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1. Genomic variation of European beech reveals signals of local adaptation despite high levels of phenotypic plasticity

Author

Desanka Lazic, Cornelia Geßner, Katharina J. Liepe, Isabelle Lesur-Kupin, Malte Mader, Céline Blanc-Jolivet, Dušan Gömöry, Mirko Liesebach, Santiago C. González-Martínez, Matthias Fladung, Bernd Degen, and Niels A. Müller

Subjects
Science
Abstract

Abstract Local adaptation is key for ecotypic differentiation and species evolution. Understanding underlying genomic patterns can allow the prediction of future maladaptation and ecosystem stability. Here, we report the whole-genome resequencing of 874 individuals from 100 range-wide populations of European beech (Fagus sylvatica L.), an important forest tree species in Europe. We show that genetic variation closely mirrors geography with a clear pattern of isolation-by-distance. Genome-wide analyses for genotype-environment associations (GEAs) identify relatively few potentially adaptive variants after correcting for an overwhelming signal of statistically significant but non-causal GEAs. We characterize the single high confidence genomic region and pinpoint a candidate gene possibly involved in winter temperature adaptation via modulation of spring phenology. Surprisingly, allelic variation at this locus does not result in any apparent fitness differences in a common garden. More generally, reciprocal transplant experiments across large climate distances suggest extensive phenotypic plasticity. Nevertheless, we find indications of polygenic adaptation which may be essential in natural ecosystems. This polygenic signal exhibits broad- and fine-scale variation across the landscape, highlighting the relevance of spatial resolution. In summary, our results emphasize the importance, but also exemplify the complexity, of employing natural genetic variation for forest conservation under climate change.

Published
2024
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2. Apelin-13 administration allows for norepinephrine sparing in a rat model of cecal ligation and puncture-induced septic shock

Author

William Salvail, Dany Salvail, Frédéric Chagnon, and Olivier Lesur

Subjects
Apelin, Norepinephrine, Septic shock, Experimental model, Cecal ligation and puncture, Medical emergencies. Critical care. Intensive care. First aid, RC86-88.9
Abstract

Abstract Background Infusion of exogenous catecholamines (i.e., norepinephrine [NE] and dobutamine) is a recommended treatment for septic shock with myocardial dysfunction. However, sustained catecholamine infusion is linked to cardiac toxicity and impaired responsiveness. Several pre-clinical and clinical studies have investigated the use of alternative vasopressors in the treatment of septic shock, with limited benefits and generally no effect on mortality. Apelin-13 (APL-13) is an endogenous positive inotrope and vasoactive peptide and has been demonstrated cardioprotective with vasomodulator and sparing life effects in animal models of septic shock. A primary objective of this study was to evaluate the NE-sparing effect of APL-13 infusion in an experimental sepsis-induced hypotension. Methods For this goal, sepsis was induced by cecal ligation and puncture (CLP) in male rats and the arterial blood pressure (BP) monitored continuously via a carotid catheter. Monitoring, fluid resuscitation and experimental treatments were performed on conscious animals. Based on pilot assays, normal saline fluid resuscitation (2.5 mL/Kg/h) was initiated 3 h post-CLP and maintained up to the endpoint. Thus, titrated doses of NE, with or without fixed-doses of APL-13 or the apelin receptor antagonist F13A co-infusion were started when 20% decrease of systolic BP (SBP) from baseline was achieved, to restore SBP values ≥ 115 ± 1.5 mmHg (baseline average ± SEM). Results A reduction in mean NE dose was observed with APL-13 but not F13A co-infusion at pre-determined treatment time of 4.5 ± 0.5 h (17.37 ± 1.74 µg/Kg/h [APL-13] vs. 25.64 ± 2.61 µg/Kg/h [Control NE] vs. 28.60 ± 4.79 µg/Kg/min [F13A], P = 0.0491). A 60% decrease in NE infusion rate over time was observed with APL-13 co-infusion, (p = 0.008 vs NE alone), while F13A co-infusion increased the NE infusion rate over time by 218% (p = 0.003 vs NE + APL-13). Associated improvements in cardiac function are likely mediated by (i) enhanced left ventricular end-diastolic volume (0.18 ± 0.02 mL [Control NE] vs. 0.30 ± 0.03 mL [APL-13], P = 0.0051), stroke volume (0.11 ± 0.01 mL [Control NE] vs. 0.21 ± 0.01 mL [APL-13], P

Published
2024
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3. Resilience of genetic diversity in forest trees over the Quaternary

Author

Milesi, Pascal, Kastally, Chedly, Dauphin, Benjamin, Cervantes, Sandra, Bagnoli, Francesca, Budde, Katharina B., Cavers, Stephen, Fady, Bruno, Faivre-Rampant, Patricia, González-Martínez, Santiago C., Grivet, Delphine, Gugerli, Felix, Jorge, Véronique, Lesur Kupin, Isabelle, Ojeda, Dario I., Olsson, Sanna, Opgenoorth, Lars, Pinosio, Sara, Plomion, Christophe, Rellstab, Christian, Rogier, Odile, Scalabrin, Simone, Scotti, Ivan, Vendramin, Giovanni G., Westergren, Marjana, Lascoux, Martin, and Pyhäjärvi, Tanja

Published
2024
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7. Whole-genome screening for near-diagnostic genetic markers for four western European white oak species identification

Author

Antoine Kremer, Adline Delcamp, Isabelle Lesur, Stefanie Wagner, Christian Rellstab, Erwan Guichoux, and Thibault Leroy

Subjects
Quercus, Diagnosticity, Genetic differentiation, Pool-seq data, Captured sequences, Forestry, SD1-669.5
Abstract

Abstract Key message Mining genome-wide DNA sequences enabled the discovery of near-diagnostic markers for species assignment in four European white oaks (Quercus petraea (Matt.) Liebl., Quercus pubescens Willd., Quercus pyrenaica Willd., and Quercus robur L.) despite their low interspecific differentiation. Near-diagnostic markers are almost fully fixed in one species and absent in the three others. As a result, only a handful of markers are needed for species identification, making this genetic assay a very promising operational taxonomic assignment procedure in research and forestry. Context Identifying species in the European white oak complex has been a long-standing concern in taxonomy, evolution, forest research, and management. Quercus petraea (Matt.) Liebl., Q. robur L., Q. pubescens Willd., and Q. pyrenaica Willd. are part of this species complex in western temperate Europe and hybridize in mixed stands, challenging species identification. Aims Our aim was to identify near-diagnostic single-nucleotide polymorphisms (SNPs) for each of the four species that are suitable for routine use and rapid diagnosis in research and applied forestry. Methods We first scanned existing whole-genome and target-capture data sets in a reduced number of samples (training set) to identify candidate diagnostic SNPs, i.e., genomic positions being characterized by a reference allele in one species and by the alternative allele in all other species. Allele frequencies of the candidates SNPs were then explored in a larger, range-wide sample of populations in each species (validation step). Results We found a subset of 38 SNPs (10 for Q. petraea, 7 for Q. pubescens, 9 for Q. pyrenaica, and 12 for Q. robur) that showed near-diagnostic features across their species distribution ranges with Q. pyrenaica and Q. pubescens exhibiting the highest (0.876) and lowest (0.747) diagnosticity, respectively. Conclusions We provide a new, efficient, and reliable molecular tool for the identification of the species Q. petraea, Q. robur, Q. pubescens, and Q. pyrenaica, which can be used as a routine tool in forest research and management. This study highlights the resolution offered by whole-genome sequencing data to design near-diagnostic marker sets for taxonomic assignment, even for species complexes with relatively low differentiation.

Published
2024
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9. Lack of association between classical HLA genes and asymptomatic SARS-CoV-2 infection

