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2. EuroPineDB: a high-coverage web database for maritime pine transcriptome

Author

Cantón Francisco R, Ordás Ricardo, Soto Álvaro, Cervera M Teresa, Collada Carmen, Perdiguero Pedro, Guevara M Ángeles, Flores-Monterroso Arantxa, Bautista Rocío, Díaz-Moreno Sara M, Villalobos David P, Guerrero-Fernández Darío, Canales Javier, Fernández-Pozo Noé, Avila Concepción, Cánovas Francisco M, and Claros M Gonzalo

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Pinus pinaster is an economically and ecologically important species that is becoming a woody gymnosperm model. Its enormous genome size makes whole-genome sequencing approaches are hard to apply. Therefore, the expressed portion of the genome has to be characterised and the results and annotations have to be stored in dedicated databases. Description EuroPineDB is the largest sequence collection available for a single pine species, Pinus pinaster (maritime pine), since it comprises 951 641 raw sequence reads obtained from non-normalised cDNA libraries and high-throughput sequencing from adult (xylem, phloem, roots, stem, needles, cones, strobili) and embryonic (germinated embryos, buds, callus) maritime pine tissues. Using open-source tools, sequences were optimally pre-processed, assembled, and extensively annotated (GO, EC and KEGG terms, descriptions, SNPs, SSRs, ORFs and InterPro codes). As a result, a 10.5× P. pinaster genome was covered and assembled in 55 322 UniGenes. A total of 32 919 (59.5%) of P. pinaster UniGenes were annotated with at least one description, revealing at least 18 466 different genes. The complete database, which is designed to be scalable, maintainable, and expandable, is freely available at: http://www.scbi.uma.es/pindb/. It can be retrieved by gene libraries, pine species, annotations, UniGenes and microarrays (i.e., the sequences are distributed in two-colour microarrays; this is the only conifer database that provides this information) and will be periodically updated. Small assemblies can be viewed using a dedicated visualisation tool that connects them with SNPs. Any sequence or annotation set shown on-screen can be downloaded. Retrieval mechanisms for sequences and gene annotations are provided. Conclusions The EuroPineDB with its integrated information can be used to reveal new knowledge, offers an easy-to-use collection of information to directly support experimental work (including microarray hybridisation), and provides deeper knowledge on the maritime pine transcriptome.

Published
2011
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3. AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences

Author

Claros M Gonzalo, Cantón Francisco R, Villalobos David P, Bautista Rocío, and Guerrero Darío

Subjects
Biology (General), QH301-705.5, Genetics, QH426-470
Abstract

Abstract Background Multiple sequence alignments are used to study gene or protein function, phylogenetic relations, genome evolution hypotheses and even gene polymorphisms. Virtually without exception, all available tools focus on conserved segments or residues. Small divergent regions, however, are biologically important for specific quantitative polymerase chain reaction, genotyping, molecular markers and preparation of specific antibodies, and yet have received little attention. As a consequence, they must be selected empirically by the researcher. AlignMiner has been developed to fill this gap in bioinformatic analyses. Results AlignMiner is a Web-based application for detection of conserved and divergent regions in alignments of conserved sequences, focusing particularly on divergence. It accepts alignments (protein or nucleic acid) obtained using any of a variety of algorithms, which does not appear to have a significant impact on the final results. AlignMiner uses different scoring methods for assessing conserved/divergent regions, Entropy being the method that provides the highest number of regions with the greatest length, and Weighted being the most restrictive. Conserved/divergent regions can be generated either with respect to the consensus sequence or to one master sequence. The resulting data are presented in a graphical interface developed in AJAX, which provides remarkable user interaction capabilities. Users do not need to wait until execution is complete and can.even inspect their results on a different computer. Data can be downloaded onto a user disk, in standard formats. In silico and experimental proof-of-concept cases have shown that AlignMiner can be successfully used to designing specific polymerase chain reaction primers as well as potential epitopes for antibodies. Primer design is assisted by a module that deploys several oligonucleotide parameters for designing primers "on the fly". Conclusions AlignMiner can be used to reliably detect divergent regions via several scoring methods that provide different levels of selectivity. Its predictions have been verified by experimental means. Hence, it is expected that its usage will save researchers' time and ensure an objective selection of the best-possible divergent region when closely related sequences are analysed. AlignMiner is freely available at http://www.scbi.uma.es/alignminer.

