dynamics (seed exchange networks) in an emblematic indigenous fruit tree species from Central Africa, the African plum tree (Dacryodes edulis, Burseraceae), within the urban context of Yaoundé. We further evaluate the consequences of these social dynamics on the distribution of the genetic diversity of the species in the city. Urban trees were planted predominantly using seeds sourced from outside the city, resulting in a level of genetic diversity as high in Yaoundé as in a whole region of production of the species. Debating the different drivers that foster the genetic diversity in planted urban trees, the study argued that cities and urban dwellers can unconsciously act as effective guardians of indigenous tree genetic diversity.
Published: 2021

19. Metabolic and inflammatory reprogramming of macrophages by ONC201 translates in a pro-inflammatory environment even in presence of glioblastoma cells

Author: Claudius Witzler, Carsten Geiß, Wolfram Ruf, Gernot Poschet, and Anne Régnier-Vigouroux
Subjects: 0301 basic medicine, Pyridines, Immunology, 610 Medizin, Glutamic Acid, Antineoplastic Agents, Mitochondrion, Biology, 570 Life sciences, 03 medical and health sciences, 0302 clinical medicine, Immune system, Cell Line, Tumor, Dopamine receptor D2, 610 Medical sciences, Tumor Microenvironment, Humans, Immunology and Allergy, Macrophage, Receptors, Dopamine D5, Tumor microenvironment, Receptors, Dopamine D2, Macrophages, Imidazoles, Mitochondria, Cell biology, Gene Expression Regulation, Neoplastic, Pyrimidines, 030104 developmental biology, Drug Resistance, Neoplasm, Tumor progression, Dopamine receptor, Energy Metabolism, Glioblastoma, Reprogramming, Transcription Factor CHOP, Signal Transduction, 030215 immunology, 570 Biowissenschaften
Abstract: Tumor-associated macrophages facilitate tumor progression and resistance to therapy. Their capacity for metabolic and inflammatory reprogramming represents an attractive therapeutic target. ONC201/TIC10 is an anticancer molecule that antagonizes the dopamine receptor D2 and affects mitochondria integrity in tumor cells. We examined whether ONC201 induces a metabolic and pro-inflammatory switch in primary human monocyte-derived macrophages that reactivates their antitumor activities, thus enhancing the onco-toxicity of ONC201. Contrary to glioblastoma cells, macrophages exhibited a low ratio of dopamine receptors D2/D5 gene expression and were resistant to ONC201 cytotoxicity. Macrophages responded to ONC201 with a severe loss of mitochondria integrity, a switch to glycolytic ATP production, alterations in glutamate transport, and a shift towards a pro-inflammatory profile. Treatment of macrophages-glioblastoma cells co-cultures with ONC201 induced similar alterations in glutamatergic and inflammatory gene expression profiles of macrophages. It induced as well metabolic changes and a pro-inflammatory switch of the co-culture milieu. However, these changes did not translate into increased onco-toxicity. This study provides the first evidence that ONC201 affects macrophage immunometabolism and leads to a pro-inflammatory tumor environment. This speaks in favor of implementing ONC201 in combinatorial therapies and warrants further investigation of the mechanisms of action of ONC201 in macrophages and other immune cells.
Published: 2021
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20. MYC Dosage Compensation is Mediated by miRNA-Transcription Factor Interactions in Aneuploid Cancer

Author: Rodrigo Mora-Rodriguez, Torres-Calvo Jorge, Francisco Siles-Canales, ManSai Acón, Yendry Oses-Vargas, Pedro Mendes, Jose Guevara-Coto, Oviedo Guillermo, Carsten Geiß, Jorge L. Arias-Arias, Gloriana Vásquez-Vargas, Steve Quirós-Barrantes, Andrés Segura-Castillo, and Anne Régnier-Vigouroux
Subjects: Genome instability, Dosage compensation, Colorectal cancer, microRNA, Cancer cell, Cancer research, medicine, Cancer, Biology, medicine.disease, Gene dosage, Transcription factor
Abstract: Cancer complexity is consequence of genomic instability leading to aneuploidy. We hypothesize that dosage compensation of critical genes arise from systems-level properties for cancer cells to withstand the negative effects of aneuploidy. We developed a computational platform to identify a network of miRNAs and transcription factors interacting with candidate dosage-compensated genes using NCI-60 multi-omic data. We next constructed a mathematical model where the property of dosage compensation emerged for MYC and STAT3 and was dependent on the kinetic parameters of their feedback and feed-forward interactions with four miRNAs. We developed a genetic tug-of-war approach by overexpressing an exogenous MYC sequence to experimentally validate MYC dosage compensation circuits as demonstrated by the over-expression of the three microRNAs involved and the respective down-regulation of endogenous MYC. In addition, MYC overexpression or inhibition of its compensating miRNAs led to dosage-dependent cytotoxicity in MYC-amplified colon cancer cells. The study of TCGA breast cancer patient data indicated that MYC dosage compensation could lead to lower patient survival, highlighting the potential of targeting gene dosage compensation to prevent aneuploid cancer progression.
Published: 2021

21. Species-level ichthyoplankton dynamics for 97 fishes in two major river basins of the Amazon using quantitative metabarcoding

Author: Jesus Nunez, Jhon Alvarado, Homero Sánchez, Carlos Angulo, Diana Castro Ruiz, José Vertiz, Guido Miranda, Gérard Cochonneau, Yves Vigouroux, Fabrice Duponchelle, Jean-François Renno, Cédric Mariac, Eduardo Mejia, Werner Chota-Macuyama, Carmen Rosa García-Dávila, Mayra Flores, Guillain Estivals, Aurea García Vásquez, Christian Nolorbe, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Institut de Recherche pour le Développement (IRD), Géosciences Environnement Toulouse (GET), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-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), Instituto de Ecologia (IE), Universidad Mayor de San Andrés (UMSA), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), 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), 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)-Observatoire Midi-Pyrénées (OMP), 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), and Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Amazonian, [SDE.MCG]Environmental Sciences/Global Changes, Fisheries, Drainage basin, flood regime, population, larvae, Biology, system, insights, 010603 evolutionary biology, 01 natural sciences, phenology, Ucayali, 03 medical and health sciences, siluriformes, Rivers, Genetics, Seasonal breeder, Animals, deforestation, 14. Life underwater, capture, Ecology, Evolution, Behavior and Systematics, biodiversity, geography, geography.geographical_feature_category, Flood myth, Amazon rainforest, Phenology, Fishes, conservation, Ichthyoplankton, biology.organism_classification, Maranon, Fishery, fish larvae, upper parana, 030104 developmental biology, Larva, metabarcoding, Freshwater fish, Seasons, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: WOS:000653259400001; International audience; The Amazon basin holds the world's largest freshwater fish diversity. Information on the intensity and timing of reproductive ecology of Amazonian fish is scant. We use a metabarcoding method by capture using a single probe to quantify species-level ichthyoplankton dynamics. We sampled the Maranon and the Ucayali rivers in Peru monthly for 2 years. We identified 97 species that spawned mainly during the flood start, the flood end or the receding periods, although some species had spawning activity in more than one period. This information was new for 40 of the species in the Amazon basin and 80 species in Peru. Most species ceased spawning for a month during a strong hydrological anomaly in January 2016, demonstrating the rapidity with which they react to environmental modifications during the breeding season. We also document another unreported event in the Amazon basin, the inverse phenology of species belonging to one genus (Triportheus). Overall larval flow in the Maranon was more than twice that of the Ucayali, including for most commercial species (between two and 20 times higher), whereas the Ucayali accounts for similar to 80% of the fisheries landings in the region. Our results are discussed in the light of the main anthropogenic threats to fishes, hydropower dam construction and the Hidrovia Amazonica, and should serve as a pre-impact baseline.
Published: 2021

22. Next-generation sequencing in a series of 80 fetuses with complex cardiac malformations and/or heterotaxy

Author: Julien Thevenon, Sophie Blesson, Sylvie Manouvrier Hanu, Chloé Quélin, Florence Fellmann, Nicolas Chassaing, Fabienne Giuliano, Laetitia Lambert, Caroline Rooryck-Thambo, Pierre-Simon Jouk, Sylvie Di Filippo, Alexandre Vasiljevic, Christine Francannet, Daphné Lehalle, Audrey Putoux, Anna‐Gaëlle Giguet‐Valard, Sophie Naudion, Salima El Chehadeh, Estelle Colin, Viorica Ciorna‐Monferrato, Bruno Reversade, Lionel Van Maldergem, Fanny Morice-Picard, Renaud Touraine, Sébastien Moutton, Jocelyne Attia, Laurent Pasquier, A. Vigouroux-Castera, Catherine Yardin, Tania Attié-Bitach, Carine Abel, Hui Liu, Sylvie Odent, Christelle Cabrol, Florence Petit, Philippe Khau Van Kien, Thomas Simonet, Catherine Vincent-Delorme, Jean Chiesa, Juliette Piard, Anne Bazin, Mélanie Fradin, Bertrand Isidor, Loubna El Zein, Patrice Bouvagnet, Marie-Pierre Brechard, Emmanuelle Szenker-Ravi, Sophie Scheidecker, Claire Beneteau, and ACS - Heart failure & arrhythmias
Subjects: Heart Defects, Congenital, Male, midline anomaly, Heterozygote, medicine.medical_specialty, Genetic counseling, Consanguinity, Heterotaxy Syndrome, Biology, DNA sequencing, 03 medical and health sciences, consanguinity, Genetics, medicine, Humans, Family, Family history, Genetics (clinical), 030304 developmental biology, 0303 health sciences, Fetus, Obstetrics, Homozygote, 030305 genetics & heredity, High-Throughput Nucleotide Sequencing, heterotaxy, congenital heart defects, Cardiac malformations, Pedigree, fetus, Parental consanguinity, Cytogenetic Analysis, Mutation, Female, next-generation sequencing, Heterotaxy
Abstract: Herein, we report the screening of a large panel of genes in a series of 80 fetuses with congenital heart defects (CHDs) and/or heterotaxy and no cytogenetic anomalies. There were 49 males (61%/39%), with a family history in 28 cases (35%) and no parental consanguinity in 77 cases (96%). All fetuses had complex CHD except one who had heterotaxy and midline anomalies while 52 cases (65%) had heterotaxy in addition to CHD. Altogether, 29 cases (36%) had extracardiac and extra-heterotaxy anomalies. A pathogenic variant was found in 10/80 (12.5%) cases with a higher percentage in the heterotaxy group (8/52 cases, 15%) compared with the non-heterotaxy group (2/28 cases, 7%), and in 3 cases with extracardiac and extra-heterotaxy anomalies (3/29, 10%). The inheritance was recessive in six genes (DNAI1, GDF1, MMP21, MYH6, NEK8, and ZIC3) and dominant in two genes (SHH and TAB2). A homozygous pathogenic variant was found in three cases including only one case with known consanguinity. In conclusion, after removing fetuses with cytogenetic anomalies, next-generation sequencing discovered a causal variant in 12.5% of fetal cases with CHD and/or heterotaxy. Genetic counseling for future pregnancies was greatly improved. Surprisingly, unexpected consanguinity accounts for 20% of cases with identified pathogenic variants.
Published: 2020