Author

Astrid Marchal, Elizabeth T. Cirulli, Iva Neveux, Evangelos Bellos, Ryan S. Thwaites, Kelly M. Schiabor Barrett, Yu Zhang, Ivana Nemes-Bokun, Mariya Kalinova, Andrew Catchpole, Stuart G. Tangye, András N. Spaan, Justin B. Lack, Jade Ghosn, Charles Burdet, Guy Gorochov, Florence Tubach, Pierre Hausfater, Clifton L. Dalgard, Shen-Ying Zhang, Qian Zhang, Christopher Chiu, Jacques Fellay, Joseph J. Grzymski, Vanessa Sancho-Shimizu, Laurent Abel, Jean-Laurent Casanova, Aurélie Cobat, Alexandre Bolze, Alessandro Aiuti, Saleh Al-Muhsen, Fahd Al-Mulla, Ali Amara, Mark S. Anderson, Evangelos Andreakos, Andrés A. Arias, Lisa M. Arkin, Hagit Baris Feldman, Paul Bastard, Alexandre Belot, Catherine M. Biggs, Dusan Bogunovic, Anastasiia Bondarenko, Alessandro Borghesi, Ahmed A. Bousfiha, Petter Brodin, Yenan Bryceson, Manish J. Butte, Giorgio Casari, John Christodoulou, Roger Colobran, Antonio Condino-Neto, Stefan N. Constantinescu, Megan A. Cooper, Murkesh Desai, Beth A. Drolet, Xavier Duval, Jamila El Baghdadi, Philippine Eloy, Sara Espinosa-Padilla, Carlos Flores, José Luis Franco, Antoine Froidure, Peter K. Gregersen, Bodo Grimbacher, Filomeen Haerynck, David Hagin, Rabih Halwani, Lennart Hammarström, James R. Heath, Elena W.Y. Hsieh, Eystein Husebye, Kohsuke Imai, Yuval Itan, Emmanuelle Jouanguy, Elżbieta Kaja, Timokratis Karamitros, Kai Kisand, Cheng-Lung Ku, Yu-Lung Lau, Yun Ling, Carrie L. Lucas, Tom Maniatis, Davood Mansouri, László Maródi, France Mentré, Isabelle Meyts, Joshua D. Milner, Kristina Mironska, Trine H. Mogensen, Tomohiro Morio, Lisa F.P. Ng, Luigi D. Notarangelo, Antonio Novelli, Giuseppe Novelli, Cliona O'Farrelly, Satoshi Okada, Keisuke Okamoto, Tayfun Ozcelik, Qiang Pan-Hammarström, Jean W. Pape, Rebeca Perez de Diego, Jordi Perez-Tur, David S. Perlin, Graziano Pesole, Anna M. Planas, Carolina Prando, Aurora Pujol, Anne Puel, Lluis Quintana-Murci, Sathishkumar Ramaswamy, Laurent Renia, Igor Resnick, Carlos Rodríguez-Gallego, Anna Sediva, Mikko R.J. Seppänen, Mohammad Shahrooei, Anna Shcherbina, Ondrej Slaby, Andrew L. Snow, Pere Soler-Palacín, Vassili Soumelis, Ivan Tancevski, Ahmad Abou Tayoun, Şehime Gülsün Temel, Christian Thorball, Pierre Tiberghien, Sophie Trouillet-Assant, Stuart E. Turvey, K. M. Furkan Uddin, Mohammed J. Uddin, Diederik van de Beek, Donald C. Vinh, Horst von Bernuth, Joost Wauters, Mayana Zatz, Pawel Zawadzki, Serge Bureau, Yannick Vacher, Anne Gysembergh-Houal, Lauren Demerville, Abla Benleulmi-Chaachoua, Sebastien Abad, Radhiya Abassi, Abdelrafie Abdellaoui, Abdelkrim Abdelmalek, Hendy Abdoul, Helene Abergel, Fariza Abeud, Sophie Abgrall, Noemie Abisror, Marylise Adechian, Nordine Aderdour, Hakeem Farid Admane, Frederic Adnet, Sara Afritt, Helene Agostini, Claire Aguilar, Sophie Agut, Tommaso Francesco Aiello, Marc Ait Kaci, Hafid Ait Oufella, Gokula Ajeenthiravasan, Virginie Alauzy, Fanny Alby-Laurent, Lucie Allard, Marie-Alexandra Alyanakian, Blanca Amador Borrero, Sabrina Amam, Lucile Amrouche, Marc Andronikof, Dany Anglicheau, Nadia Anguel, Djillali Annane, Mohammed Aounzou, Caroline Aparicio, Gladys Aratus, Jean-Benoit Arlet, Jeremy Arzoine, Elisabeth Aslangul, Mona Assefi, Adeline Aubry, Laetitia Audiffred, Etienne Audureau, Christelle Nathalie Auger, Jean-Charles Auregan, Celine Awotar, Sonia Ayllon Milla, Delphine Azan, Laurene Azemar, Billal Azzouguen, Marwa Bachir Elrufaai, Aïda Badsi, Prissile Bakouboula, Coline Balcerowiak, Fanta Balde, Elodie Baldivia, Eliane-Flore Bangamingo, Amandine Baptiste, Fanny Baran-Marszak, Caroline Barau, Nathalie Barget, Flore Baronnet, Romain Barthelemy, Jean-Luc Baudel, Camille Baudry, Elodie Baudry, Laurent Beaugerie, Adel Belamri, Nicolas Belaube, Rhida Belilita, Pierre Bellassen, Rawan Belmokhtar, Isabel Beltran, Ruben Benainous, Mourad Benallaoua, Robert Benamouzig, Amélie Benbara, Jaouad Benhida, Anis Benkhelouf, Jihene Benlagha, Chahinez Benmostafa, Skander Benothmane, Miassa Bentifraouine, Laurence Berard, Quentin Bernier, Enora Berti, Astrid Bertier, Laure Berton, Simon Bessis, Alexandra Beurton, Celine Bianco, Clara Bianquis, Frank Bidar, Philippe Blanche, Clarisse Blayau, Alexandre Bleibtreu, Emmanuelle Blin, Coralie Bloch-Queyrat, Marie-Christophe Boissier, Diane Bollens, Marion Bolzoni, Rudy pierre Bompard, Nicolas Bonnet, Justine Bonnouvrier, Shirmonecrystal Botha, Wissam Boucenna, Fatiha Bouchama, Olivier Bouchaud, Hanane Bouchghoul, Taoueslylia Boudjebla, Noel Boudjema, Catherine Bouffard, Adrien Bougle, Meriem Bouguerra, Leila Bouras, Agnes Bourcier, Anne Bourgarit Durand, Anne Bourrier, Fabrice Bouscarat, Diane Bouvry, Nesrine Bouziri, Ons Bouzrara, Sarah Bribier, Delphine Brugier, Melanie Brunel, Eida Bui, Anne Buisson, Iryna Bukreyeva, Côme Bureau, Jacques Cadranel, Johann Cailhol, Ruxandra Calin, Clara Campos Vega, Pauline Canavaggio, Marta Cancella, Delphine Cantin, Albert Cao, Lionel Carbillon, Nicolas Carlier, Clementine Cassard, Guylaine Castor, Marion Cauchy, Olivier Cha, Benjamin Chaigne, Salima Challal, Karine Champion, Patrick Chariot, Julie Chas, Simon Chauveau, Anthony Chauvin, Clement Chauvin, Nathalie Chavarot, Kamélia Chebbout, Mustapha Cherai, Ilaria Cherubini, Amelie Chevalier, Thibault Chiarabini, Thierry Chinet, Richard Chocron, Pascaline Choinier, Juliette Chommeloux, Christophe Choquet, Laure Choupeaux, Benjamin Chousterman, Dragosmarius Ciocan, Ada Clarke, Gaëlle Clavere, Florian Clavier, Karine Clement, Sebastien Clerc, Yves Cohen, Fleur Cohen, Adrien Cohen, Audrey Coilly, Hester Colboc, Pauline Colin, Magalie Collet, Chloé Comarmond, Emeline Combacon, Alain Combes, Celine Comparon, Jean-Michel Constantin, Hugues Cordel, Anne-Gael Cordier, Adrien Costantini, Nathalie Costedoat Chalumeau, Camille Couffignal, Doriane Coupeau, Alain Creange, Yannie Cuvillier Lamarre, Charlène Da Silveira, Sandrine Dautheville Guibal El Kayani, Nathalie De Castro, Yann De Rycke, Lucie Del Pozo, Quentin Delannoy, Mathieu Delay, Robin Deleris, Juliette Delforge, Laëtitia Delphine, Noemie Demare, Sophie Demeret, Alexandre Demoule, Aurore Deniau, François Depret, Sophie Derolez, Ouda Derradji, Nawal Derridj, Vincent Descamps, Lydia Deschamps, Celine Desconclois, Cyrielle Desnos, Karine Desongins, Robin Dhote, Benjamin Diallo, Morgane Didier, Myriam Diemer, Stephane Diez, Juliette Djadi-Prat, Fatima-Zohra Djamouri Monnory, Siham Djebara, Naoual Djebra, Minette Djietcheu, Hadjer Djillali, Nouara Djouadi, Severine Donneger, Catarina Dos Santos, Nathalie Dournon, Martin Dres, Laura Droctove, Marie Drogrey, Margot Dropy, Elodie Drouet, Valérie Dubosq, Evelyne Dubreucq, Estelle Dubus, Boris Duchemann, Thibault Duchenoy, Emmanuel Dudoignon, Romain Dufau, Florence Dumas, Clara Duran, Emmanuelle Duron, Antoine Durrbach, Claudine Duvivier, Nathan Ebstein, Jihane El Khalifa, Alexandre Elabbadi, Caroline Elie, Gabriel Ernotte, Anne Esling, Martin Etienne, Xavier Eyer, Muriel Sarah Fartoukh, Takoua Fayali, Marion Fermaut, Arianna Fiorentino, Souha Fliss, Marie-Céline Fournier, Benjamin Fournier, Hélène Francois, Olivia Freynet, Yvann Frigout, Isaure Fromont, Axelle Fuentes, Thomas Furet, Joris Galand, Marc Garnier, Agnes Gaubert, Stéphane Gaudry, Samuel Gaugain, Damien Gauthier, Maxime Gautier, Sophie Georgin-Lavialle, Daniela Geromin, Mohamed Ghalayini, Bijan Ghaleh, Myriam Ghezal, Aude Gibelin, Linda Gimeno, Benoit Girard, Bénédicte Giroux Leprieur, Doryan Gomes, Elisabete Gomes-Pires, Anne Gouge, Amel Gouja, Helene Goulet, Sylvain Goupil, Jeanne Goupil De Bouille, Julien Gras, Segolene Greffe, Lamiae Grimaldi, Paul Guedeney, Bertrand Guidet, Matthias Guillo, Mariechristelle Gulczynski, Tassadit Hadjam, Didier Haguenauer, Soumeya Hammal, Nadjib Hammoudi, Olivier Hanon, Anarole Harrois, Coraline Hautem, Guillaume Hekimian, Nicholas Heming, Olivier Hermine, Sylvie Ho, Marie Houllier, Benjamin Huot, Tessa Huscenot, Wafa Ibn Saied, Ghilas Ikherbane, Meriem Imarazene, Patrick Ingiliz, Lina Iratni, Stephane Jaureguiberry, Jean-Francois Jean-Marc, Deleena Jeyarajasingham, Pauline Jouany, Veronique Jouis, Clement Jourdaine, Ouifiya Kafif, Rim Kallala, Sandrine Katsahian, Lilit Kelesyan, Vixra Keo, Flora Ketz, Warda Khamis, Enfel Khelili, Mehdi Khellaf, Christy Gaëlla Kotokpo Youkou, Ilias Kounis, Gaelle Kpalma, Jessica Krause, Vincent Labbe, Karine Lacombe, Jean-Marc Lacorte, Anne Gaelle Lafont, Emmanuel Lafont, Lynda Lagha, Lionel Lamhaut, Aymeric Lancelot, Cecilia Landman, Fanny Lanternier, Cecile Larcheveque, Caroline Lascoux Combe, Ludovic Lassel, Benjamin Laverdant, Christophe Lavergne, Jean-Rémi Lavillegrand, Pompilia Lazureanu, Loïc Le Guennec, Lamia Leberre, Claire Leblanc, Marion Leboyer, Francois Lecomte, Marine Lecorre, Romain Leenhardt, Marylou Lefebvre, Bénédicte Lefebvre, Paul Legendre, Anne Leger, Laurence Legros, Justyna Legrosse, Sébastien Lehuunghia, Julien Lemarec, Jeremie Leporrier-Ext, Manon Lesein, Hubert Lesur, Vincent Levy, Albert Levy, Edwige Lopes, Amanda Lopes, Vanessa Lopez, Julien Lopinto, Olivier Lortholary, Badr Louadah, Bénédicte Loze, Marie-Laure Lucas, Axelle Lucasamichi, Liem Binh Luong, Arouna Magazimama-Ext, David Maingret, Lakhdar Mameri, Philippe Manivet, Cylia Mansouri, Estelle Marcault, Jonathan Marey, Nathalie Marin, Clémence Marois, Olivier Martin, Lou Martineau, Cannelle Martinez-Lopez, Pierre Martyniuck, Pauline Mary De Farcy, Nessrine Marzouk, Rafik Masmoudi, Alexandre Mebazaa, Frédéric Mechai, Fabio Mecozzi, Chamseddine Mediouni, Bruno Megarbane, Mohamed Meghadecha, Élodie Mejean, Arsene Mekinian, Nour Mekki Abdelhadi, Rania Mekni, Thinhinan Sabrina Meliti, Breno Melo Lima, Paris Meng, Soraya Merbah, Fadhila Messani, Yasmine Messaoudi, Baboo-Irwinsingh Mewasing, Lydia Meziane, Carole Michelot-Burger, Françoise Mignot, Fadi Hillary Minka, Makoto Miyara, Pierre Moine, Jean-Michel Molina, Anaïs Montegnies-Boulet, Alexandra Monti, Claire Montlahuc, Anne-Lise Montout, Alexandre Moores, Caroline Morbieu, Helene Mortelette, Stéphane Mouly, Rosita Muzaffar, Cherifa Iness Nacerddine, Marine Nadal, Hajer Nadif, Kladoum Nassarmadji, Pierre Natella, Sandrine Ndingamondze, Stefan Neraal, Caroline Nguyen, Bao N'Guyen, Isabelle Nion Larmurier, Luc Nlomenyengue, Nicolas Noel, Hilario Nunes, Edris Omar, Zineb Ouazene, Elise Ouedraogo, Wassila Ouelaa, Anissa Oukhedouma, Yasmina Ould Amara, Herve Oya, Johanna Oziel, Thomas Padilla, Elena Paillaud, Solenne Paiva, Beatrice Parfait, Perrine Parize, Christophe Parizot, Antoine Parrot, Arthur Pavot, Laetitia Peaudecerf, Frédéric Pene, Marion Pepin, Julie Pernet, Claire Pernin, Mylène Petit, Olivier Peyrony, Marie-Pierre Pietri, Olivia Pietri, Marc Pineton De Chambrun, Michelle Pinson, Claire Pintado, Valentine Piquard, Christine Pires, Benjamin Planquette, Sandrine Poirier, Anne-Laure Pomel, Stéphanie Pons, Diane Ponscarme, Annegaelle Pourcelot, Valérie Pourcher, Anne Pouvaret, Florian Prever, Miresta Previlon, Margot Prevost, Marie-Julie Provoost, Cyril Quemeneur, Cédric Rafat, Agathe Rami, Brigitte Ranque, Maurice Raphael, Jean Herle Raphalen, Anna Rastoin, Mathieu Raux, Amani Rebai, Michael Reby, Alexis Regent, Asma Regrag, Matthieu Resche-Rigon, Quentin Ressaire, Christian Richard, Mariecaroline Richard, Maxence Robert, Benjamin Rohaut, Camille Rolland-Debord, Jacques Ropers, Anne-Marie Roque-Afonso, Charlotte Rosso, Mélanie Rousseaux, Nabila Rousseaux, Swasti Roux, Lorène Roux, Claire Rouzaud, Antoine Rozes, Emma Rubenstein, Jean-Marc Sabate, Sheila Sabet, Sophie-Caroline Sacleux, Nathalie Saidenberg Kermanach, Faouzi Saliba, Dominique Salmon, Laurent Savale, Guillaume Savary, Rebecca Sberro, Anne Scemla, Frederic Schlemmer, Mathieu Schwartz, Saïd Sedfi, Samia Sefir-Kribel, Philippe Seksik, Pierre Sellier, Agathe Selves, Nicole Sembach, Luca Semerano, Marie-Victoire Senat, Damien Sene, Alexandra Serris, Lucile Sese, Naima Sghiouar, Johanna Sigaux, Martin Siguier, Johanne Silvain, Noémie Simon, Tabassome Simon, Lina Innes Skandri, Miassa Slimani, Aurélie Snauwaert, Harry Sokol, Heithem Soliman, Nisrine Soltani, Benjamin Soyer, Gabriel Steg, Lydia Suarez, Tali-Anne Szwebel, Kossi Taffame, Yacine Tandjaoui-Lambiotte, Claire Tantet, Mariagrazia Tateo, Igor Theodose, Pierre clement Thiebaud, Caroline Thomas, Kelly Tiercelet, Julie Tisserand, Carole Tomczak, Krystel Torelino, Fatima Touam-Ext, Lilia Toumi, Gustave Toury, Mireille Toy-Miou, Olivia Tran Dinh Thanh Lien, Alexy Trandinh, Jean-Marc Treluyer, Baptiste Trinque, Jennifer Truchot, Sarah Tubiana, Simone Tunesi, Matthieu Turpin, Agathe Turpin, Tomas Urbina, Rafael Usubillaga Narvaez, Yurdagul Uzunhan, Prabakar Vaittinadaayar, Arnaud Valent, Maelle Valentian, Nadia Valin, Hélène Vallet, Marina Vaz, Miguel-Alejandro Vazquezibarra, Benoit Vedie, Laetitia Velly, Celine Verstuyft, Cedric Viallette, Eric Vicaut, Dorothee Vignes, Damien Vimpere, Myriam Virlouvet, Guillaume Voiriot, Lena Voisot, Emmanuel Weiss, Nicolas Weiss, Anaïs Winchenne, Youri Yordanov, Lara Zafrani, Mohamad Zaidan, Wissem Zaidi, Cathia Zak, Aida Zarhrate-Ghoul, Ouassila Zatout, Suzanne Zeino, Michel Zeitouni, Naïma Zemirli, Lorene Zerah, Ounsa Zia, Marianne Ziol, Oceane Zolario, Julien Zuber, Claire Andrejak, François Angoulvant, Delphine Bachelet, Marie Bartoli, Romain Basmaci, Sylvie Behillil, Marine Beluze, Dehbia Benkerrou, Krishna Bhavsar, Lila Bouadma, Sabelline Bouchez, Maude Bouscambert, Minerva Cervantes-Gonzalez, Anissa Chair, Catherine Chirouze, Alexandra Coelho, Sandrine Couffin-Cadiergues, Eric d’Ortenzio, Marie-Pierre Debray, Laurene Deconinck, Dominique Deplanque, Diane Descamps, Mathilde Desvallée, Alpha Diallo, Alphonsine Diouf, Céline Dorival, François Dubos, Brigitte Elharrar, Vincent Enouf, Hélène Esperou, Marina Esposito-Farese, Manuel Etienne, Eglantine Ferrand Devouge, Nathalie Gault, Alexandre Gaymard, Tristan Gigante, Morgane Gilg, Jérémie Guedj, Alexandre Hoctin, Isabelle Hoffmann, Ikram Houas, Jean-Sébastien Hulot, Salma Jaafoura, Florentia Kaguelidou, Sabrina Kali, Antoine Khalil, Coralie Khan, Cédric Laouénan, Samira Laribi, Minh Le, Quentin Le Hingrat, Soizic Le Mestre, Hervé Le Nagard, François-Xavier Lescure, Sophie Letrou, Yves Levy, Bruno Lina, Guillaume Lingas, Jean-Christophe Lucet, Denis Malvy, Marina Mambert, Amina Meziane, Hugo Mouquet, Jimmy Mullaert, Nadège Neant, Duc Nguyen, Marion Noret, Saad Nseir, Aurélie Papadopoulos, Christelle Paul, Nathan Peiffer-Smadja, Thomas Perpoint, Ventzislava Petrov-Sanchez, Gilles Peytavin, Huong Pham, Olivier Picone, Oriane Puéchal, Christian Rabaud, Manuel Rosa-Calatrava, Bénédicte Rossignol, Patrick Rossignol, Carine Roy, Marion Schneider, Richa Su, Coralie Tardivon, Marie-Capucine Tellier, François Téoulé, Olivier Terrier, Jean-François Timsit, Christelle Tual, Sylvie Van Der Werf, Noémie Vanel, Aurélie Veislinger, Benoit Visseaux, Aurélie Wiedemann, Yazdan Yazdanpanah, Loubna Alavoine, Charlotte Charpentier, Aline Dechanet, Jean-Luc Ecobichon, Wahiba Frezouls, Nadhira Houhou, Jonathan Lehacaut, Pauline Manchon, Mariama Nouroudine, Caroline Quintin, Michael Thy, Sylvie van der Werf, Valérie Vignali, Abir Chahine, Nawal Waucquier, Maria-Claire Migaud, Félix Djossou, Mayka Mergeay-Fabre, Aude Lucarelli, Magalie Demar, Léa Bruneau, Patrick Gérardin, Adrien Maillot, Christine Payet, Bruno Laviolle, Fabrice Laine, Christophe Paris, Mireille Desille-Dugast, Julie Fouchard, Thierry Pistone, Pauline Perreau, Valérie Gissot, Carole L.E. Goas, Samatha Montagne, Lucie Richard, Kévin Bouiller, Maxime Desmarets, Alexandre Meunier, Marilou Bourgeon, Benjamin Lefévre, Hélène Jeulin, Karine Legrand, Sandra Lomazzi, Bernard Tardy, Amandine Gagneux-Brunon, Frédérique Bertholon, Elisabeth Botelho-Nevers, Christelle Kouakam, Leturque Nicolas, Layidé Roufai, Karine Amat, Hélène Espérou, Samia Hendou, Giuseppe Foti, Giuseppe Citerio, Ernesto Contro, Alberto Pesci, Maria Grazia Valsecchi, Marina Cazzaniga, Giacomo Bellani, Jorge Abad, Giulia Accordino, Micol Angelini, Sergio Aguilera-Albesa, Aina Aguiló-Cucurull, Esra Akyüz Özkan, Ilad Alavi Darazam, Jonathan Antonio Roblero Albisures, Juan C. Aldave, Miquel Alfonso Ramos, Taj Ali Khan, Anna Aliberti, Seyed Alireza Nadji, Gulsum Alkan, Suzan A. AlKhater, Jerome Allardet-Servent, Luis M. Allende, Rebeca Alonso-Arias, Mohammed S. Alshahrani, Laia Alsina, Zahir Amoura, Arnau Antolí, Romain Arrestier, Mélodie Aubart, Teresa Auguet, Iryna Avramenko, Gökhan Aytekin, Axelle Azot, Seiamak Bahram, Fanny Bajolle, Fausto Baldanti, Aurélie Baldolli, Maite Ballester, Benoit Barrou, Federica Barzaghi, Sabrina Basso, Gulsum Iclal Bayhan, Liliana Bezrodnik, Agurtzane Bilbao, Geraldine Blanchard-Rohner, Ignacio Blanco, Adeline Blandinières, Daniel Blázquez-Gamero, Marketa Bloomfield, Mireia Bolivar-Prados, Raphael Borie, Elisabeth Botdhlo-Nevers, Aurore Bousquet, David Boutolleau, Claire Bouvattier, Oksana Boyarchuk, Juliette Bravais, M. Luisa Briones, Marie-Eve Brunner, Raffaele Bruno, Maria Rita P. Bueno, Huda Bukhari, Jacinta Bustamante, Juan José Cáceres Agra, Ruggero Capra, Raphael Carapito, Maria Carrabba, Carlos Casasnovas, Marion Caseris, Irene Cassaniti, Martin Castelle, Francesco Castelli, Martín Castillo de Vera, Mateus V. Castro, Emilie Catherinot, Jale Bengi Celik, Alessandro Ceschi, Martin Chalumeau, Bruno Charbit, Cécile Boulanger, Père Clavé, Bonaventura Clotet, Anna Codina, Cloé Comarmond, Patrizia Comoli, Angelo G. Corsico, Taner Coşkuner, Aleksandar Cvetkovski, Cyril Cyrus, David Dalmau, François Danion, David Ross Darley, Vincent Das, Nicolas Dauby, Stéphane Dauger, Paul De Munte, Loic de Pontual, Amin Dehban, Geoffroy Delplancq, Isabelle Desguerre, Antonio Di Sabatino, Jean-Luc Diehl, Stephanie Dobbelaere, Elena Domínguez-Garrido, Clément Dubost, Olov Ekwall, Şefika Elmas Bozdemir, Marwa H. Elnagdy, Melike Emiroglu, Akifumi Endo, Emine Hafize Erdeniz, Selma Erol Aytekin, Maria Pilar Etxart Lasa, Romain Euvrard, Giovanna Fabio, Laurence Faivre, Antonin Falck, Muriel Fartoukh, Morgane Faure, Miguel Fernandez Arquero, Ricard Ferrer, Jose Ferreres, Bruno Francois, Victoria Fumadó, Kitty S.C. Fung, Francesca Fusco, Alenka Gagro, Blanca Garcia Solis, Pierre Garçon, Pascale Gaussem, Zeynep Gayretli, Juana Gil-Herrera, Laurent Gilardin, Audrey Giraud Gatineau, Mònica Girona-Alarcón, Karen Alejandra Cifuentes Godínez, Jean-Christophe Goffard, Nacho Gonzales, Luis I. Gonzalez-Granado, Rafaela González-Montelongo, Antoine Guerder, Belgin Gülhan, Victor Daniel Gumucio, Leif Gunnar Hanitsch, Jan Gunst, Marta Gut, Jérôme Hadjadj, Selda Hancerli, Tetyana Hariyan, Nevin Hatipoglu, Deniz Heppekcan, Elisa Hernandez-Brito, Po-ki Ho, María Soledad Holanda-Peña, Juan P. Horcajada, Sami Hraiech, Linda Humbert, Ivan F.N. Hung, Alejandro D. Iglesias, Antonio Íñigo-Campos, Matthieu Jamme, María Jesús Arranz, Marie-Thérèse Jimeno, Iolanda Jordan, Saliha Kanık-Yüksek, Yalcin Kara, Aydın Karahan, Adem Karbuz, Kadriye Kart Yasar, Ozgur Kasapcopur, Kenichi Kashimada, Sevgi Keles, Yasemin Kendir Demirkol, Yasutoshi Kido, Can Kizil, Ahmet Osman Kılıç, Adam Klocperk, Antonia Koutsoukou, Zbigniew J. Król, Hatem Ksouri, Paul Kuentz, Arthur M.C. Kwan, Yat Wah M. Kwan, Janette S.Y. Kwok, Jean-Christophe Lagier, David S.Y. Lam, Vicky Lampropoulou, Fleur Le Bourgeois, Yee-Sin Leo, Rafael Leon Lopez, Daniel Leung, Michael Levin, Michael Levy, Romain Lévy, Zhi Li, Daniele Lilleri, Edson Jose Adrian Bolanos Lima, Agnes Linglart, Eduardo López-Collazo, José M. Lorenzo-Salazar, Céline Louapre, Catherine Lubetzki, Kwok-Cheung Lung, Charles-Edouard Luyt, David C. Lye, Cinthia Magnone, Enrico Marchioni, Carola Marioli, Majid Marjani, Laura Marques, Jesus Marquez Pereira, Andrea Martín-Nalda, David Martínez Pueyo, Javier Martinez-Picado, Iciar Marzana, Carmen Mata-Martínez, Alexis Mathian, Larissa R.B. Matos, Gail V. Matthews, Julien Mayaux, Raquel McLaughlin-Garcia, Philippe Meersseman, Jean-Louis Mège, Armand Mekontso-Dessap, Isabelle Melki, Federica Meloni, Jean-François Meritet, Paolo Merlani, Özge Metin Akcan, Mehdi Mezidi, Isabelle Migeotte, Maude Millereux, Matthieu Million, Tristan Mirault, Clotilde Mircher, Mehdi Mirsaeidi, Yoko Mizoguchi, Bhavi P. Modi, Francesco Mojoli, Elsa Moncomble, Abián Montesdeoca Melián, Antonio Morales Martinez, Francisco Morandeira, Pierre-Emmanuel Morange, Clémence Mordacq, Guillaume Morelle, Stéphane J. Mouly, Adrián Muñoz-Barrera, Cyril Nafati, Shintaro Nagashima, Yu Nakagama, Bénédicte Neven, João Farela Neves, Yuk-Yung Ng, Hubert Nielly, Yeray Novoa Medina, Esmeralda Nuñez Cuadros, Semsi Nur Karabela, J. Gonzalo Ocejo-Vinyals, Mehdi Oualha, Amani Ouedrani, Tayfun Özçelik, Aslinur Ozkaya-Parlakay, Michele Pagani, Maria Papadaki, Philippe Parola, Tiffany Pascreau, Stéphane Paul, Estela Paz-Artal, Sigifredo Pedraza, Nancy Carolina González Pellecer, Silvia Pellegrini, Rebeca Pérez de Diego, Xosé Luis Pérez-Fernández, Aurélien Philippe, Quentin Philippot, Adrien Picod, Marc Pineton de Chambrun, Antonio Piralla, Laura Planas-Serra, Dominique Ploin, Julien Poissy, Géraldine Poncelet, Garyphallia Poulakou, Marie S. Pouletty, Persia Pourshahnazari, Jia Li Qiu-Chen, Paul Quentric, Thomas Rambaud, Didier Raoult, Violette Raoult, Anne-Sophie Rebillat, Claire Redin, Léa Resmini, Pilar Ricart, Jean-Christophe Richard, Raúl Rigo-Bonnin, Nadia Rivet, Jacques G. Rivière, Gemma Rocamora-Blanch, Mathieu P. Rodero, Carlos Rodrigo, Luis Antonio Rodriguez, Carlos Rodriguez-Gallego, Agustí Rodriguez-Palmero, Carolina Soledad Romero, Anya Rothenbuhler, Damien Roux, Nikoletta Rovina, Flore Rozenberg, Yvon Ruch, Montse Ruiz, Maria Yolanda Ruiz del Prado, Juan Carlos Ruiz-Rodriguez, Joan Sabater-Riera, Kai Saks, Maria Salagianni, Oliver Sanchez, Adrián Sánchez-Montalvá, Silvia Sánchez-Ramón, Laire Schidlowski, Agatha Schluter, Julien Schmidt, Matthieu Schmidt, Catharina Schuetz, Cyril E. Schweitzer, Francesco Scolari, Luis Seijo, Analia Gisela Seminario, Piseth Seng, Sevtap Senoglu, Mikko Seppänen, Alex Serra Llovich, Virginie Siguret, Eleni Siouti, David M. Smadja, Nikaia Smith, Ali Sobh, Xavier Solanich, Jordi Solé-Violán, Catherine Soler, Betül Sözeri, Giulia Maria Stella, Yuriy Stepanovskiy, Annabelle Stoclin, Fabio Taccone, Jean-Luc Taupin, Simon J. Tavernier, Loreto Vidaur Tello, Benjamin Terrier, Guillaume Thiery, Karolina Thorn, Caroline Thumerelle, Imran Tipu, Martin Tolstrup, Gabriele Tomasoni, Julie Toubiana, Josep Trenado Alvarez, Vasiliki Triantafyllia, Jesús Troya, Owen T.Y. Tsang, Liina Tserel, Eugene Y.K. Tso, Alessandra Tucci, Şadiye Kübra Tüter Öz, Matilde Valeria Ursini, Takanori Utsumi, Pierre Vabres, Juan Valencia-Ramos, Ana Maria Van Den Rym, Isabelle Vandernoot, Valentina Velez-Santamaria, Silvia Patricia Zuniga Veliz, Mateus C. Vidigal, Sébastien Viel, Cédric Villain, Marie E. Vilaire-Meunier, Judit Villar-García, Audrey Vincent, Dimitri Van der Linden, Alla Volokha, Fanny Vuotto, Els Wauters, Alan K.L. Wu, Tak-Chiu Wu, Aysun Yahşi, Osman Yesilbas, Mehmet Yildiz, Barnaby E. Young, Ufuk Yükselmiş, Marco Zecca, Valentina Zuccaro, Jens Van Praet, Bart N. Lambrecht, Eva Van Braeckel, Cédric Bosteels, Levi Hoste, Eric Hoste, Fré Bauters, Jozefien De Clercq, Catherine Heijmans, Hans Slabbynck, Leslie Naesens, Benoit Florkin, Mary-Anne Young, Amanda Willis, Paloma Lapuente-Suanzes, Ana de Andrés-Martín, Matilda Berkell, Valerio Carelli, Alessia Fiorentino, Surbhi Malhotra, Alessandro Mattiaccio, Tommaso Pippucci, Marco Seri, Evelina Tacconelli, Michiel van Agtmael, Anne Geke Algera, Brent Appelman, Frank van Baarle, Diane Bax, Martijn Beudel, Harm Jan Bogaard, Marije Bomers, Peter Bonta, Lieuwe Bos, Michela Botta, Justin de Brabander, Godelieve de Bree, Sanne de Bruin, David T.P. Buis, Marianna Bugiani, Esther Bulle, Osoul Chouchane, Alex Cloherty, Mirjam Dijkstra, Dave A. Dongelmans, Romein W.G. Dujardin, Paul Elbers, Lucas Fleuren, Suzanne Geerlings, Theo Geijtenbeek, Armand Girbes, Bram Goorhuis, Martin P. Grobusch, Florianne Hafkamp, Laura Hagens, Jorg Hamann, Vanessa Harris, Robert Hemke, Sabine M. Hermans, Leo Heunks, Markus Hollmann, Janneke Horn, Joppe W. Hovius, Menno D. de Jong, Rutger Koning, Endry H.T. Lim, Niels van Mourik, Jeaninne Nellen, Esther J. Nossent, Frederique Paulus, Edgar Peters, Dan A.I. Pina-Fuentes, Tom van der Poll, Bennedikt Preckel, Jan M. Prins, Jorinde Raasveld, Tom Reijnders, Maurits C.F. J. de Rotte, Michiel Schinkel, Marcus J. Schultz, Femke A.P. Schrauwen, Alex Schuurmans, Jaap Schuurmans, Kim Sigaloff, Marleen A. Slim, Patrick Smeele, Marry Smit, Cornelis S. Stijnis, Willemke Stilma, Charlotte Teunissen, Patrick Thoral, Anissa M. Tsonas, Pieter R. Tuinman, Marc van der Valk, Denise P. Veelo, Carolien Volleman, Heder de Vries, Lonneke A. Vught, Michèle van Vugt, Dorien Wouters, A.H. Zwinderman, Matthijs C. Brouwer, W. Joost Wiersinga, Alexander P.J. Vlaar, Miranda F. Tompkins, Camille Alba, Daniel N. Hupalo, John Rosenberger, Gauthaman Sukumar, Matthew D. Wilkerson, Xijun Zhang, Justin Lack, Andrew J. Oler, Kerry Dobbs, Ottavia M. Delmonte, Jeffrey J. Danielson, Andrea Biondi, Laura Rachele Bettini, Mariella D’Angiò, Ilaria Beretta, Luisa Imberti, Alessandra Sottini, Virginia Quaresima, Eugenia Quiros-Roldan, Camillo Rossi, Riccardo Castagnoli, Daniela Montagna, Amelia Licari, and Gian Luigi Marseglia