Published
2010
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4. SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read

Author

Pérez-Trabado Guillermo, Cantón Francisco R, Fernández-Pozo Noé, Lara Antonio J, Falgueras Juan, and Claros M Gonzalo

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background High-throughput automated sequencing has enabled an exponential growth rate of sequencing data. This requires increasing sequence quality and reliability in order to avoid database contamination with artefactual sequences. The arrival of pyrosequencing enhances this problem and necessitates customisable pre-processing algorithms. Results SeqTrim has been implemented both as a Web and as a standalone command line application. Already-published and newly-designed algorithms have been included to identify sequence inserts, to remove low quality, vector, adaptor, low complexity and contaminant sequences, and to detect chimeric reads. The availability of several input and output formats allows its inclusion in sequence processing workflows. Due to its specific algorithms, SeqTrim outperforms other pre-processors implemented as Web services or standalone applications. It performs equally well with sequences from EST libraries, SSH libraries, genomic DNA libraries and pyrosequencing reads and does not lead to over-trimming. Conclusions SeqTrim is an efficient pipeline designed for pre-processing of any type of sequence read, including next-generation sequencing. It is easily configurable and provides a friendly interface that allows users to know what happened with sequences at every pre-processing stage, and to verify pre-processing of an individual sequence if desired. The recommended pipeline reveals more information about each sequence than previously described pre-processors and can discard more sequencing or experimental artefacts.

Published
2010
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5. PreP+07: improvements of a user friendly tool to preprocess and analyse microarray data

Author

Claros M Gonzalo, Muñoz-Merida Antonio, Martin-Requena Victoria, and Trelles Oswaldo

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Nowadays, microarray gene expression analysis is a widely used technology that scientists handle but whose final interpretation usually requires the participation of a specialist. The need for this participation is due to the requirement of some background in statistics that most users lack or have a very vague notion of. Moreover, programming skills could also be essential to analyse these data. An interactive, easy to use application seems therefore necessary to help researchers to extract full information from data and analyse them in a simple, powerful and confident way. Results PreP+07 is a standalone Windows XP application that presents a friendly interface for spot filtration, inter- and intra-slide normalization, duplicate resolution, dye-swapping, error removal and statistical analyses. Additionally, it contains two unique implementation of the procedures – double scan and Supervised Lowess-, a complete set of graphical representations – MA plot, RG plot, QQ plot, PP plot, PN plot – and can deal with many data formats, such as tabulated text, GenePix GPR and ArrayPRO. PreP+07 performance has been compared with the equivalent functions in Bioconductor using a tomato chip with 13056 spots. The number of differentially expressed genes considering p-values coming from the PreP+07 and Bioconductor Limma packages were statistically identical when the data set was only normalized; however, a slight variability was appreciated when the data was both normalized and scaled. Conclusion PreP+07 implementation provides a high degree of freedom in selecting and organizing a small set of widely used data processing protocols, and can handle many data formats. Its reliability has been proven so that a laboratory researcher can afford a statistical pre-processing of his/her microarray results and obtain a list of differentially expressed genes using PreP+07 without any programming skills. All of this gives support to scientists that have been using previous PreP releases since its first version in 2003.

