CX3CR1+ CD115+ CD135+ common macrophage/DC precursors and the role of CX3CR1 in their response to inflammation

CX3CR1 expression is associated with the commitment of CSF-1R+ myeloid precursors to the macrophage/dendritic cell (DC) lineage. However, the relationship of the CSF-1R+ CX3CR1+ macrophage/DC precursor (MDP) with other DC precursors and the role of CX3CR1 in macrophage and DC development remain unclear. We show that MDPs give rise to conventional DCs (cDCs), plasmacytoid DCs (PDCs), and monocytes, including Gr1+ inflammatory monocytes that differentiate into TipDCs during infection. CX3CR1 deficiency selectively impairs the recruitment of blood Gr1+ monocytes in the spleen after transfer and during acute Listeria monocytogenes infection but does not affect the development of monocytes, cDCs, and PDCs

Assessing walking posture with geometric morphometrics: Effects of rearing environment in pigs

International audienceRearing social animals like pigs in isolation from conspecifics can have consequences on behaviour and physiology. The aim of this experiment was to determine whether rearing conditions affect body postures. We adapted a method for quantitative evaluation of postures based on geometric morphometrics, developed in horses, for pigs and applied it in different conditions. Forty eight 75-day old females were reared either alone in 2.25 m2 pens (IH, N = 24 animals and 4 groups) or in groups of four in 4.64 m2 pens (GH, N = 24) for two weeks. They were habituated to human handling (stroking, speaking) and marking on their backs every day, and tested individually once a day for 10 min in a corridor outside the home pen during the two subsequent weeks. We observed their behaviour and posture during the first exposure to the test (novelty), and the fourth and fifth (after habituation). On the sixth and seventh tests, a familiar stockperson was present in the corridor (human presence). Before each test, the animals were marked with seven landmarks along their length, corresponding to anatomical points and easily located. An experimenter took pictures of the animals walking along the corridor, and these pictures were transferred to tps software for analysis. GH animals were more often active in the rearing pen than IH (median (IQ) 15% of observations [12-20%] versus 2% [0-13%]; P < 0.05). All animals except one IH initiated contact with the handler during the last sessions of handling (Fisher's exact test, ns). Principal Component Analyses revealed significant effects of rearing and testing conditions on pigs’ behaviour and posture. Novelty led to fewer vocalisations and more exploration for IH than GH animals (P < 0.05), but there were no differences between treatments after habituation to the testing situation. The backs of IH animals were more rounded than those of GH (P < 0.05; dimension 1 of PCA), independently of the test condition. Human presence had no effect on posture. In conclusion, the method based on geometric morphometrics that we developed to study pig posture detected variations in walking posture in pigs associated with rearing conditions. Postures might reflect affective states in pigs, as shown in other species, but further studies are needed to verify thi

