Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Rarity of monodominance in hyperdiverse Amazonian forests
Steege, Hans Ter; Henkel, Terry W. ; Helal, Nora ; Marimon, Beatriz S. ; Marimon-Junior, Ben Hur ; Huth, Andreas ; Groeneveld, Jürgen ; Sabatier, Daniel ; Souza Coelho, Luiz de; Andrade Lima Filho, Diogenes de; Salomão, Rafael P. ; Amaral, Iêda Leão ; Almeida Matos, Francisca Dionízia de; Castilho, Carolina V. ; Phillips, Oliver L. ; Guevara, Juan Ernesto ; Jesus Veiga Carim, Marcelo de; Cárdenas López, Dairon ; Magnusson, William E. ; Wittmann, Florian ; Irume, Mariana Victória ; Martins, Maria Pires ; Silva Guimarães, José Renan da; Molino, Jean François ; Bánki, Olaf S. ; Piedade, Maria Teresa Fernandez ; Pitman, Nigel C.A. ; Mendoza, Abel Monteagudo ; Ramos, José Ferreira ; Luize, Bruno Garcia ; Moraes de Leão Novo, Evlyn Márcia ; Núñez Vargas, Percy ; Silva, Thiago Sanna Freire ; Venticinque, Eduardo Martins ; Manzatto, Angelo Gilberto ; Reis, Neidiane Farias Costa ; Terborgh, John ; Casula, Katia Regina ; Honorio Coronado, Euridice N. ; Montero, Juan Carlos ; Feldpausch, Ted R. ; Duque, Alvaro ; Costa, Flávia R.C. ; Arboleda, Nicolás Castaño ; Schöngart, Jochen ; Killeen, Timothy J. ; Vasquez, Rodolfo ; Mostacedo, Bonifacio ; Demarchi, Layon O. ; Assis, Rafael L. ; Baraloto, Chris ; Engel, Julien ; Petronelli, Pascal ; Castellanos, Hernán ; Medeiros, Marcelo Brilhante de; Quaresma, Adriano ; Simon, Marcelo Fragomeni ; Andrade, Ana ; Camargo, José Luís ; Laurance, Susan G.W. ; Laurance, William F. ; Rincón, Lorena M. ; Schietti, Juliana ; Sousa, Thaiane R. ; Sousa Farias, Emanuelle de; Lopes, Maria Aparecida ; Magalhães, José Leonardo Lima ; Mendonça Nascimento, Henrique Eduardo ; Lima de Queiroz, Helder ; Aymard C, Gerardo A. ; Brienen, Roel ; Revilla, Juan David Cardenas ; Vieira, Ima Célia Guimarães ; Cintra, Bruno Barçante Ladvocat ; Stevenson, Pablo R. ; Feitosa, Yuri Oliveira ; Duivenvoorden, Joost F. ; Mogollón, Hugo F. ; Araujo-Murakami, Alejandro ; Ferreira, Leandro Valle ; Lozada, José Rafael ; Comiskey, James A. ; Toledo, José Julio de; Damasco, Gabriel ; Dávila, Nállarett ; Draper, Freddie ; García-Villacorta, Roosevelt ; Lopes, Aline ; Vicentini, Alberto ; Alonso, Alfonso ; Dallmeier, Francisco ; Gomes, Vitor H.F. ; Lloyd, Jon ; Neill, David ; Aguiar, Daniel Praia Portela de; Arroyo, Luzmila ; Carvalho, Fernanda Antunes ; Souza, Fernanda Coelho de; Amaral, Dário Dantas do; Feeley, Kenneth J. ; Gribel, Rogerio ; Pansonato, Marcelo Petratti ; Barlow, Jos ; Berenguer, Erika ; Ferreira, Joice ; Fine, Paul V.A. ; Guedes, Marcelino Carneiro ; Jimenez, Eliana M. ; Licona, Juan Carlos ; Peñuela Mora, Maria Cristina ; Villa, Boris ; Cerón, Carlos ; Maas, Paul ; Silveira, Marcos ; Stropp, Juliana ; Thomas, Raquel ; Baker, Tim R. ; Daly, Doug ; Dexter, Kyle G. ; Huamantupa-Chuquimaco, Isau ; Milliken, William ; Pennington, Toby ; Ríos Paredes, Marcos ; Fuentes, Alfredo ; Klitgaard, Bente ; Pena, José Luis Marcelo ; Peres, Carlos A. ; Silman, Miles R. ; Tello, J.S. ; Chave, Jerome ; Cornejo Valverde, Fernando ; Fiore, Anthony Di; Hilário, Renato Richard ; Phillips, Juan Fernando ; Rivas-Torres, Gonzalo ; Andel, Tinde R. van; Hildebrand, Patricio von; Noronha, Janaína Costa ; Barbosa, Edelcilio Marques ; Barbosa, Flávia Rodrigues ; Matos Bonates, Luiz Carlos de; Sá Carpanedo, Rainiellen de; Dávila Doza, Hilda Paulette ; Fonty, Émile ; GómeZárate Z, Ricardo ; Gonzales, Therany ; Gallardo Gonzales, George Pepe ; Hoffman, Bruce ; Junqueira, André Braga ; Malhi, Yadvinder ; Andrade Miranda, Ires Paula de; Pinto, Linder Felipe Mozombite ; Prieto, Adriana ; Jesus Rodrigues, Domingos de; Rudas, Agustín ; Ruschel, Ademir R. ; Silva, Natalino ; Vela, César I.A. ; Vos, Vincent Antoine ; Zent, Egleé L. ; Zent, Stanford ; Weiss Albuquerque, Bianca ; Cano, Angela ; Carrero Márquez, Yrma Andreina ; Correa, Diego F. ; Costa, Janaina Barbosa Pedrosa ; Flores, Bernardo Monteiro ; Galbraith, David ; Holmgren, Milena ; Kalamandeen, Michelle ; Nascimento, Marcelo Trindade ; Oliveira, Alexandre A. ; Ramirez-Angulo, Hirma ; Rocha, Maira ; Scudeller, Veridiana Vizoni ; Sierra, Rodrigo ; Tirado, Milton ; Umaña Medina, Maria Natalia ; Heijden, Geertje van der; Vilanova Torre, Emilio ; Vriesendorp, Corine ; Wang, Ophelia ; Young, Kenneth R. ; Ahuite Reategui, Manuel Augusto ; Baider, Cláudia ; Balslev, Henrik ; Cárdenas, Sasha ; Casas, Luisa Fernanda ; Farfan-Rios, William ; Ferreira, Cid ; Linares-Palomino, Reynaldo ; Mendoza, Casimiro ; Mesones, Italo ; Torres-Lezama, Armando ; Giraldo, Ligia Estela Urrego ; Villarroel, Daniel ; Zagt, Roderick ; Alexiades, Miguel N. ; Oliveira, Edmar Almeida de; Garcia-Cabrera, Karina ; Hernandez, Lionel ; Palacios Cuenca, Walter ; Pansini, Susamar ; Pauletto, Daniela ; Ramirez Arevalo, Freddy ; Sampaio, Adeilza Felipe ; Valderrama Sandoval, Elvis H. ; Valenzuela Gamarra, Luis ; Levesley, Aurora ; Pickavance, Georgia ; Melgaço, Karina - \ 2019