Published
2009
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8. Decreased mortality among patients with catheter-related bloodstream infections at Catalan hospitals (2010–2019)

Author

Badia-Cebada, L., Peñafiel, J., López-Contreras, J., Pomar, V., Martínez, J.A., Santana, G., Cuquet, J., Montero, M.M., Hidalgo-López, C., Andrés, M., Gimenez, M., Quesada, M.D., Vaqué, M., Iftimie, S., Gudiol, C., Pérez, R., Coloma, A., Marron, A., Barrufet, P., Marimon, M., Lérida, A., Clarós, M., Ramírez-Hidalgo, M.F., Garcia Pardo, G., Martinez, M.J., Chamarro, E.L., Jiménez-Martínez, E., Hornero, A., Limón, E., López, M., Calbo, E., Pujol, M., and Gasch, O.

Published
2022
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11. Micro-Variations from RNA-seq Experiments for Non-model Organisms

Author

Espinosa, Elena, Arroyo, Macarena, Larrosa, Rafael, Manchado, Manuel, Claros, M. Gonzalo, Bautista, Rocí­o, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Rojas, Ignacio, editor, Valenzuela, Olga, editor, Rojas, Fernando, editor, Herrera, Luis Javier, editor, and Ortuño, Francisco, editor

Published
2020
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14. Research and reflection competences in Initial Teacher Education

Author

González Ramírez, Carolina, Cárdenas- Claros, M´ónica, Venegas , René, González Ramírez, Carolina, Cárdenas- Claros, M´ónica, and Venegas , René

Abstract

Research studies have assessed the development of research and reflection skills of pre-service teachers and for this several surveys, questionnaires and inventories have been designed. However, their authors do not necessarily report validity and reliability indexes of such instruments. This limits the possibilities of conducting replication studies, conducting meta-analyses and limits the understanding and development of this research area. Accordingly, in this paper we report the findings of two studies. Study 1 introduces the Research and Reflection Competences in Initial Teacher Education Questionnaire (RRC-ITE) to the research community by describing the design, piloting and validation measures undertaken. In Study 2 the RRC-ITE questionnaire is used to assess the research and reflection competences of 162 pre-service teachers from Chile. Results show that the participants lack knowledge about (1) research design, (2) data collection and data analysis procedures, (3) ethical considerations and (4) issue identification. Findings also show that pre-service teachers perceive to be highly-competent in transversal competences to do with collaborative work, decision-making, and reflection. Avenues for further research along with study limitations are also described. &nbsp, Estudios recientes han valorado el grado de desarrollo de competencias de investigación y reflexión de profesores en formación y para ello han diseñado diversos cuestionarios, inventarios y escalas de percepción. Sin embargo, sus autores no declaran los grados de validez y confiabilidad de dichos instrumentos lo que dificulta su replicabilidad, la construcción de metaanálisis y limita el avance de esta área del conocimiento. De acuerdo con lo anterior, se presentan dos estudios: el primero, describe el proceso de diseño y validación del Cuestionario de Competencias de Investigación y Reflexión en la Formación Inicial Docente (CCIR-FID) con el propósito de facilitar su aplicación en otros contextos. El segundo, busca determinar el nivel de competencias de investigación y reflexión que 162 profesores en formación declaran poseer a partir de la aplicación del CCIR-FID. Los hallazgos indican que el CCIR-FID es un instrumento confiable y replicable. Además, se identifican cuatro competencias descendidas: (1) falta de conocimiento de herramientas para el análisis de datos cualitativos y cuantitativos, (2) conocimiento sobre metodología para el tratamiento y análisis de datos cualitativos, (3) falta de conocimiento sobre consideraciones éticas y (4) identificación de problemas de investigación. Asimismo, las competencias mayormente desarrolladas atienden a competencias transversales como trabajo colaborativo, toma de decisiones y competencias de reflexión. Proyecciones del estudio al igual que limitaciones también se describen.

