A global database of soil nematode abundance and functional group composition
Hoogen, Johan van den; Geisen, Stefan ; Wall, Diana H. ; Wardle, David A. ; Traunspurger, Walter ; Goede, Ron G.M. de; Adams, Byron J. ; Ahmad, Wasim ; Ferris, Howard ; Bardgett, Richard D. ; Bonkowski, Michael ; Campos-Herrera, Raquel ; Cares, Juvenil E. ; Caruso, Tancredi ; Brito Caixeta, Larissa de; Chen, Xiaoyun ; Costa, Sofia R. ; Creamer, Rachel ; Cunha e Castro, José Mauro da; Dam, Marie ; Djigal, Djibril ; Escuer, Miguel ; Griffiths, Bryan S. ; Gutiérrez, Carmen ; Hohberg, Karin ; Kalinkina, Daria ; Kardol, Paul ; Kergunteuil, Alan ; Korthals, Gerard ; Krashevska, Valentyna ; Kudrin, Alexey A. ; Li, Qi ; Liang, Wenju ; Magilton, Matthew ; Marais, Mariette ; Martín, José Antonio Rodríguez ; Matveeva, Elizaveta ; Mayad, El Hassan ; Mzough, E. ; Mulder, Christian ; Mullin, Peter ; Neilson, Roy ; Nguyen, Duong T.A. ; Nielsen, Uffe N. ; Okada, Hiroaki ; Rius, Juan Emilio Palomares ; Pan, Kaiwen ; Peneva, Vlada ; Pellissier, Loïc ; Silva, Julio Carlos Pereira da; Pitteloud, Camille ; Powers, Thomas O. ; Powers, Kirsten ; Quist, Casper W. ; Rasmann, Sergio ; Moreno, Sara Sánchez ; Scheu, Stefan ; Setälä, Heikki ; Sushchuk, Anna ; Tiunov, Alexei V. ; Trap, Jean ; Vestergård, Mette ; Villenave, Cecile ; Waeyenberge, Lieven ; Wilschut, Rutger A. ; Wright, Daniel G. ; Keith, Aidan M. ; Yang, Jiuein ; Schmidt, Olaf ; Bouharroud, R. ; Ferji, Z. ; Putten, Wim H. van der; Routh, Devin ; Crowther, Thomas W. - \ 2020
Scientific Data 7 (2020)1. - ISSN 2052-4463
As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns.
NEOTROPICAL XENARTHRANS: a data set of occurrence of xenarthran species in the Neotropics
Santos, Paloma Marques ; Bocchiglieri, Adriana ; Chiarello, Adriano Garcia ; Paglia, Adriano Pereira ; Moreira, Adryelle ; Souza, Agnis Cristiane de; Abba, Agustin Manuel ; Paviolo, Agustin ; Gatica, Ailin ; Medeiro, Akyllan Zoppi ; Costa, Alan Nilo ; Gallina, Alberto Gonzalez ; Yanosky, Alberto A. ; Jesus, Alejandro ; Bertassoni, Alessandra ; Rocha, Alessandro ; Bovo, Alex Augusto Abreu ; Bager, Alex ; Mol, Alexandra Cravino ; Martensen, Alexandre Camargo ; Faustino, Alexandre Casagrande ; Lopes, Alexandre Martins Costa ; Percequillo, Alexandre Reis ; Vogliotti, Alexandre ; Keuroghlian, Alexine ; Colina, María Alicia de la; Devlin, Allison L. ; García-Olaechea, Alvaro ; Sánchez, Amadeo ; Srbek-Araujo, Ana Carolina ; Ochoa, Ana Cecilia ; Oliveira, Ana Cristina Mendes ; Lacerda, Ana Cristyna Reis ; Campelo, Ana Kellen Nogueira ; Oliveira Paschoal, Ana Maria de; Costa, Ana Raíssa Cunha ; Meiga, Ana Yoko Ykeuti ; Jesus, Anamélia Souza ; Feijó, Anderson ; Hirsch, André ; Silva, André Luiz Ferreira da; Botelho, André Luis Moura ; Regolin, André Luis ; Lanna, André Monnerat ; Nunes, André Valle ; Kindel, Andreas ; Moraes, Andreia Magro ; Gatti, Andressa ; Noss, Andrew J. ; Nobre, Andrezza Bellotto ; Montanarin, Anelise ; Deffaci, Ângela Camila ; Albuquerque, Anna Carolina Figueiredo de; Oliveira, Anne Karoline de; Mangione, Antonio Marcelo ; Pontes, Antonio Rossano Mendes ; Bertoldi, Ariane Teixeira ; Calouro, Armando Muniz ; Desbiez, Arnaud L.J. ; Fernandes, Arthur ; Ferreguetti, Atilla Colombo ; Silva, Maria Augusta Andrade da; Zimbres, Barbara ; Luciano, Beatriz Fernandes Lima ; Thoisy, Benoit de; Niebuhr, Bernardo Brandão S. ; Papi, Bernardo ; Gómez-Valencia, Bibiana ; Santos, Bráulio