23. Formation and diversification of a paradigm biosynthetic gene cluster in plants

Author: Anne Osbourn, Zhenhua Liu, Lionel Hill, Pirita Paajanen, Marielle Vigouroux, Levi Yant, Jitender Cheema, and James Reed
Subjects: 0106 biological sciences, 0301 basic medicine, Plant genetics, Science, Arabidopsis, Secondary Metabolism, General Physics and Astronomy, Diversification (marketing strategy), Genes, Plant, 01 natural sciences, Genome, Article, Evolutionary genetics, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, 03 medical and health sciences, Gene cluster, lcsh:Science, Gene, Chromosomal inversion, Multidisciplinary, Natural selection, biology, Arabidopsis Proteins, Haplotype, General Chemistry, biology.organism_classification, Triterpenes, Biosynthetic Pathways, 030104 developmental biology, Evolutionary biology, Multigene Family, lcsh:Q, Genome, Plant, 010606 plant biology & botany
Abstract: Numerous examples of biosynthetic gene clusters (BGCs), including for compounds of agricultural and medicinal importance, have now been discovered in plant genomes. However, little is known about how these complex traits are assembled and diversified. Here, we examine a large number of variants within and between species for a paradigm BGC (the thalianol cluster), which has evolved recently in a common ancestor of the Arabidopsis genus. Comparisons at the species level reveal differences in BGC organization and involvement of auxiliary genes, resulting in production of species-specific triterpenes. Within species, the thalianol cluster is primarily fixed, showing a low frequency of deleterious haplotypes. We further identify chromosomal inversion as a molecular mechanism that may shuffle more distant genes into the cluster, so enabling cluster compaction. Antagonistic natural selection pressures are likely involved in shaping the occurrence and maintenance of this BGC. Our work sheds light on the birth, life and death of complex genetic and metabolic traits in plants., How plant biosynthetic gene clusters (BGCs) form and evolve remains unclear. Here, via examining available genomes within and between Arabidopsis species, the authors show that the thalianol BGC has evolved recently and is still dynamically evolving through involvement of auxiliary genes and chromosomal inversions.
Published: 2020

24. Talin dissociates from RIAM and associates to vinculin sequentially in response to the actomyosin force

Author: Véronique Henriot, Clémence Vigouroux, Christophe Le Clainche, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Dynamique du cytosquelette et motilité (ACTIN), Département Biochimie, Biophysique et Biologie Structurale (B3S), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ANR-16-CE13-0007,PHAGOMECANO,Mécanotransduction associée à la phagocytose dépendante des intégrines(2016), ANR-18-CE13-0026,RECAMECA,Etude des liens moléculaires entre la force du cytosquelette d'actomyosine, la régulation des intégrines et les propriétés de la matrice extracellulaire grâce à une reconstitution in vitro(2018), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), and Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Talin, 0301 basic medicine, Cell biology, animal structures, Science, [SDV]Life Sciences [q-bio], Biophysics, General Physics and Astronomy, macromolecular substances, Biochemistry, Mechanical stretching, environment and public health, Article, General Biochemistry, Genetics and Molecular Biology, Adhesion strength, 03 medical and health sciences, 0302 clinical medicine, Genes, Reporter, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Muscle, Skeletal, lcsh:Science, Cytoskeleton, Adaptor Proteins, Signal Transducing, Multidisciplinary, biology, Chemistry, Membrane Proteins, Actomyosin, General Chemistry, Vinculin, Recombinant Proteins, Molecular Imaging, 3. Good health, Luminescent Proteins, 030104 developmental biology, Microscopy, Fluorescence, embryonic structures, biology.protein, lcsh:Q, Rabbits, biological phenomena, cell phenomena, and immunity, 030217 neurology & neurosurgery
Abstract: Cells reinforce adhesion strength and cytoskeleton anchoring in response to the actomyosin force. The mechanical stretching of talin, which exposes cryptic vinculin-binding sites, triggers this process. The binding of RIAM to talin could regulate this mechanism. However, the mechanosensitivity of the talin-RIAM complex has never been tested. It is also not known whether RIAM controls the mechanosensitivity of the talin-vinculin complex. To address these issues, we designed an in vitro microscopy assay with purified proteins in which the actomyosin force controls RIAM and vinculin-binding to talin. We demonstrate that actomyosin triggers RIAM dissociation from several talin domains. Actomyosin also provokes the sequential exchange of RIAM for vinculin on talin. The effect of RIAM on this force-dependent binding of vinculin to talin varies from one talin domain to another. This mechanism could allow talin to biochemically code a wide range of forces by selecting different combinations of partners., Force-dependent formation of the talin-vinculin complex reinforces actin anchoring to focal adhesions, but how different talin-binding proteins respond to force is unclear. Here authors use an in vitro microscopy assay and show that the actomyosin force triggers the dissociation of RIAM from several talin domains.
Published: 2020

25. Characterization of the first tetrameric transcription factor of the GntR superfamily with allosteric regulation from the bacterial pathogen Agrobacterium fabrum

Author: Armelle Vigouroux, Anaïs Naretto, Pierre Legrand, Aurélie Di Cicco, Ludovic Vial, Daniel Lévy, Sébastien Renoud, Céline Lavire, Jeanne Doré, Magali Aumont-Nicaise, Solange Moréra, Thibault Meyer, Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Synchroton Soleil, Division Experience/Ligne Nanoscopium, L'Orme des Merisiers, Gif-sur-Yvette, ANR-10-INSB-05-01 INSB ANR-10-INSB-0501, Universite de LyonED341-E2M2French Ministere de l'Education Nationale, de l'Enseignement Superieur et de la RechercheFrench National Research Infrastructure France BioImagingANR10-INBS-04Centre National de la Recherche Scientifique (CNRS)European Commission, Synchrotron SOLEIL (SSOLEIL), Laboratoire Physico-Chimie Curie [Institut Curie] (PCC), Institut Curie [Paris]-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Microbiologie et enzymologie structurale (MESB3S), Département Biochimie, Biophysique et Biologie Structurale (B3S), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Mesures d'interactions protéine-protéine (PIM), Département Plateforme (PF I2BC), Centre de recherche de l'Institut Curie [Paris], and Institut Curie [Paris]
Subjects: Models, Molecular, Coumaric Acids, Protein Conformation, AcademicSubjects/SCI00010, [SDV]Life Sciences [q-bio], Allosteric regulation, Repressor, Agrobacterium, Biology, Crystallography, X-Ray, Sodium Citrate, 03 medical and health sciences, Allosteric Regulation, Bacterial Proteins, Protein Domains, Transcription (biology), Structural Biology, Genetics, Transcriptional regulation, Genes, Synthetic, Binding site, Promoter Regions, Genetic, Transcription factor, Tetrahydrofolates, 030304 developmental biology, 0303 health sciences, Binding Sites, Effector, 030302 biochemistry & molecular biology, Gene Expression Regulation, Bacterial, DNA binding site, Repressor Proteins, Zinc, Biochemistry, Multigene Family, Protein Multimerization
Abstract: A species-specific region, denoted SpG8-1b allowing hydroxycinnamic acids (HCAs) degradation is important for the transition between the two lifestyles (rhizospheric versus pathogenic) of the plant pathogen Agrobacterium fabrum. Indeed, HCAs can be either used as trophic resources and/or as induced-virulence molecules. The SpG8-1b region is regulated by two transcriptional regulators, namely, HcaR (Atu1422) and Atu1419. In contrast to HcaR, Atu1419 remains so far uncharacterized. The high-resolution crystal structures of two fortuitous citrate complexes, two DNA complexes and the apoform revealed that the tetrameric Atu1419 transcriptional regulator belongs to the VanR group of Pfam PF07729 subfamily of the large GntR superfamily. Until now, GntR regulators were described as dimers. Here, we showed that Atu1419 represses three genes of the HCAs catabolic pathway. We characterized both the effector and DNA binding sites and identified key nucleotides in the target palindrome. From promoter activity measurement using defective gene mutants, structural analysis and gel-shift assays, we propose N5,N10-methylenetetrahydrofolate as the effector molecule, which is not a direct product/substrate of the HCA degradation pathway. The Zn2+ ion present in the effector domain has both a structural and regulatory role. Overall, our work shed light on the allosteric mechanism of transcription employed by this GntR repressor.
Published: 2020