TRY plant trait database – enhanced coverage and open access

Plant traits—the morphological, anatomical, physiological, biochemical and phenological characteristics of plants—determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits—almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.Rest of authors: Decky Junaedi, Robert R. Junker, Eric Justes, Richard Kabzems, Jeffrey Kane, Zdenek Kaplan, Teja Kattenborn, Lyudmila Kavelenova, Elizabeth Kearsley, Anne Kempel, Tanaka Kenzo, Andrew Kerkhoff, Mohammed I. Khalil, Nicole L. Kinlock, Wilm Daniel Kissling, Kaoru Kitajima, Thomas Kitzberger, Rasmus Kjøller, Tamir Klein, Michael Kleyer, Jitka Klimešová, Joice Klipel, Brian Kloeppel, Stefan Klotz, Johannes M. H. Knops, Takashi Kohyama, Fumito Koike, Johannes Kollmann, Benjamin Komac, Kimberly Komatsu, Christian König, Nathan J. B. Kraft, Koen Kramer, Holger Kreft, Ingolf Kühn, Dushan Kumarathunge, Jonas Kuppler, Hiroko Kurokawa, Yoko Kurosawa, Shem Kuyah, Jean-Paul Laclau, Benoit Lafleur, Erik Lallai, Eric Lamb, Andrea Lamprecht, Daniel J. Larkin, Daniel Laughlin, Yoann Le Bagousse-Pinguet, Guerric le Maire, Peter C. le Roux, Elizabeth le Roux, Tali Lee, Frederic Lens, Simon L. Lewis, Barbara Lhotsky, Yuanzhi Li, Xine Li, Jeremy W. Lichstein, Mario Liebergesell, Jun Ying Lim, Yan-Shih Lin, Juan Carlos Linares, Chunjiang Liu, Daijun Liu, Udayangani Liu, Stuart Livingstone, Joan Llusià, Madelon Lohbeck, Álvaro López-García, Gabriela Lopez-Gonzalez, Zdeňka Lososová, Frédérique Louault, Balázs A. Lukács, Petr Lukeš, Yunjian Luo, Michele Lussu, Siyan Ma, Camilla Maciel Rabelo Pereira, Michelle Mack, Vincent Maire, Annikki Mäkelä, Harri Mäkinen, Ana Claudia Mendes Malhado, Azim Mallik, Peter Manning, Stefano Manzoni, Zuleica Marchetti, Luca Marchino, Vinicius Marcilio-Silva, Eric Marcon, Michela Marignani, Lars Markesteijn, Adam Martin, Cristina Martínez-Garza, Jordi Martínez-Vilalta, Tereza Mašková, Kelly Mason, Norman Mason, Tara Joy Massad, Jacynthe Masse, Itay Mayrose, James McCarthy, M. Luke McCormack, Katherine McCulloh, Ian R. McFadden, Brian J. McGill, Mara Y. McPartland, Juliana S. Medeiros, Belinda Medlyn, Pierre Meerts, Zia Mehrabi, Patrick Meir, Felipe P. L. Melo, Maurizio Mencuccini, Céline Meredieu, Julie Messier, Ilona Mészáros, Juha Metsaranta, Sean T. Michaletz, Chrysanthi Michelaki, Svetlana Migalina, Ruben Milla, Jesse E. D. Miller, Vanessa Minden, Ray Ming, Karel Mokany, Angela T. Moles, Attila Molnár V, Jane Molofsky, Martin Molz, Rebecca A. Montgomery, Arnaud Monty, Lenka Moravcová, Alvaro Moreno-Martínez, Marco Moretti, Akira S. Mori, Shigeta Mori, Dave Morris, Jane Morrison, Ladislav Mucina, Sandra Mueller, Christopher D. Muir, Sandra Cristina Müller, François Munoz, Isla H. Myers-Smith, Randall W. Myster, Masahiro Nagano, Shawna Naidu, Ayyappan Narayanan, Balachandran Natesan, Luka Negoita, Andrew S. Nelson, Eike Lena Neuschulz, Jian Ni, Georg Niedrist, Jhon Nieto, Ülo Niinemets, Rachael Nolan, Henning Nottebrock, Yann Nouvellon, Alexander Novakovskiy, The Nutrient Network, Kristin Odden Nystuen, Anthony O'Grady, Kevin O'Hara, Andrew O'Reilly-Nugent, Simon Oakley, Walter Oberhuber, Toshiyuki Ohtsuka, Ricardo Oliveira, Kinga Öllerer, Mark E. Olson, Vladimir Onipchenko, Yusuke Onoda, Renske E. Onstein, Jenny C. Ordonez, Noriyuki Osada, Ivika Ostonen, Gianluigi Ottaviani, Sarah Otto, Gerhard E. Overbeck, Wim A. Ozinga, Anna T. Pahl, C. E. Timothy Paine, Robin J. Pakeman, Aristotelis C. Papageorgiou, Evgeniya Parfionova, Meelis Pärtel, Marco Patacca, Susana Paula, Juraj Paule, Harald Pauli, Juli G. Pausas, Begoña Peco, Josep Penuelas, Antonio Perea, Pablo Luis Peri, Ana Carolina Petisco-Souza, Alessandro Petraglia, Any Mary Petritan, Oliver L. Phillips, Simon Pierce, Valério D. Pillar, Jan Pisek, Alexandr Pomogaybin, Hendrik Poorter, Angelika Portsmuth, Peter Poschlod, Catherine Potvin, Devon Pounds, A. Shafer Powell, Sally A. Power, Andreas Prinzing, Giacomo Puglielli, Petr Pyšek, Valerie Raevel, Anja