Subjects
HLA, association, asymptomatic infection, COVID-19, population stratification, Genetics, QH426-470
Abstract

Summary: Human genetic studies of critical COVID-19 pneumonia have revealed the essential role of type I interferon-dependent innate immunity to SARS-CoV-2 infection. Conversely, an association between the HLA-B∗15:01 allele and asymptomatic SARS-CoV-2 infection in unvaccinated individuals was recently reported, suggesting a contribution of pre-existing T cell-dependent adaptive immunity. We report a lack of association of classical HLA alleles, including HLA-B∗15:01, with pre-omicron asymptomatic SARS-CoV-2 infection in unvaccinated participants in a prospective population-based study in the United States (191 asymptomatic vs. 945 symptomatic COVID-19 cases). Moreover, we found no such association in the international COVID Human Genetic Effort cohort (206 asymptomatic vs. 574 mild or moderate COVID-19 cases and 1,625 severe or critical COVID-19 cases). Finally, in the Human Challenge Characterisation study, the three HLA-B∗15:01 individuals infected with SARS-CoV-2 developed symptoms. As with other acute primary infections studied, no classical HLA alleles favoring an asymptomatic course of SARS-CoV-2 infection were identified.

Published
2024
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10. Estimation of contemporary effective population size in plant populations: Limitations of genomic datasets

Author

Roberta Gargiulo, Véronique Decroocq, Santiago C. González‐Martínez, Ivan Paz‐Vinas, Jean‐Marc Aury, Isabelle Lesur Kupin, Christophe Plomion, Sylvain Schmitt, Ivan Scotti, and Myriam Heuertz

Subjects
conservation genomics, effective population size, GONE, linkage disequilibrium, plants, Evolution, QH359-425
Abstract

Abstract Effective population size (Ne) is a pivotal evolutionary parameter with crucial implications in conservation practice and policy. Genetic methods to estimate Ne have been preferred over demographic methods because they rely on genetic data rather than time‐consuming ecological monitoring. Methods based on linkage disequilibrium (LD), in particular, have become popular in conservation as they require a single sampling and provide estimates that refer to recent generations. A software program based on the LD method, GONE, looks particularly promising to estimate contemporary and recent‐historical Ne (up to 200 generations in the past). Genomic datasets from non‐model species, especially plants, may present some constraints to the use of GONE, as linkage maps and reference genomes are seldom available, and SNP genotyping is usually based on reduced‐representation methods. In this study, we use empirical datasets from four plant species to explore the limitations of plant genomic datasets when estimating Ne using the algorithm implemented in GONE, in addition to exploring some typical biological limitations that may affect Ne estimation using the LD method, such as the occurrence of population structure. We show how accuracy and precision of Ne estimates potentially change with the following factors: occurrence of missing data, limited number of SNPs/individuals sampled, and lack of information about the location of SNPs on chromosomes, with the latter producing a significant bias, previously unexplored with empirical data. We finally compare the Ne estimates obtained with GONE for the last generations with the contemporary Ne estimates obtained with the programs currentNe and NeEstimator.