26. Amazonian mammal monitoring using aquatic environmental DNA

Author: Jérôme Murienne, Opale Coutant, Alice Valentini, Cécile Richard-Hansen, Sébastien Brosse, Tony Dejean, Benoit de Thoisy, Régis Vigouroux, and Jean-Baptiste Decotte
Subjects: 0106 biological sciences, 0301 basic medicine, Arboreal locomotion, Sampling efficiency, Amazonian, Fauna, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Aquatic species, Genetics, Animals, DNA Barcoding, Taxonomic, Environmental DNA, Transect, Ecology, Evolution, Behavior and Systematics, Mammals, Ecology, Water, Biodiversity, DNA, Environmental, French Guiana, 030104 developmental biology, Geography, Mammal, Species richness, Biotechnology, Environmental Monitoring
Abstract: Environmental DNA (eDNA) metabarcoding has emerged as one of the most efficient methods to assess aquatic species presence. While the method can in theory be used to investigate nonaquatic fauna, its development for inventorying semi-aquatic and terrestrial fauna is still at an early stage. Here we investigated the potential of aquatic eDNA metabarcoding for inventorying mammals in Neotropical environments, be they aquatic, semi-aquatic or terrestrial. We collected aquatic eDNA in 96 sites distributed along three Guianese watersheds and compared our inventories to expected species distributions and field observations derived from line transects located throughout French Guiana. Species occurrences and emblematic mammalian fauna richness patterns were consistent with the expected distribution of fauna and our results revealed that aquatic eDNA metabarcoding brings additional data to line transect samples for diurnal nonaquatic (terrestrial and arboreal) species. Aquatic eDNA also provided data on species not detectable in line transect surveys such as semi-aquatic, aquatic and nocturnal terrestrial and arboreal species. Although the application of eDNA to inventory mammals still needs some developments to optimize sampling efficiency, it can now be used as a complement to traditional surveys.
Published: 2020

27. The Viral Hemorrhagic Septicemia Virus (VHSV) Markers of Virulence in Rainbow Trout (Oncorhynchus mykiss)

Author: Estelle Vigouroux, Michel Brémont, Joëlle Cabon, Thierry Morin, Lénaïg Louboutin, Valentina Panzarin, Stéphane Biacchesi, Yannick Blanchard, Niels Jørgen Olesen, Anna Luiza Farias Alencar, Argelia Cuenca, Emilie Mérour, Laury Baillon, Virologie et Immunologie Moléculaires (VIM (UR 0892)), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Ploufragan-Plouzané-Niort [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), DTU Aqua, National Institute of Aquatic Resources, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Project: 291815,EC:FP7:KBBE,FP7-ERANET-2011-RTD,ANIHWA(2012), and Technical University of Denmark [Lyngby] (DTU)
Subjects: Viral hemorragic septicemia virus, Microbiology (medical), novirhabdovirus, animal diseases, lcsh:QR1-502, Virulence, Virulence markers, Microbiology, lcsh:Microbiology, Virus, Novirhabdovirus, 03 medical and health sciences, SDG 3 - Good Health and Well-being, 14. Life underwater, viral hemorrhagic septicemia virus, 030304 developmental biology, Cytopathic effect, 0303 health sciences, biology, VHSV, 030306 microbiology, virulence markers, biology.organism_classification, rainbow trout, Reverse genetics, Trout, Rainbow trout, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Viral hemorrhagic septicemia
Abstract: International audience; Viral hemorrhagic septicemia virus (VHSV) is a highly contagious virus leading to high mortality in a large panel of freshwater and marine fish species. VHSV isolates originating from marine fish show low pathogenicity in rainbow trout. The analysis of several nearly complete genome sequences from marine and freshwater isolates displaying varying levels of virulence in rainbow trout suggested that only a limited number of amino acid residues might be involved in regulating the level of virulence. Based on a recent analysis of 55 VHSV strains, which were entirely sequenced and phenotyped in vivo in rainbow trout, several amino acid changes putatively involved in virulence were identified. In the present study, these amino acid changes were introduced, alone or in combination, in a highly-virulent VHSV 23-75 genome backbone by reverse genetics. A total of 35 recombinant VHSV variants were recovered and characterized for virulence in trout by bath immersion. Results confirmed the important role of the NV protein (R116S) and highlighted a major contribution of the nucleoprotein N (K46G and A241E) in regulating virulence. Single amino acid changes in these two proteins drastically affect virus pathogenicity in rainbow trout. This is particularly intriguing for the N variant (K46G) which is unable to establish an active infection in the fins of infected trout, the main portal of entry of VHSV in this species, allowing further spread in its host. In addition, salmonid cell lines were selected to assess the kinetics of replication and cytopathic effect of recombinant VHSV and discriminate virulent and avirulent variants. In conclusion, three major virulence markers were identified in the NV and N proteins. These markers explain almost all phenotypes (92.7%) observed in trout for the 55 VHSV strains analyzed in the present study and herein used for the backward validation of virulence markers. The identification of VHSV specific virulence markers in this species is of importance both to predict the in vivo phenotype of viral isolates with targeted diagnostic tests and to improve prophylactic methods such as the development of safer live-attenuated vaccines.
Published: 2020

28. SARS-CoV-2 phylodynamics differentiates the effectiveness of non-pharmaceutical interventions

Author: Bruno Lina, Julie Teresa Shapiro, Thierry Wirth, Philippe Vanhems, Jean-Philippe Rasigade, Laurence Josset, Grégory Destras, Yoann Vigouroux, Charlene Coquisart, Antonin Bal, and Anais Barray
Subjects: medicine.medical_specialty, Viral phylodynamics, Coronavirus disease 2019 (COVID-19), Environmental health, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Intervention (counseling), Public health, Pandemic, medicine, Psychological intervention, Biology
Abstract: Quantifying the effectiveness of large-scale non-pharmaceutical interventions against COVID-19 is critical to adapting responses against future waves of the pandemic. By combining phylogenetic data of 5,198 SARS-CoV-2 genomes with the chronology of non-pharmaceutical interventions in 57 countries, we examine how interventions and combinations thereof alter the divergence rate of viral lineages, which is directly related to the epidemic reproduction number. Home containment and education lockdown had the largest independent impacts and were predicted to reduce the reproduction number by 35% and 26%, respectively. However, we find that in contexts with a reproduction number >2, no individual intervention is sufficient to stop the epidemic and increasingly stringent intervention combinations may be required. Our phylodynamic approach can complement epidemiological models to inform public health strategies against COVID-19.
Published: 2020
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29. GWAS unveils features between early- and late-flowering pearl millets

Author: Leila Zekraoui, Ousmane Sy, Ndjido Ardo Kane, Amadou Fofana, Desalegn D. Serba, Diaga Diouf, Cécile Berthouly-Salazar, Mame Codou Gueye, Oumar Diack, Hamidou Tall, Yves Vigouroux, Ghislain Kanfany, Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), Kansas State University, Diversité, adaptation, développement des plantes (UMR DIADE), 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 [France-Sud])-Université de Montpellier (UM), and Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)
Subjects: Candidate gene, Pennisetum, lcsh:QH426-470, lcsh:Biotechnology, Climate, India, Single-nucleotide polymorphism, Flowers, engineering.material, Biology, Morphotypes, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Flowering, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Pearl millet, 03 medical and health sciences, 0302 clinical medicine, lcsh:TP248.13-248.65, Genetics, GWAS, Genetic Association Studies, 030304 developmental biology, 0303 health sciences, Genetic diversity, Diversity, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], food and beverages, Phenotypic trait, Senegal, lcsh:Genetics, Plant Breeding, Evolutionary biology, Genetic structure, engineering, Gene pool, Adaptation, Pearl, 030217 neurology & neurosurgery, Biotechnology, Research Article
Abstract: Background Pearl millet, a nutritious food for around 100 million people in Africa and India, displays extensive genetic diversity and a high degree of admixture with wild relatives. Two major morphotypes can be distinguished in Senegal: early-flowering Souna and late-flowering Sanio. Phenotypic variabilities related to flowering time play an important role in the adaptation of pearl millet to climate variability. A better understanding of the genetic makeup of these variabilities would make it possible to breed pearl millet to suit regions with different climates. The aim of this study was to characterize the genetic basis of these phenotypic differences. Results We defined a core collection that captures most of the diversity of cultivated pearl millets in Senegal and includes 60 early-flowering Souna and 31 late-flowering Sanio morphotypes. Sixteen agro-morphological traits were evaluated in the panel in the 2016 and 2017 rainy seasons. Phenological and phenotypic traits related with yield, flowering time, and biomass helped differentiate early- and late-flowering morphotypes. Further, using genotyping-by-sequencing (GBS), 21,663 single nucleotide polymorphisms (SNPs) markers with more than 5% of minor allele frequencies were discovered. Sparse non-negative matrix factorization (sNMF) analysis confirmed the genetic structure in two gene pools associated with differences in flowering time. Two chromosomal regions on linkage groups (LG 3) (~ 89.7 Mb) and (LG 6) (~ 68.1 Mb) differentiated two clusters among the early-flowering Souna. A genome-wide association study (GWAS) was used to link phenotypic variation to the SNPs, and 18 genes were linked to flowering time, plant height, tillering, and biomass (P-value < 2.3E-06). Conclusions The diversity of early- and late-flowering pearl millet morphotypes in Senegal was captured using a heuristic approach. Key phenological and phenotypic traits, SNPs, and candidate genes underlying flowering time, tillering, biomass yield and plant height of pearl millet were identified. Chromosome rearrangements in LG3 and LG6 were inferred as a source of variation in early-flowering morphotypes. Using candidate genes underlying these features between pearl millet morphotypes will be of paramount importance in breeding for resilience to climatic variability.
Published: 2020

30. Quick and cheap technique to cryopreserve Welsh pony embryo

Author: Thierry Blard, Thierry Gascogne, Michèle Magistrini, S. Vigouroux, Philippe Barrière, Fabrice Reigner, Florence Guignot, Yvan Gaude, Isabelle Couty, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité Expérimentale de Physiologie Animale de l‘Orfrasiére (UE PAO), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Guignot, Florence
Subjects: 040301 veterinary sciences, Equine, Pony, [SDV]Life Sciences [q-bio], 0402 animal and dairy science, Embryo, 04 agricultural and veterinary sciences, Biology, 040201 dairy & animal science, language.human_language, [SDV] Life Sciences [q-bio], 0403 veterinary science, Andrology, Welsh, biology.animal, language, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2020

31. Are we neglecting earth while conquering space? Effects of aluminized solid rocket fuel combustion on the physiology of a tropical freshwater invertebrate