A. ; Lima, Breno Campelo ; Oliveira, Bruna Gomes ; Santos, Bruna Silva ; Campos, Bruno Augusto Torres Parahyba ; Leles, Bruno ; Albuquerque França, Bruno Rodrigo de; Lim, Burton ; Oliveira, Caetano Troncoso ; Cantagallo, Camila ; Lara, Camila Clozato ; Lima, Camila Silveira ; Gestich, Carla Cristina ; Melo-Soares, Carla Danielle de; Peres, Carlos A. ; Kasper, Carlos Benhur ; Candia-Gallardo, Carlos ; Angelo, Carlos De; Fragoso, Carlos Eduardo ; Freitas, Carlos Henrique de; Salvador, Carlos Henrique ; Brocardo, Carlos R. ; Melo, Carolina Depolito ; Leuchtenberger, Caroline ; Braga, Caryne ; Sánchez-Lalinde, Catalina ; Bueno, Cecília ; Luna, Cecília Licarião ; Rojano, Cesar ; Hurtado, Cindy Meliza ; Santos, Cinthya Chiva dos; Tellaeche, Cintia ; Rosa, Clarissa ; Campos, Claudia Bueno de; Silva, Cláudia Regina ; Kanda, Claudia Zukeran ; Jenkins, Clinton N. ; McDonough, Colleen ; Trinca, Cristiano Trapé ; Cunha, Cristina Jaques da; Widmer, Cynthia Elisa ; Santos, Cyntia ; Buscariol, Daiane ; Carreira, Daiane Cristina ; Carvalho, Danianderson Rodrigues ; Silva Ferraz, Daniel da; Casali, Daniel ; Thornton, Daniel ; Vasconcellos, Daniela Rodrigues ; Barcelos, Daniele ; Brown, Danielle ; Ramos, Daniella Leal ; Moreira, Danielle Oliveira ; Yogui, Débora Regina ; Faria, Deborah ; Sana, Denis Alessio ; Mattia, Denise Lidoro de; Henz, Denison José ; Friedeberg, Diana B. ; Carvalho, Diana Letícia Kruger Pacheco ; Astúa, Diego ; Queirolo, Diego ; Varela, Diego M. ; Eaton, Donald P. ; Dias, Douglas Matos ; Rivadeneira, Edgar Federico ; Rocha, Ednaldo Cândido ; Abreu-Júnior, Edson Fiedler de; Carrano, Eduardo ; Santos, Eduardo Marques ; Setz, Eleonore Zulnara Freire ; Carvalho, Elildo Alves Ribeiro ; Almeida Chiquito, Elisandra de; Matos Cardoso, Elizandra de; Mendonça, Eloisa Neves ; Bastiani, Elvira D'; Vieira, Emerson M. ; Ramalho, Emiliano Esterci ; Guijosa-Guadarrama, Emiliano ; González, Enrique ; Maggiorini, Erica Vanessa ; Fischer, Erich ; Aguiar, Erick Francisco ; Castro, Érika Paula ; Peña-Cuéllar, Erika de la; Viveiros de Castro, Ernesto B. ; Brítez, Evelyn Beatriz ; Vanderhoeven, Ezequiel Andres ; Pedó, Ezequiel ; Rocha, Fabiana Lopes ; Girardi, Fabiane ; Oliveira Roque, Fabio de; Mazim, Fábio Dias ; Barros, Fabio Monteiro de; Martello, Felipe ; Fantacini, Felipe Moreli ; Pedrosa, Felipe ; Peters, Felipe Bortolotto ; Abra, Fernanda Delborgo ; Azevedo, Fernanda Cavalcanti de; Silva Santos, Fernanda da; Silva, Fernanda Guedes da; Teixeira, Fernanda Zimmermann ; Perini, Fernando Araujo ; Passos, Fernando C. ; Carvalho, Fernando ; Azevedo, Fernando Cesar Cascelli de; Pinho, Fernando Ferreira de; Gonçalves, Fernando ; Lima, Fernando ; Contreras-Moreno, Fernando M. ; Pedroni, Fernando ; Tortato, Fernando Rodrigo ; Santos, Filipe Pereira Rego ; Caruso, Flavia ; Tirelli, Flávia Pereira ; Miranda, Flávia Regina ; Rodrigues, Flávio Henrique Guimarães ; Ubaid, Flávio Kulaif ; Palmeira, Francesca Belem Lopes ; Silva, Franciane Almeida da; Grotta-Neto, Francisco ; Souza, Franco Leandro de; Costa, Francys Emanuelle ; Pérez-Garduza, Freddy ; Delsuc, Frédéric ; Lemos, Frederico ; Pinto, Fredy Ramirez ; Boaglio, Gabriel Ivan ; Massocato, Gabriel Fávero ; Preuss, Gabriel ; Hofmann, Gabriel Selbach ; Aguiar, Gabriel Lima ; Oliveira, Gabriela Schuck ; Duarte, Gabriela Teixeira ; Beca, Gabrielle ; Giné, Gastón Andrés Fernandez ; Batista, Graziele Oliveira ; Gil, Guillermo Eduardo ; Gonsioroski, Gustavo ; Secco, Helio ; Medeiros, Hugo Reis ; Coelho, Igor Pfeifer ; Franceschi, Ingridi Camboim ; Bernardi, Itiberê ; Torre, Antonio de la; Zocche, Jairo José ; Seibert, Jardel Brandão ; Faria Falcão, Jéssica Caroline de; Dias, Jéssica Helena Mangueira ; Nodari, Joana Zorzal ; Oliveira, João Alves ; Giovanelli, João Gabriel Ribeiro ; Favoretti, João Paulo Pandini ; Polisar, John ; Sponchiado, Jonas ; Cherem, Jorge José ; Ramírez, José Fernando Moreira ; Toledo, José Julio de; Duarte, José Maurício Barbanti ; Matos, Jose Roberto de; Arrabal, Juan Pablo ; Faria Oshima, Júlia Emi de; Ribeiro, Juliana Fernandes ; Bogoni, Juliano André ; Pacheco, Julio Javier Chacón ; Schuchmann, Karl L. ; Ferraz, Katia M.P.M.B. ; Santos Everton, Laís dos; Bailey, Larissa L. ; Gonçalves, Larissa Oliveira ; Cullen, Laury ; Andrade, Layla Reis de; Trevelin, Leonardo Carreira ; Bonjorne, Lilian ; Almeida Rodrigues, Livia de; Leuzinger, Lucas ; Perillo, Lucas Neves ; Araújo, Luciana Souza ; Hufnagel, Ludmila ; Ribeiro, Ludmilla Oliveira ; Bernardo, Luis Renato Rezende ; Oliveira-Santos, Luiz Gustavo Rodrigues ; Varzinczak, Luiz Henrique ; Borges, Luiz Henrique Medeiros ; Guimarães, Luiza Neves ; Möcklinghoff, Lydia ; Oliveira, Marcela Alvares ; Magioli, Marcelo ; Assis Jardim, Márcia Maria de; Oliveira, Márcio Leite de; Tortato, Marcos Adriano ; Dums, Marcos ; Iezzi, Maria Eugenia ; Pereira, Maria João Ramos ; Jorge, Maria Luísa ; Castro Morini, Maria Santina de; Landis, Mariana Bueno ; Xavier, Mariana Sampaio ; Barros, Marília A.S. ; Silva, Marina Lima da; Rivero, Marina ; Zanin, Marina ; Marques, Marinêz Isaac ; Alves, Mario Henrique ; Bitetti, Mario S. Di; Alvarez, Martín R. ; Graipel, Maurício Eduardo ; Godoi, Mauricio Neves ; Benedetti, Maximiliano Augusto ; Beltrão, Mayara Guimarães ; Monteiro, Miguel Coutinho Moretta ; Paula, Milton José de; Perilli, Miriam Lucia Lages ; Silva, Murillo Prado da; Villar, Nacho ; Albuquerque, Natasha Moraes De; Canassa, Nathália F. ; Filho, Newton Mota ; Rosa Oliveira, Nicole da; Pasqualotto, Nielson ; Cáceres, Nilton Carlos ; Attias, Nina ; Favarini, Marina Ochoa ; Ribeiro, Otávio Santi ; Gonçalves, Pablo Rodrigues ; Rocha, Patrício Adriano da; Condé, Paula Alves ; Akkawi, Paula ; Cruz, Paula ; Lira, Paula Koeler ; Ferreira, Paula Modenesi ; Arroyo-Gerala, Paulina ; Hartmann, Paulo Afonso ; Tarso Zuquim Antas, Paulo de; Marinho, Paulo Henrique ; Faria Peres, Pedro Henrique de; Peña-Mondragón, Juan Luis ; Lombardi, Pryscilla Moura ; Souza Laurindo, Rafael de; Alves, Rafael Souza Cruz ; Grangeiro, Raissa Danielle Praxedes ; Silva, Ramon Lima ; Beltrão-Mendes, Raone ; Bonikowski, Renata Twardowsky Ramalho ; Reppucci, Juan ; Arrais, Ricardo Corassa ; Sampaio, Ricardo ; Sartorello, Ricardo ; Bovendorp, Ricardo Siqueira ; McNab, Roan ; Hack, Robson Odeli Espíndola ; Magalhães, Rodolfo Assis ; Araújo, Rodrigo Costa ; Almeida Nobre, Rodrigo de; Pérez, Rodrigo Raúl León ; Massara, Rodrigo Lima ; Paula, Rogério Cunha de; Anleu, Rony García ; Marques, Rosane Vieira ; Dornas, Rubem ; Rolim, Samir Gonçalves ; Cavalcanti, Sandra M.C. ; Lima, Saulo Ramos ; Ballari, Sebastián A. ; Santamaría, Silvia Benito ; Silva, Sofia Marques ; Age, Stefani Gabrieli ; Godim, Tayana ; Sobral-Souza, Thadeu ; Maccarini, Thiago Bernardes ; Rodrigues, Thiago Ferreira ; Piovezan, Ubiratan ; Cunha Tavares, Valéria da; Quiroga, Verónica Andrea ; Krepschi, Victor Gasperotto ; Filho, Vilmar Picinatto ; Galvão Bastazini, Vinícius Augusto ; Oliveira Gasparotto, Vinicius Peron de; Orsini, Vinicius Santana ; Guedes Layme, Viviane Maria ; Hannibal, Wellington ; Dáttilo, Wesley ; Carvalho, William Douglas de; Loughry, William James ; Blanco, Yamil Edgardo Di; Núñez-Regueiro, Mauricio M. ; Giubbina, Marina Furlan ; Passamani, Marcelo ; Alagão Querido, Luciano Carramaschi de; Costa Toledo, Gustavo Alvez da; Ribeiro, Igor Kintopp ; Quintilham, Lucas ; Bustos, Soledad de; Maza, Javier de la; Lima Neto, Jorge Ferreira ; Kossel de Andrade Silva, Katyucha Von; Sartorello, Leonardo ; Rampim, Lilian Elaine ; Marás, Gustavo A. ; Camino, Micaela ; Freitas-Junior, Mozart ; Perovic, Pablo Gaston ; Paolino, Roberta Montanheiro ; Ferreira, Scarlat Dalva ; Towns, Valeria ; Esperandio, Isadora Beraldi ; Aximoff, Izar ; Beduschi, Júlia ; Guenther, Mariana ; Cassia Bianchi, Rita de; Keuroghlian-Eaton, Sean ; Mendes, Sérgio Lucena ; Fatima Cunha, Lerrane de; Cirignoli, Sebastián ; Ciocheti, Giordano ; Prado, Helena Alves do; Fernandes-Ferreira, Hugo ; Mendes de Sena, Liana Mara ; Yamane, Marcelo Hideki ; Brennand, Pamella G.G. ; Silva, Rayana Diniz da; Escobar, Santiago ; Endo, Whaldener ; Hurtado, Rafael Reyna ; Gontijo, Nila Rássia Costa ; Marsh, Laura K. ; Severo, Magnus Machado ; Pardo, Julia Martinez ; Costa, Sebastián Andrés ; Melo, Geruza Leal ; Santana, Gindomar Gomes ; Miranda Mourão, Guilherme de; Gaspari, Gustavo Gabirele ; Duarte, Herbert ; Cabral, Hugo ; Silva, Leonardo Henrique da; Mendonça, Luana ; Barbosa, Lucas Lobo ; Santos, Manuela Vieira dos; Moraes, Marcela Figuerêdo Duarte ; Gordo, Marcelo ; Versiani, Natalia Fraguas ; Cantero, Nicolás ; Pays, Olivier ; Guedes, Patrícia Gonçalves ; Colas-Rosas, Paul François ; Ribeiro, Paulo ; Renaud, Pierre Cyril ; Hoogesteijn, Rafael Jan ; Ayala, Rodrigo ; Cunha, Rogério Grassetto Teixeira da; Schaub, Roxane ; Laurito, Sabrina ; Betkowski, Samuel Eurich ; Cortez, Sara ; Silva, Shirley Seixas Pereira ; Oliveira, Tadeu Gomes de; Spironello, Wilson Roberto ; Gengler, Nicholas ; Hidalgo, Mircea Mihart ; Juárez, Rugieri ; Iglesias, Jesús A. ; Anacleto, Teresa Cristina ; Souza Fialho, Marcos de; Cavicchioli, Guilherme ; Beccato, Maria Angélica Barbosa ; Silva, Marcelo da; Neto, Omar Correia ; Lopes, Karine Galisteo Diemer ; Godoy, Leandro Perez ; Luiz, Micheli Ribeiro ; Rojas Bonzi, Viviana B. ; Ferreira, Guilherme Braga ; Oliveira, Marcelo Juliano Rabelo ; Hinojosa, Javier ; Oliveira, Luiz Flamarion Barbosa de; Nagy-Reis, Mariana Baldy ; Ramirez, Sixto Fernández ; Concone, Henrique Villas Boas ; Mourthe, Italo ; Martínez-Lanfranco, Juan A. ; Zanoni, Juliani Bruna ; Moreira, Tainah Cruz ; Guarderas, Zoila Vega ; Bazilio, Sérgio ; Cervini, Marcelo ; Pinheiro, Marcell Soares ; Morato, Ronaldo Gonçalves ; Peroni, Nivaldo ; Trigo, Tatiane Campos ; Machado, Ricardo Bomfim ; Gaspari, Fernando ; Koenemann, Joceleia G. ; Rudolf, Juan Carlos ; Benchimol, Maíra ; Vieira, Marcus Vinícius ; Retta, Lucía Martínez ; Santiago, Pablo Gerardo Fernández ; Ciccia, Paula Gonzalez ; Estrela, Pedro Cordeiro ; Carvalho, Santiago ; Esbérard, Carlos Eduardo Lustosa ; Cruz, Yaribeth Bravata de la; Castro-Prieto, Jessica ; Braga, Ricardo Miranda ; Cartes, Jose Luis ; Andrade-Núñez, María José ; Denkiewicz, Natalia Mariana ; Falconi, Nereyda ; Pezzuti, Juarez Carlos Brito ; Castillo Cordero, Hugo Fernando del; Sousa, Luziene Conceição