Scientific Reports 9 (2019). - ISSN 2045-2322

Tropical forests are known for their high diversity. Yet, forest patches do occur in the tropics where a single tree species is dominant. Such "monodominant" forests are known from all of the main tropical regions. For Amazonia, we sampled the occurrence of monodominance in a massive, basin-wide database of forest-inventory plots from the Amazon Tree Diversity Network (ATDN). Utilizing a simple defining metric of at least half of the trees ≥ 10 cm diameter belonging to one species, we found only a few occurrences of monodominance in Amazonia, and the phenomenon was not significantly linked to previously hypothesized life history traits such wood density, seed mass, ectomycorrhizal associations, or Rhizobium nodulation. In our analysis, coppicing (the formation of sprouts at the base of the tree or on roots) was the only trait significantly linked to monodominance. While at specific locales coppicing or ectomycorrhizal associations may confer a considerable advantage to a tree species and lead to its monodominance, very few species have these traits. Mining of the ATDN dataset suggests that monodominance is quite rare in Amazonia, and may be linked primarily to edaphic factors.

Patterns of nitrogen-fixing tree abundance in forests across Asia and America
Menge, Duncan N.L. ; Chisholm, Ryan A. ; Davies, Stuart J. ; Abu Salim, Kamariah ; Allen, David ; Alvarez, Mauricio ; Bourg, Norm ; Brockelman, Warren Y. ; Bunyavejchewin, Sarayudh ; Butt, Nathalie ; Cao, Min ; Chanthorn, Wirong ; Chao, Wei Chun ; Clay, Keith ; Condit, Richard ; Cordell, Susan ; Silva, João Batista da; Dattaraja, H.S. ; Andrade, Ana Cristina Segalin de; Oliveira, Alexandre A. de; Ouden, Jan den; Drescher, Michael ; Fletcher, Christine ; Giardina, Christian P. ; Savitri Gunatilleke, C.V. ; Gunatilleke, I.A.U.N. ; Hau, Billy C.H. ; He, Fangliang ; Howe, Robert ; Hsieh, Chang Fu ; Hubbell, Stephen P. ; Inman-Narahari, Faith M. ; Jansen, Patrick A. ; Johnson, Daniel J. ; Kong, Lee Sing ; Král, Kamil ; Ku, Chen Chia ; Lai, Jiangshan ; Larson, Andrew J. ; Li, Xiankun ; Li, Yide ; Lin, Luxiang ; Lin, Yi Ching ; Liu, Shirong ; Lum, Shawn K.Y. ; Lutz, James A. ; Ma, Keping ; Malhi, Yadvinder ; McMahon, Sean ; McShea, William ; Mi, Xiangcheng ; Morecroft, Michael ; Myers, Jonathan A. ; Nathalang, Anuttara ; Novotny, Vojtech ; Ong, Perry ; Orwig, David A. ; Ostertag, Rebecca ; Parker, Geoffrey ; Phillips, Richard P. ; Abd. Rahman, Kassim ; Sack, Lawren ; Sang, Weiguo ; Shen, Guochun ; Shringi, Ankur ; Shue, Jessica ; Su, Sheng Hsin ; Sukumar, Raman ; Fang Sun, I. ; Suresh, H.S. ; Tan, Sylvester ; Thomas, Sean C. ; Toko, Pagi S. ; Valencia, Renato ; Vallejo, Martha I. ; Vicentini, Alberto ; Vrška, Tomáš ; Wang, Bin ; Wang, Xihua ; Weiblen, George D. ; Wolf, Amy ; Xu, Han ; Yap, Sandra ; Zhu, Li ; Fung, Tak - \ 2019
Journal of Ecology 107 (2019)6. - ISSN 0022-0477 - p. 2598 - 2610.
forest - legume - nitrogen fixation - nutrient limitation - Smithsonian ForestGEO - symbiosis

Symbiotic nitrogen (N)-fixing trees can provide large quantities of new N to ecosystems, but only if they are sufficiently abundant. The overall abundance and latitudinal abundance distributions of N-fixing trees are well characterised in the Americas, but less well outside the Americas. Here, we characterised the abundance of N-fixing trees in a network of forest plots spanning five continents, ~5,000 tree species and ~4 million trees. The majority of the plots (86%) were in America or Asia. In addition, we examined whether the observed pattern of abundance of N-fixing trees was correlated with mean annual temperature and precipitation. Outside the tropics, N-fixing trees were consistently rare in the forest plots we examined. Within the tropics, N-fixing trees were abundant in American but not Asian forest plots (~7% versus ~1% of basal area and stems). This disparity was not explained by mean annual temperature or precipitation. Our finding of low N-fixing tree abundance in the Asian tropics casts some doubt on recent high estimates of N fixation rates in this region, which do not account for disparities in N-fixing tree abundance between the Asian and American tropics. Synthesis. Inputs of nitrogen to forests depend on symbiotic nitrogen fixation, which is constrained by the abundance of N-fixing trees. By analysing a large dataset of ~4 million trees, we found that N-fixing trees were consistently rare in the Asian tropics as well as across higher latitudes in Asia, America and Europe. The rarity of N-fixing trees in the Asian tropics compared with the American tropics might stem from lower intrinsic N limitation in Asian tropical forests, although direct support for any mechanism is lacking. The paucity of N-fixing trees throughout Asian forests suggests that N inputs to the Asian tropics might be lower than previously thought.

Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds
Nunes-Nesi, Adriano ; Alseekh, Saleh ; Oliveira Silva, Franklin Magnum de; Omranian, Nooshin ; Lichtenstein, Gabriel ; Mirnezhad, Mohammad ; González, Roman R.R. ; y Garcia, Julia Sabio ; Conte, Mariana ; Leiss, Kirsten A. ; Klinkhamer, Peter G.L. ; Nikoloski, Zoran ; Carrari, Fernando ; Fernie, Alisdair R. - \ 2019
Metabolomics 15 (2019)4. - ISSN 1573-3882
Leaf metabolism - Metabolite network - Metabolite QTL - Tomato

Introduction: To date, most studies of natural variation and metabolite quantitative trait loci (mQTL) in tomato have focused on fruit metabolism, leaving aside the identification of genomic regions involved in the regulation of leaf metabolism. Objective: This study was conducted to identify leaf mQTL in tomato and to assess the association of leaf metabolites and physiological traits with the metabolite levels from other tissues. Methods: The analysis of components of leaf metabolism was performed by phenotypying 76 tomato ILs with chromosome segments of the wild species Solanum pennellii in the genetic background of a cultivated tomato (S. lycopersicum) variety M82. The plants were cultivated in two different environments in independent years and samples were harvested from mature leaves of non-flowering plants at the middle of the light period. The non-targeted metabolite profiling was obtained by gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). With the data set obtained in this study and already published metabolomics data from seed and fruit, we performed QTL mapping, heritability and correlation analyses. Results: Changes in metabolite contents were evident in the ILs that are potentially important with respect to stress responses and plant physiology. By analyzing the obtained data, we identified 42 positive and 76 negative mQTL involved in carbon and nitrogen metabolism. Conclusions: Overall, these findings allowed the identification of S. lycopersicum genome regions involved in the regulation of leaf primary carbon and nitrogen metabolism, as well as the association of leaf metabolites with metabolites from seeds and fruits.

Tomato Chlorotic Spot Virus (TCSV) Putatively Incorporated a Genomic Segment of Groundnut Ringspot Virus (GRSV) Upon a Reassortment Event
Silva, João Marcos Fagundes ; Oliveira, Athos Silva de; Almeida, Mariana Martins Severo de; Kormelink, Richard ; Nagata, Tatsuya ; Resende, Renato Oliveira - \ 2019
Viruses 11 (2019)2. - ISSN 1999-4915
groundnut ringspot virus - reassortment - tomato chlorotic spot virus - tospovirus - virus evolution

Tomato chlorotic spot virus (TCSV) and groundnut ringspot virus (GRSV) share several genetic and biological traits. Both of them belong to the genus Tospovirus (family Peribunyaviridae), which is composed by viruses with tripartite RNA genome that infect plants and are transmitted by thrips (order Thysanoptera). Previous studies have suggested several reassortment events between these two viruses, and some speculated that they may share one of their genomic segments. To better understand the intimate evolutionary history of these two viruses, we sequenced the genomes of the first TCSV and GRSV isolates ever reported. Our analyses show that TCSV and GRSV isolates indeed share one of their genomic segments, suggesting that one of those viruses may have emerged upon a reassortment event. Based on a series of phylogenetic and nucleotide diversity analyses, we conclude that the parental genotype of the M segment of TCSV was either eliminated due to a reassortment with GRSV or it still remains to be identified.

Biodiversity recovery of Neotropical secondary forests
Rozendaal, Danaë M.A. ; Bongers, Frans ; Aide, T.M. ; Alvarez-Dávila, Esteban ; Ascarrunz, Nataly ; Balvanera, Patricia ; Becknell, Justin M. ; Bentos, Tony V. ; Brancalion, Pedro H.S. ; Cabral, George A.L. ; Calvo-Rodriguez, Sofia ; Chave, Jerome ; César, Ricardo G. ; Chazdon, Robin L. ; Condit, Richard ; Dallinga, Jorn S. ; Almeida-Cortez, Jarcilene S. De; Jong, Ben de; Oliveira, Alexandre De; Denslow, Julie S. ; Dent, Daisy H. ; Dewalt, Saara J. ; Dupuy, Juan Manuel ; Durán, Sandra M. ; Dutrieux, Loïc P. ; Espírito-Santo, Mario M. ; Fandino, María C. ; Fernandes, G.W. ; Finegan, Bryan ; García, Hernando ; Gonzalez, Noel ; Moser, Vanessa Granda ; Hall, Jefferson S. ; Hernández-Stefanoni, José Luis ; Hubbell, Stephen ; Jakovac, Catarina C. ; Hernández, Alma Johanna ; Junqueira, André B. ; Kennard, Deborah ; Larpin, Denis ; Letcher, Susan G. ; Licona, Juan-Carlos ; Lebrija-trejos, Edwin ; Marín-Spiotta, Erika ; Martínez-Ramos, Miguel ; Massoca, Paulo E.S. ; Meave, Jorge A. ; Mesquita, Rita C.G. ; Mora, Francisco ; Müller, Sandra C. ; Muñoz, Rodrigo ; Oliveira Neto, Silvio Nolasco De; Norden, Natalia ; Nunes, Yule R.F. ; Ochoa-Gaona, Susana ; Ortiz-Malavassi, Edgar ; Ostertag, Rebecca ; Peña-Caros, Marielos ; Pérez-García, Eduardo A. ; Piotto, Daniel ; Powers, Jennifer S. ; Aguilar-Cano, José ; Rodriguez-Buritica, Susana ; Rodríguez-Velázquez, Jorge ; Romero-Romero, Marco Antonio ; Ruíz, Jorge ; Sanchez-Azofeifa, Arturo ; Almeida, Arlete Silva De; Silver, Whendee L. ; Schwartz, Naomi B. ; Thomas, William Wayt ; Toledo, Marisol ; Uriarte, Maria ; Sá Sampaio, Everardo Valadares De; Breugel, Michiel van; Wal, Hans van der; Martins, Sebastião Venâncio ; Veloso, Maria D.M. ; Vester, Hans F.M. ; Vicentini, Alberto ; Vieira, Ima C.G. ; Villa, Pedro ; Williamson, G.B. ; Zanini, Kátia J. ; Zimmerman, Jess ; Poorter, Lourens - \ 2019
Science Advances 5 (2019)3. - ISSN 2375-2548 - 10 p.