Author: Regis Vigouroux, Montserrat Solé, Georgina A. Rivera-Ingraham, Katherina Brokordt, Madalena Andrade, Jehan-Hervé Lignot, Rosa Freitas, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Université de Montpellier (UM), Centro de Estudios Avanzados en Zonas Aridas (CEAZA), and Agencia Estatal de Investigación (España)
Subjects: Environmental Engineering, Antioxidant, Health, Toxicology and Mutagenesis, medicine.medical_treatment, [SDE.MCG]Environmental Sciences/Global Changes, 0208 environmental biotechnology, Glutathione reductase, Fresh Water, 02 engineering and technology, Aluminum oxide, 010501 environmental sciences, 01 natural sciences, Sink (geography), Antioxidants, Acidification, Respiration, medicine, Environmental Chemistry, Homeostasis, Animals, 0105 earth and related environmental sciences, geography, geography.geographical_feature_category, biology, Chemistry, Aquatic ecosystem, Freshwater shrimp, Public Health, Environmental and Occupational Health, General Medicine, General Chemistry, biology.organism_classification, Pollution, Crustacean, Invertebrates, 6. Clean water, 020801 environmental engineering, Crustaceans, French Guiana, Oxidative Stress, Environmental chemistry, Toxicity, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Propergol toxicity, Biomarkers, Water Pollutants, Chemical
Abstract: 12 pages, 6 figures, Space launchers often use aluminized-solid fuel (“propergol”) as propellant and its combustion releases tons of Al2O3 and HCl that sink in terrestrial and aquatic environments, polluting and decreasing water pH. We studied the impact of these events on the biochemical/physiological performance of the freshwater shrimp Macrobrachium jelskii, with wild specimens collected from a non-impacted site in French Guiana. In the laboratory, shrimps were exposed for one week to: i) undisturbed conditions; ii) Al2O3 exposure (0.5 mg L−1) at normal pH (6.6); iii) decreased pH (4.5) (mimicking HCl release in the environment) with no Al2O3; or iv) Al2O3 0.5 mg L−1 and pH 4.5, representing the average conditions found in the water bodies around the Ariane 5 launch pad. Results showed that shrimps bioaccumulated aluminium (Al) regardless of water pH. The combined effect of Al2O3 and low pH caused the most impact: acetylcholinesterase and carboxylesterase activities decreased, indicating neurotoxicity and reduced detoxification capacity, respectively. Animal respiration was enhanced with Al2O3 and pH variations alone, but the synergic interaction of both stressors caused respiration to decrease, suggesting metabolic depression. Oxidative damage followed a similar pattern to respiration rates across conditions, suggesting free radical-mediation in Al toxicity. Antioxidant activities varied among enzymes, with glutathione reductase being the most impacted by Al2O3 exposure. This study shows the importance of addressing space ports’ impact on the environment, setting the bases for selecting the most appropriate biomarkers for future monitoring programs using a widespread and sensitive crustacean in the context of an increasing space-oriented activity across the world, With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)
Published: 2020

32. Aquaporins are main contributors of root hydraulic conductivity in pearl millet [Pennisetum glaucum (L) R. Br.]

Author: Pablo Affortit, C. de la Fuente Canto, Cédric Mariac, Yves Vigouroux, Vincent Vadez, Alexandre Grondin, Laurent Laplaze, Christine Tranchant-Dubreuil, and Pascal Gantet
Subjects: 0106 biological sciences, 2. Zero hunger, Gene isoform, 0303 health sciences, Water transport, Water stress, Aquaporin, Biology, engineering.material, 01 natural sciences, Cell biology, 03 medical and health sciences, Hydraulic conductivity, engineering, Water-use efficiency, Gene, Pearl, 030304 developmental biology, 010606 plant biology & botany
Abstract: Pearl millet is a key cereal for food security in arid and semi-arid regions but its yield is increasingly threatened by water stress. Physiological mechanisms consisting in saving water or increasing water use efficiency can alleviate that stress. Aquaporins (AQP) are water channels contributing to plant hydraulic balance that are supposedly involved in these mechanisms by mediating root water transport. However, AQP remain largely uncharacterized in pearl millet. Here, we studied AQP function in root water transport in two pearl millet lines contrasting for water use efficiency (WUE). We observed that these lines were also contrasting for root hydraulic conductivity (Lpr) and AQP contribution to Lpr, the line with lower WUE showing significantly higher AQP contribution to Lpr. To investigate the AQP isoforms contributing to Lpr, we developed genomic approaches to first identify the entire AQP family in pearl millet and second study the plasma membrane intrinsic proteins (PIP) gene expression profile. We identified and annotated 33 AQP genes in pearl millet among which ten encoded PIP isoforms. PgPIP1-3 and PgPIP1-4 were significantly more expressed in the line showing lower WUE, higher Lpr and higher AQP contribution to Lpr. Overall, our study suggests that AQP from the PIP1 family are the main contributor of Lpr in pearl millet and are possibly associated to whole plant water use mechanisms. This study paves the way for further investigations on AQP functions in pearl millet hydraulics and adaptation to environmental stresses.The newly sequenced nucleotide sequences reported in this article have been submitted to GenBank under the submission number 2333840 (TPA grp467567). Assignment of GenBank accession number is in process.
Published: 2020
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33. Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Author: Ndjido Ardo Kane, Yves Vigouroux, Denisa Šimoníková, Leila Zekraoui, Jaroslav Dolezel, Nagarajan Kathiresan, Sandrine Causse, Michael Abrouk, Thomas Wicker, Sandrine Arribat, Claire Billot, Stéphane Cauet, Simon G. Krattinger, Jana Cizkova, Sylvie Vancoppenolle, Adeline Barnaud, E. Hribova, Hélène Bergès, Philippe Cubry, Jan Bettgenhaeuser, Mathieu Gueye, Hanin Ibrahim Ahmed, Liubov Gapa, Nora Scarcelli, Yveline Pailles, Jan J. Wieringa, Christian Leclerc, Marie Couderc, University of Zurich, Barnaud, Adeline, Krattinger, Simon G, King Abdullah University of Science and Technology (KAUST), Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Naturalis Biodiversity Center [Leiden], Institut Fondamental d'Afrique Noire (IFAN), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Senegalese Agricultural Research Institute, LMI Adaptation des Plantes et microorganismes associés aux Stress Environnementaux [Dakar] (LAPSE), Institut de Recherche pour le Développement (IRD), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universität Zürich [Zürich] = University of Zurich (UZH), European Regional Development Fund OPVVV project 'Plants as a tool for sustainable development' CZ.02.1.01/0.0/0.0/16_019/0000827, ANR-16-IDEX-0006,MUSE,MUSE(2016), ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Digitaria, General Physics and Astronomy, 580 Plants (Botany), 01 natural sciences, Plant breeding, F30 - Génétique et amélioration des plantes, Domestication, 0302 clinical medicine, 10126 Department of Plant and Microbial Biology, lcsh:Science, 2. Zero hunger, Molecular breeding, 0303 health sciences, Multidisciplinary, Diversité génétique (comme ressource), Agroforestry, Domestication des plantes, phytogénétique, food and beverages, Agriculture, 3100 General Physics and Astronomy, Genome, Plant, Agricultural genetics, Plant domestication, Science, Climate Change, Context (language use), 1600 General Chemistry, Genetics and Molecular Biology, Biology, Article, General Biochemistry, Genetics and Molecular Biology, génomique, Evolution, Molecular, 03 medical and health sciences, Ressource génétique végétale, Variation génétique, Species Specificity, 1300 General Biochemistry, Genetics and Molecular Biology, 10211 Zurich-Basel Plant Science Center, Selection, Genetic, 030304 developmental biology, Changement climatique, Genetic diversity, business.industry, Genetic Variation, Molecular Sequence Annotation, Digitaria exilis, General Chemistry, 15. Life on land, biology.organism_classification, Amélioration des plantes, 030104 developmental biology, Crop diversity, 13. Climate action, General Biochemistry, Africa, lcsh:Q, business, Edible Grain, 030217 neurology & neurosurgery, 010606 plant biology & botany
Abstract: Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments., Fonio millet is a fast growing orphan cereal crop with a great potential for dryland agriculture. Here, the authors report chromosome-scale reference genome assembly and population genomic resources to shed light on genetic diversity, population structure and domestication of fonio millet.
Published: 2020

34. Applications of emerging stable isotopes and elemental markers for geographical and varietal recognition of Romanian and French honeys

Author: Ioana Feher, Gabriela Cristea, Romulus Puscas, Laetitia Gaillard, Audrey Vigouroux, Francois Guyon, Dana Alina Magdas, and Adriana Dehelean
Subjects: Magnetic Resonance Spectroscopy, Rare earth, Biology, Oxygen Isotopes, 01 natural sciences, Analytical Chemistry, Isotopic signature, 0404 agricultural biotechnology, Isotopes, Carbon Isotopes, Stable isotope ratio, business.industry, Romania, fungi, 010401 analytical chemistry, food and beverages, Water, 04 agricultural and veterinary sciences, General Medicine, Honey, 040401 food science, 0104 chemical sciences, Biotechnology, Fermentation, Identification (biology), Metals, Rare Earth, France, business, Food Analysis, Food Science
Abstract: The research towards the identification of new authenticity markers is crucial to fight against fraudulent activities on honey, one of the top ten most falsified food commodities. This work proposes an association of stable isotopes and elemental content as markers for honey authentication, with respect to its floral and geographical origin. Emerging markers like isotopic signature of honey water alongside with carbon and hydrogen isotopic ratios of ethanol obtained from honey fermentation and Rare Earth Elements, were used to develop new recognition models. Thus, the efficiency of the discrimination potential of these emerging markers was discussed individually and in association. This approach proved its effectiveness for geographical differentiation (>98%) and the role of the emerging markers in these classifications was an essential one, especially of: (D/H)I, δ2H, δ18O, La, Ce and Pr. Floral recognition was realized in a lower percentage revealing the suitability of these markers mainly for geographical classification.
Published: 2020