Published
2024
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13. Lack of association between classical HLA genes and asymptomatic SARS-CoV-2 infection

Author

Abel, Laurent, Aiuti, Alessandro, Al-Muhsen, Saleh, Al-Mulla, Fahd, Amara, Ali, Anderson, Mark S., Andreakos, Evangelos, Arias, Andrés A., Arkin, Lisa M., Feldman, Hagit Baris, Bastard, Paul, Belot, Alexandre, Biggs, Catherine M., Bogunovic, Dusan, Bolze, Alexandre, Bondarenko, Anastasiia, Borghesi, Alessandro, Bousfiha, Ahmed A., Brodin, Petter, Bryceson, Yenan, Butte, Manish J., Casanova, Jean-Laurent, Casari, Giorgio, Christodoulou, John, Cobat, Aurélie, Colobran, Roger, Condino-Neto, Antonio, Constantinescu, Stefan N., Cooper, Megan A., Dalgard, Clifton L., Desai, Murkesh, Drolet, Beth A., Duval, Xavier, El Baghdadi, Jamila, Eloy, Philippine, Espinosa-Padilla, Sara, Fellay, Jacques, Flores, Carlos, Franco, José Luis, Froidure, Antoine, Gorochov, Guy, Gregersen, Peter K., Grimbacher, Bodo, Haerynck, Filomeen, Hagin, David, Halwani, Rabih, Hammarström, Lennart, Heath, James R., Hsieh, Elena W.Y., Husebye, Eystein, Imai, Kohsuke, Itan, Yuval, Jouanguy, Emmanuelle, Kaja, Elżbieta, Karamitros, Timokratis, Kisand, Kai, Ku, Cheng-Lung, Lau, Yu-Lung, Ling, Yun, Lucas, Carrie L., Maniatis, Tom, Mansouri, Davood, Maródi, László, Mentré, France, Meyts, Isabelle, Milner, Joshua D., Mironska, Kristina, Mogensen, Trine H., Morio, Tomohiro, Ng, Lisa F.P., Notarangelo, Luigi D., Novelli, Antonio, Novelli, Giuseppe, O'Farrelly, Cliona, Okada, Satoshi, Okamoto, Keisuke, Ozcelik, Tayfun, Pan-Hammarström, Qiang, Pape, Jean W., Perez de Diego, Rebeca, Perez-Tur, Jordi, Perlin, David S., Pesole, Graziano, Planas, Anna M., Prando, Carolina, Pujol, Aurora, Puel, Anne, Quintana-Murci, Lluis, Ramaswamy, Sathishkumar, Renia, Laurent, Resnick, Igor, Rodríguez-Gallego, Carlos, Sancho-Shimizu, Vanessa, Sediva, Anna, Seppänen, Mikko R.J., Shahrooei, Mohammad, Shcherbina, Anna, Slaby, Ondrej, Snow, Andrew L., Soler-Palacín, Pere, Soumelis, Vassili, Spaan, András N., Tancevski, Ivan, Tangye, Stuart G., Tayoun, Ahmad Abou, Temel, Şehime Gülsün, Thorball, Christian, Tiberghien, Pierre, Trouillet-Assant, Sophie, Turvey, Stuart E., Uddin, K. M. Furkan, Uddin, Mohammed J., van de Beek, Diederik, Vinh, Donald C., von Bernuth, Horst, Wauters, Joost, Zatz, Mayana, Zawadzki, Pawel, Zhang, Qian, Zhang, Shen-Ying, Bureau, Serge, Vacher, Yannick, Gysembergh-Houal, Anne, Demerville, Lauren, Benleulmi-Chaachoua, Abla, Abad, Sebastien, Abassi, Radhiya, Abdellaoui, Abdelrafie, Abdelmalek, Abdelkrim, Abdoul, Hendy, Abergel, Helene, Abeud, Fariza, Abgrall, Sophie, Abisror, Noemie, Adechian, Marylise, Aderdour, Nordine, Admane, Hakeem Farid, Adnet, Frederic, Afritt, Sara, Agostini, Helene, Aguilar, Claire, Agut, Sophie, Aiello, Tommaso Francesco, Kaci, Marc Ait, Oufella, Hafid Ait, Ajeenthiravasan, Gokula, Alauzy, Virginie, Alby-Laurent, Fanny, Allard, Lucie, Alyanakian, Marie-Alexandra, Borrero, Blanca Amador, Amam, Sabrina, Amrouche, Lucile, Andronikof, Marc, Anglicheau, Dany, Anguel, Nadia, Annane, Djillali, Aounzou, Mohammed, Aparicio, Caroline, Aratus, Gladys, Arlet, Jean-Benoit, Arzoine, Jeremy, Aslangul, Elisabeth, Assefi, Mona, Aubry, Adeline, Audiffred, Laetitia, Audureau, Etienne, Auger, Christelle Nathalie, Auregan, Jean-Charles, Awotar, Celine, Milla, Sonia Ayllon, Azan, Delphine, Azemar, Laurene, Azzouguen, Billal, Elrufaai, Marwa Bachir, Badsi, Aïda, Bakouboula, Prissile, Balcerowiak, Coline, Balde, Fanta, Baldivia, Elodie, Bangamingo, Eliane-Flore, Baptiste, Amandine, Baran-Marszak, Fanny, Barau, Caroline, Barget, Nathalie, Baronnet, Flore, Barthelemy, Romain, Baudel, Jean-Luc, Baudry, Camille, Baudry, Elodie, Beaugerie, Laurent, Belamri, Adel, Belaube, Nicolas, Belilita, Rhida, Bellassen, Pierre, Belmokhtar, Rawan, Beltran, Isabel, Benainous, Ruben, Benallaoua, Mourad, Benamouzig, Robert, Benbara, Amélie, Benhida, Jaouad, Benkhelouf, Anis, Benlagha, Jihene, Benmostafa, Chahinez, Benothmane, Skander, Bentifraouine, Miassa, Berard, Laurence, Bernier, Quentin, Berti, Enora, Bertier, Astrid, Berton, Laure, Bessis, Simon, Beurton, Alexandra, Bianco, Celine, Bianquis, Clara, Bidar, Frank, Blanche, Philippe, Blayau, Clarisse, Bleibtreu, Alexandre, Blin, Emmanuelle, Bloch-Queyrat, Coralie, Boissier, Marie-Christophe, Bollens, Diane, Bolzoni, Marion, Bompard, Rudy pierre, Bonnet, Nicolas, Bonnouvrier, Justine, Botha, Shirmonecrystal, Boucenna, Wissam, Bouchama, Fatiha, Bouchaud, Olivier, Bouchghoul, Hanane, Boudjebla, Taoueslylia, Boudjema, Noel, Bouffard, Catherine, Bougle, Adrien, Bouguerra, Meriem, Bouras, Leila, Bourcier, Agnes, Durand, Anne Bourgarit, Bourrier, Anne, Bouscarat, Fabrice, Bouvry, Diane, Bouziri, Nesrine, Bouzrara, Ons, Bribier, Sarah, Brugier, Delphine, Brunel, Melanie, Bui, Eida, Buisson, Anne, Bukreyeva, Iryna, Bureau, Côme, Cadranel, Jacques, Cailhol, Johann, Calin, Ruxandra, Vega, Clara Campos, Canavaggio, Pauline, Cancella, Marta, Cantin, Delphine, Cao, Albert, Carbillon, Lionel, Carlier, Nicolas, Cassard, Clementine, Castor, Guylaine, Cauchy, Marion, Cha, Olivier, Chaigne, Benjamin, Challal, Salima, Champion, Karine, Chariot, Patrick, Chas, Julie, Chauveau, Simon, Chauvin, Anthony, Chauvin, Clement, Chavarot, Nathalie, Chebbout, Kamélia, Cherai, Mustapha, Cherubini, Ilaria, Chevalier, Amelie, Chiarabini, Thibault, Chinet, Thierry, Chocron, Richard, Choinier, Pascaline, Chommeloux, Juliette, Choquet, Christophe, Choupeaux, Laure, Chousterman, Benjamin, Ciocan, Dragosmarius, Clarke, Ada, Clavere, Gaëlle, Clavier, Florian, Clement, Karine, Clerc, Sebastien, Cohen, Yves, Cohen, Fleur, Cohen, Adrien, Coilly, Audrey, Colboc, Hester, Colin, Pauline, Collet, Magalie, Comarmond, Chloé, Combacon, Emeline, Combes, Alain, Comparon, Celine, Constantin, Jean-Michel, Cordel, Hugues, Cordier, Anne-Gael, Costantini, Adrien, Chalumeau, Nathalie Costedoat, Couffignal, Camille, Coupeau, Doriane, Creange, Alain, Lamarre, Yannie Cuvillier, Da Silveira, Charlène, Guibal El Kayani, Sandrine Dautheville, De Castro, Nathalie, De Rycke, Yann, Del Pozo, Lucie, Delannoy, Quentin, Delay, Mathieu, Deleris, Robin, Delforge, Juliette, Delphine, Laëtitia, Demare, Noemie, Demeret, Sophie, Demoule, Alexandre, Deniau, Aurore, Depret, François, Derolez, Sophie, Derradji, Ouda, Derridj, Nawal, Descamps, Vincent, Deschamps, Lydia, Desconclois, Celine, Desnos, Cyrielle, Desongins, Karine, Dhote, Robin, Diallo, Benjamin, Didier, Morgane, Diemer, Myriam, Diez, Stephane, Djadi-Prat, Juliette, Djamouri Monnory, Fatima-Zohra, Djebara, Siham, Djebra, Naoual, Djietcheu, Minette, Djillali, Hadjer, Djouadi, Nouara, Donneger, Severine, Santos, Catarina Dos, Dournon, Nathalie, Dres, Martin, Droctove, Laura, Drogrey, Marie, Dropy, Margot, Drouet, Elodie, Dubosq, Valérie, Dubreucq, Evelyne, Dubus, Estelle, Duchemann, Boris, Duchenoy, Thibault, Dudoignon, Emmanuel, Dufau, Romain, Dumas, Florence, Duran, Clara, Duron, Emmanuelle, Durrbach, Antoine, Duvivier, Claudine, Ebstein, Nathan, El Khalifa, Jihane, Elabbadi, Alexandre, Elie, Caroline, Ernotte, Gabriel, Esling, Anne, Etienne, Martin, Eyer, Xavier, Fartoukh, Muriel Sarah, Fayali, Takoua, Fermaut, Marion, Fiorentino, Arianna, Fliss, Souha, Fournier, Marie-Céline, Fournier, Benjamin, Francois, Hélène, Freynet, Olivia, Frigout, Yvann, Fromont, Isaure, Fuentes, Axelle, Furet, Thomas, Galand, Joris, Garnier, Marc, Gaubert, Agnes, Gaudry, Stéphane, Gaugain, Samuel, Gauthier, Damien, Gautier, Maxime, Georgin-Lavialle, Sophie, Geromin, Daniela, Ghalayini, Mohamed, Ghaleh, Bijan, Ghezal, Myriam, Gibelin, Aude, Gimeno, Linda, Girard, Benoit, Leprieur, Bénédicte Giroux, Gomes, Doryan, Gomes-Pires, Elisabete, Gouge, Anne, Gouja, Amel, Goulet, Helene, Goupil, Sylvain, De Bouille, Jeanne Goupil, Gras, Julien, Greffe, Segolene, Grimaldi, Lamiae, Guedeney, Paul, Guidet, Bertrand, Guillo, Matthias, Gulczynski, Mariechristelle, Hadjam, Tassadit, Haguenauer, Didier, Hammal, Soumeya, Hammoudi, Nadjib, Hanon, Olivier, Harrois, Anarole, Hausfater, Pierre, Hautem, Coraline, Hekimian, Guillaume, Heming, Nicholas, Hermine, Olivier, Ho, Sylvie, Houllier, Marie, Huot, Benjamin, Huscenot, Tessa, Saied, Wafa Ibn, Ikherbane, Ghilas, Imarazene, Meriem, Ingiliz, Patrick, Iratni, Lina, Jaureguiberry, Stephane, Jean-Marc, Jean-Francois, Jeyarajasingham, Deleena, Jouany, Pauline, Jouis, Veronique, Jourdaine, Clement, Kafif, Ouifiya, Kallala, Rim, Katsahian, Sandrine, Kelesyan, Lilit, Keo, Vixra, Ketz, Flora, Khamis, Warda, Khelili, Enfel, Khellaf, Mehdi, Kotokpo Youkou, Christy Gaëlla, Kounis, Ilias, Kpalma, Gaelle, Krause, Jessica, Labbe, Vincent, Lacombe, Karine, Lacorte, Jean-Marc, Lafont, Anne Gaelle, Lafont, Emmanuel, Lagha, Lynda, Lamhaut, Lionel, Lancelot, Aymeric, Landman, Cecilia, Lanternier, Fanny, Larcheveque, Cecile, Combe, Caroline Lascoux, Lassel, Ludovic, Laverdant, Benjamin, Lavergne, Christophe, Lavillegrand, Jean-Rémi, Lazureanu, Pompilia, Le Guennec, Loïc, Leberre, Lamia, Leblanc, Claire, Leboyer, Marion, Lecomte, Francois, Lecorre, Marine, Leenhardt, Romain, Lefebvre, Marylou, Lefebvre, Bénédicte, Legendre, Paul, Leger, Anne, Legros, Laurence, Legrosse, Justyna, Lehuunghia, Sébastien, 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Makoto, Moine, Pierre, Molina, Jean-Michel, Montegnies-Boulet, Anaïs, Monti, Alexandra, Montlahuc, Claire, Montout, Anne-Lise, Moores, Alexandre, Morbieu, Caroline, Mortelette, Helene, Mouly, Stéphane, Muzaffar, Rosita, Nacerddine, Cherifa Iness, Nadal, Marine, Nadif, Hajer, Nassarmadji, Kladoum, Natella, Pierre, Ndingamondze, Sandrine, Neraal, Stefan, Nguyen, Caroline, N'Guyen, Bao, Larmurier, Isabelle Nion, Nlomenyengue, Luc, Noel, Nicolas, Nunes, Hilario, Omar, Edris, Ouazene, Zineb, Ouedraogo, Elise, Ouelaa, Wassila, Oukhedouma, Anissa, Amara, Yasmina Ould, Oya, Herve, Oziel, Johanna, Padilla, Thomas, Paillaud, Elena, Paiva, Solenne, Parfait, Beatrice, Parize, Perrine, Parizot, Christophe, Parrot, Antoine, Pavot, Arthur, Peaudecerf, Laetitia, Pene, Frédéric, Pepin, Marion, Pernet, Julie, Pernin, Claire, Petit, Mylène, Peyrony, Olivier, Pietri, Marie-Pierre, Pietri, Olivia, De Chambrun, Marc Pineton, Pinson, Michelle, Pintado, Claire, Piquard, Valentine, Pires, Christine, Planquette, Benjamin, Poirier, Sandrine, Pomel, Anne-Laure, Pons, Stéphanie, Ponscarme, Diane, Pourcelot, Annegaelle, Pourcher, Valérie, Pouvaret, Anne, Prever, Florian, Previlon, Miresta, Prevost, Margot, Provoost, Marie-Julie, Quemeneur, Cyril, Rafat, Cédric, Rami, Agathe, Ranque, Brigitte, Raphael, Maurice, Raphalen, Jean Herle, Rastoin, Anna, Raux, Mathieu, Rebai, Amani, Reby, Michael, Regent, Alexis, Regrag, Asma, Resche-Rigon, Matthieu, Ressaire, Quentin, Richard, Christian, Richard, Mariecaroline, Robert, Maxence, Rohaut, Benjamin, Rolland-Debord, Camille, Ropers, Jacques, Roque-Afonso, Anne-Marie, Rosso, Charlotte, Rousseaux, Mélanie, Rousseaux, Nabila, Roux, Swasti, Roux, Lorène, Rouzaud, Claire, Rozes, Antoine, Rubenstein, Emma, Sabate, Jean-Marc, Sabet, Sheila, Sacleux, Sophie-Caroline, Kermanach, Nathalie Saidenberg, Saliba, Faouzi, Salmon, Dominique, Savale, Laurent, Savary, Guillaume, Sberro, Rebecca, Scemla, Anne, Schlemmer, Frederic, Schwartz, Mathieu, Sedfi, Saïd, 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Luisa, Brunner, Marie-Eve, Bruno, Raffaele, Bueno, Maria Rita P., Bukhari, Huda, Bustamante, Jacinta, Cáceres Agra, Juan José, Capra, Ruggero, Carapito, Raphael, Carrabba, Maria, Casasnovas, Carlos, Caseris, Marion, Cassaniti, Irene, Castelle, Martin, Castelli, Francesco, Castillo de Vera, Martín, Castro, Mateus V., Catherinot, Emilie, Celik, Jale Bengi, Ceschi, Alessandro, Chalumeau, Martin, Charbit, Bruno, Boulanger, Cécile, Clavé, Père, Clotet, Bonaventura, Codina, Anna, Comarmond, Cloé, Comoli, Patrizia, Corsico, Angelo G., Coşkuner, Taner, Cvetkovski, Aleksandar, Cyrus, Cyril, Dalmau, David, Danion, François, Darley, David Ross, Das, Vincent, Dauby, Nicolas, Dauger, Stéphane, De Munte, Paul, de Pontual, Loic, Dehban, Amin, Delplancq, Geoffroy, Desguerre, Isabelle, Di Sabatino, Antonio, Diehl, Jean-Luc, Dobbelaere, Stephanie, Domínguez-Garrido, Elena, Dubost, Clément, Ekwall, Olov, Bozdemir, Şefika Elmas, Elnagdy, Marwa H., Emiroglu, Melike, Endo, Akifumi, Erdeniz, Emine Hafize, Aytekin, Selma Erol, Etxart Lasa, Maria Pilar, Euvrard, Romain, Fabio, Giovanna, Faivre, Laurence, Falck, Antonin, Fartoukh, Muriel, Faure, Morgane, Arquero, Miguel Fernandez, Ferrer, Ricard, Ferreres, Jose, Francois, Bruno, Fumadó, Victoria, Fung, Kitty S.C., Fusco, Francesca, Gagro, Alenka, Solis, Blanca Garcia, Garçon, Pierre, Gaussem, Pascale, Gayretli, Zeynep, Gil-Herrera, Juana, Gilardin, Laurent, Gatineau, Audrey Giraud, Girona-Alarcón, Mònica, Cifuentes Godínez, Karen Alejandra, Goffard, Jean-Christophe, Gonzales, Nacho, Gonzalez-Granado, Luis I., González-Montelongo, Rafaela, Guerder, Antoine, Gülhan, Belgin, Gumucio, Victor Daniel, Hanitsch, Leif Gunnar, Gunst, Jan, Gut, Marta, Hadjadj, Jérôme, Hancerli, Selda, Hariyan, Tetyana, Hatipoglu, Nevin, Heppekcan, Deniz, Hernandez-Brito, Elisa, Ho, Po-ki, Holanda-Peña, María Soledad, Horcajada, Juan P., Hraiech, Sami, Humbert, Linda, Hung, Ivan F.N., Iglesias, Alejandro D., Íñigo-Campos, Antonio, Jamme, Matthieu, Arranz, María Jesús, Jimeno, Marie-Thérèse, Jordan, Iolanda, Kanık-Yüksek, Saliha, Kara, Yalcin, Karahan, Aydın, Karbuz, Adem, Yasar, Kadriye Kart, Kasapcopur, Ozgur, Kashimada, Kenichi, Keles, Sevgi, Demirkol, Yasemin Kendir, Kido, Yasutoshi, Kizil, Can, Kılıç, Ahmet Osman, Klocperk, Adam, Koutsoukou, Antonia, Król, Zbigniew J., Ksouri, Hatem, Kuentz, Paul, Kwan, Arthur M.C., Kwan, Yat Wah M., Kwok, Janette S.Y., Lagier, Jean-Christophe, Lam, David S.Y., Lampropoulou, Vicky, Le Bourgeois, Fleur, Leo, Yee-Sin, Lopez, Rafael Leon, Leung, Daniel, Levin, Michael, Levy, Michael, Lévy, Romain, Li, Zhi, Lilleri, Daniele, Adrian Bolanos Lima, Edson Jose, Linglart, Agnes, López-Collazo, Eduardo, Lorenzo-Salazar, José M., Louapre, Céline, Lubetzki, Catherine, Lung, Kwok-Cheung, Luyt, Charles-Edouard, Lye, David C., Magnone, Cinthia, Marchioni, Enrico, Marioli, Carola, Marjani, Majid, Marques, Laura, Pereira, Jesus Marquez, Martín-Nalda, Andrea, Pueyo, David Martínez, Martinez-Picado, Javier, Marzana, Iciar, Mata-Martínez, Carmen, Mathian, Alexis, Matos, Larissa R.B., Matthews, Gail V., Mayaux, Julien, McLaughlin-Garcia, Raquel, Meersseman, Philippe, Mège, Jean-Louis, Mekontso-Dessap, Armand, Melki, Isabelle, Meloni, Federica, Meritet, Jean-François, Merlani, Paolo, Akcan, Özge Metin, Mezidi, Mehdi, Migeotte, Isabelle, Millereux, Maude, Million, Matthieu, Mirault, Tristan, Mircher, Clotilde, Mirsaeidi, Mehdi, Mizoguchi, Yoko, Modi, Bhavi P., Mojoli, Francesco, Moncomble, Elsa, Melián, Abián Montesdeoca, Martinez, Antonio Morales, Morandeira, Francisco, Morange, Pierre-Emmanuel, Mordacq, Clémence, Morelle, Guillaume, Mouly, Stéphane J., Muñoz-Barrera, Adrián, Nafati, Cyril, Nagashima, Shintaro, Nakagama, Yu, Neven, Bénédicte, Neves, João Farela, Ng, Yuk-Yung, Hubert Nielly, Medina, Yeray Novoa, Cuadros, Esmeralda Nuñez, Karabela, Semsi Nur, Ocejo-Vinyals, J. 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J., Schinkel, Michiel, Schultz, Marcus J., Schrauwen, Femke A.P., Schuurmans, Alex, Schuurmans, Jaap, Sigaloff, Kim, Slim, Marleen A., Smeele, Patrick, Smit, Marry, Stijnis, Cornelis S., Stilma, Willemke, Teunissen, Charlotte, Thoral, Patrick, Tsonas, Anissa M., Tuinman, Pieter R., van der Valk, Marc, Veelo, Denise P., Volleman, Carolien, de Vries, Heder, Vught, Lonneke A., van Vugt, Michèle, Wouters, Dorien, Zwinderman, A.H., Brouwer, Matthijs C., Wiersinga, W. Joost, Vlaar, Alexander P.J., Tompkins, Miranda F., Alba, Camille, Hupalo, Daniel N., Rosenberger, John, Sukumar, Gauthaman, Wilkerson, Matthew D., Zhang, Xijun, Lack, Justin, Oler, Andrew J., Dobbs, Kerry, Delmonte, Ottavia M., Danielson, Jeffrey J., Biondi, Andrea, Bettini, Laura Rachele, D’Angiò, Mariella, Beretta, Ilaria, Imberti, Luisa, Sottini, Alessandra, Quaresima, Virginia, Quiros-Roldan, Eugenia, Rossi, Camillo, Castagnoli, Riccardo, Montagna, Daniela, Licari, Amelia, Marseglia, Gian Luigi, Marchal, Astrid, Cirulli, Elizabeth T., Neveux, Iva, Bellos, Evangelos, Thwaites, Ryan S., Schiabor Barrett, Kelly M., Zhang, Yu, Nemes-Bokun, Ivana, Kalinova, Mariya, Catchpole, Andrew, Lack, Justin B., Chiu, Christopher, and Grzymski, Joseph J.