Old-growth tropical forests harbor an immense diversity of tree species but are rapidly being cleared, while secondary forests that regrow on abandoned agricultural lands increase in extent. We assess how tree species richness and composition recover during secondary succession across gradients in environmental conditions and anthropogenic disturbance in an unprecedented multisite analysis for the Neotropics. Secondary forests recover remarkably fast in species richness but slowly in species composition. Secondary forests take a median time of five decades to recover the species richness of old-growth forest (80% recovery after 20 years) based on rarefaction analysis. Full recovery of species composition takes centuries (only 34% recovery after 20 years). A dual strategy that maintains both old-growth forests and species-rich secondary forests is therefore crucial for biodiversity conservation in human-modified tropical landscapes.
Optimizing ex situ genetic resource collections for European livestock conservation
Oliveira Silva, Rafael De; Ahmadi, Bouda Vosough ; Hiemstra, Sipke Joost ; Moran, Dominic - \ 2019
Journal of Animal Breeding and Genetics 136 (2019)1. - ISSN 0931-2668 - p. 63 - 73.
cryoconservation - ex situ conservation - gene bank - livestock diversity - optimization

Ex situ collections offer the potential to reduce extinction risks, affording option to society in maintaining future breeding opportunities for productivity and heritage traits. However, how much should we be seeking to collect and conserve in gene banks, and where? We developed a mathematical model to optimize logistical decisions of breed conservation choices and to evaluate alternative scenarios for efficiently re-allocating genetic materials currently stored in different European gene banks, allowing for cross-country collections, cost and cryogenic capacity differentials. We show how alternative allocations for the breeds that are currently stored in 11 European gene banks could reduce overall conservation costs by around 20% by selecting cryogenic banks that have relatively lower combination of fixed and collection costs, and are geographically closer to collection regions. Our results show that centralizing collections in one gene bank would double the costs, relative to collective European collections approaches. We also calculate marginal costs of collections and show that increasing diversity within the gene banks implies in higher costs per conserved breed.

Influence of synthesis method on molybdenum carbide crystal structure and catalytic performance in stearic acid hydrodeoxygenation
Souza Macedo, Luana ; Oliveira, Ricardo R. ; Haasterecht, Tomas van; Teixeira da Silva, Victor ; Bitter, Harry - \ 2019
Applied Catalysis B-Environmental 241 (2019). - ISSN 0926-3373 - p. 81 - 88.
Crystal structure - Hydrodeoxygenation - Molybdenum carbide - Site density - Synthesis method

The role of the synthesis method of molybdenum carbide nanoparticle catalysts supported on carbon nanofibers on crystal structure and on catalytic performance in hydrodeoxygenation of stearic acid was investigated. We obtained the cubic phase of molybdenum carbide (α-MoC1-x) by impregnating carbon nanofibers with a solution of (NH4)2MoO4, then exposing them to 20% CH4/H2 at 650 °C for 2 h. When increasing the Mo loading from 7.5 wt% to 20 wt% or using the carbothermal reduction method, i.e. using carbon from the support to reduce the (NH4)2MoO4 precursor at 800 °C for 6 h, the hexagonal phase (β-Mo2C) resulted. Experiments with stearic acid hydrodeoxygenation showed that both phases (7.5 wt% Mo) displayed similar intrinsic activities. However, α-MoC1-x/CNF reached 80% stearic acid conversion after 240 min while the β-Mo2C/CNF catalyst attained the same conversion after 360 min. CO chemisorption results showed that α-MoC1-x/CNF and β-Mo2C/CNF have a similar number of potential active sites (66 and 56 μmol g−1, respectively). We attribute the difference in catalytic performance between α-MoC1-x/CNF and β-Mo2C/CNF to differences in the catalyst's crystal structure, more specifically, the associated site density. The face-centered cubic α-MoC1-x/CNF has a lower site density (0.1096 Mo atoms Ų) than the hexagonal close-packed β-Mo2C/CNF (0.1402 Mo atoms Ų), making the Mo atoms at the surface of the α-MoC1-x phase more accessible for large reactant molecules such as stearic acid thus allowing its convertion in shorter times.

Carbon supported metal-carbides and metal phosphide for biomass-based conversions
Bitter, J.H. ; Souza Macêdo, L. ; Oliveira Jr, R.R. ; Haasterecht, T. van; Auxiliadora, M. ; Baldanza, S. ; Teixeira da Silva, V. - \ 2018
Volatile organic molecules from Fusarium oxysporum strain 21 with nematicidal activity against Meloidogyne incognita
Terra, Willian César ; Campos, Vicente Paulo ; Martins, Samuel Julio ; Costa, Lilian Simara Abreu S. ; Silva, Júlio Carlos Pereira da; Barros, Aline Ferreira ; Lopez, Liliana Estupiñan ; Santos, Thaisa Conrado Nunes ; Smant, Geert ; Oliveira, Denilson Ferreira - \ 2018
Crop Protection 106 (2018). - ISSN 0261-2194 - p. 125 - 131.