35. New Anti-Müllerian Hormone Target Genes Involved in Granulosa Cell Survival in Women With Polycystic Ovary Syndrome

Author: Stéphane Fabre, Alice Pierre, Emmanuelle Mathieu d'Argent, Corinne Vigouroux, Nathalie di Clemente, Carine Genet, Chrystèle Racine, Camille Bourgneuf, Charlotte Dupont, Christelle Hennequet-Antier, Danielle Monniaux, Julien Sarry, Florence Plisson-Petit, Centre de Recherche Saint-Antoine (CRSA), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut de Cardiométabolisme et Nutrition = Institute of Cardiometabolism and Nutrition [CHU Pitié Salpêtrière] (IHU ICAN), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), CHU Tenon [AP-HP], Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Biologie Fonctionnelle et Adaptative (BFA (UMR_8251 / U1133)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Ligue nationale contre le cancerN/ref: RS16/75-41, ANR-12-BSV1-0034,AMHAROC,L'hormone anti-Müllérienne ovarienne : régulation, activité et implication dans le syndrome des ovaires polykystiques(2012), Fabre, Stéphane, BLANC - L'hormone anti-Müllérienne ovarienne : régulation, activité et implication dans le syndrome des ovaires polykystiques - - AMHAROC2012 - ANR-12-BSV1-0034 - BLANC - VALID, Centre de Recherche Saint-Antoine (CR Saint-Antoine), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), and Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Anti-Mullerian Hormone, endocrine system diseases, Endocrinology, Diabetes and Metabolism, Clinical Biochemistry, Apoptosis, Anti-Müllerian hormone, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Biochemistry, Mice, 0302 clinical medicine, Endocrinology, Cells, Cultured, 0303 health sciences, [SDV.BDLR.RS] Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, 030219 obstetrics & reproductive medicine, biology, Granulosa cells apoptosis, Polycystic ovary, female genital diseases and pregnancy complications, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Female, hormones, hormone substitutes, and hormone antagonists, Polycystic Ovary Syndrome, Adult, endocrine system, medicine.medical_specialty, Cell Survival, Granulosa cell, Mice, Transgenic, [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, Follicle atresia, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, 03 medical and health sciences, Follicle, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Internal medicine, medicine, Animals, Humans, Gene, 030304 developmental biology, Cell Proliferation, Granulosa Cells, urogenital system, Biochemistry (medical), [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, medicine.disease, Mice, Inbred C57BL, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Gene Expression Regulation, Atresia, Case-Control Studies, biology.protein, Target genes, Hormone
Abstract: Purpose A protective effect of anti-Müllerian hormone (AMH) on follicle atresia was recently demonstrated using long-term treatments, but this effect has never been supported by mechanistic studies. This work aimed to gain an insight into the mechanism of action of AMH on follicle atresia and on how this could account for the increased follicle pool observed in women with polycystic ovary syndrome (PCOS). Methods In vivo and in vitro experiments were performed to study the effects of AMH on follicle atresia and on the proliferation and apoptosis of granulosa cells (GCs). RNA-sequencing was carried out to identify new AMH target genes in GCs. The expression of some of these genes in GCs from control and PCOS women was compared using microfluidic real time quantitative RT-PCR. Results A short-term AMH treatment prevented follicle atresia in prepubertal mice. Consistent with this result, AMH inhibited apoptosis and promoted proliferation of different models of GCs. Moreover, integrative biology analyses of 965 AMH target genes identified in 1 of these GC models, confirmed that AMH had initiated a gene expression program favoring cell survival and proliferation. Finally, on 43 genes selected among the most up- and down-regulated AMH targets, 8 were up-regulated in GCs isolated from PCOS women, of which 5 are involved in cell survival. Main conclusions Our results provide for the first time cellular and molecular evidence that AMH protects follicles from atresia by controlling GC survival and suggest that AMH could participate in the increased follicle pool of PCOS patients.
Published: 2020

36. Revisiting the role of Dcc in visual system development with a novel eye clearing method

Author: Robin J. Vigouroux, Kim T. Nguyen-Ba-Charvet, Alain Chédotal, Quénol Cesar, Institut de la Vision, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU), Nguyen-Ba-Charvet, Kim, and Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: 0301 basic medicine, Retinal degeneration, genetic structures, Deleted in Colorectal Cancer, Visual system, neuroscience, Mice, 0302 clinical medicine, Biology (General), light sheet microscopy, axon guidance, General Neuroscience, General Medicine, DCC Receptor, visual development, Cell biology, medicine.anatomical_structure, Optic nerve, Medicine, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Research Article, tissue clearing, QH301-705.5, Science, Biology, Retinal ganglion, Retina, General Biochemistry, Genetics and Molecular Biology, developmental biology, 03 medical and health sciences, medicine, Animals, Visual Pathways, [SDV.NEU] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], mouse, Melanins, Retinal pigment epithelium, retinal development, General Immunology and Microbiology, fungi, medicine.disease, eye diseases, 030104 developmental biology, Mutation, retinal degeneration, Axon guidance, sense organs, 030217 neurology & neurosurgery
Abstract: International audience; The Deleted in Colorectal Carcinoma (Dcc) receptor plays a critical role in optic nerve development. Whilst Dcc is expressed postnatally in the eye, its function remains unknown as Dcc knockouts die at birth. To circumvent this drawback, we generated an eye-specific Dcc mutant. To study the organization of the retina and visual projections in these mice, we also established EyeDISCO, a novel tissue clearing protocol that removes melanin allowing 3D imaging of whole eyes and visual pathways. We show that in the absence of Dcc, some ganglion cell axons stalled at the optic disc, whereas others perforated the retina, separating photoreceptors from the retinal pigment epithelium. A subset of visual axons entered the CNS, but these projections are perturbed. Moreover, Dcc-deficient retinas displayed a massive postnatal loss of retinal ganglion cells and a large fraction of photoreceptors. Thus, Dcc is essential for the development and maintenance of the retina.
Published: 2020

37. A new multimetric index for the evaluation of water ecological quality of French Guiana streams based on benthic diatoms

Author: François Delmas, Régis Vigouroux, Anne Eulin-Garrigue, David Carayon, Environnement, territoires et infrastructures (UR ETBX), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), HYDRECO GUYANE FRA, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), and Ecosystèmes aquatiques et changements globaux (UR EABX)
Subjects: 0106 biological sciences, Overseas department, Fauna, General Decision Sciences, 010501 environmental sciences, Generalist and specialist species, 010603 evolutionary biology, 01 natural sciences, media_common.cataloged_instance, 14. Life underwater, European union, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, Local adaptation, media_common, GUYANE, Ecology, biology, ECOLOGICAL STATUS, 15. Life on land, biology.organism_classification, BIOTIC, Diatom, Geography, Water Framework Directive, Benthic zone, BIOASSESMENT, [SDE]Environmental Sciences
Abstract: International audience; The Water Framework Directive (WFD) requires European Union Member States to monitor the ecological quality of their water bodies through the responses of key biological compartments to anthropogenic alteration in the aquatic environment. French Guiana is a French overseas department located in the Amazonian part of South America. Despite its geographical remoteness, this department is a European territory like all the other French overseas departments and is therefore subjected to the requirements of the WFD. Previous work over the past decade, especially on benthic diatoms, have led to the development of several new biological indices specifically adapted to the biogeographic conditions (geological substrates, climate, local fauna and flora) of each of these overseas territories. However, work has progressed at a slower rate on the diatoms of French Guiana, due to the particular natural conditions that lead to very specific and still largely unknown diatomic communities. Since no convenient local system was available, an evaluation system based on a local adaptation of a generalist diatom index (SPI) has been previously set up to assess the ecological state of French Guiana's watercourses, despite obvious weaknesses linked to the biogeographical mismatch of the ecological profiles of many taxa. The increase in the quantity of data gathered through Guyanese monitoring networks over the past 9 years, as well as the progress made on diatom taxonomy, allowed the development of the new French Guiana Diatomic Index (FGDI) presented in this paper. A methodology adapted to the Guyanese context has been developed based on (i) a reduction in the number of taxa taken into account in diatom communities and on (ii) the search for alert taxa in a multimetric approach. The FGDI allows a relevant and consistent ecological status evaluation of French Guiana's streams based on benthic diatoms following the WFD framework and, due to its multimetric construction, it also allows a comprehensive ecological diagnosis which will be of great benefit for water managers.
Published: 2020

38. Coalescent Models of Demographic History: Application to Plant Domestication

Author: Olivier François, Concetta Burgarella, Philippe Cubry, Yves Vigouroux, Université Grenoble Alpes (UGA), Translational Innovation in Medicine and Complexity / Recherche Translationnelle et Innovation en Médecine et Complexité - UMR 5525 (TIMC ), 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 Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Biologie Computationnelle et Modélisation (TIMC-BCM ), and Université Grenoble Alpes (UGA)-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 Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )
Subjects: 0106 biological sciences, 2. Zero hunger, 0303 health sciences, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Range (biology), Demographic history, food and beverages, Inference, 15. Life on land, Biology, 010603 evolutionary biology, 01 natural sciences, Field (geography), Coalescent theory, 03 medical and health sciences, Evolutionary biology, Approximate Bayesian computation, Domestication, ComputingMilieux_MISCELLANEOUS, Selection (genetic algorithm), 030304 developmental biology
Abstract: A detailed understanding of the origins of domesticated species is important for many disciplines. Recent advances in this field have been made with the use of genome-wide polymorphisms and improved statistical methods. In this chapter, we review the most important developments of coalescent models for the inference of demographic history from genome-wide data. These methods include sequential Markovian models, range expansion models, and approximate Bayesian computation. We summarize the applications of the methods to some major cultivated cereals, including rice, maize, and millet. Then we discuss extensions of these methods that would better incorporate the interaction of demographic processes with selection and inclusion of gene flow with wild related species.
Published: 2020