Published
2024

15. EuroPineDB: a high-coverage web database for maritime pine transcriptome

Author

Fernández-Pozo, Noé, Canales, Javier, Guerrero-Fernández, Darío, Villalobos, David P., Díaz-Moreno, Sara M., Bautista, Rocío, Flores-Monterroso, Arantxa, Guevara, M. Ángeles, Perdiguero Jiménez, Pedro, Collada, Carmen, Cervera, M. Teresa, Soto, Álvaro, Ordás, Ricardo, Cantón, Francisco R., Ávila, Concepción, Cánovas, Francisco M., Claros, M. Gonzalo, Fernández-Pozo, Noé, Canales, Javier, Guerrero-Fernández, Darío, Villalobos, David P., Díaz-Moreno, Sara M., Bautista, Rocío, Flores-Monterroso, Arantxa, Guevara, M. Ángeles, Perdiguero Jiménez, Pedro, Collada, Carmen, Cervera, M. Teresa, Soto, Álvaro, Ordás, Ricardo, Cantón, Francisco R., Ávila, Concepción, Cánovas, Francisco M., and Claros, M. Gonzalo

Abstract

Acknowledgements The authors gratefully acknowledge the computer resources and technical support provided by the Plataforma Andaluza de Bioinformática of the University of Málaga, Spain. This study was supported by the Spanish Ministerio de Ciencia e Innovación [AGL2009-12139-C02-02, BIO2009-07490], the European Union [PLE2009-0016] and the Junta de Andalucía [CVI-6075 and BIO-114]., Pinus pinaster is an economically and ecologically important species that is becoming a woody gymnosperm model. Its enormous genome size makes whole-genome sequencing approaches are hard to apply. Therefore, the expressed portion of the genome has to be characterised and the results and annotations have to be stored in dedicated databases.Description: EuroPineDB is the largest sequence collection available for a single pine species, Pinus pinaster (maritime pine), since it comprises 951 641 raw sequence reads obtained from non-normalised cDNA libraries and high-throughput sequencing from adult (xylem, phloem, roots, stem, needles, cones, strobili) and embryonic (germinated embryos, buds, callus) maritime pine tissues. Using open-source tools, sequences were optimally pre-processed, assembled, and extensively annotated (GO, EC and KEGG terms, descriptions, SNPs, SSRs, ORFs and InterPro codes). As a result, a 10.5× P. pinaster genome was covered and assembled in 55 322 UniGenes. A total of 32 919 (59.5%) of P. pinaster UniGenes were annotated with at least one description, revealing at least 18 466 different genes. The complete database, which is designed to be scalable, maintainable, and expandable, is freely available at: http://www.scbi.uma.es/pindb/. It can be retrieved by gene libraries, pine species, annotations, UniGenes and microarrays (i.e., the sequences are distributed in two-colour microarrays; this is the only conifer database that provides this information) and will be periodically updated. Small assemblies can be viewed using a dedicated visualisation tool that connects them with SNPs. Any sequence or annotation set shown on-screen can be downloaded. Retrieval mechanisms for sequences and gene annotations are provided.Conclusions: The EuroPineDB with its integrated information can be used to reveal new knowledge, offers an easy-to-use collection of information to directly support experimental work (including microarray hybridisation), and provides deepe, Depto. de Genética, Fisiología y Microbiología, Fac. de Ciencias Biológicas, TRUE, pub

Published
2024

17. Structural and Functional Features of Glutathione Reductase Transcripts from Olive (Olea europaea L.) Seeds

Author

Lima-Cabello, Elena, Martínez-Beas, Isabel, García-Quirós, Estefanía, Carmona, Rosario, Gonzalo Claros, M., Jimenez-Lopez, Jose Carlos, de Dios Alché, Juan, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Rojas, Ignacio, editor, Valenzuela, Olga, editor, Rojas, Fernando, editor, and Ortuño, Francisco, editor

Published
2019
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18. Expression Change Correlations Between Transposons and Their Adjacent Genes in Lung Cancers Reveal a Genomic Location Dependence and Highlights Cancer-Significant Genes