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2024
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15. PKM2 diverts glycolytic flux in dependence on mitochondrial one-carbon cycle

Author

Mohaned Benzarti, Laura Neises, Anais Oudin, Christina Krötz, Elodie Viry, Ernesto Gargiulo, Coralie Pulido, Maryse Schmoetten, Vitaly Pozdeev, Nadia I. Lorenz, Michael W. Ronellenfitsch, David Sumpton, Marc Warmoes, Christian Jaeger, Antoine Lesur, Björn Becker, Etienne Moussay, Jerome Paggetti, Simone P. Niclou, Elisabeth Letellier, and Johannes Meiser

Subjects
CP: Cancer, CP: Metabolism, Biology (General), QH301-705.5
Abstract

Summary: Modeling tumor metabolism in vitro remains challenging. Here, we used galactose as an in vitro tool compound to mimic glycolytic limitation. In contrast to the established idea that high glycolytic flux reduces pyruvate kinase isozyme M2 (PKM2) activity to support anabolic processes, we have discovered that glycolytic limitation also affects PKM2 activity. Surprisingly, despite limited carbon availability and energetic stress, cells induce a near-complete block of PKM2 to divert carbons toward serine metabolism. Simultaneously, TCA cycle flux is sustained, and oxygen consumption is increased, supported by glutamine. Glutamine not only supports TCA cycle flux but also serine synthesis via distinct mechanisms that are directed through PKM2 inhibition. Finally, deleting mitochondrial one-carbon (1C) cycle reversed the PKM2 block, suggesting a potential formate-dependent crosstalk that coordinates mitochondrial 1C flux and cytosolic glycolysis to support cell survival and proliferation during nutrient-scarce conditions.

Published
2024
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16. Proteomic analysis of horse hair extracts provides no evidence for the existence of a hypoallergenic Curly Horse breed

Author

Bente Janssen‐Weets, Antoine Lesur, Gunnar Dittmar, François Bernardin, Eva Zahradnik, Monika Raulf, François Hentges, Carsten Bindslev‐Jensen, Markus Ollert, and Christiane Hilger

Subjects
American Bashkir Curly Horse, Equ c 1, horse allergens, horse proteome, hypoallergenic breeds, Immunologic diseases. Allergy, RC581-607
Abstract

Abstract Background The American Bashkir Curly Horse is frequently advertised to horse‐allergic riders and claimed to be a so‐called hypoallergenic breed that elicits fewer symptoms. Previous studies quantifying selected allergens in different breeds did not find a reduced allergen content in Curly Horses. Here, we provide a comprehensive proteomic analysis of horse hair extracts and a molecular analysis of the major allergen Equ c 1 with the aim of identifying differences in the Curly Horse breed that might explain their presumed reduced allergenic potential. Methods Horse hair extracts were prepared from Curly and American Quarter Horse breeds, separated by gender and castration status, extracts from other breeds served as controls. Extracts and native Equ c 1 (nEqu c 1) were analyzed by mass spectrometry. IgE‐binding capacities of nEqu c 1 and its recombinant variants were tested by ELISA using sera of patients sensitized to horses. Structures and ligand binding abilities were analyzed by computational modeling and fluorescence quenching assays. Results All known respiratory horse allergens are present in hair extracts of Curly and Quarter Horses and share identical allergen‐specific peptides. Lipocalin allergens are the most abundant proteins in horse hair extracts and contain several post‐translational modifications. We identified two new variants of Equ c 1 that have similar IgE‐binding capacities but show structural differences in their binding cavities and altered ligand binding behavior. There are no differences in IgE‐binding of Equ c 1 derived from Curly Horses compared to other horse breeds. Conclusion Our data do not support the claim that Curly Horses are less allergenic than other breeds.

Published
2024
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17. Synthesis of trehalose-based chemical tools for the study of the mycobacterial membrane

Author

Lesur, Emilie, Rollando, Paulin, Guianvarc’h, Dominique, and Bourdreux, Yann

Subjects
Chemical reporter, Metabolic labeling, Bioorthogonal probe, Trehalose, Mycomembrane, Corynebacteriales, Biochemistry, QD415-436, Physical and theoretical chemistry, QD450-801, Mathematics, QA1-939
Abstract

Corynebacteriales including the causative agent of many diseases such as tuberculosis are known to be extremely resistant against external stress as well as to antibiotic treatments which is believed to be related to the singular architecture of their mycomembrane. Over the last decades, both bioorthogonal chemical reporters and fluorescent probes for the metabolic labeling of bacterial cell glycans were developed including several trehalose-based probes to study the dynamics of mycomembrane components. This review presents an exhaustive view on the reported syntheses of trehalose-based probes enabling the study of the mycomembrane biogenesis.

Published
2023
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19. PKM2 diverts glycolytic flux in dependence on mitochondrial one-carbon cycle

Author

Benzarti, Mohaned, Neises, Laura, Oudin, Anais, Krötz, Christina, Viry, Elodie, Gargiulo, Ernesto, Pulido, Coralie, Schmoetten, Maryse, Pozdeev, Vitaly, Lorenz, Nadia I., Ronellenfitsch, Michael W., Sumpton, David, Warmoes, Marc, Jaeger, Christian, Lesur, Antoine, Becker, Björn, Moussay, Etienne, Paggetti, Jerome, Niclou, Simone P., Letellier, Elisabeth, and Meiser, Johannes

Published
2024
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20. Formate overflow drives toxic folate trapping in MTHFD1 inhibited cancer cells

Author

Green, Alanna C., Marttila, Petra, Kiweler, Nicole, Chalkiadaki, Christina, Wiita, Elisée, Cookson, Victoria, Lesur, Antoine, Eiden, Kim, Bernardin, François, Vallin, Karl S. A., Borhade, Sanjay, Long, Maeve, Ghahe, Elahe Kamali, Jiménez-Alonso, Julio J., Jemth, Ann-Sofie, Loseva, Olga, Mortusewicz, Oliver, Meyers, Marianne, Viry, Elodie, Johansson, Annika I., Hodek, Ondřej, Homan, Evert, Bonagas, Nadilly, Ramos, Louise, Sandberg, Lars, Frödin, Morten, Moussay, Etienne, Slipicevic, Ana, Letellier, Elisabeth, Paggetti, Jérôme, Sørensen, Claus Storgaard, Helleday, Thomas, Henriksson, Martin, and Meiser, Johannes

Published
2023
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21. Fluid face but not gender: Enfacement illusion through digital face filters does not affect gender identity.