39. Guinea yam (Dioscoreaspp., Dioscoreaceae) wild relatives identified using whole plastome phylogenetic analyses

Author: Jan J. Wieringa, Yves Vigouroux, Nora Scarcelli, Thomas L. P. Couvreur, Bonaventure Sonké, Jacqueline Magwé-Tindo, and Louis Zapfack
Subjects: 0301 basic medicine, biology, Phylogenetic tree, Dioscoreaceae, Plant Science, 15. Life on land, biology.organism_classification, Maximum parsimony, 03 medical and health sciences, Monophyly, 030104 developmental biology, Crop wild relative, Genus, Phylogenetics, Botany, Dioscorea, Ecology, Evolution, Behavior and Systematics
Abstract: The genus Dioscorea (Dioscoreaceae) contains several economically important species for human consumption, medical and pharmaceutical uses. The phylogeny of this genus is not yet resolved. As a result, the relationships between cultivated yams and their wild relatives are not well understood and this negatively impacts the understanding of cultivated yams' evolution. Here, we reconstructed the phylogenetic relationships of the main African cultivated species with all West African species in order to better circumscribe the Crop Wild Relatives of African yams. Complete chloroplast genomes of 57 individuals representing all know 17 Dioscorea species from West Africa were reconstructed. Phylogenetic analyses recovered using neighbourjoining, maximum parsimony or maximum likelihood approaches were highly congruent. We recovered six monophyletic groups corresponding to seven botanical sections. All species were clearly distinct except within the Enantiophyllum section, where it was not possible to separate the two main cultivated species (D. rotundata and D. cayenensis) from their closest wild relatives (D. abyssinica, D. praehensilis and D. sagittifolia). Dioscorea baya was well differentiated but closely related to the cultivated clade. We therefore suggest its integration within the yam Crop Wild Relative complex.
Published: 2018

40. A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9

Author: Varun Khanna, Lun Cui, François Rousset, Hugo Varet, David Bikard, Antoine Vigouroux, Biologie de Synthèse - Synthetic biology, Institut Pasteur [Paris], Sorbonne Université (SU), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This work was supported by the European Research Council (ERC) under the Europe Union’s Horizon 2020 research and innovation program (grant agreement No. [677823]), the French Government’s Investissement d’Avenir program, Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ [ANR-10-LABX-62-IBEID], and the Pasteur-Weizmann consortium and Pasteur-Roux Fellowship to L.C., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 677823,H2020,ERC-2015-STG,CRISPAIR(2016), Institut Pasteur [Paris] (IP), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Transcription, Genetic, Science, 030106 microbiology, General Physics and Astronomy, Computational biology, Biology, medicine.disease_cause, General Biochemistry, Genetics and Molecular Biology, Homology (biology), Article, 03 medical and health sciences, Species Specificity, CRISPR-Associated Protein 9, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene expression, medicine, Escherichia coli, Nucleotide, Clustered Regularly Interspaced Short Palindromic Repeats, Guide RNA, lcsh:Science, Gene, Psychological repression, chemistry.chemical_classification, Multidisciplinary, Cas9, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, General Chemistry, RNA, Bacterial, 030104 developmental biology, chemistry, lcsh:Q, CRISPR-Cas Systems, RNA, Guide, Kinetoplastida
Abstract: High-throughput CRISPR-Cas9 screens have recently emerged as powerful tools to decipher gene functions and genetic interactions. Here we use a genome-wide library of guide RNAs to direct the catalytically dead Cas9 (dCas9) to block gene transcription in Escherichia coli. Using a machine-learning approach, we reveal that guide RNAs sharing specific 5-nucleotide seed sequences can produce strong fitness defects or even kill E. coli regardless of the other 15 nucleotides of guide sequence. This effect occurs at high dCas9 concentrations and can be alleviated by tuning the expression of dCas9 while maintaining strong on-target repression. Our results also highlight the fact that off-targets with as little as nine nucleotides of homology to the guide RNA can strongly block gene expression. Altogether this study provides important design rules to safely use dCas9 in E. coli., CRISPR interference (CRISPRi) is a method for targeted silencing of transcription that requires the coexpression of protein dCas9 and a customized guide RNA. Here, Cui et al. show that certain guide RNAs induce toxicity in E. coli, and provide design rules to minimize off-target effects.
Published: 2018

41. The lipodystrophic hotspot lamin A p.R482W mutation deregulates the mesodermal inducer T/Brachyury and early vascular differentiation gene networks

Author: Marie Garcia, Anne-Claire Guénantin, Anja R. Oldenburg, Emilie Capel, Jean-Sébastien Hulot, Jonas Paulsen, Nolwenn Briand, Akshay Shah, Corinne Vigouroux, Matthieu Mantecon, Philippe Collas, and Dorota Jeziorowska
Subjects: Adult, Fetal Proteins, Male, 0301 basic medicine, Brachyury, Adolescent, Induced Pluripotent Stem Cells, Primary Cell Culture, Polycomb-Group Proteins, Locus (genetics), Biology, Mesoderm, LMNA, 03 medical and health sciences, Genetics, Humans, Cell Lineage, Gene Regulatory Networks, Epigenetics, Induced pluripotent stem cell, Molecular Biology, Genetics (clinical), Regulation of gene expression, Endothelial Cells, Gene Expression Regulation, Developmental, Cell Differentiation, General Medicine, Fibroblasts, Middle Aged, Lamin Type A, Lipodystrophy, Familial Partial, Cell biology, 030104 developmental biology, Case-Control Studies, Mutation, embryonic structures, Nuclear lamina, Female, T-Box Domain Proteins, Lamin, Protein Binding, Signal Transduction
Abstract: The p.R482W hotspot mutation in A-type nuclear lamins causes familial partial lipodystrophy of Dunnigan-type (FPLD2), a lipodystrophic syndrome complicated by early onset atherosclerosis. Molecular mechanisms underlying endothelial cell dysfunction conferred by the lamin A mutation remain elusive. However, lamin A regulates epigenetic developmental pathways and mutations could perturb these functions. Here, we demonstrate that lamin A R482W elicits endothelial differentiation defects in a developmental model of FPLD2. Genome modeling in fibroblasts from patients with FPLD2 caused by the lamin A R482W mutation reveals repositioning of the mesodermal regulator T/Brachyury locus towards the nuclear center relative to normal fibroblasts, suggesting enhanced activation propensity of the locus in a developmental model of FPLD2. Addressing this issue, we report phenotypic and transcriptional alterations in mesodermal and endothelial differentiation of induced pluripotent stem cells we generated from a patient with R482W-associated FPLD2. Correction of the LMNA mutation ameliorates R482W-associated phenotypes and gene expression. Transcriptomics links endothelial differentiation defects to decreased Polycomb-mediated repression of the T/Brachyury locus and over-activation of T target genes. Binding of the Polycomb repressor complex 2 to T/Brachyury is impaired by the mutated lamin A network, which is unable to properly associate with the locus. This leads to a deregulation of vascular gene expression over time. By connecting a lipodystrophic hotspot lamin A mutation to a disruption of early mesodermal gene expression and defective endothelial differentiation, we propose that the mutation rewires the fate of several lineages, resulting in multi-tissue pathogenic phenotypes.
Published: 2018

42. 4q25 microdeletion encompassing PITX2 : A patient presenting with tetralogy of Fallot and dental anomalies without ocular features

Author: P Calvas, S. El Hout, Nicolas Chassaing, C. Zazo Seco, Adeline Vigouroux, Laurence Bouneau, P. Vande Perre, O. Patat, D. Bourgeois, Unité différenciation épidermique et auto-immunité rhumatoïde (UDEAR), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), and CHU Toulouse [Toulouse]
Subjects: Male, 0301 basic medicine, Pediatrics, MESH: Epidermal Growth Factor / genetics, Glaucoma, Haploinsufficiency, 030105 genetics & heredity, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Child, Genotype, Eye Abnormalities, PITX2, Child, Genetics (clinical), Tetralogy of Fallot, MESH: Tetralogy of Fallot / pathology, Genetics, 4q25, Eye Diseases, Hereditary, MESH: Tooth Abnormalities / pathology, MESH: Fatty Acid Elongases, General Medicine, MESH: Tooth Abnormalities / genetics, Tetralogy of fallot, Phenotype, Penetrance, Pedigree, 3. Good health, MESH: Acetyltransferases / genetics, Female, MESH: Chromosomes, Human, Pair 4 / genetics, MESH: Haploinsufficiency, Chromosome Deletion, Chromosomes, Human, Pair 4, Adult, congenital, hereditary, and neonatal diseases and abnormalities, medicine.medical_specialty, Fatty Acid Elongases, MESH: Pedigree, MESH: Chromosome Deletion, MESH: Eye Diseases, Hereditary, Biology, Glutamyl Aminopeptidase, MESH: Phenotype, MESH: Transcription Factors / genetics, 03 medical and health sciences, stomatognathic system, Acetyltransferases, Anterior Eye Segment, medicine, Humans, MESH: Anterior Eye Segment / abnormalities, MESH: Homeodomain Proteins / genetics, Homeodomain Proteins, MESH: Humans, Epidermal Growth Factor, Axenfeld-rieger syndrome, MESH: Glutamyl Aminopeptidase / genetics, Tooth Abnormalities, Point mutation, MESH: Eye Abnormalities / pathology, MESH: Adult, medicine.disease, MESH: Male, eye diseases, stomatognathic diseases, 030104 developmental biology, MESH: Tetralogy of Fallot / genetics, MESH: Eye Abnormalities / genetics, sense organs, MESH: Female, Transcription Factors, MESH: Anterior Eye Segment / pathology
Abstract: International audience; Axenfeld-Rieger syndrome (ARS) is a heterogeneous clinical entity transmitted in an autosomal dominant manner. The main feature, Axenfeld-Rieger Anomaly (ARA), is a malformation of the anterior segment of the eye that can lead to glaucoma and impair vision. Extra-ocular defects have also been reported. Point mutations of FOXC1 and PITX2 are responsible for about 40% of the ARS cases. We describe the phenotype of a patient carrying a deletion encompassing the 4q25 locus containing PITX2 gene. This child presented with a congenital heart defect (Tetralogy of Fallot, TOF) and no signs of ARA. He is the first patient described with TOF and a complete deletion of PITX2 (arr[GRCh37]4q25(110843057-112077858)x1, involving PITX2, EGF, ELOVL6 and ENPEP) inherited from his ARS affected mother. In addition, to our knowledge, he is the first patient reported with no ocular phenotype associated with haploinsufficiency of PITX2. We compare the phenotype and genotype of this patient to those of five other patients carrying 4q25 deletions. Two of these patients were enrolled in the university hospital in Toulouse, while the other three were already documented in DECIPHER. This comparative study suggests both an incomplete penetrance of the ocular malformation pattern in patients carrying PITX2 deletions and a putative association between TOF and PITX2 haploinsufficiency.
Published: 2018

