CD8(+) T-Cell Responses to Trypanosoma cruzi Are Highly Focused on Strain-Variant trans-Sialidase Epitopes

CD8(+) T cells are crucial for control of a number of medically important protozoan parasites, including Trypanosoma cruzi, the agent of human Chagas disease. Yet, in contrast to the wealth of information from viral and bacterial infections, little is known about the antigen specificity or the general development of effector and memory T-cell responses in hosts infected with protozoans. In this study we report on a wide-scale screen for the dominant parasite peptides recognized by CD8(+) T cells in T. cruzi–infected mice and humans. This analysis demonstrates that in both hosts the CD8(+) T-cell response is highly focused on epitopes encoded by members of the large trans-sialidase family of genes. Responses to a restricted set of immunodominant peptides were especially pronounced in T. cruzi–infected mice, with more than 30% of the CD8(+) T-cell response at the peak of infection specific for two major groups of trans-sialidase peptides. Experimental models also demonstrated that the dominance patterns vary depending on the infective strain of T. cruzi, suggesting that immune evasion may be occurring at a population rather than single-parasite level

Socioeconomic position links circulatory microbiota differences with biological age

Imbalanced nutrition is associated with accelerated ageing, possibly mediated by microbiota. An analysis of the circulatory microbiota obtained from the leukocytes of participants in the MRC Twenty-07 general population cohort was performed. We now report that in this cohort, the most biologically aged exhibit a significantly higher abundance of circulatory pathogenic bacteria, including Neisseria, Rothia and Porphyromonas, while those less biologically aged possess more circulatory salutogenic (defined as being supportive of human health and wellbeing) bacteria, including Lactobacillus, Lachnospiraceae UCG-004 and Kocuria. The presence of these salutogenic bactreria is consistent with a capacity to metabolise and produce Nrf2 agonists. We also demonstrate that associated one carbon metabolism, notably betaine levels, did not vary with chronological age, but displayed a difference with socioeconomic position (SEP). Those at lower SEP possessed significantly lower betaine levels indicative of a poorer diet and poorer health span and consistent with reduced global DNA methylation levels in this group. Our data suggest a clear route to improving age related health and resilience based on dietary modulation of the microbiota

Reduced anthropogenic aerosol radiative forcing caused by biogenic new particle formation

The magnitude of aerosol radiative forcing caused by anthropogenic emissions depends on the baseline state of the atmosphere under pristine preindustrial conditions. Measurements show that particle formation in atmospheric conditions can occur solely from biogenic vapors. Here, we evaluate the potential effect of this source of particles on preindustrial cloud condensation nuclei (CCN) concentrations and aerosol-cloud radiative forcing over the industrial period. Model simulations show that the pure biogenic particle formation mechanism has a much larger relative effect on CCN concentrations in the preindustrial atmosphere than in the present atmosphere because of the lower aerosol concentrations. Consequently, preindustrial cloud albedo is increased more than under present day conditions, and therefore the cooling forcing of anthropogenic aerosols is reduced. The mechanism increases CCN concentrations by 20-100% over a large fraction of the preindustrial lower atmosphere, and the magnitude of annual global mean radiative forcing caused by changes of cloud albedo since 1750 is reduced by 0.22 W m-2 (27%) to -0.60 W m-2. Model uncertainties, relatively slow formation rates, and limited available ambient measurements make it difficult to establish the significance of a mechanism that has its dominant effect under preindustrial conditions. Our simulations predict more particle formation in the Amazon than is observed. However, the first observation of pure organic nucleation has now been reported for the free troposphere. Given the potentially significant effect on anthropogenic forcing, effort should be made to better understand such naturally driven aerosol processes

An original phylogenetic approach identified mitochondrial haplogroup T1a1 as inversely associated with breast cancer risk in BRCA2 mutation carriers

Introduction: Individuals carrying pathogenic mutations in the BRCA1 and BRCA2 genes have a high lifetime risk of breast cancer. BRCA1 and BRCA2 are involved in DNA double-strand break repair, DNA alterations that can be caused by exposure to reactive oxygen species, a main source of which are mitochondria. Mitochondrial genome variations affect electron transport chain efficiency and reactive oxygen species production. Individuals with different mitochondrial haplogroups differ in their metabolism and sensitivity to oxidative stress. Variability in mitochondrial genetic background can alter reactive oxygen species production, leading to cancer risk. In the present study, we tested the hypothesis that mitochondrial haplogroups modify breast cancer risk in BRCA1/2 mutation carriers. Methods: We genotyped 22,214 (11,421 affected, 10,793 unaffected) mutation carriers belonging to the Consortium of Investigators of Modifiers of BRCA1/2 for 129 mitochondrial polymorphisms using the iCOGS array. Haplogroup inference and association detection were performed using a phylogenetic approach. ALTree was applied to explore the reference mitochondrial evolutionary tree and detect subclades enriched in affected or unaffected individuals. Results: We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01). Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03). We also identified three potential susceptibility loci, including G13708A/rs28359178, which has demonstrated an inverse association with familial breast cancer risk. Conclusions: This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects.Peer reviewe

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

Carbon sequestration potential of second-growth forest regeneration in the Latin American tropics

Regrowth of tropical secondary forests following complete or nearly complete removal of forest vegetation actively stores carbon in aboveground biomass, partially counterbalancing carbon emissions from deforestation, forest degradation, burning of fossil fuels, and other anthropogenic sources. We estimate the age and spatial extent of lowland second-growth forests in the Latin American tropics and model their potential aboveground carbon accumulation over four decades. Our model shows that, in 2008, second-growth forests (1 to 60 years old) covered 2.4 million km2 of land (28.1%of the total study area).Over 40 years, these lands can potentially accumulate a total aboveground carbon stock of 8.48 Pg C (petagrams of carbon) in aboveground biomass via low-cost natural regeneration or assisted regeneration, corresponding to a total CO2 sequestration of 31.09 Pg CO2. This total is equivalent to carbon emissions from fossil fuel use and industrial processes in all of Latin America and the Caribbean from1993 to 2014. Ten countries account for 95% of this carbon storage potential, led by Brazil, Colombia, Mexico, and Venezuela. We model future land-use scenarios to guide national carbon mitigation policies. Permitting natural regeneration on 40% of lowland pastures potentially stores an additional 2.0 Pg C over 40 years. Our study provides information and maps to guide national-level forest-based carbon mitigation plans on the basis of estimated rates of natural regeneration and pasture abandonment. Coupled with avoided deforestation and sustainable forestmanagement, natural regeneration of second-growth forests provides a low-costmechanism that yields a high carbon sequestration potential with multiple benefits for biodiversity and ecosystem services. © 2016 The Authors

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

Parasite Strain–Dependent Dominance Patterns in T. cruzi–Infected Mice

<p>B6 mice were infected with 1,000 Brazil, 1,000 Y, or 10,000 CL strain T. cruzi and stained with TSKB20/K^b (top) or TSKB18/K^b (bottom) tetramers as described in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.0020077#s4" target="_blank">Materials and Methods</a>. Data shown are a combination of two separate experiments with three or four mice per group per experiment.</p