Author

Luca Provenzano, Hanna Gohlke, Gianluca Saetta, Ilaria Bufalari, Bigna Lenggenhager, and Marte Roel Lesur

Subjects
Medicine, Science
Abstract

It has been shown that observing a face being touched or moving in synchrony with our own face increases self-identification with the former which might alter both cognitive and affective processes. The induction of this phenomenon, termed enfacement illusion, has often relied on laboratory tools that are unavailable to a large audience. However, digital face filters applications are nowadays regularly used and might provide an interesting tool to study similar mechanisms in a wider population. Digital filters are able to render our faces in real time while changing important facial features, for example, rendering them more masculine or feminine according to normative standards. Recent literature using full-body illusions has shown that participants' own gender identity shifts when embodying a different gendered avatar. Here we studied whether participants' filtered faces, observed while moving in synchrony with their own face, may induce an enfacement illusion and if so, modulate their gender identity. We collected data from 35 female and 33 male participants who observed a stereotypically gender mismatched version of themselves either moving synchronously or asynchronously with their own face on a screen. Our findings showed a successful induction of the enfacement illusion in the synchronous condition according to a questionnaire addressing the feelings of ownership, agency and perceived similarity. However, we found no evidence of gender identity being modulated, neither in explicit nor in implicit measures of gender identification. We discuss the distinction between full-body and facial processing and the relevance of studying widely accessible devices that may impact the sense of a bodily self and our cognition, emotion and behaviour.

Published
2024
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22. The name of the game: palaeoproteomics and radiocarbon dates further refine the presence and dispersal of caprines in eastern and southern Africa

Author

Louise Le Meillour, Antoine Zazzo, Séverine Zirah, Olivier Tombret, Véronique Barriel, Kathryn W. Arthur, John W. Arthur, Jessie Cauliez, Louis Chaix, Matthew C. Curtis, Diane Gifford-Gonzalez, Imogen Gunn, Xavier Gutherz, Elisabeth Hildebrand, Lamya Khalidi, Marie Millet, Peter Mitchell, Jacqueline Studer, Emmanuelle Vila, Frido Welker, David Pleurdeau, and Joséphine Lesur

Subjects
Africa, zooarchaeology, hunters–gatherers, pastoralism, palaeoproteomics, radiocarbon dating, Science
Abstract

We report the first large-scale palaeoproteomics research on eastern and southern African zooarchaeological samples, thereby refining our understanding of early caprine (sheep and goat) pastoralism in Africa. Assessing caprine introductions is a complicated task because of their skeletal similarity to endemic wild bovid species and the sparse and fragmentary state of relevant archaeological remains. Palaeoproteomics has previously proved effective in clarifying species attributions in African zooarchaeological materials, but few comparative protein sequences of wild bovid species have been available. Using newly generated type I collagen sequences for wild species, as well as previously published sequences, we assess species attributions for elements originally identified as caprine or ‘unidentifiable bovid’ from 17 eastern and southern African sites that span seven millennia. We identified over 70% of the archaeological remains and the direct radiocarbon dating of domesticate specimens allows refinement of the chronology of caprine presence in both African regions. These results thus confirm earlier occurrences in eastern Africa and the systematic association of domesticated caprines with wild bovids at all archaeological sites. The combined biomolecular approach highlights repeatability and accuracy of the methods for conclusive contribution in species attribution of archaeological remains in dry African environments.

Published
2023
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23. Oak stands along an elevation gradient have different molecular strategies for regulating bud phenology

Author

Gregoire Le Provost, Céline Lalanne, Isabelle Lesur, Jean-Marc Louvet, Sylvain Delzon, Antoine Kremer, Karine Labadie, Jean-Marc Aury, Corinne Da Silva, Thomas Moritz, and Christophe Plomion

Subjects
Response to temperature, Bud phenology, Elevation cline, Gene expression, Hormone quantification, Sessile oak, Botany, QK1-989
Abstract

Abstract Background Global warming raises serious concerns about the persistence of species and populations locally adapted to their environment, simply because of the shift it produces in their adaptive landscape. For instance, the phenological cycle of tree species may be strongly affected by higher winter temperatures and late frost in spring. Given the variety of ecosystem services they provide, the question of forest tree adaptation has received increasing attention in the scientific community and catalyzed research efforts in ecology, evolutionary biology and functional genomics to study their adaptive capacity to respond to such perturbations. Results In the present study, we used an elevation gradient in the Pyrenees Mountains to explore the gene expression network underlying dormancy regulation in natural populations of sessile oak stands sampled along an elevation cline and potentially adapted to different climatic conditions mainly driven by temperature. By performing analyses of gene expression in terminal buds we identified genes displaying significant dormancy, elevation or dormancy-by-elevation interaction effects. Our Results highlighted that low- and high-altitude populations have evolved different molecular strategies for minimizing late frost damage and maximizing the growth period, thereby increasing potentially their respective fitness in these contrasting environmental conditions. More particularly, population from high elevation overexpressed genes involved in the inhibition of cell elongation and delaying flowering time while genes involved in cell division and flowering, enabling buds to flush earlier were identified in population from low elevation. Conclusion Our study made it possible to identify key dormancy-by-elevation responsive genes revealing that the stands analyzed in this study have evolved distinct molecular strategies to adapt their bud phenology in response to temperature.

Published
2023
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24. The authors reply

Author

Angriman, Federico, Muttalib, Fiona, Lamontagne, François, Adhikari, Neill K. J., Chassé, Michaël, Aslanian, Pierre, Bélisle, Sylvain, Cailhier, Jean-François, Martin Carrier, François, Charbonney, Emmanuel, Denault, André, Girard, Martin, Guimond, Jean-Gilles, Halwagi, Antoine, Hébert, Paul, Kolan, Christophe, Ouellet, Caroline, Robillard, Nicholas, Benettaib, Fatna, Boumahni, Dounia, Lebrasseur, Martine, Salamé, Maya, Cantin, Marie-Ève, Archambault, Patrick, Drouin, Christine, Duquet-Deblois, Estel, Noël-Hunter, Monia, Dubé, Jean-Nicolas, Bériault, Marie-Josée, Chacon, Marco, Claveau, David, Naud, Jean-François, Rodrigue, Élise, Tapss, Danielle, Toupin, Guylaine, Ting Wang, Han, Brosseau, Marc, Laufer, Brian, Marquis, François, Toupin, Francis, Tassy, Danaë, Cheung, Vincent, Toun, Sam-Ang, Lamontagne, François, D’Aragon, Frédérick, Bérard, Dominique, Grondin-Beaudoin, Brian, Leclair, Marc-André, Lesur, Olivier, Mayette, Michaël, Poulin, Yannick, Quiroz Martinez, Hector, St-Arnaud, Charles, Carbonneau, Elaine, Bélisle, Julie, Bouchard, Marie-Pier, Côté, Line, Ladouceur, Marylène, Marchand, Joannie, Naisby, Alexandra, Robert-Petit, Louise, Thibault, Marie-Ève, Charbonney, Emmanuel, Albert, Martin, Bernard, Francis, Cavayas, Alexandros, Serri, Karim, Williamson, David, Williams, Virginie, Lainer Palacios, Julia, Lauzier, François, Francoeur, Charles, Leblanc, Guillaume, St-Onge, Maude, Turgeon, Alexis, Bellemare, David, Boulanger, Marie-Claude, Cloutier, Eve, Guilbault, Gabrielle, Thibeault, Frédérique, Belley-Côté, Emilie, Fox-Robichaud, Alison, Meade, Maureen, Whitlock, Richard, Hand, Lori, Hayward, Leah, Mullen, Courtney, Savija, Nevena, Lellouche, François, Simon, Mathieu, Tung Sia, Ying, Lizotte, Patricia, Rochwerg, Bram, Millen, Tina, Maslove, David, Gordon Boyd, J., Drover, John, Muscedere, John, Sibley, Stephanie, Boyd, Tracy, Hunt, Miranda, Mele, Tina, Bentall, Tracey, ElKhatib, Chadia, Shahin, Jason, Khwaja, Kosar, Campisi, Josie, Alam, Norine, Rahgoshai, Raham, Mehta, Sangeeta, Detsky, Michael, Shah, Sumesh, Kohli, Sonny, Cui, Fulan, Khera, Vikas, McConachie, David, Rehsia, Sachdeep, Bharti, Dalisha, Perez, Adic, James Kutsogiannis, Demetrios, Chowdhury, Raiyan, Davidow, Jon, Johnston, Curtis, Kim, Michael, Macala, Kimberley, Marcushamer, Sam, Markland, Darren, Matheson, Doug, Parker, Arabesque, Paton-Gay, Damian, Hewer, Tayne, Thompson, Patrica, Cook, Deborah, Al-Hazzani, Waleed, Duan, Erick, Ligori, Tania, Soth, Mark, Clarke, France, Copland, Mary, Matic, Karlo, Adhikari, Neill KJ, Amaral, Andre, Cuthbertson, Brian H, Fowler, Robert A, Piquette, Dominique, Scales, Damon C, Tillmann, Bourke, Wunsch, Hannah, Marinoff, Nicole, Kamra, Maneesha, Kaur, Navjot, Murali, Deeptha, Sabananthan, Thivya, Sugumaran, Thuva, Seely, Andrew, English, Shane, Meggison, Hilary, Microys, Sherissa, Millington, Scott, Sarti, Aimee, Haines, Jessica, Miezitis, Sydney, Porteous, Rebecca, Watpool, Irene, Del Sorbo, Lorenzo, Fan, Eddy, Granton, John, Abdelhady, Hesham, Romagnuolo, Tina, Rewa, Oleksa, Bagshaw, Sean, Meier, Michael, Sligl, Wendy, Baig, Nadia, Wood, Gordon, Ovakim, Daniel, Auld, Fiona, Carney, Gayle, Parfett, Deborah, Leblanc, Rémi, Poirier, Matthieu, Theriault, Theophile, Williston, Maryse, Caissie Collette, Jackie, Carriere, Melanie, Daigle, Melissa, Gaudet, Bernise, Morin, Karine, Ouellette-Bernier, Lola, Poitras, Julie, Robichaud, Melanie, Rockburn, Joanne, Mekontso Dessap, Armand, Arrestier, Romain, Bagate, François, Bendib, Ines, Benelli, Brice, Berti, Enora, Bertier, Astrid, Cavaleiro, Pedro, de Prost, Nicolas, Gendreau, Segolene, Hartman, Otto, Haudebourg, Anne-Fleur, Lopinto, Julien, Masi, Paul, Michaud, Gaël, Razazi, Keyvan, Tuffet, Samuel, Alves, Aline, Nait Chabane, Luiza, Ouali, Fariza, Ouedraogo, Rachida, Annane, Djillali, Abdeladim, Lilia, Bounab, Rania, Heming, Nicholas, Maxime, Virginie, Moine, Pierre, Bossard, Isabelle, Jourdier, Segolene, Mahiou, Siline, Tessa, Hayette, McGuinness, Shay, Ball, Jonathan, Hennessy, Immanuel, Hogan, Maurice, Butler, Magdalena, Cowdrey, Keri-Anne, Gilder, Eileen, Parke, Rachael, Ryan, Samantha, Woollett, Melissa, Van Der Poll, Andrew, Benson-Cooper, Kerry, Chen, Jonathan, Freeman, Kirk, Harley, David, Harvey, Dave, Hourigan, Craig, Julian, Kylie, Lo, Stephen, McArthur, Colin, Miller, Stuart, Pointer, Chris, Anthony Smith, Rex, Tincknell, Laura, McConnochie, Rachael, Simmonds, Catherine, Shaw, Geoffrey, Betteridge, Toby, Burke, Brandon, Closey, David, Crombie, Rosalind, Davidson, Neil, Henderson, Louise, Henderson, Seton, Hitchings, Louise, Knight, David, Quigley, Christine, Ritzema Carter, Jay, Roberts, Jessica, Townend, Katherine, Doyle, Tara, Mehrtens, Jan, Morgan, Stacey, Morris, Anna, Van Der Heyden, Kymbalee, Twardowski, Pawel, Dvoracek, Martin, Renner, Markus, Silverman, David, Smith, Myles, Monica Stephens, Katherine, Albert Waibel, Hansjörg, Wiebe, Stefan, Woolley, Mark, Eden, Amie, France, Dawn, Buehner, Ulrike, Erin Williams, Katallah Kramer, Browne, Troy, Callender, Owen, Chen, Jonathan, Farrell, Susanne, Higson, Vicky, Jackson, David, Keet, Owen, Goodson, Jennifer, Martynoga, Robert, Byrne, Kelly, Butler, Amelia, Trask, Kara, Mans, Gay, Termaat, Jonathan, Young, Paul, Barnes, Colin, Barry, Ben, Grayson, Kim, Moore, James, Psirides, Alex, Sturland, Shawn, Tietjens, Kate, Ure, Bob, Walker, Laurence, Wright, Jason, Aguilar-Dano, April, Delaney, Kirsha, Lawrence, Cassie, Lesona, Mildred, Millington, Alexandra, Navarra, Leanlove, Olatunji, Shaanti, Sol Cruz, Raulle, Sol Cruz, Rhoze, Young, Chelsea, Day, Andrew, Cook, Deborah J, Guyatt, Gordon H, Sprague, Sheila, Cohen, Dian, Heyland, Daren K, Lamontagne, François, Masse, Marie-Hélène, Ménard, Julie, Adhikari, Neill KJ, Pinto, Ruxandra, Kanji, Salmaan, Battista, Marie-Claude, Annane, Djillali, Tirupakuzhi Vijayaraghavan, Bharath Kumar, McGuinness, Shay, Parke, Rachael, and Arabi, Yaseen

Published
2023
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25. Formate promotes invasion and metastasis in reliance on lipid metabolism

Author

Catherine Delbrouck, Nicole Kiweler, Oleg Chen, Vitaly I. Pozdeev, Lara Haase, Laura Neises, Anaïs Oudin, Aymeric Fouquier d’Hérouël, Ruolin Shen, Lisa Schlicker, Rashi Halder, Antoine Lesur, Anne Schuster, Nadja I. Lorenz, Christian Jaeger, Maureen Feucherolles, Gilles Frache, Martyna Szpakowska, Andy Chevigne, Michael W. Ronellenfitsch, Etienne Moussay, Marie Piraud, Alexander Skupin, Almut Schulze, Simone P. Niclou, Elisabeth Letellier, and Johannes Meiser

Subjects
CP: Cancer, CP: Metabolism, Biology (General), QH301-705.5
Abstract

Summary: Metabolic rewiring is essential for cancer onset and progression. We previously showed that one-carbon metabolism-dependent formate production often exceeds the anabolic demand of cancer cells, resulting in formate overflow. Furthermore, we showed that increased extracellular formate concentrations promote the in vitro invasiveness of glioblastoma cells. Here, we substantiate these initial observations with ex vivo and in vivo experiments. We also show that exposure to exogeneous formate can prime cancer cells toward a pro-invasive phenotype leading to increased metastasis formation in vivo. Our results suggest that the increased local formate concentration within the tumor microenvironment can be one factor to promote metastases. Additionally, we describe a mechanistic interplay between formate-dependent increased invasiveness and adaptations of lipid metabolism and matrix metalloproteinase activity. Our findings consolidate the role of formate as pro-invasive metabolite and warrant further research to better understand the interplay between formate and lipid metabolism.