de; Gaspari Júnior, Roque Lázaro de; Santos-Filho, Manoel ; Almeida, Josué Santos ; Thompson, Jeffrey J. ; Santos, Juliana Silveira dos; Pereira-Ribeiro, Juliane ; Burs, Kathrin ; Silva, Kena Ferrari Moreira da; Velilla, Marianela ; Silva, Marina Xavier da; Sancha, Noé U. de la; Pinheiro, Paula Fabiana ; Castilho, Pedro Volkmer de; Bercê, William ; Assis, Julia Camara ; Tonetti, Vinicius Rodrigues ; Alves-Eigenheer, Milene ; Chinem, Simonne ; Honda, Laura K. ; Godoy Bergallo, Helena de; Alberici, Vinicius ; Wallace, Robert ; Campos Krauer, Juan Manuel ; Ribeiro, Milton Cezar ; Galetti, Mauro - \ 2019
Ecology 100 (2019)7. - ISSN 0012-9658
biodiversity hotspot - cingulata - forest fragmentation - habitat loss - neotropical mammals - neotropical region - pilosa - xenarthra
Xenarthrans—anteaters, sloths, and armadillos—have essential functions for ecosystem maintenance, such as insect control and nutrient cycling, playing key roles as ecosystem engineers. Because of habitat loss and fragmentation, hunting pressure, and conflicts with domestic dogs, these species have been threatened locally, regionally, or even across their full distribution ranges. The Neotropics harbor 21 species of armadillos, 10 anteaters, and 6 sloths. Our data set includes the families Chlamyphoridae (13), Dasypodidae (7), Myrmecophagidae (3), Bradypodidae (4), and Megalonychidae (2). We have no occurrence data on Dasypus pilosus (Dasypodidae). Regarding Cyclopedidae, until recently, only one species was recognized, but new genetic studies have revealed that the group is represented by seven species. In this data paper, we compiled a total of 42,528 records of 31 species, represented by occurrence and quantitative data, totaling 24,847 unique georeferenced records. The geographic range is from the southern United States, Mexico, and Caribbean countries at the northern portion of the Neotropics, to the austral distribution in Argentina, Paraguay, Chile, and Uruguay. Regarding anteaters, Myrmecophaga tridactyla has the most records (n = 5,941), and Cyclopes sp. have the fewest (n = 240). The armadillo species with the most data is Dasypus novemcinctus (n = 11,588), and the fewest data are recorded for Calyptophractus retusus (n = 33). With regard to sloth species, Bradypus variegatus has the most records (n = 962), and Bradypus pygmaeus has the fewest (n = 12). Our main objective with Neotropical Xenarthrans is to make occurrence and quantitative data available to facilitate more ecological research, particularly if we integrate the xenarthran data with other data sets of Neotropical Series that will become available very soon (i.e., Neotropical Carnivores, Neotropical Invasive Mammals, and Neotropical Hunters and Dogs). Therefore, studies on trophic cascades, hunting pressure, habitat loss, fragmentation effects, species invasion, and climate change effects will be possible with the Neotropical Xenarthrans data set. Please cite this data paper when using its data in publications. We also request that researchers and teachers inform us of how they are using these data
Genetic determinism of flowering regularity over years in an apple multi-family population
Durand, J.B. ; Allard, A. ; Guitton, B. ; Weg, E. van de; Bink, M.C.A.M. ; Costes, E. - \ 2018
In: International Symposium on Flowering, Fruit Set and Alternate Bearing. - ISHS (Acta Horticulturae 1229) - ISBN 9789462612266 - p. 15 - 22.
