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335 results on '"Claros M"'

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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14. 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

24. 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

28. Post-discharge surgical site infections after uncomplicated elective colorectal surgery: impact and risk factors. The experience of the VINCat Program

Author

Castellana, D., Barcenilla, Fernando, Garcia, G., Antúnez, R., Rebull, J., Domenech, M.F., Domenech, D., Garcia, D., Lérida, A., Martin, L., Oller, B., Sopena, N., Almirante, B., Ferrer, C., Pérez, R., Obradors, F., Mestre, G., Berbel, C., Serrat, P., Palau, E., Iborra, M.I., Zaragoza, M., Garcia, Á., Grabulosa, L., Pericàs, F., Burgas, M.C., Girbal, P., Gonzalez, M., Villegas, M.L., Ferrer, L., Moreno, M.J., Nicolás, C., Navarro, A., Angas, J., Ros, M.T., Smithson, A., Porrón, C., Nolla, M., Rovira, M., Escudero, L.R., Conde, M., Espinosa, J.J., Serrate, G., Falgueras, L., Fernández, I., Cruz, A.J., Ferrer Díaz de Brito, V., Peña, I., Agustí, C., Pagespetit, L., Santamaría, M.A., Rifà, J., Pinyana, A., Herranz, M., Gil, M.J., Beltran, J.M., Sanjurjo, E., Vazquez, R.M., Cuquet, J., Morcillo, M.Á., Hernández, R., Errando, X., Moreno, E., Ferrer, R., Casas, A., Ramos, C., Roura, I., López, A.F., Castro, A., Pérez, À., Espinach, J., Castander, D., Paradiñeiro, J.C., Clarós, M., Jofré, M., Montardit, I., Batlle, R., Cotura, A., Pomar, V., López-Contreras, J., de La Cruz, P., Aguilar, L., Calbet, J., Sabaté, S., Montilla, C., Camps, R., Garcia Penche, R.M., Coll, M.R., Caro, S., Ginesta, D., Doménech, T., Gisbert, J.C., Redón, E., Tricas, J.M., Marrón, A., Brugues, M., Martinez, S., Cuscó, M., Estrada, O., Vidal, E., Roura, J., Colomer, À., Calsina, M., Vaqué, M., Guillemat, M., Armengol, E.C., Vilà, B., Garcia, A., Limón, E., Shaw, E., Badia, J.M., Piriz, M., Escofet, R., Gudiol, F., and Pujol, M.

Published
2014
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29. 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., Bullones, Amanda, Raga, Veronica, Romero-Aranda, Maria R., Espinosa, Jesus, Triviño, Juan C., Bernet, Guillermo P., Traverso, Jose A., Carbonell, Emilio A., Claros, M. Gonzalo, and Belver, Andres

Subjects
ROOTSTOCKS, LOCUS (Genetics), CITRUS, TRANSCRIPTOMES, GENE expression, GENES
Abstract

The excessive accumulation of chloride (Cl−) in leaves due to salinity is frequently related to decreased yield in citrus. Two salt tolerance experiments to detect quantitative trait loci (QTLs) for leaf concentrations of Cl−, Na+, and other traits using the same reference progeny derived from the salt-tolerant Cleopatra mandarin (Citrus reshni) and the disease-resistant donor Poncirus trifoliata were performed with the aim to identify repeatable QTLs that regulate leaf Cl− (and/or Na+) exclusion across independent experiments in citrus, as well as potential candidate genes involved. A repeatable QTL controlling leaf Cl− was detected in chromosome 6 (LCl-6), where 23 potential candidate genes coding for transporters were identified using the C. clementina genome as reference. Transcriptomic analysis revealed two important candidate genes coding for a member of the nitrate transporter 1/peptide transporter family (NPF5.9) and a major facilitator superfamily (MFS) protein. Cell wall biosynthesis- and secondary metabolism-related processes appeared to play a significant role in differential gene expression in LCl-6. Six likely gene candidates were mapped in LCl-6, showing conserved synteny in C. reshni. In conclusion, markers to select beneficial Cleopatra mandarin alleles of likely candidate genes in LCl-6 to improve salt tolerance in citrus rootstock breeding programs are provided. [ABSTRACT FROM AUTHOR]

Published
2023
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35. Forest Disturbances

Author

Broadbent, E. N., Zarin, D. J., Asner, G. P., Peña-Claros, M., Cooper, A., and Littell, R.