Author

Arroyo, Macarena, Larrosa, Rafael, Claros, M. Gonzalo, Bautista, Rocío, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Rojas, Ignacio, editor, Valenzuela, Olga, editor, Rojas, Fernando, editor, and Ortuño, Francisco, editor

Published
2019
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19. De novo Transcriptome Assembly of Solea senegalensis v5.0 Using TransFlow

Author

Córdoba-Caballero, José, Seoane-Zonjic, Pedro, Manchado, Manuel, Gonzalo Claros, M., Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Rojas, Ignacio, editor, Valenzuela, Olga, editor, Rojas, Fernando, editor, and Ortuño, Francisco, editor

Published
2019
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21. NearTrans Can Identify Correlated Expression Changes Between Retrotransposons and Surrounding Genes in Human Cancer

Author

Larrosa, Rafael, Arroyo, Macarena, Bautista, Rocío, López-Rodríguez, Carmen María, Claros, M. Gonzalo, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, Rojas, Ignacio, editor, and Ortuño, Francisco, editor

Published
2018
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22. Obtaining the Most Accurate de novo Transcriptomes for Non-model Organisms: The Case of Castanea sativa

Author

Espigares, Marina, Seoane, Pedro, Bautista, Rocío, Quintana, Julia, Gómez, Luis, Claros, M. Gonzalo, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Rojas, Ignacio, editor, and Ortuño, Francisco, editor

Published
2017
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23. Identification and in silico Analysis of Glutathione Reductase Transcripts Expressed in Olive (Olea europaea L.) Pollen and Pistil

Author

García-Quirós, Estefanía, Carmona, Rosario, Zafra, Adoración, Gonzalo Claros, M., Alché, Juan de Dios, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Rojas, Ignacio, editor, and Ortuño, Francisco, editor

Published
2017
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24. Persistent effects of pre-Columbian plant domestication on Amazonian forest composition

Author

Levis, C., Costa, F. R. C., Bongers, F., Peña-Claros, M., Clement, C. R., Junqueira, A. B., Neves, E. G., Tamanaha, E. K., Figueiredo, F. O. G., Salomão, R. P., Castilho, C. V., Magnusson, W. E., Phillips, O. L., Guevara, J. E., Sabatier, D., Molino, J.-F., López, D. Cárdenas, Mendoza, A. M., Pitman, N. C. A., Duque, A., Vargas, P. Núñez, Zartman, C. E., Vasquez, R., Andrade, A., Camargo, J. L., Feldpausch, T. R., Laurance, S. G. W., Laurance, W. F., Killeen, T. J., Nascimento, H. E. Mendonça, Montero, J. C., Mostacedo, B., Amaral, I. L., Vieira, I. C. Guimarães, Brienen, R., Castellanos, H., Terborgh, J., de Jesus Veiga Carim, M., da Silva Guimarães, J. R., de Souza Coelho, L., de Almeida Matos, F. D., Wittmann, F., Mogollón, H. F., Damasco, G., Dávila, N., García-Villacorta, R., Coronado, E. N. H., Emilio, T., de Andrade Lima Filho, D., Schietti, J., Souza, P., Targhetta, N., Comiskey, J. A., Marimon, B. S., Marimon, B.-H., Neill, D., Alonso, A., Arroyo, L., Carvalho, F. A., de Souza, F. C., Dallmeier, F., Pansonato, M. P., Duivenvoorden, J. F., Fine, P. V. A., Stevenson, P. R., Araujo-Murakami, A., Aymard C., G. A., Baraloto, C., do Amaral, D. D., Engel, J., Henkel, T. W., Maas, P., Petronelli, P., Revilla, J. D. Cardenas, Stropp, J., Daly, D., Gribel, R., Paredes, M. Ríos, Silveira, M., Thomas-Caesar, R., Baker, T. R., da Silva, N. F., Ferreira, L. V., Peres, C. A., Silman, M. R., Cerón, C., Valverde, F. C., Di Fiore, A., Jimenez, E. M., Mora, M. C. Peñuela, Toledo, M., Barbosa, E. M., de Matos Bonates, L. C., Arboleda, N. C., de Sousa Farias, E., Fuentes, A., Guillaumet, J.-L., Jørgensen, P. Møller, Malhi, Y., de Andrade Miranda, I. P., Phillips, J. F., Prieto, A., Rudas, A., Ruschel, A. R., Silva, N., von Hildebrand, P., Vos, V. A., Zent, E. L., Zent, S., Cintra, B. B. L., Nascimento, M. T., Oliveira, A. A., Ramirez-Angulo, H., Ramos, J. F., Rivas, G., Schöngart, J., Sierra, R., Tirado, M., van der Heijden, G., Torre, E. V., Wang, O., Young, K. R., Baider, C., Cano, A., Farfan-Rios, W., Ferreira, C., Hoffman, B., Mendoza, C., Mesones, I., Torres-Lezama, A., Medina, M. N. U., van Andel, T. R., Villarroel, D., Zagt, R., Alexiades, M. N., Balslev, H., Garcia-Cabrera, K., Gonzales, T., Hernandez, L., Huamantupa-Chuquimaco, I., Manzatto, A. G., Milliken, W., Cuenca, W. P., Pansini, S., Pauletto, D., Arevalo, F. R., Reis, N. F. Costa, Sampaio, A. F., Giraldo, L. E. Urrego, Sandoval, E. H. Valderrama, Gamarra, L. Valenzuela, Vela, C. I. A., and ter Steege, H.