Bayes factor - Biennial bearing - Entropy - Floral induction - Malus × domestica - Markov models - Pedigree based analysis
Irregular flowering over years is commonly observed in fruit trees and is assumed to be, at least partly, under genetic control. This study aimed at predicting genotype flowering behaviours and at detecting QTL associated to regularity, in a multi-family apple tree population. Successions of vegetative and floral annual shoots (AS) were observed along axes in trees belonging to five apple related full-sib families, observed at two experimental sites. Sequences were analysed using Markovian and linear mixed models including year and site effects. Indices of flowering regularity, periodicity and synchronicity were estimated, at tree and axis scales. First indices were derived from the biennial bearing index (BBI). A second index was the autoregressive correlation coefficient between flowering in consecutive years. A third index quantified the synchronicity of meristems within the trees through the measure of differences in the predictability of flowering over years, from a probabilistic viewpoint. These three types of indices were used to predict tree behaviour and to detect QTL with a Bayesian pedigree-based analysis, using an integrated genetic map containing 6,849 SNPs. The combination of the three indices efficiently predicted and classified the genotype behaviours despite few miss-classifications. Four common QTLs for BBIs and auto-regressive coefficient were highlighted (on LG4, 5, 8 and 10) and one for synchronicity (on LG9) in the integrated multi-family map, thus revealing the complex genetic architecture of the considered traits. This study proposes a posteriori sampling of axes within trees as a relevant and time-saving method to estimate tree flowering behaviours. Coupled to appropriate statistical indices, it is efficient to evaluate the tree breeding values for flowering regularity. In apple tree, biennial bearing appeared to result from high AS synchronism in flowering i.e., with all axes alternatively flowering or not in a given year, whereas regularity resulted from either asynchronous alternating or regular flowering of AS.
microRNA 193a-5p Regulates Levels of Nucleolar- and Spindle-associated Protein 1 to Suppress Hepatocarcinogenesis
Roy, Sanchari ; Hooiveld, Guido J. ; Seehawer, Marco ; Caruso, Stefano ; Heinzmann, Florian ; Schneider, Anne T. ; Frank, Anna K. ; Cardenas, David Vargas ; Sonntag, Roland ; Luedde, Mark ; Trautwein, Christian ; Stein, Ilan ; Pikarsky, Eli ; Loosen, Sven ; Tacke, Frank ; Ringelhan, Marc ; Avsaroglu, Seda Kilinc ; Goga, Andrei ; Buendia, Marie-Annick ; Vucur, Mihael ; Heikenwalder, Mathias ; Zucman-Rossi, Jessica ; Zender, Lars ; Roderburg, Christoph ; Luedde, Tom - \ 2018
Gastroenterology 155 (2018)6. - ISSN 0016-5085 - p. 1951 - 1966.
Background & Aims: We performed an integrated analysis to identify microRNAs (miRNAs) and mRNAs with altered expression in liver tumors from 3 mouse models of hepatocellular carcinoma (HCC) and human tumor tissues. Methods: We analyzed miRNA and mRNA expression profiles of liver tissues from mice with diethylnitrosamine-induced hepatocarcinogenesis, conditional expression of lymphotoxin alpha and lymphotoxin beta , or inducible expression of a Myc transgene (Tet-O-Myc mice), as well as male C57BL/6 mice (controls). miRNA mimics were expressed and miRNAs and mRNAs were knocked down in human (Huh7, Hep3B, JHH2) hepatoma cell lines; cells were analyzed for viability, proliferation, apoptosis, migration, and invasion. Cells were grown as xenograft tumors in nude mice and analyzed. We combined in-silico target gene prediction with mRNA profiles from all 3 mouse models. We quantified miRNA levels in 146 fresh-frozen tissues from patients (125 HCCs, 17 matched non-tumor tissues, and 4 liver samples from patients without cancer) and published human data sets and tested correlations with patient survival times using Kaplan-Meier curves and the log-rank test. Levels of NUSAP1 mRNA were quantified in 237 HCCs and 5 non-tumor liver samples using the Taqman assay. Results: Levels of the microRNA 193a-5p (MIR193A-5p) were reduced in liver tumors from all 3 mouse tumor models and in human HCC samples, compared with non-tumor liver tissues. Expression of a MIR193A-5p mimic in hepatoma cells reduced proliferation, survival, migration, and invasion and their growth as xenograft tumors in nude mice. We found nucleolar and spindle associated protein 1 (NUSAP1) to be a target of MIR193A-5p; HCC cells and tissues with low levels of MIR193A-5p had increased expression of NUSAP1. Increased levels of NUSAP1 in HCC samples correlated with shorter survival times of patients. Knockdown of NUSAP1 in Huh7 cells reduced proliferation, survival, migration, and growth as xenograft tumors in nude mice. Hydrodynamic tail-vein injections of a small hairpin RNA against NUSAP1 reduced growth of AKT1-MYC–induced tumors in mice. Conclusions: MIR193A-5p appears to prevent liver tumorigenesis by reducing levels of NUSAP1. Levels of MIR193A-5p are reduced in mouse and human HCC cells and tissues, leading to increased levels of NUSAP1, associated with shorter survival times of patients. Integrated analyses of miRNAs and mRNAs in tumors from mouse models can lead to identification of therapeutic targets in humans.