Published
2006

38. Long-term decline of the Amazon carbon sink

Author

Brienen, R. J. W., Phillips, O. L., Feldpausch, T. R., Gloor, E., Baker, T. R., Lloyd, J., Lopez-Gonzalez, G., Monteagudo-Mendoza, A., Malhi, Y., Lewis, S. L., Vásquez Martinez, R., Alexiades, M., Álvarez Dávila, E., Alvarez-Loayza, P., Andrade, A., Aragão, L. E. O. C., Araujo-Murakami, A., Arets, E. J. M. M., Arroyo, L., Aymard, G. A. C., Bánki, O. S., Baraloto, C., Barroso, J., Bonal, D., Boot, R. G. A., Camargo, J. L. C., Castilho, C. V., Chama, V., Chao, K. J., Chave, J., Comiskey, J. A., Cornejo Valverde, F., da Costa, L., de Oliveira, E. A., Di Fiore, A., Erwin, T. L., Fauset, S., Forsthofer, M., Galbraith, D. R., Grahame, E. S., Groot, N., Hérault, B., Higuchi, N., Honorio Coronado, E. N., Keeling, H., Killeen, T. J., Laurance, W. F., Laurance, S., Licona, J., Magnussen, W. E., Marimon, B. S., Marimon-Junior, B. H., Mendoza, C., Neill, D. A., Nogueira, E. M., Núñez, P., Pallqui Camacho, N. C., Parada, A., Pardo-Molina, G., Peacock, J., Peña-Claros, M., Pickavance, G. C., Pitman, N. C. A., Poorter, L., Prieto, A., Quesada, C. A., Ramírez, F., Ramírez-Angulo, H., Restrepo, Z., Roopsind, A., Rudas, A., Salomão, R. P., Schwarz, M., Silva, N., Silva-Espejo, J. E., Silveira, M., Stropp, J., Talbot, J., ter Steege, H., Teran-Aguilar, J., Terborgh, J., Thomas-Caesar, R., Toledo, M., Torello-Raventos, M., Umetsu, R. K., van der Heijden, G. M. F., van der Hout, P., Guimarães Vieira, I. C., Vieira, S. A., Vilanova, E., Vos, V. A., and Zagt, R. J.

Published
2015
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50. Insights into ROS‐dependent signalling underlying transcriptomic plant responses to the herbicide 2,4‐D.

Author

Romero‐Puertas, María C., Peláez‐Vico, Maria Ángeles, Pazmiño, Diana M., Rodríguez‐Serrano, María, Terrón‐Camero, Laura, Bautista, Rocío, Gómez‐Cadenas, Aurelio, Claros, M. Gonzalo, León, José, and Sandalio, Luisa M.

Subjects
PROTEOLYSIS, AUXIN, UBIQUITINATION, INDOLEACETIC acid, HERBICIDES, REACTIVE oxygen species, TRANSCRIPTOMES, WEED control
Abstract

The synthetic auxin 2,4‐dichlorophenoxyacetic acid (2,4‐D) functions as an agronomic weed control herbicide. High concentrations of 2,4‐D induce plant growth defects, particularly leaf epinasty and stem curvature. Although the 2,4‐D triggered reactive oxygen species (ROS) production, little is known about its signalling. In this study, by using a null mutant in peroxisomal acyl CoA oxidase 1 (acx1‐2), we identified acyl‐coenzyme A oxidase 1 (ACX1) as one of the main sources of ROS production and, in part, also causing the epinastic phenotype following 2,4‐D application. Transcriptomic analyses of wild type (WT) plants after treatment with 2,4‐D revealed a ROS‐related peroxisomal footprint in early plant responses, while other organelles, such as mitochondria and chloroplasts, are involved in later responses. Interestingly, a group of 2,4‐D‐responsive ACX1‐dependent transcripts previously associated with epinasty is related to auxin biosynthesis, metabolism, and signalling. We found that the auxin receptor auxin signalling F‐box 3 (AFB3), a component of Skp, Cullin, F‐box containing complex (SCF) (ASK‐cullin‐F‐box) E3 ubiquitin ligase complexes, which mediates auxin/indole acetic acid (AUX/IAA) degradation by the 26S proteasome, acts downstream of ACX1 and is involved in the epinastic phenotype induced by 2,4‐D. We also found that protein degradation associated with ubiquitin E3‐RING and E3‐SCF‐FBOX in ACX1‐dependent signalling in plant responses to 2,4‐D is significantly regulated over longer treatment periods. Summary Statement: 2,4‐D induced a reactive oxygen species (ROS)‐related peroxisomal footprint in early plant responses. ACX1 is one of the main sources of ROS production and associated epinasty phenotype following 2,4‐D application in plants. ACX1‐dependent signalling in plant responses to 2,4‐D point to protein degradation associated with auxin signalling at the early response and with ubiquitin E3‐RING and E3‐SCF‐FBOX/proteasome as key processes in the development of epinasty over longer treatment periods. [ABSTRACT FROM AUTHOR]

Published
2022
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