Bioprospecting - Fusarium oxysporum - Plant-parasitic nematodes - Volatiles
Volatile organic compounds (VOCs) produced by microorganisms are potential alternatives for the development of new nematicides. In a previous study, we identified VOCs produced by Fusarium oxysporum strain 21 (F.o–21). In this study, we tested the eight most abundant VOCs produced by F.o-21 against Meloidogyne incognita. Compounds 2-methylbutyl acetate (1), 3-methylbutyl acetate (2), ethyl acetate (7), and 2-methylpropyl acetate (8) led to in vitro mortality of 100%, 91%, 100%, and 82%, respectively, in second-stage juveniles (J2) of M. incognita at a concentration of 500 μg/mL. The lethal concentration (LC50) for compounds 1, 2, 7, and 8 in M. incognita J2, was 236, 198, 213, and 218 μg/mL, respectively. Under the same conditions, the commercial nematicide called carbofuran (2,3-dihydro-2,2-dimethyl-1-benzofuran-7-yl N-methyl carbamate) showed an LC50 of 191 μg/mL. Eggs exposed to compounds 2 and 7, for 72 h showed up to a 90% reduction in hatching, and the compounds 1, 2, 7, and 8 reduced M. incognita infectivity by 52%, 52%, 36% and 41%, respectively. When the compounds were applied in tomato seedlings infested by M. incognita, compound 1 reduced the number of galls per root gram by 22% when compared to the negative control (without the application of nematicide). The compound 2-methylbutyl acetate (1) showed potential to be used in the field after improvements in the application technology.
The NSm proteins of phylogenetically related tospoviruses trigger Sw-5b–mediated resistance dissociated of their cell-to-cell movement function
Leastro, Mikhail Oliveira ; Oliveira, Athos Silva De; Pallás, Vicente ; Sánchez-Navarro, Jesús A. ; Kormelink, Richard ; Resende, Renato Oliveira - \ 2017
Virus Research 240 (2017). - ISSN 0168-1702 - p. 25 - 34.
Avr - Hypersensitive response - NS protein - Resistance - Sw-5b gene - Tospovirus

The cell-to-cell movement protein (NSM) in members of the tospovirus species Tomato spotted wilt virus (TSWV) has been recently identified as the effector of the single dominant Sw-5b resistance gene from tomato (Solanum lycopersicum L.). Although most TSWV isolates shows a resistance-inducing (RI) phenotype, regular reports have appeared on the emergence of resistance-breaking (RB) isolates in tomato fields, and suggested a strong association with two point mutations (C118Y and T120N) in the NSM protein. In this study the Sw-5b gene has been demonstrated to confer not only resistance against TSWV but to members of five additional, phylogenetically-related tospovirus species classified within the so-called “American” evolutionary clade, i.e. Alstroemeria necrotic streak virus (ANSV), Chrysanthemum stem necrosis virus (CSNV), Groundnut ringspot virus (GRSV), Impatiens necrotic spot virus (INSV) and Tomato chlorotic spot virus (TCSV). Remarkably, a member of the species Bean necrotic mosaic virus (BeNMV), a recently discovered tospovirus classified in a distinct American subclade and circulating on the American continent, did not trigger a Sw-5b-mediated hypersensitive (HR) response. Introduction of point mutations C118Y and T120N into the NSM protein of TSWV, TCSV and CSNV abrogated the ability to trigger Sw-5b-mediated HR in both transgenic-N. benthamiana and tomato isolines harboring the Sw-5b gene whereas it had no effect on BeNMV NSM. Truncated versions of TSWV NSM lacking motifs associated with tubule formation, cell-to-cell or systemic viral movement were made and tested for triggering of resistance. HR was still observed with truncated NSM proteins lacking 50 amino acids (out of 301) from either the amino- or carboxy-terminal end. These data altogether indicate the importance of amino acid residues C118 and T120 in Sw-5b-mediated HR only for the NSM proteins from one cluster of tospoviruses within the American clade, and that the ability to support viral cell-to-cell movement is not required for effector functionality.

A footprint of desiccation tolerance in the genome of Xerophyta viscosa
Dias Costa, M.C. ; Silva Artur, M.A. ; Maia de Oliveira, Julio ; Jonkheer, Eef ; Derks, Martijn ; Nijveen, H. ; Williams, B. ; Mundree, Sagadevan ; Jiménez-Gómez, José M. ; Hesselink, T. ; Schijlen, E.G.W.M. ; Ligterink, W. ; Oliver, Melvin J. ; Farrant, Jill M. ; Hilhorst, H.W.M. - \ 2017
Nature Plants 3 (2017). - ISSN 2055-026X - 10 p.
Desiccation tolerance is common in seeds and various other organisms, but only a few angiosperm species possess vegetative desiccation tolerance. These ‘resurrection species’ may serve as ideal models for the ultimate design of crops with enhanced drought tolerance. To understand the molecular and genetic mechanisms enabling vegetative desiccation tolerance, we produced a high-quality whole-genome sequence for the resurrection plant Xerophyta viscosa and assessed transcriptome changes during its dehydration. Data revealed induction of transcripts typically associated with desiccation
tolerance in seeds and involvement of orthologues of ABI3 and ABI5, both key regulators of seed maturation. Dehydration resulted in both increased, but predominantly reduced, transcript abundance of genomic ‘clusters of desiccation-associated genes’ (CoDAGs), reflecting the cessation of growth that allows for the expression of desiccation tolerance. Vegetative
desiccation tolerance in X. viscosa was found to be uncoupled from drought-induced senescence. We provide strong support for the hypothesis that vegetative desiccation tolerance arose by redirection of genetic information from
desiccation-tolerant seeds.
Cell death triggering and effector recognition by Sw-5 SD-CNL proteins from resistant and susceptible tomato isolines to Tomato spotted wilt virus
Silva de Oliveira, A. ; Koolhaas, Ivo ; Boiteux, L.S. ; Caldararu, O. ; Petrescu, A.J. ; Resende, R. ; Kormelink, R.J.M. - \ 2016
Molecular Plant Pathology 17 (2016)9. - ISSN 1464-6722 - p. 1442 - 1454.