Published
2023
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27. Pyruvate dehydrogenase fuels a critical citrate pool that is essential for Th17 cell effector functions

Author

Soriano-Baguet, Leticia, Grusdat, Melanie, Kurniawan, Henry, Benzarti, Mohaned, Binsfeld, Carole, Ewen, Anouk, Longworth, Joseph, Bonetti, Lynn, Guerra, Luana, Franchina, Davide G., Kobayashi, Takumi, Horkova, Veronika, Verschueren, Charlène, Helgueta, Sergio, Gérard, Deborah, More, Tushar H., Henne, Antonia, Dostert, Catherine, Farinelle, Sophie, Lesur, Antoine, Gérardy, Jean-Jacques, Jäger, Christian, Mittelbronn, Michel, Sinkkonen, Lasse, Hiller, Karsten, Meiser, Johannes, and Brenner, Dirk

Published
2023
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28. Association between physical activity and neoadjuvant chemotherapy completion and pathologic complete response in primary breast cancer: the CANTO study

Author

Baker, Jennifer L., Di Meglio, Antonio, Gbenou, Arnauld S., El Mouhebb, Mayssam, Iyengar, Neil M., Michiels, Stefan, Cottu, Paul, Lerebours, Florence, Coutant, Charles, Lesur, Anne, Tredan, Oliver, Vanlemmens, Laurence, Jouannaud, Christelle, Hrab, Iona, Everhard, Sibille, Martin, Anne-Laure, Arveux, Patrick, Fabrice, Andre, Vaz-Luis, Ines, and Jones, Lee W.

Published
2022
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29. IV Vitamin C in Adults With Sepsis: A Bayesian Reanalysis of a Randomized Controlled Trial*

Author

Angriman, Federico, Muttalib, Fiona, Lamontagne, François, Adhikari, Neill K. J., Chassé, Michaël, Aslanian, Pierre, Bélisle, Sylvain, Cailhier, Jean-François, Carrier, François Martin, Charbonney, Emmanuel, Denault, André, Girard, Martin, Guimond, Jean-Gilles, Halwagi, Antoine, Hébert, Paul, Kolan, Christophe, Ouellet, Caroline, Robillard, Nicholas, Benettaib, Fatna, Boumahni, Dounia, Lebrasseur, Martine, Salamé, Maya, Cantin, Marie-Ève, Archambault, Patrick, Drouin, Christine, Dubé, Jean-Nicolas, Bériault, Marie-Josée, Chacon, Marco, Claveau, David, Naud, Jean-François, Rodrigue, Élise, Ting Wang, Han, Brosseau, Marc, Laufer, Brian, Marquis, François, Toupin, Francis, Lamontagne, François, D’Aragon, Frédérick, Bérard, Dominique, Grondin-Beaudoin, Brian, Leclair, Marc-André, Lesur, Olivier, Mayette, Michaël, Poulin, Yannick, Quiroz Martinez, Hector, St-Arnaud, Charles, Charbonney, Emmanuel, Albert, Martin, Bernard, Francis, Cavayas, Alexandros, Serri, Karim, Williamson, David, Duquet-Deblois, Estel, Noël-Hunter, Monia, Tapss, Danielle, Toupin, Guylaine, Tassy, Danaë, Cheung, Vincent, Toun, Sam-Ang, Carbonneau, Elaine, Bélisle, Julie, Bouchard, Marie-Pier, Côté, Line, Ladouceur, Marylène, Marchand, Joannie, Naisby, Alexandra, Robert-Petit, Louise, Thibault, Marie-Ève, Williams, Virginie, Lainer Palacios, Julia, Charbonney, Emmanuel, Albert, Martin, Bernard, Francis, Cavayas, Alexandros, Serri, Karim, Williamson, David, Lauzier, François, Francoeur, Charles, Leblanc, Guillaume, St-Onge, Maude, Turgeon, Alexis, Belley-Côté, Emilie, Fox-Robichaud, Alison, Meade, Maureen, Whitlock, Richard, Lellouche, François, Simon, Mathieu, Tung Sia, Ying, Rochwerg, Bram, Maslove, David, Gordon Boyd, J., Drover, John, Muscedere, John, Sibley, Stephanie, Mele, Tina, Shahin, Jason, Khwaja, Kosar, Mehta, Sangeeta, Detsky, Michael, Kohli, Sonny, Cui, Fulan, Khera, Vikas, McConachie, David, Rehsia, Sachdeep, James Kutsogiannis, Demetrios, Chowdhury, Raiyan, Davidow, Jon, Johnston, Curtis, Kim, Michael, Macala, Kimberley, Marcushamer, Sam, Markland, Darren, Matheson, Doug, Parker, Arabesque, Paton-Gay, Damian, Cook, Deborah, Al-Hazzani, Waleed, Duan, Erick, Ligori, Tania, Soth, Mark, Adhikari, Neill KJ, Amaral, Andre, Cuthbertson, Brian H, Fowler, Robert A, Piquette, Dominique, Scales, Damon C, Tillmann, Bourke, Wunsch, Hannah, Seely, Andrew, English, Shane, Meggison, Hilary, Microys, Sherissa, Millington, Scott, Sarti, Aimee, Del Sorbo, Lorenzo, Fan, Eddy, Granton, John, Rewa, Oleksa, Bagshaw, Sean, Meier, Michael, Sligl, Wendy, Wood, Gordon, Ovakim, Daniel, Leblanc, Rémi, Poirier, Matthieu, Theriault, Theophile, Williston, Maryse, Bellemare, David, Boulanger, Marie-Claude, Cloutier, Eve, Guilbault, Gabrielle, Thibeault, Frédérique, Hand, Lori, Hayward, Leah, Mullen, Courtney, Savija, Nevena, Lizotte, Patricia, Millen, Tina, Boyd, Tracy, Hunt, Miranda, Bentall, Tracey, ElKhatib, Chadia, Campisi, Josie, Alam, Norine, Rahgoshai, Raham, Shah, Sumesh, Bharti, Dalisha, Perez, Adic, Hewer, Tayne, Thompson, Patrica, Clarke, France, Copland, Mary, Matic, Karlo, Marinoff, Nicole, Kamra, Maneesha, Kaur, Navjot, Murali, Deeptha, Sabananthan, Thivya, Sugumaran, Thuva, Haines, Jessica, Miezitis, Sydney, Porteous, Rebecca, Watpool, Irene, Abdelhady, Hesham, Romagnuolo, Tina, Baig, Nadia, Auld, Fiona, Carney, Gayle, Parfett, Deborah, Caissie Collette, Jackie, Carriere, Melanie, Daigle, Melissa, Gaudet, Bernise, Morin, Karine, Ouellette-Bernier, Lola, Poitras, Julie, Robichaud, Melanie, Rockburn, Joanne, Mekontso Dessap, Armand, Arrestier, Romain, Bagate, François, Bendib, Ines, Benelli, Brice, Berti, Enora, Bertier, Astrid, Cavaleiro, Pedro, de Prost, Nicolas, Gendreau, Segolene, Hartman, Otto, Haudebourg, Anne-Fleur, Lopinto, Julien, Masi, Paul, Michaud, Gaël, Razazi, Keyvan, Tuffet, Samuel, Annane, Djillali, Abdeladim, Lilia, Bounab, Rania, Heming, Nicholas, Maxime, Virginie, Moine, Pierre, Alves, Aline, Nait Chabane, Luiza, Ouali, Fariza, Ouedraogo, Rachida, Bossard, Isabelle, Jourdier, Segolene, Mahiou, Siline, Tessa, Hayette, McGuinness, Shay, Ball, Jonathan, Hennessy, Immanuel, Hogan, Maurice, Van Der Poll, Andrew, Benson-Cooper, Kerry, Chen, Jonathan, Freeman, Kirk, Harley, David, Harvey, Dave, Hourigan, Craig, Julian, Kylie, Lo, Stephen, McArthur, Colin, Miller, Stuart, Pointer, Chris, Anthony Smith, Rex, Tincknell, Laura, Shaw, Geoffrey, Betteridge, Toby, Burke, Brandon, Closey, David, Crombie, Rosalind, Davidson, Neil, Henderson, Louise, Henderson, Seton, Hitchings, Louise, Knight, David, Quigley, Christine, Ritzema Carter, Jay, Roberts, Jessica, Townend, Katherine, Twardowski, Pawel, Dvoracek, Martin, Renner, Markus, Silverman, David, Smith, Myles, Monica Stephens, Katherine, Albert Waibel, Hansjörg, Wiebe, Stefan, Woolley, Mark, Buehner, Ulrike, Kramer, Katallah, Browne, Troy, Callender, Owen, Chen, Jonathan, Farrell, Susanne, Higson, Vicky, Jackson, David, Keet, Owen, Martynoga, Robert, Byrne, Kelly, Young, Paul, Barnes, Colin, Barry, Ben, Grayson, Kim, Moore, James, Psirides, Alex, Sturland, Shawn, Tietjens, Kate, Ure, Bob, Walker, Laurence, Wright, Jason, Butler, Magdalena, Cowdrey, Keri-Anne, Gilder, Eileen, Parke, Rachael, Ryan, Samantha, Woollett, Melissa, McConnochie, Rachael, Simmonds, Catherine, Doyle, Tara, Mehrtens, Jan, Morgan, Stacey, Morris, Anna, Van Der Heyden, Kymbalee, Eden, Amie, France, Dawn, Williams, Erin, Goodson, Jennifer, Butler, Amelia, Trask, Kara, Mans, Gay, Termaat, Jonathan, Aguilar-Dano, April, Delaney, Kirsha, Lawrence, Cassie, Lesona, Mildred, Millington, Alexandra, Navarra, Leanlove, Olatunji, Shaanti, Cruz, Raulle Sol, Cruz, Rhoze Sol, Young, Chelsea, Day, Andrew, Cook, Deborah J, Guyatt, Gordon H, Sprague, Sheila, Cohen, Dian, Heyland, Daren K, Lamontagne, François, Masse, Marie-Hélène, Ménard, Julie, Adhikari, Neill KJ, Pinto, Ruxandra, Kanji, Salmaan, Battista, Marie-Claude, Annane, Djillali, Vijayaraghavan, Bharath Kumar Tirupakuzhi, McGuinness, Shay, Parke, Rachael, and Arabi, Yaseen

Published
2023
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32. Proteomic consequences of TDA1 deficiency in Saccharomyces cerevisiae: Protein kinase Tda1 is essential for Hxk1 and Hxk2 serine 15 phosphorylation

Author

Henry Müller, Antoine Lesur, Gunnar Dittmar, Marc Gentzel, and Karina Kettner

Subjects
Medicine, Science
Abstract

Abstract Hexokinase 2 (Hxk2) of Saccharomyces cerevisiae is a dual function hexokinase, acting as a glycolytic enzyme and being involved in the transcriptional regulation of glucose-repressible genes. Relief from glucose repression is accompanied by phosphorylation of Hxk2 at serine 15, which has been attributed to the protein kinase Tda1. To explore the role of Tda1 beyond Hxk2 phosphorylation, the proteomic consequences of TDA1 deficiency were investigated by difference gel electrophoresis (2D-DIGE) comparing a wild type and a Δtda1 deletion mutant. To additionally address possible consequences of glucose repression/derepression, both were grown at 2% and 0.1% (w/v) glucose. A total of eight protein spots exhibiting a minimum twofold enhanced or reduced fluorescence upon TDA1 deficiency was detected and identified by mass spectrometry. Among the spot identities are—besides the expected Hxk2—two proteoforms of hexokinase 1 (Hxk1). Targeted proteomics analyses in conjunction with 2D-DIGE demonstrated that TDA1 is indispensable for Hxk2 and Hxk1 phosphorylation at serine 15. Thirty-six glucose-concentration-dependent protein spots were identified. A simple method to improve spot quantification, approximating spots as rotationally symmetric solids, is presented along with new data on the quantities of Hxk1 and Hxk2 and their serine 15 phosphorylated forms at high and low glucose growth conditions. The Δtda1 deletion mutant exhibited no altered growth under high or low glucose conditions or on alternative carbon sources. Also, invertase activity, serving as a reporter for glucose derepression, was not significantly altered. Instead, an involvement of Tda1 in oxidative stress response is suggested.

Published
2022
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33. Ventriculo-arterial (un)coupling in septic shock: Impact of current and upcoming hemodynamic drugs

Author

Zoé Demailly, Emmanuel Besnier, Fabienne Tamion, and Olivier Lesur

Subjects
ventriculo-arterial coupling, sepsis, hemodynamic drugs, norepinephrine (NE), dobutamine, levosimendan, Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract

Sepsis is an archetype of distributive shock and combines different levels of alterations in preload, afterload, and often cardiac contractility. The use of hemodynamic drugs has evolved over the past few years, along with the invasive and non-invasive tools used to measure these components in real time. However, none of them is impeccable, which is why the mortality of septic shock remains too high. The concept of ventriculo-arterial coupling (VAC) allows for the integration of these three fundamental macroscopic hemodynamic components. In this mini review, we discuss the knowledge, tools, and limitations of VAC measurement, along with the evidence supporting ventriculo-arterial uncoupling in septic shock. Finally, the impact of recommended hemodynamic drugs and molecules on VAC is detailed.

Published
2023
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34. Magnetically Driven Turbulence in the Inner Regions of Protoplanetary Disks

Author

David G. Rea, Jacob B. Simon, Daniel Carrera, Geoffroy Lesur, Wladimir Lyra, Debanjan Sengupta, Chao-Chin Yang, and Andrew N. Youdin

Subjects
Planet formation, Magnetohydrodynamics, Accretion, Protoplanetary disks, Magnetohydrodynamical simulations, Astrophysics, QB460-466
Abstract

Given the important role turbulence plays in the settling and growth of dust grains in protoplanetary disks, it is crucial that we determine whether these disks are turbulent and to what extent. Protoplanetary disks are weakly ionized near the midplane, which has led to a paradigm in which largely laminar magnetic field structures prevail deeper in the disk, with angular momentum being transported via magnetically launched winds. Yet, there has been little exploration of the precise behavior of the gas within the bulk of the disk. We carry out 3D, local shearing box simulations that include all three low-ionization effects (ohmic diffusion, ambipolar diffusion, and the Hall effect) to probe the nature of magnetically driven gas dynamics 1–30 au from the central star. We find that gas turbulence can persist with a generous yet physically motivated ionization prescription (order unity Elsässer numbers). The gas velocity fluctuations range from 0.03 to 0.09 of the sound speed c _s at the disk midplane to ∼ c _s near the disk surface, and are dependent on the initial magnetic field strength. However, the turbulent velocities do not appear to be strongly dependent on the field polarity, and thus appear to be insensitive to the Hall effect. The midplane turbulence has the potential to drive dust grains to collision velocities exceeding their fragmentation limit, and likely reduces the efficacy of particle clumping in the midplane, though it remains to be seen if this level of turbulence persists in disks with lower ionization levels.