Rammig, Johannes Ransijn, Courtenay A. Ray, Peter B. Reich, Markus Reichstein, Douglas E. B. Reid, Maxime Réjou-Méchain, Victor Resco de Dios, Sabina Ribeiro, Sarah Richardson, Kersti Riibak, Matthias C. Rillig, Fiamma Riviera, Elisabeth M. R. Robert, Scott Roberts, Bjorn Robroek, Adam Roddy, Arthur Vinicius Rodrigues, Alistair Rogers, Emily Rollinson, Victor Rolo, Christine Römermann, Dina Ronzhina, Christiane Roscher, Julieta A. Rosell, Milena Fermina Rosenfield, Christian Rossi, David B. Roy, Samuel Royer-Tardif, Nadja Rüger, Ricardo Ruiz-Peinado, Sabine B. Rumpf, Graciela M. Rusch, Masahiro Ryo, Lawren Sack, Angela Saldaña, Beatriz Salgado-Negret, Roberto Salguero-Gomez, Ignacio Santa-Regina, Ana Carolina Santacruz-García, Joaquim Santos, Jordi Sardans, Brandon Schamp, Michael Scherer-Lorenzen, Matthias Schleuning, Bernhard Schmid, Marco Schmidt, Sylvain Schmitt, Julio V. Schneider, Simon D. Schowanek, Julian Schrader, Franziska Schrodt, Bernhard Schuldt, Frank Schurr, Galia Selaya Garvizu, Marina Semchenko, Colleen Seymour, Julia C. Sfair, Joanne M. Sharpe, Christine S. Sheppard, Serge Sheremetiev, Satomi Shiodera, Bill Shipley, Tanvir Ahmed Shovon, Alrun Siebenkäs, Carlos Sierra, Vasco Silva, Mateus Silva, Tommaso Sitzia, Henrik Sjöman, Martijn Slot, Nicholas G. Smith, Darwin Sodhi, Pamela Soltis, Douglas Soltis, Ben Somers, Grégory Sonnier, Mia Vedel Sørensen, Enio Egon Sosinski Jr, Nadejda A. Soudzilovskaia, Alexandre F. Souza, Marko Spasojevic, Marta Gaia Sperandii, Amanda B. Stan, James Stegen, Klaus Steinbauer, Jörg G. Stephan, Frank Sterck, Dejan B. Stojanovic, Tanya Strydom, Maria Laura Suarez, Jens-Christian Svenning, Ivana Svitková, Marek Svitok, Miroslav Svoboda, Emily Swaine, Nathan Swenson, Marcelo Tabarelli, Kentaro Takagi, Ulrike Tappeiner, Rubén Tarifa, Simon Tauugourdeau, Cagatay Tavsanoglu, Mariska te Beest, Leho Tedersoo, Nelson Thiffault, Dominik Thom, Evert Thomas, Ken Thompson, Peter E. Thornton, Wilfried Thuiller, Lubomír Tichý, David Tissue, Mark G. Tjoelker, David Yue Phin Tng, Joseph Tobias, Péter Török, Tonantzin Tarin, José M. Torres-Ruiz, Béla Tóthmérész, Martina Treurnicht, Valeria Trivellone, Franck Trolliet, Volodymyr Trotsiuk, James L. Tsakalos, Ioannis Tsiripidis, Niklas Tysklind, Toru Umehara, Vladimir Usoltsev, Matthew Vadeboncoeur, Jamil Vaezi, Fernando Valladares, Jana Vamosi, Peter M. van Bodegom, Michiel van Breugel, Elisa Van Cleemput, Martine van de Weg, Stephni van der Merwe, Fons van der Plas, Masha T. van der Sande, Mark van Kleunen, Koenraad Van Meerbeek, Mark Vanderwel, Kim André Vanselow, Angelica Vårhammar, Laura Varone, Maribel Yesenia Vasquez Valderrama, Kiril Vassilev, Mark Vellend, Erik J. Veneklaas, Hans Verbeeck, Kris Verheyen, Alexander Vibrans, Ima Vieira, Jaime Villacís, Cyrille Violle, Pandi Vivek, Katrin Wagner, Matthew Waldram, Anthony Waldron, Anthony P. Walker, Martyn Waller, Gabriel Walther, Han Wang, Feng Wang, Weiqi Wang, Harry Watkins, James Watkins, Ulrich Weber, James T. Weedon, Liping Wei, Patrick Weigelt, Evan Weiher, Aidan W. Wells, Camilla Wellstein, Elizabeth Wenk, Mark Westoby, Alana Westwood, Philip John White, Mark Whitten, Mathew Williams, Daniel E. Winkler, Klaus Winter, Chevonne Womack, Ian J. Wright, S. Joseph Wright, Justin Wright, Bruno X. Pinho, Fabiano Ximenes, Toshihiro Yamada, Keiko Yamaji, Ruth Yanai, Nikolay Yankov, Benjamin Yguel, Kátia Janaina Zanini, Amy E. Zanne, David Zelený, Yun-Peng Zhao, Jingming Zheng, Ji Zheng, Kasia Ziemińska, Chad R. Zirbel, Georg Zizka, Irié Casimir Zo-Bi, Gerhard Zotz, Christian Wirth.Max Planck Institute for Biogeochemistry; Max Planck Society; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; International Programme of Biodiversity Science (DIVERSITAS); International Geosphere-Biosphere Programme (IGBP); Future Earth; French Foundation for Biodiversity Research (FRB); GIS ‘Climat, Environnement et Société'.http://wileyonlinelibrary.com/journal/gcbhj2021Plant Production and Soil Scienc