Only a limited number of dominant resistance genes acting against plant viruses have been cloned, and further functional studies of these have been almost entirely limited to the resistance genes Rx against Potato virus X (PVX) and N against Tobacco mosaic virus (TMV). Recently, the cell-to-cell movement protein (NSM) of Tomato spotted wilt virus (TSWV) has been identified as the avirulence determinant (Avr) of Sw-5b-mediated resistance, a dominant resistance gene which belongs to the class of SD-CC-NB-LRR (Solanaceae domain-coiled coil-nucleotide-binding-leucine-rich repeat, SD-CNL) resistance genes. On transient expression of the NSM protein in tomato and transgenic Nicotiana benthamiana harbouring the Sw-5b gene, a hypersensitive cell death response (HR) is triggered. Here, it is shown that high accumulation of the Sw-5b protein in N. benthamiana leaves, achieved by co-expression of the Sw-5b protein with RNA silencing suppressors (RSSs), leads to auto-activity in the absence of NSM. In a similar approach, Sw-5a, the highest conserved paralogue of Sw-5b from Solanum peruvianum, also triggered HR by auto-activation, whereas the highest conserved orthologue from susceptible S. lycopersicum, named Sw-5aS, did not. However, neither of the last two homologues was able to trigger an NSM-dependent HR. Truncated and mutated versions of these Sw-5 proteins revealed that the NB-ARC [nucleotide-binding adaptor shared by Apaf-1 (from humans), R proteins and CED-4 (from nematodes)] domain is sufficient for the triggering of HR and seems to be suppressed by the SD-CC domain. Furthermore, a single mutation was sufficient to restore auto-activity within the NB-ARC domain of Sw-5aS. When the latter domain was fused to the Sw-5b LRR domain, NSM-dependent HR triggering was regained, but not in the presence of its own Sw-5aS LRR domain. Expression analysis in planta revealed a nucleocytoplasmic localization pattern of Sw-5b, in which the SD-CC domain seems to be required for nuclear translocation. Although the Sw-5 N-terminal CC domain, in contrast with Rx, contains an additional SD, most findings from this study support a conserved role of domains within NB-LRR (NLR) proteins against plant viruses.
Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests
Wagner, Fabien H. ; Hérault, Bruno ; Bonal, Damien ; Stahl, Clément ; Anderson, Liana O. ; Baker, Timothy R. ; Becker, Gabriel Sebastian ; Beeckman, Hans ; Boanerges Souza, Danilo ; Botosso, Paulo Cesar ; Bowman, David M.J.S. ; Bräuning, Achim ; Brede, Benjamin ; Brown, Foster Irving ; Camarero, Jesus Julio ; Camargo, Plínio Barbosa ; Cardoso, Fernanda C.G. ; Carvalho, Fabrício Alvim ; Castro, Wendeson ; Chagas, Rubens Koloski ; Chave, Jérome ; Chidumayo, Emmanuel N. ; Clark, Deborah A. ; Costa, Flavia Regina Capellotto ; Couralet, Camille ; Silva Mauricio, Paulo Henrique Da; Dalitz, Helmut ; Castro, Vinicius Resende De; Freitas Milani, Jaçanan Eloisa De; Oliveira, Edilson Consuelo De; Souza Arruda, Luciano De; Devineau, Jean-Louis ; Drew, David M. ; Dünisch, Oliver ; Durigan, Giselda ; Elifuraha, Elisha ; Fedele, Marcio ; Ferreira Fedele, Ligia ; Figueiredo Filho, Afonso ; Finger, César Augusto Guimarães ; Franco, Augusto César ; Freitas Júnior, João Lima ; Galvão, Franklin ; Gebrekirstos, Aster ; Gliniars, Robert ; Lima De Alencastro Graça, Paulo Maurício ; Griffiths, Anthony D. ; Grogan, James ; Guan, Kaiyu ; Homeier, Jürgen ; Kanieski, Maria Raquel ; Kho, Lip Khoon ; Koenig, Jennifer ; Kohler, Sintia Valerio ; Krepkowski, Julia ; Lemos-filho, José Pires ; Lieberman, Diana ; Lieberman, Milton Eugene ; Lisi, Claudio Sergio ; Longhi Santos, Tomaz ; López Ayala, José Luis ; Maeda, Eduardo Eijji ; Malhi, Yadvinder ; Maria, Vivian R.B. ; Marques, Marcia C.M. ; Marques, Renato ; Maza Chamba, Hector ; Mbwambo, Lawrence ; Melgaço, Karina Liana Lisboa ; Mendivelso, Hooz Angela ; Murphy, Brett P. ; O'Brien, Joseph J. ; Oberbauer, Steven F. ; Okada, Naoki ; Pélissier, Raphaël ; Prior, Lynda D. ; Roig, Fidel Alejandro ; Ross, Michael ; Rossatto, Davi Rodrigo ; Rossi, Vivien ; Rowland, Lucy ; Rutishauser, Ervan ; Santana, Hellen ; Schulze, Mark ; Selhorst, Diogo ; Silva, Williamar Rodrigues ; Silveira, Marcos ; Spannl, Susanne ; Swaine, Michael D. ; Toledo, José Julio ; Toledo, Marcos Miranda ; Toledo, Marisol ; Toma, Takeshi ; Tomazello Filho, Mario ; Valdez Hernández, Juan Ignacio ; Verbesselt, Jan ; Vieira, Simone Aparecida ; Vincent, Grégoire ; Volkmer De Castilho, Carolina ; Volland, Franziska ; Worbes, Martin ; Zanon, Magda Lea Bolzan ; Aragão, Luiz E.O.C. - \ 2016
Biogeosciences 13 (2016)8. - ISSN 1726-4170 - p. 2537 - 2562.
The seasonal climate drivers of the carbon cycle in tropical forests remain poorly known, although these forests account for more carbon assimilation and storage than any other terrestrial ecosystem. Based on a unique combination of seasonal pan-tropical data sets from 89 experimental sites (68 include aboveground wood productivity measurements and 35 litter productivity measurements), their associated canopy photosynthetic capacity (enhanced vegetation index, EVI) and climate, we ask how carbon assimilation and aboveground allocation are related to climate seasonality in tropical forests and how they interact in the seasonal carbon cycle. We found that canopy photosynthetic capacity seasonality responds positively to precipitation when rainfall is  < 2000 mm yr−1 (water-limited forests) and to radiation otherwise (light-limited forests). On the other hand, independent of climate limitations, wood productivity and litterfall are driven by seasonal variation in precipitation and evapotranspiration, respectively. Consequently, light-limited forests present an asynchronism between canopy photosynthetic capacity and wood productivity. First-order control by precipitation likely indicates a decrease in tropical forest productivity in a drier climate in water-limited forest, and in current light-limited forest with future rainfall  < 2000 mm yr−1.