Published
2017

25. Combining Genetic and Transcriptomic Approaches to Identify Transporter-Coding Genes as Likely Responsible for a Repeatable Salt Tolerance QTL in Citrus

Author

Asins, Maria J., primary, Bullones, Amanda, additional, Raga, Veronica, additional, Romero-Aranda, Maria R., additional, Espinosa, Jesus, additional, Triviño, Juan C., additional, Bernet, Guillermo P., additional, Traverso, Jose A., additional, Carbonell, Emilio A., additional, Claros, M. Gonzalo, additional, and Belver, Andres, additional

Published
2023
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32. Automatic Workflow for the Identification of Constitutively-Expressed Genes Based on Mapped NGS Reads

Author

Carmona, Rosario, Seoane, Pedro, Zafra, Adoración, Jiménez-Quesada, María José, Alché, Juan de Dios, Claros, M. Gonzalo, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Ortuño, Francisco, editor, and Rojas, Ignacio, editor

Published
2016
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34. Warming, drought, and disturbances lead to shifts in functional composition: a millennial-scale analysis for Amazonian and Andean sites

Author

van der Sande, M., Bush, M., Åkesson, C., Berrio, J., Correia Metrio, A., Flantua, S., Hooghiemstra, H., Maezumi, S., McMichael, C., Montoya, E., Mosblech, N., de Novaes Nascimento, M., Peña-Claros, M., Poorter, L., Raczka, M., and Gosling, W.