Priorities for research in soil ecology
Eisenhauer, Nico ; Antunes, Pedro M. ; Bennett, Alison E. ; Birkhofer, Klaus ; Bissett, Andrew ; Bowker, Matthew A. ; Caruso, Tancredi ; Chen, Baodong ; Coleman, David C. ; Boer, Wietse de; Ruiter, Peter de; DeLuca, Thomas H. ; Frati, Francesco ; Griffiths, Bryan S. ; Hart, Miranda M. ; Hättenschwiler, Stephan ; Haimi, Jari ; Heethoff, Michael ; Kaneko, Nobuhiro ; Kelly, Laura C. ; Leinaas, Hans Petter ; Lindo, Zoë ; Macdonald, Catriona ; Rillig, Matthias C. ; Ruess, Liliane ; Scheu, Stefan ; Schmidt, Olaf ; Seastedt, Timothy R. ; Straalen, Nico M. van; Tiunov, Alexei V. ; Zimmer, Martin ; Powell, Jeff R. - \ 2017
Pedobiologia 63 (2017). - ISSN 0031-4056 - p. 1 - 7.
Aboveground-belowground interactions - Biodiversity–ecosystem functioning - Biogeography - Chemical ecology - Climate change - Ecosystem services - Global change - Microbial ecology - Novel environments - Plant-microbe interactions - Soil biodiversity - Soil food web - Soil management - Soil processes
The ecological interactions that occur in and with soil are of consequence in many ecosystems on the planet. These interactions provide numerous essential ecosystem services, and the sustainable management of soils has attracted increasing scientific and public attention. Although soil ecology emerged as an independent field of research many decades ago, and we have gained important insights into the functioning of soils, there still are fundamental aspects that need to be better understood to ensure that the ecosystem services that soils provide are not lost and that soils can be used in a sustainable way. In this perspectives paper, we highlight some of the major knowledge gaps that should be prioritized in soil ecological research. These research priorities were compiled based on an online survey of 32 editors of Pedobiologia – Journal of Soil Ecology. These editors work at universities and research centers in Europe, North America, Asia, and Australia. The questions were categorized into four themes: (1) soil biodiversity and biogeography, (2) interactions and the functioning of ecosystems, (3) global change and soil management, and (4) new directions. The respondents identified priorities that may be achievable in the near future, as well as several that are currently achievable but remain open. While some of the identified barriers to progress were technological in nature, many respondents cited a need for substantial leadership and goodwill among members of the soil ecology research community, including the need for multi-institutional partnerships, and had substantial concerns regarding the loss of taxonomic expertise.
Stable isotape ratios of H, C, N an O in Italian citrus juices
Bontempo, L. ; Caruso, R. ; Fiorillo, M. ; Gambino, G.L. ; Perini, M. ; Simoni, M. ; Traulo, P. ; Wehrens, H.R.M.J. ; Gagliano, G. ; Camin, F. - \ 2014
Journal of Mass Spectrometry 49 (2014)9. - ISSN 1076-5174 - p. 785 - 791.