43. Glycogen Synthase Kinase 3 Regulates the Genesis of Displaced Retinal Ganglion Cells3

Author: Jerome E. Roger, Parth Shah, Muriel Perron, Anand Swaroop, Sophie Lourdel, Catherine Hottin, Elena Kisseleff, Leah Thomas, Robin J. Vigouroux, and Alain Chédotal
Subjects: Retinal Ganglion Cells, Biology, Retinal ganglion, Retina, Mice, chemistry.chemical_compound, GSK-3, post-translational modifications, medicine, Animals, retinal development, General Neuroscience, displaced ganglion cells, Retinal, General Medicine, glycogen synthase kinase 3, Axons, Cell biology, cell death, medicine.anatomical_structure, chemistry, Retinal ganglion cell, medial terminal nucleus, Inner nuclear layer, Optomotor response, Sensory and Motor Systems, sense organs, Neural development, Research Article: New Research
Abstract: Glycogen synthase kinase 3 (GSK3) proteins (GSK3α and GSK3β) are key mediators of signaling pathways, with crucial roles in coordinating fundamental biological processes during neural development. Here we show that the complete loss of GSK3 signaling in mouse retinal progenitors leads to microphthalmia with broad morphologic defects. A single wild-type allele of eitherGsk3αorGsk3βis able to rescue this phenotype. In this genetic context, all cell types are present in a functional retina. However, we unexpectedly detected a large number of cells in the inner nuclear layer expressing retinal ganglion cell (RGC)-specific markers (called displaced RGCs, dRGCs) when at least one allele ofGsk3αis expressed. The excess of dRGCs leads to an increased number of axons projecting into the ipsilateral medial terminal nucleus, an area of the brain belonging to the non-image-forming visual circuit and poorly targeted by RGCs in wild-type retina. Transcriptome analysis and optomotor response assay suggest that at least a subset of dRGCs inGsk3mutant mice are direction-selective RGCs. Our study thus uncovers a unique role of GSK3 in controlling the production of ganglion cells in the inner nuclear layer, which correspond to dRGCs, a rare and poorly characterized retinal cell type.
Published: 2021

44. Histologic analysis has a prognostical value in colorectal biopsies assessed for suspicion of graft-versus-host disease

Author: Catherine Mohr, Harold IpKan Fong, Jean-francois Goussot, Noel Milpied, Marion Marty, Claire Bréal, Reza Tabrizi, Sébastien Cossin, Fanny Sauvestre, Stephane Vigouroux, and Genevieve Belleannee
Subjects: Adult, Male, medicine.medical_specialty, Adolescent, Colon, Biopsy, medicine.medical_treatment, Graft vs Host Disease, Rectum, Kaplan-Meier Estimate, Hematopoietic stem cell transplantation, Sensitivity and Specificity, Gastroenterology, Pathology and Forensic Medicine, Young Adult, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, medicine, Humans, Molecular Biology, Grading (tumors), Aged, Retrospective Studies, Observer Variation, medicine.diagnostic_test, biology, business.industry, Hematopoietic Stem Cell Transplantation, Chromogranin A, Retrospective cohort study, Cell Biology, General Medicine, Middle Aged, Prognosis, medicine.disease, surgical procedures, operative, medicine.anatomical_structure, Graft-versus-host disease, 030220 oncology & carcinogenesis, biology.protein, Female, Histopathology, business, Follow-Up Studies, 030215 immunology
Abstract: Gastrointestinal (GI) graft-versus-host-disease (GVHD) is a common and severe complication of allogeneic hematopoietic stem cell transplantation, but clinical and histological features are unspecific. The aim of this study was to correlate the histological GI GVHD grade with the clinical outcomes. In a retrospective study of 112 patients with clinically suspected GI GVHD, colonic biopsies were reviewed by three pathologists without knowledge of the corresponding clinical data and classified in four scores, according to the NIH Consensus Project recommendations: no GVHD, possible, probable, and unequivocal GVHD. At the end of the study, the histological and clinical data were confronted with the following results: clinical diagnosis of GI GVHD was established for 70 patients (62.5%) and histological scores correlated well with the clinical diagnosis (p
Published: 2017

45. Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

Author: Jun Wang, Katrien M. Devos, Jianping Wang, Andrew H. Paterson, Cédric Mariac, Xinming Liang, Wenbin Chen, Dadakhalandar Doddamani, Sunil Gupta, Om Parkash Yadav, Rattan Yadav, Eric Lyons, Rajeev K. Varshney, Arindam Ghatak, Wolfram Weckwerth, C. Tom Hash, He Zhang, Mame Codou Gueye, Dev Paudel, Abhishek Rathore, Palak Chaturvedi, R. S. Mahala, Christian Dupuy, Xun Xu, Jeffrey L. Bennetzen, Guangyi Fan, Swapan K. Datta, Yusheng Zhao, Somashekhar Punnuri, Annapurna Chitikineni, Ndjido Ardo Kane, Mohan A. V. S. K. Katta, Falalou Hamidou, Francesca Sparvoli, Jason G. Wallace, Mahendar Thudi, Edward S. Buckler, Joann A. Conner, Prasad Bajaj, Xiyin Wang, Ramanjulu Sunkar, Peggy Ozias-Akins, Marie Couderc, Bharat P. Singh, Trilochan Mohapatra, Stefania Grando, Xin Liu, Bénédicte Rhoné, Vanika Garg, K. D. Mungra, Hari D. Upadhyaya, Chengcheng Shi, Peng Qi, Philippe Cubry, Yong Jiang, Hao Wang, Karen R. Harris-Shultz, Sabarinath Subramaniam, Yves Vigouroux, Jérémy Clotault, Cécile Berthouly-Salazar, Shifeng Cheng, Jochen C. Reif, Neetin Desai, Rakesh K. Srivastava, Institut des Mondes Africains (IMAF), Université Paris 1 Panthéon-Sorbonne (UP1)-Institut de Recherche pour le Développement (IRD)-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)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), ANR-13-BSV7-0017,AfriCrop,Etude de l'histoire évolutive des plantes domestiquées africaines(2013), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Numerical modeling and high performance computing for evolution problems in complex domains and heterogeneous media (NACHOS), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Alexandre Dieudonné (JAD), Université Côte d'Azur (UCA)-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 Côte d'Azur (UCA)-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), Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Recherches Forestières Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), 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 Paris 1 Panthéon-Sorbonne (UP1)-Institut de Recherche pour le Développement (IRD)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE), Unité de Mécanique (UME), École Nationale Supérieure de Techniques Avancées (ENSTA Paris), State Key Laboratory of Fine Chemicals, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Alexandre Dieudonné (LJAD), Université Nice Sophia Antipolis (1965 - 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 Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 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 Côte d'Azur (UCA), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Université d'Angers (UA)-AGROCAMPUS OUEST-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université Panthéon-Sorbonne (UP1)-Institut de Recherche pour le Développement (IRD)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, genome sequence, [SDV]Life Sciences [q-bio], adaptation, Applied Microbiology and Biotechnology, hybridism, Conserved Sequence, 2. Zero hunger, Agriculture, Staple food, genetic diversity, Genomics, hybridations, Phenotype, diversité génétique, pennisetum glaucum, Molecular Medicine, Desert Climate, pearl millet, Genome, Plant, Biotechnology, Agricultural genetics, Pennisetum, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Drought tolerance, Biomedical Engineering, Bioengineering, Biology, Genes, Plant, milieu aride, Article, domestication, 03 medical and health sciences, Quantitative Trait, Heritable, Mil (Cenchrus americanus), Genetic variation, Plant breeding, Domestication, Millet (Cenchrus americanus), Genetic diversity, Base Sequence, Genetic Variation, Molecular Sequence Annotation, 15. Life on land, Arid, arid environment, Plant Breeding, 030104 developmental biology, Agronomy, Next-generation sequencing, Hybridization, Genetic, Genome-Wide Association Study
Abstract: Draft genome, 994 re-sequenced lines and GWAS for yield-traits provide a resource of genetics and genomics tools for pearl millet researchers and breeders. Supplementary information The online version of this article (doi:10.1038/nbt.3943) contains supplementary material, which is available to authorized users., Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop. Supplementary information The online version of this article (doi:10.1038/nbt.3943) contains supplementary material, which is available to authorized users.
Published: 2017

46. Disentangling spatial and environmental determinants of fish species richness and assemblage structure in Neotropical rainforest streams

Author: Kévin Cilleros, Sébastien Brosse, Luc Allard, and Régis Vigouroux
Subjects: 0106 biological sciences, geography, geography.geographical_feature_category, Ecology, 010604 marine biology & hydrobiology, Drainage basin, Biodiversity, Rainforest, STREAMS, Aquatic Science, Biology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Habitat, Temperate climate, Freshwater fish, Species richness
Abstract: Freshwater ecology templates were developed in temperate streams, but whether they also apply to tropical streams that harbour a higher biological diversity than their temperate counterparts remains uncertain. This is particularly true for tropical fish assemblages inhabiting small streams that have been less studied than larger, higher-order lowland streams. Here, we disentangled the strength of spatial (longitudinal and environmental) drivers, and scale-specific (drainage basin, reach and local scale) determinants of species richness and composition of freshwater fish assemblages inhabiting small streams in French Guiana. We found that species richness increased from upstream to downstream but also with increasing local habitat structural diversity independently of stream position in the upstream–downstream gradient. This pattern was shared by the two most speciose fish orders (Characiformes and Siluriformes), demonstrating that species addition rather than species replacement shaped species richness in these assemblages. Species composition of fish assemblages was determined equally by their spatial structure within drainage and by the environment, and assemblages differed both with distance and along an upstream–downstream gradient. The environmental effect on species assemblages indicated by the fact that almost all environmental descriptors had slight but nonetheless significant effects on assemblage composition, probably reflecting species-specific responses to the local environment. In contrast, despite a strong micro-endemism between drainages for some taxa, assemblages were only slightly affected by river drainage identity, since widespread species were a common constituent of assemblages in all rivers. We identified five species assemblages characterising different local habitat features from torrential areas to lowland muddy areas. We also distinguished fish assemblages from confluence areas with larger rivers, which differed from the other five assemblages. The fish zonation patterns we report can constitute a benchmark for future studies measuring the impact of anthropogenic disturbances on Neotropical forest streams.
Published: 2017