Published
2024
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37. Monitoring Breast Cancer Care Quality at National and Local Level Using the French National Cancer Cohort

Author

Houzard, Sophie, Courtois, Emilie, Le Bihan Benjamin, Christine, Erbault, Marie, Arnould, Laurent, Barranger, Emmanuel, Coussy, Florence, Couturaud, Benoît, Cutuli, Bruno, de Cremoux, Patricia, de Reilhac, Pia, de Seze, Chantal, Foucaut, Aude-Marie, Gompel, Anne, Honoré, Stéphane, Lesur, Anne, Mathelin, Carole, Verzaux, Laurent, and Bousquet, Philippe-Jean

Published
2022
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38. Pyruvate dehydrogenase fuels a critical citrate pool that is essential for Th17 cell effector functions

Author

Leticia Soriano-Baguet, Melanie Grusdat, Henry Kurniawan, Mohaned Benzarti, Carole Binsfeld, Anouk Ewen, Joseph Longworth, Lynn Bonetti, Luana Guerra, Davide G. Franchina, Takumi Kobayashi, Veronika Horkova, Charlène Verschueren, Sergio Helgueta, Deborah Gérard, Tushar H. More, Antonia Henne, Catherine Dostert, Sophie Farinelle, Antoine Lesur, Jean-Jacques Gérardy, Christian Jäger, Michel Mittelbronn, Lasse Sinkkonen, Karsten Hiller, Johannes Meiser, and Dirk Brenner

Subjects
CP: Immunology, CP: Metabolism, Biology (General), QH301-705.5
Abstract

Summary: Pyruvate dehydrogenase (PDH) is the central enzyme connecting glycolysis and the tricarboxylic acid (TCA) cycle. The importance of PDH function in T helper 17 (Th17) cells still remains to be studied. Here, we show that PDH is essential for the generation of a glucose-derived citrate pool needed for Th17 cell proliferation, survival, and effector function. In vivo, mice harboring a T cell-specific deletion of PDH are less susceptible to developing experimental autoimmune encephalomyelitis. Mechanistically, the absence of PDH in Th17 cells increases glutaminolysis, glycolysis, and lipid uptake in a mammalian target of rapamycin (mTOR)-dependent manner. However, cellular citrate remains critically low in mutant Th17 cells, which interferes with oxidative phosphorylation (OXPHOS), lipid synthesis, and histone acetylation, crucial for transcription of Th17 signature genes. Increasing cellular citrate in PDH-deficient Th17 cells restores their metabolism and function, identifying a metabolic feedback loop within the central carbon metabolism that may offer possibilities for therapeutically targeting Th17 cell-driven autoimmunity.

Published
2023
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39. Are petrous bones just a repository of ancient biomolecules? Investigating biosystematic signals in sheep petrous bones using 3D geometric morphometrics

Author

Bader, Camille, Mallet, Christophe, Chahoud, Jwana, Amane, Agraw, De Cupere, Bea, Berthon, Remi, Lavenne, Franck, Mohaseb, Azadeh, Davoudi, Hossein, Albesso, Moussab, Fathi, Homa, Vuillien, Manon, Lesur, Joséphine, Helmer, Daniel, Gourichon, Lionel, Hanotte, Olivier, Mashkour, Marjan, Vila, Emmanuelle, and Cucchi, Thomas

Published
2022
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42. A phase III randomized trial of weight loss to reduce cancer-related fatigue among overweight and obese breast cancer patients: MEDEA Study design

Author

Di Meglio, Antonio, Martin, Elise, Crane, Tracy E., Charles, Cecile, Barbier, Aude, Raynard, Bruno, Mangin, Anthony, Tredan, Olivier, Bouleuc, Carole, Cottu, Paul H., Vanlemmens, Laurence, Segura-Djezzar, Carine, Lesur, Anne, Pistilli, Barbara, Joly, Florence, Ginsbourger, Thomas, Coquet, Bernadette, Pauporte, Iris, Jacob, Guillemette, Sirven, Aude, Bonastre, Julia, Ligibel, Jennifer A., Michiels, Stefan, and Vaz-Luis, Ines

Published
2022
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43. A phase III randomized trial of weight loss to reduce cancer-related fatigue among overweight and obese breast cancer patients: MEDEA Study design

Author

Antonio Di Meglio, Elise Martin, Tracy E. Crane, Cecile Charles, Aude Barbier, Bruno Raynard, Anthony Mangin, Olivier Tredan, Carole Bouleuc, Paul H. Cottu, Laurence Vanlemmens, Carine Segura-Djezzar, Anne Lesur, Barbara Pistilli, Florence Joly, Thomas Ginsbourger, Bernadette Coquet, Iris Pauporte, Guillemette Jacob, Aude Sirven, Julia Bonastre, Jennifer A. Ligibel, Stefan Michiels, and Ines Vaz-Luis

Subjects
Breast cancer, Cancer-related fatigue, Body mass index, Overweight, Obesity, Weight loss, Medicine (General), R5-920
Abstract

Abstract Background Elevated body mass index (BMI) represents a risk factor for cancer-related fatigue (CRF). Weight loss interventions are feasible and safe in cancer survivors, leading to improved cardio-metabolic and quality of life (QOL) outcomes and modulating inflammatory biomarkers. Randomized data are lacking showing that a lifestyle intervention aimed at weight loss, combining improved diet, exercise, and motivational counseling, reduces CRF. Motivating to Exercise and Diet, and Educating to healthy behaviors After breast cancer (MEDEA) is a multi-center, randomized controlled trial evaluating the impact of weight loss on CRF in overweight or obese survivors of breast cancer. Herein, we described the MEDEA methodology. Methods Patients (N = 220) with stage I–III breast cancer and BMI ≥ 25 kg/m2, within 12 months of primary treatment, and able to walk ≥ 400 m are eligible to enroll. Participants are randomized 1:1 to health education alone vs. a personalized telephone-based weight loss intervention plus health education. Both arms receive a health education program focusing on healthy living. Patients in the intervention arm are paired with an individual lifestyle coach, who delivers the intervention through 24 semi-structured telephone calls over 1 year. Intervention goals include weight loss ≥ 10% of baseline, caloric restriction of 500–1000 Kcal/day, and increased physical activity (PA) to 150 (initial phase) and 225–300 min/week (maintenance phase). The intervention is based on the social cognitive theory and is adapted from the Breast Cancer Weight Loss trial (BWEL, A011401). The primary endpoint is the difference in self-reported CRF (EORTC QLQ-C30) between arms. Secondary endpoints include the following: QOL (EORTC QLQ-C30, -BR45, -FA12), anxiety, and depression (HADS); weight and BMI, dietary habits and quality, PA, and sleep; health care costs (hospital-admissions, all-drug consumption, sick leaves) and cost-effectiveness (cost per quality-adjusted life-year); and patient motivation and satisfaction. The primary analysis of MEDEA will compare self-reported CRF at 12 months post-randomization between arms, with 80.0% power (two-sided α = 0.05) to detect a standardized effect size of 0.40. Discussion MEDEA will test the impact of a weight loss intervention on CRF among overweight or obese BC survivors, potentially providing additional management strategies and contributing to establish weight loss support as a new standard of clinical care. Trial registration ClinicalTrials.gov NCT04304924

Published
2022
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44. Genome‐wide evolutionary response of European oaks during the Anthropocene

Author

Dounia Saleh, Jun Chen, Jean‐Charles Leplé, Thibault Leroy, Laura Truffaut, Benjamin Dencausse, Céline Lalanne, Karine Labadie, Isabelle Lesur, Didier Bert, Frédéric Lagane, François Morneau, Jean‐Marc Aury, Christophe Plomion, Martin Lascoux, and Antoine Kremer

Subjects
Anthropocene, evolution, linked selection, Little Ice Age, Quercus petraea, Evolution, QH359-425
Abstract

Abstract The pace of tree microevolution during Anthropocene warming is largely unknown. We used a retrospective approach to monitor genomic changes in oak trees since the Little Ice Age (LIA). Allelic frequency changes were assessed from whole‐genome pooled sequences for four age‐structured cohorts of sessile oak (Quercus petraea) dating back to 1680, in each of three different oak forests in France. The genetic covariances of allelic frequency changes increased between successive time periods, highlighting genome‐wide effects of linked selection. We found imprints of parallel linked selection in the three forests during the late LIA, and a shift of selection during more recent time periods of the Anthropocene. The changes in allelic covariances within and between forests mirrored the documented changes in the occurrence of extreme events (droughts and frosts) over the last 300 years. The genomic regions with the highest covariances were enriched in genes involved in plant responses to pathogens and abiotic stresses (temperature and drought). These responses are consistent with the reported sequence of frost (or drought) and disease damage ultimately leading to the oak dieback after extreme events. They provide support for adaptive evolution of long‐lived species during recent climatic changes. Although we acknowledge that other sources (e.g., gene flow, generation overlap) may have contributed to temporal covariances of allelic frequency changes, the consistent and correlated response across the three forests lends support to the existence of a systematic driving force such as natural selection.

Published
2022
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47. Process-Specific Blood Biomarkers and Outcomes in COVID-19 Versus Non-COVID-19 ARDS (APEL–COVID Study): A Prospective, Observational Cohort Study.

Author

Lesur, Olivier, Segal, Eric David, Rego, Kevin, Mercat, Alain, Asfar, Pierre, and Chagnon, Frédéric

Abstract

Background: Severe acute respiratory syndrome (SARS) and acute respiratory distress syndrome (ARDS) are often considered separate clinico-radiological entities. Whether these conditions also present a single process-specific systemic biomolecular phenotype and how this relates to patient outcomes remains unknown. A prospective cohort study was conducted, including adult patients admitted to the ICU and general floors for COVID-19-related (COVID+) or non-COVID-19-related (COVID−) acute respiratory failure during the main phase of the pandemic. The primary objective was to study blood biomarkers and outcomes among different groups and severity subsets. Results: A total of 132 patients were included, as follows: 67 COVID+, 54 COVID− (with 11 matched control subjects for biomarker reference), and 58 of these patients allowed for further pre- and post-analysis. The baseline apelin (APL) levels were higher in COVID+ patients (p < 0.0001 vs. COVID− patients) and in SARS COVID+ patients (p ≤ 0.02 vs. ARDS), while the IL-6 levels were higher in ARDS COVID− patients (p ≤ 0.0001 vs. SARS). Multivariable logistic regression analyses with cohort biomarkers and outcome parameters revealed the following: (i) log-transformed neprilysin (NEP) activity was significantly higher in COVID+ patients (1.11 [95% CI: 0.4–1.9] vs. 0.37 [95% CI: 0.1–0.8], fold change (FC): 1.43 [95% CI: 1.04–1.97], p = 0.029) and in SARS patients (FC: 1.65 [95% CI: 1.05–2.6], p = 0.032 vs. non-SARS COVID+ patients, and 1.73 [95% CI: 1.19–2.5], p = 0.005 vs. ARDS COVID− patients) and (ii) higher lysyl oxidase (LOX) activity and APL levels were respectively associated with death and a shorter length of hospital stay in SARS COVID+ patients (Odds Ratios (OR): 1.01 [1.00–1.02], p = 0.05, and OR: −0.007 [−0.013–0.0001], p = 0.048). Conclusion: Process-specific blood biomarkers exhibited distinct profiles between COVID+ and COVID− patients, and across stages of severity. NEP and LOX activities, as well as APL levels, are particularly linked to COVID+ patients and their outcomes (ClinicalTrials.gov Identifier: NCT04632732). [ABSTRACT FROM AUTHOR]

Published
2024
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48. A strategy for studying epigenetic diversity in natural populations: proof of concept in poplar and oak.

Author

Lesur, Isabelle, Rogier, Odile, Sow, Mamadou Dia, Boury, Christophe, Duplan, Alexandre, Garnier, Abel, Senhaji-Rachik, Abdeljalil, Civan, Peter, Daron, Josquin, Delaunay, Alain, Duvaux, Ludovic, Benoit, Vanina, Guichoux, Erwan, Provost, Grégoire Le, Sanou, Edmond, Ambroise, Christophe, Plomion, Christophe, Salse, Jérôme, Segura, Vincent, and Tost, Jörg

Subjects
*WHOLE genome sequencing, *DNA methylation, *DURMAST oak, *BLACK poplar, *BIODIVERSITY
Abstract

In the last 20 years, several techniques have been developed for quantifying DNA methylation, the most studied epigenetic marks in eukaryotes, including the gold standard method, whole-genome bisulfite sequencing (WGBS). WGBS quantifies genome-wide DNA methylation but has several inconveniences rendering it less suitable for population-scale epigenetic studies. The high cost of deep sequencing and the large amounts of data generated prompted us to seek an alternative approach. Restricting studies to parts of the genome would be a satisfactory alternative had there not been a major limitation: the need to select upstream targets corresponding to differentially methylated regions as targets. Given the need to study large numbers of samples, we propose a strategy for investigating DNA methylation variation in natural populations, taking into account the structural complexity of genomes, their size, and their content in unique coding regions versus repeated regions as transposable elements. We first identified regions of highly variable DNA methylation in a subset of genotypes representative of the biological diversity in the population by WGBS. We then analysed the variations of DNA methylation in these targeted regions at the population level by sequencing capture bisulfite (SeqCapBis). The entire strategy was then validated by applying it to another species. Our strategy was developed as a proof of concept on natural populations of two forest species: Populus nigra and Quercus petraea. [ABSTRACT FROM AUTHOR]

Published
2024
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50. Apelin-13 in septic shock: effective in supporting hemodynamics in sheep but compromised by enzymatic breakdown in patients

Author

David Coquerel, Julie Lamoureux, Frédéric Chagnon, Kien Trân, Michael Sage, Etienne Fortin-Pellerin, Eugénie Delile, Xavier Sainsily, Justin Fournier, Audrey-Ann Dumont, Mannix Auger-Messier, Philippe Sarret, Eric Marsault, Jean-Paul Praud, Tamàs Fülöp, and Olivier Lesur

Subjects
Medicine, Science
Abstract

Abstract Sepsis is a prevalent life-threatening condition related to a systemic infection, and with unresolved issues including refractory septic shock and organ failures. Endogenously released catecholamines are often inefficient to maintain blood pressure, and low reactivity to exogenous catecholamines with risk of sympathetic overstimulation is well documented in septic shock. In this context, apelinergics are efficient and safe inotrope and vasoregulator in rodents. However, their utility in a larger animal model as well as the limitations with regards to the enzymatic breakdown during sepsis, need to be investigated. The therapeutic potential and degradation of apelinergics in sepsis were tested experimentally and in a cohort of patients. (1) 36 sheep with or without fecal peritonitis-induced septic shock (a large animal experimental design aimed to mimic the human septic shock paradigm) were evaluated for hemodynamic and renal responsiveness to incremental doses of two dominant apelinergics: apelin-13 (APLN-13) or Elabela (ELA), and (2) 52 subjects (33 patients with sepsis/septic shock and 19 healthy volunteers) were investigated for early levels of endogenous apelinergics in the blood, the related enzymatic degradation profile, and data regarding sepsis outcome. APLN-13 was the only one apelinergic which efficiently improved hemodynamics in both healthy and septic sheep. Endogenous apelinergic levels early rose, and specific enzymatic breakdown activities potentially threatened endogenous apelin system reactivity and negatively impacted the outcome in human sepsis. Short-term exogenous APLN-13 infusion is helpful in stabilizing cardiorenal functions in ovine septic shock; however, this ability might be impaired by specific enzymatic systems triggered during the early time course of human sepsis. Strategies to improve resistance of APLN-13 to degradation and/or to overcome sepsis-induced enzymatic breakdown environment should guide future works.

Published
2021
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