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Transplantation hépatique pour métastases endocrines (analyse d'une série multicentrique française de 85 patients transplantés)

Introduction Les tumeurs endocrines (TE) forment un groupe de tumeurs rares, hétérogènes et souvent métastatiques au moment du diagnostic. Parmi ces dernières, seules 20% seront réséquables. Certaines équipes ont donc proposé la greffe comme traitement des TE métastatiques (TEM). L ablation totale du foie et la transplantation (TH) permettait de traiter à la fois la maladie et le syndrome hormonal qu elle provoquait mais aussi d améliorer la survie globale des malades M+. Les résultats de cette thérapeutique sont inhomogènes et une approche sélective des malades semble être nécessaire pour améliorer la survie. Les études publiées dans la littérature portent sur de petits effectifs avec un niveau de preuve faible. Matériel et méthode C est pourquoi nous avons colligé la quasi totalité des patients français greffés pour cette indication. Notre but était d identifier les critères pronostiques pour indiquer la TH chez les patients qui pourraient en retirer le meilleur bénéfice à l heure de la pénurie de transplants. Résultats Quatre vingt cinq patients ont été greffés hépatiques en France entre 1989 et 2005 pour TEM. Le suivi médian de cette série est 57 mois. La survie globale à 1, 5 et 10 ans était respectivement 72, 47 et 24%. La survie sans récidive était de 20% à 5 ans. Les facteurs pronostiques identifiés en analyse univariée étaient : la période d étude (avant ou après 1994), la localisation pancréatique primitive, la résection de la tumeur primitive, la sécrétion de gastrine, la réalisation d un octréoscanner prégreffe, la présence d une hépatomégalie, un envahissement tumoral de plus de 40% (TDM), la TH associée à une exentération susmésocolique, la splénectomie, le caractère R0 de la résection et la différentiation histologique. En analyse multivariée, la localisation tumorale primitive pancréatique ou digestive et la présence d une hépatomégalie métastatique ( poids foie 20% poids théorique du foie) étaient les seuls critères pronostics indépendants. Nous avons ensuite établi une échelle de gravité en pondérant chacun des critères en fonction de leur risque relatif ce qui nous a permis d en déduire un score pronostique. Discussion La TH est indiquée en cas de TEM chez les patients en bon état général (âge physiologique), symptomatiques malgré le traitement médical , en l absence de dissémination extra hépatique et avec un score pronostique 2 (survie à 5ans > 50%). Les malades qui ont une TE d origine pancréatique associée à une hépatomégalie métastatique selon notre définition sont de mauvais candidats à la greffe (survie à 5 ans : 14%). Perspectives La validité de ce modèle sera confirmée prochainement sur une autre population. L identification de facteurs histopronostiques nous permettra également d améliorer sa sensibilité et sa spécificité. Conclusion Ce score apporte une réponse simple et facilement applicable en pratique clinique pour aider le praticien dans sa prise de décision opératoire.AIX-MARSEILLE2-BU Méd/Odontol. (130552103) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