Abstract

Tropical forests are changing in composition and productivity, probably in response to changes in climate and disturbances. The responses to these multiple environmental drivers, and the mechanisms underlying the changes, remain largely unknown. Here, we use a functional trait approach on timescales of 10,000?years to assess how climate and disturbances influence the community-mean adult height, leaf area, seed mass, and wood density for eight lowland and highland forest landscapes. To do so, we combine data of eight fossil pollen records with functional traits and proxies for climate (temperature, precipitation, and El Niño frequency) and disturbances (fire and general disturbances). We found that temperature and disturbances were the most important drivers of changes in functional composition. Increased water availability (high precipitation and low El Niño frequency) generally led to more acquisitive trait composition (large leaves and soft wood). In lowland forests, warmer climates decreased community-mean height probably because of increased water stress, whereas in highland forests warmer climates increased height probably because of upslope migration of taller species. Disturbance increased the abundance of acquisitive, disturbance-adapted taxa with small seeds for quick colonization of disturbed sites, large leaves for light capture, and soft wood to attain fast height growth. Fire had weak effects on lowland forests but led to more stress-adapted taxa that are tall with fast life cycles and small seeds that can quickly colonize burned sites. Site-specific analyses were largely in line with cross-site analyses, except for varying site-level effects of El Niño frequency and fire activity, possibly because regional patterns in El Niño are not a good predictor of local changes, and charcoal abundances do not reflect fire intensity or severity. With future global changes, tropical Amazonian and Andean forests may transition toward shorter, drought- and disturbance-adapted forests in the lowlands but taller forests in the highlands. 1 Introduction 2 Materials and methods 2.1 Sites 2.2 Fossil pollen records 2.3 Functional traits 2.4 Community-mean traits 2.5 Climate 2.6 Fire activity 2.7 General disturbance 2.8 Analyses 3 Results 3.1 Adult tree height 3.2 Leaf area 3.3 Seed mass 3.4 Wood density 4 Discussion 4.1 More favorable climatic growing conditions lead to more acquisitive trait values 4.2 Fires lead to more stress-adapted species, while general disturbances lead to more acquisitive species 4.3 Adult height and LA are most responsive to climate and disturbances 4.4 Local disturbance histories determine local responses to climate and disturbances 5 Conclusions

Published
2023

35. Identification of Distinctive Variants of the Olive Pollen Allergen Ole e 5 (Cu,Zn Superoxide Dismutase) throughout the Analysis of the Olive Pollen Transcriptome

Author

Zafra, Adoración, Carmona, Rosario, Jimenez-Lopez, José C., Pulido, Amada, Claros, M. Gonzalo, de Dios Alché, Juan, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Ortuño, Francisco, editor, and Rojas, Ignacio, editor

Published
2015
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36. Identification and in silico Analysis of NADPH Oxidase Homologues Involved in Allergy from an Olive Pollen Transcriptome

Author

Jiménez-Quesada, María José, Traverso, Jose Ángel, Zafra, Adoración, Jimenez-Lopez, José C., Carmona, Rosario, Claros, M. Gonzalo, de Dios Alché, Juan, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Ortuño, Francisco, editor, and Rojas, Ignacio, editor

Published
2015
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37. DEgenes Hunter - A Self-customised Gene Expression Analysis Workflow for Non-model Organisms

Author

González Gayte, Isabel, Bautista Moreno, Rocío, Claros, M. Gonzalo, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Ortuño, Francisco, editor, and Rojas, Ignacio, editor

Published
2015
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38. Bioinformatics Analyses to Separate Species Specific mRNAs from Unknown Sequences in de novo Assembled Transcriptomes

Author

Velasco, David, Seoane, Pedro, Claros, M. Gonzalo, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Ortuño, Francisco, editor, and Rojas, Ignacio, editor

Published
2015
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43. Spatial and temporal abilities of proxies used to detect pre-Columbian Indigenous human activity in Amazonian ecosystems

Author

McMichael, C.N.H., Levis, C., Gosling, W.D., Junqueira, A.B., Piperno, D.R., Neves, E.G., Mayle, F., Peña-Claros, M., Bongers, F., McMichael, C.N.H., Levis, C., Gosling, W.D., Junqueira, A.B., Piperno, D.R., Neves, E.G., Mayle, F., Peña-Claros, M., and Bongers, F.

Abstract

Humans have been modifying ecosystems since before the Holocene began ca. 12,000 years ago, even in Neotropical regions. The Amazon was once thought to be ‘pristine’ and only lightly impacted by Indigenous people before European colonization in the Americas (e.g., pre-Columbian); however, multiple lines of evidence have shown that Indigenous human activities over the past millennia have left ecological legacies on modern ecosystems. We review the various lines of evidence used to reconstruct pre-Columbian Indigenous human activity in Amazonia, and assess the spatial and temporal resolution and limits of each one of them. We suggest that a multi-proxy approach is always preferred, and that lines of evidence that cover overlapping yet discrete spatial and temporal scales can provide a robust and comprehensive assessment of the nuances of pre-Columbian Indigenous human activities in Amazonia, and how they affect modern ecosystems.