fruit juices - mass-spectrometry - orange juice - sugar addition - snif-nmr - water - ethanol - irms - fructose - origin
Stable isotope ratios (SIRs) of C, N, H and O have been exensively used in fruit juices quality control (ENV and AOAC methods) to detect added sugar and the watering down of concentrated juice, practices prohibited by European legislation (EU Directive 2012/12). The European Fruit Juice Association (AIJN) set some reference guidelines in order to allow the judging of the genuiness of a juice. Moreover, various studies have been carried out to determine the natural variability of SIRs in fruit juices, but none of these has investigated SIRs extensively in authentic citrus juices from Italy. In this work, about 500 citrus juice samples were officially collected in Italy by the Italian Ministry of Agricultural and Forestry Policies from 1998 onwards. (D/H)I and (D/H)II in ethanol and d13Cethanol, d13Cpulp, d13Csugars, d18Ovegetalwater, d15Npulp, and d18Opulp were determined using Site-Specific Natural Isotope Fractionation-Nuclear Magnetic Resonance and Isotope Ratio Mass Spectrometry, respectively. The characteristic ranges of variability in SIRs in genuine Italian citrus juice samples are here presented as well as their relationships and compliance with the limits indicated by the AIJN and others proposed in the literature. In particular, the Italian range of values was found to be not completely in agreement with AIJN guidelines, with the risk that genuine juices could be judged as not genuine. Variety seems not to influence SIRs, whereas harvest year and region of origin have some influence on the different ratios, although their data distribution shows overlapping when principal component analysis is applied.
Development of a methodology to forecast the nutritional value of new tomato hybrids
Carli, P. ; Caruso, G. ; Fogliano, V. ; Carputo, D. ; Frusciante, L. ; Ercolano, M.R. - \ 2011
Euphytica 180 (2011)3. - ISSN 0014-2336 - p. 291 - 300.
Agronomic performance - Nutritional value - Selection methods - Solanum lycopersicum
Tomato is a food of great relevance both due to its large-scale consumption and its richness in bioactive components. It is an important component of the traditional Mediterranean diet as well as of other diets. Nowadays, concerns about human health and environment preservation have changed the objectives of tomato breeding. In this study, eight tomato F1 hybrids and their parental lines were analyzed for nutritional properties and agronomic traits using a new selection method that combines biochemical and agronomic evaluation. Eight traits contributing to the nutritional quality of tomato (lycopene, β-carotene, other carotenoids, flavonoids, phenolic acids, vitamins C and E, dry residue) and average yield were assessed in fifteen tomato genotypes. Furthermore the pathogen resistances possessed from these genotypes were, also, considered. In order to select valuable tomato hybrids, a nutritional index (IQUAN) and an agronomic index (AI) were calculated. Our results suggested that the IQUAN nutritional index may be very useful to forecast the nutritional value of F1 hybrids based on parental performance. Combining the use of the IQUAN and AI indexes, we were able to select two hybrids (MR 48 and MR 47) that contain considerable amounts of antioxidants and acceptable parameters for commercial production.
Investigation of Cyprinidherpesvirus-3 genetic diversity by a multi-locus variable number of tandem repeats analysis.
Avarre, J.C. ; Madeira, J.P. ; Santika, A. ; Zainunb, Z. ; Baud, M. ; Cabon, J. ; Caruso, D. ; Castric, J. ; Bigarré, L. ; Engelsma, M.Y. ; Maskur, M. - \ 2011
Journal of Virological Methods 173 (2011)2. - ISSN 0166-0934 - p. 320 - 327.
mediated isothermal amplification - koi-herpesvirus - common carp - r-package - virus - khv - sequences - pcr - dna - mortality
Cyprinid herpesvirus-3 (CyHV-3), or koi herpesvirus (KHV), is responsible for high mortalities in aquaculture of both common carp (Cyprinus carpio carpio) and koi carp (Cyprinus carpio koi) worldwide. The complete genomes of three CyHV-3 isolates showed more than 99% of DNA sequence identity, with the majority of differences located in short tandem repeats, also called VNTR (variable number of tandem repeats). By targeting these variations, eight loci were selected for genotyping CyHV-3 by multiple locus VNTR analysis (MLVA). CyHV-3 strains obtained after sequential in vivo infections exhibited identical MLVA profiles, whereas samples originating from a single isolate passaged 6 and 82 times in vitro exhibited mutations in two of the eight loci, suggesting a relatively slow genetic evolution rate of the VNTRs. The method was subsequently applied on 38 samples collected in Indonesia, France and the Netherlands. Globally, the isolates grouped in two main genetic clusters, each one divided in two subgroups including either CyHV-3-U/I or CyHV3-J. Interestingly, Indonesian strains were rather distant from CyHV-3-J isolate. The results of the present study indicate that these VNTR molecular markers are efficient in estimating the genetic diversity among CyHV-3 isolates and are therefore suitable for further molecular epidemiological studies.
Gravimetric monitoring of nonionic surfactant adsorption from nonaqueous media onto quartz crystal microbalance electrodes and colloidal silica.
Caruso, F. ; Rinia, H.A. ; Furlong, D.N. - \ 1996
Langmuir 12 (1996). - ISSN 0743-7463 - p. 2145 - 2152.