The Sw-5 gene cluster : analysis of tomato resistance against tospoviruses
Silva de Oliveira, A. - \ 2015
Wageningen University. Promotor(en): Monique van Oers; R. de Oliveira Resende, co-promotor(en): Richard Kormelink. - Wageningen : Wageningen University - ISBN 9789462575769 - 158
solanum lycopersicum - tomaten - ziekteresistentie - plantenvirussen - tospovirus - genen - tomatenbronsvlekkenvirus - plantenveredeling - resistentieveredeling - solanum lycopersicum - tomatoes - disease resistance - plant viruses - tospovirus - genes - tomato spotted wilt virus - plant breeding - resistance breeding
Does functional trait diversity predict aboveground biomass and productivity of tropical forests? Testing three alternative hypotheses
Finegan, B. ; Pena Claros, M. ; Silva de Oliveira, A. ; Ascarrunz, N. ; Bret-Harte, M.S. ; Carreño Rocabado, I.G. ; Casanoves, F. ; Diaz, S. ; Eguiguren Velepucha, P. ; Fernandez, F. ; Licona, J.C. ; Lorenzo, L. ; Salgado Negret, B. ; Vaz, M. ; Poorter, L. - \ 2014
green soup hypothesis - biodiversity - biomass ratio - ecosystem processes - functional traits - commiunity weighted mean - niche complementary
1. Tropical forests are globally important, but it is not clear whether biodiversity enhances carbon storage and sequestration in them. We tested this relationship focusing on components of functional trait biodiversity as predictors. 2. Data are presented for three rain forests in Bolivia, Brazil and Costa Rica. Initial above-ground biomass and biomass increments of survivors, recruits and survivors + recruits (total) were estimated for trees ≥10 cm d.b.h. in 62 and 21 1.0-ha plots, respectively. We determined relationships of biomass increments to initial standing biomass (AGBi), biomass-weighted community mean values (CWM) of eight functional traits and four functional trait variety indices (functional richness, functional evenness, functional diversity and functional dispersion). 3. The forest continuum sampled ranged from ‘slow’ stands dominated by trees with tough tissues and high AGBi, to ‘fast’ stands dominated by trees with soft, nutrient-rich leaves, lighter woods and lower AGBi. 4. We tested whether AGBi and biomass increments were related to the CWM trait values of the dominant species in the system (the biomass ratio hypothesis), to the variety of functional trait values (the niche complementarity hypothesis), or in the case of biomass increments, simply to initial standing biomass (the green soup hypothesis). 5. CWMs were reasonable bivariate predictors of AGBi and biomass increments, with CWM specific leaf area SLA, CWM leaf nitrogen content, CWM force to tear the leaf, CWM maximum adult height Hmax and CWM wood specific gravity the most important. AGBi was also a reasonable predictor of the three measures of biomass increment. In best-fit multiple regression models, CWMHmax was the most important predictor of initial standing biomass AGBi. Only leaf traits were selected in the best models for biomass increment; CWM SLA was the most important predictor, with the expected positive relationship. There were no relationships of functional variety indices to biomass increments, and AGBi was the only predictor for biomass increments from recruits. 6. Synthesis. We found no support for the niche complementarity hypothesis and support for the green soup hypothesis only for biomass increments of recruits. We have strong support for the biomass ratio hypothesis. CWMHmax is a strong driver of ecosystem biomass and carbon storage and CWM SLA, and other CWM leaf traits are especially important for biomass increments and carbon sequestration.
The Tomato spotted wilt virus cell-to-cell movement protein (NSM) triggers a hypersensitive response in Sw-5 containing resistant tomato lines and Nicotiana benthamiana transformed with the functional Sw-5b resistance gene copy.
Hallwass, M. ; Silva de Oliveira, A. ; Dianese, E.C. ; Lohuis, D. ; Boiteux, L.S. ; Inoue-Nagata, A.K. ; Resende, R.O. de; Kormelink, R.J.M. - \ 2014
Molecular Plant Pathology 15 (2014)9. - ISSN 1464-6722 - p. 871 - 880.
mosaic-virus - lycopersicon-esculentum - nonstructural protein - capsicum-chinense - coat protein - plant-cells - rna segment - tswv - tospovirus - tobacco
Although the Sw-5 gene cluster has been cloned, and Sw-5b has been identified as the functional gene copy that confers resistance to Tomato spotted wilt virus (TSWV), its avirulence (Avr) determinant has not been identified to date. Nicotiana tabacum SR1 plants transformed with a copy of the Sw-5b gene are immune without producing a clear visual response on challenge with TSWV, whereas it is shown here that N.benthamiana transformed with Sw-5b gives a rapid and conspicuous hypersensitive response (HR). Using these plants, from all structural and non-structural TSWV proteins tested, the TSWV cell-to-cell movement protein (NSM) was confirmed as the Avr determinant using a Potato virus X (PVX) replicon or a non-replicative pEAQ-HT expression vector system. HR was induced in Sw-5b-transgenic N.benthamiana as well as in resistant near-isogenic tomato lines after agroinfiltration with a functional cell-to-cell movement protein (NSM) from a resistance-inducing (RI) TSWV strain (BR-01), but not with NSM from a Sw-5 resistance-breaking (RB) strain (GRAU). This is the first biological demonstration that Sw-5-mediated resistance is triggered by the TSWV NSM cell-to-cell movement protein.
Ecosystem services research in Latin America: The state of the art.