Published
2023

44. OliveAtlas: A gene expression atlas yool for Olea europaea

Author

Ministerio de Ciencia e Innovación (España), European Commission, Junta de Andalucía, Bullones, Amanda, Castro López, Antonio Jesús, Lima Cabello, Elena, Alché Ramírez, Juan de Dios, Luque, F., Claros, M. G., Ministerio de Ciencia e Innovación (España), European Commission, Junta de Andalucía, Bullones, Amanda, Castro López, Antonio Jesús, Lima Cabello, Elena, Alché Ramírez, Juan de Dios, Luque, F., and Claros, M. G.

Abstract

The olive (Olea europaea L.) is an ancient crop of great importance in the Mediterranean basin due to the production of olive oil and table olives, which are important sources of fat and have benefits for human health. This crop is expanding and increasing its production worldwide and five olive genomes have recently been sequenced, representing a wild olive and important cultivars in terms of olive oil production, intensive agriculture, and adaptation to the East Asian climate. However, few bioinformatic and genomic resources are available to assist olive research and breeding, and there are no platforms to query olive gene expression data. Here, we present OliveAtlas, an interactive gene expression atlas for olive with multiple bioinformatics tools and visualization methods, enabling multiple gene comparison, replicate inspection, gene set enrichment, and data downloading. It contains 70 RNA-seq experiments, organized in 10 data sets representing the main olive plant organs, the pollen germination and pollen tube elongation process, and the response to a collection of biotic and abiotic stresses, among other experimental conditions. OliveAtlas is a web tool based on easyGDB with expression data based on the ‘Picual’ genome reference and gene annotation.

Published
2023

48. Diversity enhances carbon storage in tropical forests

Author

Poorter, L., van der Sande, M. T., Thompson, J., Arets, E. J. M. M., Alarcón, A., Álvarez-Sánchez, J., Ascarrunz, N., Balvanera, P., Barajas-Guzmán, G., Boit, A., Bongers, F., Carvalho, F. A., Casanoves, F., Cornejo-Tenorio, G., Costa, F. R. C., de Castilho, C. V., Duivenvoorden, J. F., Dutrieux, L. P., Enquist, B. J., Fernández-Méndez, F., Finegan, B., Gormley, L. H. L., Healey, J. R., Hoosbeek, M. R., Ibarra-Manriquez, G., Junqueira, A. B., Levis, C., Licona, J. C., Lisboa, L. S., Magnusson, W. E., Martínez-Ramos, M., Martínez-Yrizar, A., Martorano, L. G., Maskell, L. C., Mazzei, L., Meave, J. A., Mora, F., Muñoz, R., Nytch, C., Pansonato, M. P., Parr, T. W., Paz, H., Pérez-García, E. A., Rentería, L. Y., Rodríguez-Velazquez, J., Rozendaal, D. M. A., Ruschel, A. R., Sakschewski, B., Salgado-Negret, B., Schietti, J., Simões, M., Sinclair, F. L., Souza, P. F., Souza, F. C., Stropp, J., ter Steege, H., Swenson, N. G., Thonicke, K., Toledo, M., Uriarte, M., van der Hout, P., Walker, P., Zamora, N., and Peña-Claros, M.

Published
2015

50. GENote v.β: A Web Tool Prototype for Annotation of Unfinished Sequences in Non-model Eukaryotes

Author

Fernández-Pozo, Noé, Guerrero-Fernández, Darío, Bautista, Rocío, Gómez-Maldonado, Josefa, Avila, Concepción, Cánovas, Francisco M., Claros, M. Gonzalo, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, Freitas, Ana T., editor, and Navarro, Arcadi, editor

Published
2012
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