141 results on '"M. Gonzalo Claros"'
Search Results
2. Study of microRNA expression in Salmonella Typhimurium-infected porcine ileum reveals miR-194a-5p as an important regulator of the TLR4-mediated inflammatory response
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Juber Herrera-Uribe, Sara Zaldívar-López, Carmen Aguilar, Carmen Entrenas-García, Rocío Bautista, M. Gonzalo Claros, and Juan J. Garrido
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Salmonellosis ,microRNAs ,inflammation ,Toll-like receptor ,ileum ,immunity ,Veterinary medicine ,SF600-1100 - Abstract
Abstract Infection with Salmonella Typhimurium (S. Typhimurium) is a common cause of food-borne zoonosis leading to acute gastroenteritis in humans and pigs, causing economic losses to producers and farmers, and generating a food security risk. In a previous study, we demonstrated that S. Typhimurium infection produces a severe transcriptional activation of inflammatory processes in ileum. However, little is known regarding how microRNAs regulate this response during infection. Here, small RNA sequencing was used to identify 28 miRNAs differentially expressed (DE) in ileum of S. Typhimurium-infected pigs, which potentially regulate 14 target genes involved in immune system processes such as regulation of cytokine production, monocyte chemotaxis, or cellular response to interferon gamma. Using in vitro functional and gain/loss of function (mimics/CRISPR-Cas system) approaches, we show that porcine miR-194a-5p (homologous to human miR-194-5p) regulates TLR4 gene expression, an important molecule involved in pathogen virulence, recognition and activation of innate immunity in Salmonella infection.
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- 2022
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3. An innovative framework to determine the implementation level of personalized medicine: A systematic review
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Lorena Aguilera-Cobos, Patricia García-Sanz, María Piedad Rosario-Lozano, M. Gonzalo Claros, and Juan Antonio Blasco-Amaro
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personalized medicine (PM) ,health policy ,health system ,implementation ,framework ,Public aspects of medicine ,RA1-1270 - Abstract
BackgroundPersonalized medicine (PM) is now the new frontier in patient care. The application of this new paradigm extends to various pathologies and different patient care phases, such as diagnosis and treatment. Translating biotechnological advances to clinical routine means adapting health services at all levels is necessary.PurposeThis article aims to identify the elements for devising a framework that will allow the level of PM implementation in the country under study to be quantitatively and qualitatively assessed and that can be used as a guideline for future implementation plans.MethodsA systematic review was conducted per the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. The research question was: What are the domains for determining the level of implementation of PM at the national level? The domains for assessing the degree of PM implementation, which would form the framework, were established.Results19 full-text studies that met the inclusion criteria were peer-selected in the systematic review. From all the studies that were included, 37 elements—encompassed in 11 domains—were extracted for determining the degree of PM implementation. These domains and their constituent elements comprise the qualitative and quantitative assessment framework presented herein. Each of the elements can be assessed individually. On the other hand, the domains were standardized to all have the same weight in an overall assessment.ConclusionsA framework has been developed that takes a multi-factorial approach to determine the degree of implementation of PM at the national level. This framework could also be used to rank countries and their implementation strategies according to the score they receive in the application of the latter. It could also be used as a guide for developing future national PM implementation strategies.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42022338611, Identifier: CRD42022338611.
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- 2023
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4. Combining Genetic and Transcriptomic Approaches to Identify Transporter-Coding Genes as Likely Responsible for a Repeatable Salt Tolerance QTL in Citrus
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Maria J. Asins, Amanda Bullones, Veronica Raga, Maria R. Romero-Aranda, Jesus Espinosa, Juan C. Triviño, Guillermo P. Bernet, Jose A. Traverso, Emilio A. Carbonell, M. Gonzalo Claros, and Andres Belver
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QTL analysis ,Citrus reshni ,Poncirus trifoliata ,rootstock breeding ,yield ,Cl− homeostasis ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - 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.
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- 2023
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5. Chromosome anchoring in Senegalese sole (Solea senegalensis) reveals sex-associated markers and genome rearrangements in flatfish
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Israel Guerrero-Cózar, Jessica Gomez-Garrido, Concha Berbel, Juan F. Martinez-Blanch, Tyler Alioto, M. Gonzalo Claros, Pierre-Alexandre Gagnaire, and Manuel Manchado
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Medicine ,Science - Abstract
Abstract The integration of physical and high-density genetic maps is a very useful approach to achieve chromosome-level genome assemblies. Here, the genome of a male Senegalese sole (Solea senegalensis) was de novo assembled and the contigs were anchored to a high-quality genetic map for chromosome-level scaffolding. Hybrid assembled genome was 609.3 Mb long and contained 3403 contigs with a N50 of 513 kb. The linkage map was constructed using 16,287 informative SNPs derived from ddRAD sequencing in 327 sole individuals from five families. Markers were assigned to 21 linkage groups with an average number of 21.9 markers per megabase. The anchoring of the physical to the genetic map positioned 1563 contigs into 21 pseudo-chromosomes covering 548.6 Mb. Comparison of genetic and physical distances indicated that the average genome-wide recombination rate was 0.23 cM/Mb and the female-to-male ratio 1.49 (female map length: 2,698.4 cM, male: 2,036.6 cM). Genomic recombination landscapes were different between sexes with crossovers mainly concentrated toward the telomeres in males while they were more uniformly distributed in females. A GWAS analysis using seven families identified 30 significant sex-associated SNP markers located in linkage group 18. The follicle-stimulating hormone receptor appeared as the most promising locus associated with sex within a region with very low recombination rates. An incomplete penetrance of sex markers with males as the heterogametic sex was determined. An interspecific comparison with other Pleuronectiformes genomes identified a high sequence similarity between homologous chromosomes, and several chromosomal rearrangements including a lineage-specific Robertsonian fusion in S. senegalensis.