A workflow to assemble plant mitochondrial genomes using long-reads: case study in <em>Pisum sativum</em> and <em>Phaseolus vulgaris</em>

National audiencePlant mitochondrial genomes are generally not used to study evolution within and between species. They are larger than animal mitochondrial genomes and evolve by accumulating rearrangements rather than mutations [1]. These characteristics make it difficult to obtain complete assemblies using short-reads like in mammals. To address this problem, we developed and tested a plant-based assembly workflow using Nanopore and Pacbio long-reads from Pisum sativum and Phaseolus vulgaris, respectively. Nanopore long-reads from Pisum sativum whole genome sequencing and Pacbio long-reads from Phaseolus vulgaris whole genome sequencing were mapped on all mitochondrial genomes available for legumes at NCBI using minimap2. Captured reads were assembled using canu 1.8 and corrected by racon for Nanopore reads and pilon for both using available Illumina reads. Circlator was used to circularize the sequences obtained. To assess and compare gene orders, the annotation of each mitochondrial genome was done using GeSeq. A phylogeny based on mitochondrial gene order was built and showed consistency with legumes’ reported phylogeny. Illumina short reads from wild pea accessions were also mapped to the mitochondria of Pisum sativum to identify putative gene order differences. These resources pave the way for further use of legume and other plant mitochondrial data to answer evolution-related key questions

Non-excisional laser therapies for hemorrhoidal disease: a systematic review of the literature

Non-excisional laser therapies are emerging treatment for grades II and III hemorrhoidal disease (HD). However, so far, their efficiency is based on low-level evidence. Therefore, we aimed to systematically review the efficiency of non-excisional laser therapies for HD. MEDLINE/Pubmed, Web of science, Embase, and Cochrane were searched from database implementation until the April 17th, 2020. We included studies reporting at least one of surgical indicators of postoperative outcomes of laser therapies, encompassing laser hemorrhoidoplasty (LH) and hemorrhoidal laser procedure (HeLP). Fourteen studies describing LH and HeLP were included, representing 1570 patients. The main intraoperative complication was bleeding (0-1.9% of pooled patients for LH, 5.5-16.7% of pooled patients for HeLP). Postoperative complications occurred in up to 64% of patients after LH and 23.3% after HeLP. Resolution of symptoms ranged between 70 and 100% after LH and between 83.6 and 90% after HeLP. Moreover, four randomized controlled trials included in our review reported similar resolution after LH compared with hemorrhoidectomy or mucopexy and after HeLP compared with rubber band ligation. Recurrence rate was reported to range between 0 and 11.3% after LH and between 5 and 9.4% after HeLP. When compared with hemorrhoidectomy, LH showed conflicting results with one randomized controlled trial reporting similar recurrence rate, but another reporting decreased recurrences associated with hemorrhoidectomy. Laser therapies showed lower postoperative pain than hemorrhoidectomy or rubber band ligation. LH and HeLP are safe and effective techniques for the treatment of grades II and III HD