47. Cytoplasmic overexpression of RNA-binding protein HuR is a marker of poor prognosis in meningioma, and HuR knockdown decreases meningioma cell growth and resistance to hypoxia

Author: Matthieu Peyre, Fabien Rech, François Labrousse, Jean-Louis Guéant, Jean-Matthieu Casse, Guillaume Gauchotte, Laurent Vallar, Charlène Vigouroux, Rémi Houlgatte, Tony Kaoma, Déborah Helle, Jean-Michel Vignaud, Lydia Brochin, Sébastien Hergalant, Shyue-Fang Battaglia-Hsu, Nutrition-Génétique et Exposition aux Risques Environnementaux (NGERE), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lorraine (UL), Service de Pathologie [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Luxembourg Institute of Health (LIH), Service de Neurochirurgie [CHRU Nancy], Institut des Neurosciences de Montpellier (INM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Service d'Anatomie Pathologique [CHU Limoges], CHU Limoges, M2TP, Division of Biochemistry and Molecular Biology [CHRU Nancy], Centre de Ressources Biologiques - [Nancy] (CRB Nancy), Institut des Neurosciences de Montpellier - Déficits sensoriels et moteurs (INM), Service de Neurochirurgie [CHU Pitié-Salpêtrière], 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: Adult, Male, 0301 basic medicine, Cytoplasm, [SDV]Life Sciences [q-bio], Apoptosis, [SDV.CAN]Life Sciences [q-bio]/Cancer, RNA-binding protein, Kaplan-Meier Estimate, Biology, ELAV-Like Protein 1, Pathology and Forensic Medicine, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Downregulation and upregulation, Cell Line, Tumor, Biomarkers, Tumor, Gene Knockdown Techniques, Humans, ComputingMilieux_MISCELLANEOUS, Aged, Retrospective Studies, Aged, 80 and over, Observer Variation, Gene knockdown, Cell growth, Gene Expression Profiling, RNA-Binding Proteins, Middle Aged, Prognosis, Molecular biology, Cell Hypoxia, Neoplasm Proteins, Up-Regulation, Gene Expression Regulation, Neoplastic, 030104 developmental biology, HIF1A, Cell culture, 030220 oncology & carcinogenesis, Cancer research, Female, Neoplasm Grading, Meningioma, Cell Division
Abstract: HuR regulates cytoplasmic mRNA stability and translatability, and the HuR expression level has been shown to correlate with poor disease outcome in several cancer types; however, the prognostic value and potential pro-oncogenic properties of HuR in meningioma remain unclear. Thus, in the present study, we analysed 85 meningioma tissue samples to establish the relationship between HuR expression, tumour cell proliferation, and/or patient survival. In addition, we examined the anti-proliferative effects of HuR knockdown in two meningioma cell lines (IOMM-Lee and Ben-Men-1) and conducted transcriptome-wide analyses (IOMM-Lee cells) to elucidate the molecular consequences of HuR knockdown. The results of the present study showed HuR cytoplasmic expression to correlate positively with tumour grade (p = 1.2 × 10-8 ) and negatively with progression-free and overall survival (p = 0.01) time in human meningioma tissues. In vitro, siHuR-induced HuR knockdown was shown to reduce the growth of both Ben-Men-1 (p = 2 × 10-8 ) and IOMM-Lee (p = 4 × 10-9 ) cells. Transcriptome analyses revealed HuR knockdown in IOMM-Lee cells to deregulate the HIF1A signalling pathway (p = 1.5 × 10-6 ) and to up-regulate the expression of genes essential for the assembly of the cytoplasmic mRNA processing body, global genome nucleotide-excision repair, poly(A)-specific ribonuclease activity, the positive regulation of apoptosis and of cell cycle arrest, and the negative regulation of RNA splicing [p(FDR)
Published: 2017

48. Individuals, populations, and timespace

Author: Salikoko S. Mufwene and Cécile B. Vigouroux
Subjects: 060201 languages & linguistics, Ecology, Ecology (disciplines), 05 social sciences, 0507 social and economic geography, 06 humanities and the arts, Space (commercial competition), Biology, Vitality, Ecolinguistics, Variation (linguistics), Sociology of language, 0602 languages and literature, 050703 geography, Macroecology, Sociolinguistics
Abstract: In the present article we distinguish the concept ofecology of languageas articulated inMufwene (2001ff)from that ofecolinguisticsdeveloped especially byMühlhäusler (1996ff),Fill and Mühlhäusler (2001),Couto (2009), and several contributors toFill and Benz (to appear). We explain how Mufwene’secology of languageconcept, inspired primarily by macroecology, applies to language evolution. We articulate various factors internal and external to a language that bear on how it emerged phylogenetically, underwent particular structural changes, and, in some cases, may have speciated into separate varieties. The external ecology also influences the vitality of languages, rolling the dice on whether they thrive or are endangered. Because these particular phenomena have been elaborately discussed in Mufwene’s earlier publications, we devote more space to explaining how the notion oflanguage ecology, as others call it, also applies as a useful heuristic tool to qualitative sociolinguistics.
Published: 2017

49. Crop wild relative conservation: Wild yams are not that wild

Author: Nora Scarcelli, Hâna Chaïr, Sandrine Causse, Raphaël Vesta, Thomas L.P. Couvreur, Yves Vigouroux, Institut de Recherche pour le Développement (IRD [France-Sud]), Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)
Subjects: 0301 basic medicine, Introgression, [SDV]Life Sciences [q-bio], Chloroplast, F30 - Génétique et amélioration des plantes, Gene flow, Crop, 03 medical and health sciences, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Cultivar, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation, Hybrid, 2. Zero hunger, Genetic diversity, biology, food and beverages, F70 - Taxonomie végétale et phytogéographie, 15. Life on land, biology.organism_classification, 030104 developmental biology, Crop wild relatives, Dioscorea rotundata, Agronomy, Crop wild relative, NGS, Yam, P01 - Conservation de la nature et ressources foncières, Crop-to-wild gene flow
Abstract: Extension of land use has been the main way to increase agricultural production to date. Natural habitats have consequently decreased and became increasingly fragmented, putting high pressure on the wild relatives of main crops. In this study, we assessed the diversity of wild relatives and cultivated varieties of yam, Dioscorea rotundata , a tuber crop grown in West Africa. Using nuclear markers, we showed that 19% of the wild plants were in fact hybrids between wild and cultivated varieties. Using whole chloroplast sequences, our results suggest that hybridization may be even stronger, with 43% of the wild individuals presenting either chloroplast or nuclear introgression with the cultivated yams. Adaptation of agriculture to current new pathogen outbreaks and ongoing climatic changes will require mining the vast diversity found in crops wild relatives. However, our study suggests that wild yam diversity is already largely tainted by crop-to-wild gene flow. The need to focus on in-situ wild yam conservation is even more crucial, since today, ex-situ genebanks contain nearly no wild yam accessions. Data profile Microsatellite allele scoring is available as an online appendix; NGS data (.bam file) are available as SRA bioproject PRJNA383673.
Published: 2017

50. Extracellular matrix remodeling and transforming growth factor-β signaling abnormalities induced by lamin A/C variants that cause lipodystrophy

Author: Wei Wu, Corinne Vigouroux, Jacqueline Capeau, Véronique Béréziat, Caroline Le Dour, Howard J. Worman, Columbia University [New York], Institute of Geotechnical Engineering University of Natural Resources and Applied Life Sciences Feistmantelstr. 4. 1180 Vienna, CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Université Pierre et Marie Curie - Paris 6 (UPMC), Sorbonne Universités (COMUE), Institut de Cardiométabolisme et Nutrition = Institute of Cardiometabolism and Nutrition [CHU Pitié Salpêtrière] (IHU ICAN), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), and Belgian Institute for Space Aeronomy / Institut d'Aéronomie Spatiale de Belgique (BIRA-IASB)
Subjects: 0301 basic medicine, Male, medicine.medical_specialty, [SDV]Life Sciences [q-bio], adipocytes, Adipose tissue, QD415-436, Gene mutation, Biochemistry, Cell Line, Extracellular matrix, 03 medical and health sciences, Mice, 0302 clinical medicine, Endocrinology, Fibrosis, Transforming Growth Factor beta, Internal medicine, medicine, Animals, Humans, Research Articles, Aged, Aged, 80 and over, Mice, Knockout, biology, Chemistry, fibrosis, Cell Biology, Transforming growth factor beta, nuclear envelope, Middle Aged, medicine.disease, Lamin Type A, Cell biology, Extracellular Matrix, Lipodystrophy, Familial Partial, adipose tissue, 030104 developmental biology, Gene Expression Regulation, Matrix Metalloproteinase 9, 030220 oncology & carcinogenesis, Mutation, biology.protein, Lipodystrophy, Lamin, Transforming growth factor
Abstract: Mutations in the lamin A/C gene encoding nuclear lamins A and C (lamin A/C) cause familial partial lipodystrophy type 2 (FPLD2) and related lipodystrophy syndromes. These are mainly characterized by redistribution of adipose tissue associated with insulin resistance. Several reports suggest that alterations in the extracellular matrix of adipose tissue leading to fibrosis play a role in the pathophysiology of lipodystrophy syndromes. However, the extent of extracellular matrix alterations in FPLD2 remains unknown. We show significantly increased fibrosis and altered expression of genes encoding extracellular matrix proteins in cervical subcutaneous adipose tissue from a human subject with FLPD2. Similar extracellular matrix alterations occur in adipose tissue of transgenic mice expressing an FPLD2-causing human lamin A variant and in cultured fibroblasts from human subjects with FPLD2 and related lipodystrophies. These abnormalities are associated with increased transforming growth factor-β signaling and defects in matrix metalloproteinase 9 activity. Our data demonstrate that lamin A/C gene mutations responsible for FPLD2 and related lipodystrophies are associated with transforming growth factor-β activation and an extracellular matrix imbalance in adipose tissue, suggesting that targeting these alterations could be the basis of novel therapies.
Published: 2017

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