Balvanera, P. ; Uriarte, M. ; Almeida-Leñero, L. ; Altesor, A. ; DeClerck, F. ; Gardner, T. ; Hall, J. ; Lara, A. ; Laterra, P. ; Peña-Claros, M. ; Silva Matos, D.M. ; Vogl, A.L. ; Romero-Duque, L.P. ; Arreola, L.F. ; Caro-Borrero, A.P. ; Gallego, F. ; Jain, M. ; Little, C. ; Oliveira Xavier, R. de; Paruelo, J.M. ; Peinado, J.E. ; Poorter, L. - \ 2012
Ecosystem Services 2 (2012). - ISSN 2212-0416 - p. 56 - 70.
Ecosystem services science has developed at a fast rate in Latin America, a region characterized by a high biological and cultural diversity, strong emphasis in foreign investment, and high socioeconomic inequities. Here we conducted the following analyses at the regional and national scales: (1) how and when did the study of ecosystem services arise in each country?, (2) what is our present understanding of ecosystem service supply, delivery to societies, and social and economic values?, (3) what is the state of the art in integrating tradeoffs among services and in using interdisciplinary perspectives?, and (4) how has ecosystem service research been connected to policy design or management for sustainability? A large literature review (>1000 references) showed that in Latin America ES supply and links to policy have been the most frequently assessed. Overall, emphasis has been placed on a few services, namely carbon and water. Payments for ecosystem services have received considerable attention in the region, though with strong differences across nations and with important limitations in their application. The future of the ecosystem service paradigm in Latin America will largely depend on its capacity to demonstrate effectiveness in meeting both conservation and development goals.
Pindaré Basin: Tools for Sustainable Natural Resource Use, Conservation Strategies and Territorial Planning in Maranhão State, Brazil
Barreto, L. ; Silva, M. da; Rebelo, G. ; Ribeiro, M.C. ; Oliveira, A.E. ; Jongman, R.H.G. ; Brito, M.P. ; Rodrigues, E. ; Mendes, I. - \ 2011
In: Proceedings of the 8th World Congress of the International Association for Landscape Ecology on Landscape Ecology for Sustainable Environment and Culture, Beijing, China, 18-23 August 2011. - Beijing, China : IALE - p. 28 - 29.
Evolução Diurna do Balanço de Radiação na Superfície da Cidade de São Paulo, Brasil
Ferreira, M.J. ; Oliveira, A.P. ; Soares, J. ; Barbaro, E.W. ; Codato, G. ; Fonseca, F.L.A. ; Silva, M. da - \ 2007
- p. 1 - 9.
Este trabalho tem como objetivo descrever a evolução temporal das componentes do balanço de radiação na superfície da região metropolitana da cidade de São Paulo durante o ano de 2004. E avaliar a possibilidade de utilizar estimativas de satélite para representar os padrões espaciais das componentes do balanço de radiação na superfície da região metropolitana da cidade de São Paulo. As observações na plataforma micrometeorológica do Instituto de Astronomia, Geofísica e Ciências Atmosféricas são comparadas com estimativas de radiação solar global, onda longa da atmosfera e onda longa emitida pela superfície do Projeto SRB. A excelente concordância entre os valores médios mensais de radiação solar global e de onda longa emitida pela atmosfera, observados e estimados pelo satélite indica que este último pode ser considerado como representativo de toda região metropolitana da cidade de São Paulo. A evolução diurna dos valores médios mensais de radiação solar incidente e refletida pela superfície indica que o albedo da região da cidade de São Paulo varia de 0,10 a 0,12 durante o ano. A evolução diurna dos valores médios mensais de radiação de onda longa emitida pela atmosfera e pela superfície indica que a emissividade média da região urbana de São Paulo é da ordem de 0.96 e a emissividade da atmosfera é da ordem de 0,82 estando compatíveis com as estimativas de satélite. A evolução diurna dos valores médios mensais de radiação liquida indicam que a nebulosidade reduz a amplitude da radiação líquida, principalmente durante o período noturno nos meses de verão na cidade de São Paulo
Vaccination with a gE-negative bovine herpesvirus type 1 vaccine confers insufficient protection to a bovine herpesvirus type 5 challenge
Silva, A.D. ; Spilki, F.R. ; Franco, A.C. ; Esteves, P.A. ; Hubner, S.O. ; Driemeier, D. ; Oliveira, A.P. ; Rijsewijk, F.A.M. ; Roehe, P.M. - \ 2006
Vaccine 24 (2006)16. - ISSN 0264-410X - p. 3313 - 3320.
to-cell spread - glycoprotein-e - restriction-endonuclease - experimental-infection - neurological disease - nervous-system - 1.2a bhv-1.2a - in-vitro - virus - calves
In the present study, cross-protection to bovine herpesvirus type 5 (BHV-5) induced by bovine herpesvirus type 1 (BHV-1) vaccination was examined following inoculation of rabbits and calves with a glycoprotein E (gE)-negative BHV-1 vaccine and subsequent challenge with BHV-5. Rabbits (n = 5) and calves (n = 8) were vaccinated [five rabbits intranasally (IN), four calves IN and four intramuscularly (IM)] with 7.1 log10median tissue culture infective dose (TCID50) of the BHV-1 vaccine. Rabbits and calves were challenged IN [rabbits 2 weeks post-vaccination (pv); calves 5 weeks pv] with 9.1 log10 TCID50 of BHV-5. Two out of five vaccinated rabbits died after challenge with typical BHV-5 disease, as did 3/5 non-vaccinated controls. In calves, 4/8 vaccinated animals displayed mild signs of disease, whereas 6/6 non-vaccinated controls developed signs of disease, so severe that 2/6 had to be killed. Besides, nasal virus shedding post-challenge was not reduced by vaccination. At necropsy, on day 21 post-challenge, typical BHV-5 lesions were evident in brain tissues of both vaccinated and non-vaccinated calves. Dexametasone administration at 180 days post-infection did not reactivate clinical signs despite BHV-5 shedding in nasal secretions of both vaccinated and non-vaccinated calves. These results show that the BHV-1 vaccine evaluated here did not confer protection to BHV-5 in rabbits. In calves, BHV-1 vaccination did confer some protection to BHV-5 induced clinical disease, but it did not prevent infection and had no effect on nasal virus shedding or on the development of encephalitic lesions.
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