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- 2021
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6. Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole
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Israel Guerrero-Cózar, Cathaysa Perez-Garcia, Hicham Benzekri, J. J. Sánchez, Pedro Seoane, Fernando Cruz, Marta Gut, Maria Jesus Zamorano, M. Gonzalo Claros, and Manuel Manchado
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Medicine ,Science - Abstract
Abstract The Senegalese sole (Solea senegalensis) is an economically important flatfish species. In this study, a genome draft was analyzed to identify microsatellite (SSR) markers for whole-genome genotyping. A subset of 224 contigs containing SSRs were preselected and validated by using a de novo female hybrid assembly. Overall, the SSR density in the genome was 886.7 markers per megabase of genomic sequences and the dinucleotide motif was the most abundant (52.4%). In silico comparison identified a set of 108 SSRs (with di-, tetra- or pentanucleotide motifs) widely distributed in the genome and suitable for primer design. A total of 106 markers were structured in thirteen multiplex PCR assays (with up to 10-plex) and the amplification conditions were optimized with a high-quality score. Main genetic diversity statistics and genotyping reliability were assessed. A subset of 40 high polymorphic markers were selected to optimize four supermultiplex PCRs (with up to 11-plex) for pedigree analysis. Theoretical exclusion probabilities and real parentage allocation tests using parent–offspring information confirmed their robustness and effectiveness for parental assignment. These new SSR markers were combined with previously published SSRs (in total 229 makers) to construct a new and improved integrated genetic map containing 21 linkage groups that matched with the expected number of chromosomes. Synteny analysis with respect to C. semilaevis provided new clues on chromosome evolution in flatfish and the formation of metacentric and submetacentric chromosomes in Senegalese sole.
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- 2020
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7. The haustorial transcriptome of the cucurbit pathogen Podosphaera xanthii reveals new insights into the biotrophy and pathogenesis of powdery mildew fungi
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Álvaro Polonio, Pedro Seoane, M. Gonzalo Claros, and Alejandro Pérez-García
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Powdery mildew fungi ,Podosphaera xanthii ,Haustorium ,Massive-scale RNA sequencing ,Secretome ,Protein structure modeling ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Podosphaera xanthii is the main causal agent of powdery mildew disease in cucurbits and is responsible for important yield losses in these crops worldwide. Powdery mildew fungi are obligate biotrophs. In these parasites, biotrophy is determined by the presence of haustoria, which are specialized structures of parasitism developed by these fungi for the acquisition of nutrients and the delivery of effectors. Detailed molecular studies of powdery mildew haustoria are scarce due mainly to difficulties in their isolation. Therefore, their analysis is considered an important challenge for powdery mildew research. The aim of this work was to gain insights into powdery mildew biology by analysing the haustorial transcriptome of P. xanthii. Results Prior to RNA isolation and massive-scale mRNA sequencing, a flow cytometric approach was developed to isolate P. xanthii haustoria free of visible contaminants. Next, several commercial kits were used to isolate total RNA and to construct the cDNA and Illumina libraries that were finally sequenced by the Illumina NextSeq system. Using this approach, the maximum amount of information from low-quality RNA that could be obtained was used to accomplish the de novo assembly of the P. xanthii haustorial transcriptome. The subsequent analysis of this transcriptome and comparison with the epiphytic transcriptome allowed us to identify the importance of several biological processes for haustorial cells such as protection against reactive oxygen species, the acquisition of different nutrients and genetic regulation mediated by non-coding RNAs. In addition, we could also identify several secreted proteins expressed exclusively in haustoria such as cell adhesion proteins that have not been related to powdery mildew biology to date. Conclusions This work provides a novel approach to study the molecular aspects of powdery mildew haustoria. In addition, the results of this study have also allowed us to identify certain previously unknown processes and proteins involved in the biology of powdery mildews that could be essential for their biotrophy and pathogenesis.
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- 2019
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8. TransFlow: a modular framework for assembling and assessing accurate de novo transcriptomes in non-model organisms
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Pedro Seoane, Marina Espigares, Rosario Carmona, Álvaro Polonio, Julia Quintana, Enrico Cretazzo, Josefina Bota, Alejandro Pérez-García, Juan de Dios Alché, Luis Gómez, and M. Gonzalo Claros
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Transcriptome ,Assembling ,Workflow ,pipeline ,PCA ,Non-model organism ,Computer applications to medicine. Medical informatics ,R858-859.7 ,Biology (General) ,QH301-705.5 - Abstract
Abstract Background The advances in high-throughput sequencing technologies are allowing more and more de novo assembling of transcriptomes from many new organisms. Some degree of automation and evaluation is required to warrant reproducibility, repetitivity and the selection of the best possible transcriptome. Workflows and pipelines are becoming an absolute requirement for such a purpose, but the issue of assembling evaluation for de novo transcriptomes in organisms lacking a sequenced genome remains unsolved. An automated, reproducible and flexible framework called TransFlow to accomplish this task is described. Results TransFlow with its five independent modules was designed to build different workflows depending on the nature of the original reads. This architecture enables different combinations of Illumina and Roche/454 sequencing data, and can be extended to other sequencing platforms. Its capabilities are illustrated with the selection of reliable plant reference transcriptomes and the assembling six transcriptomes (three case studies for grapevine leaves, olive tree pollen, and chestnut stem, and other three for haustorium, epiphytic structures and their combination for the phytopathogenic fungus Podosphaera xanthii). Arabidopsis and poplar transcriptomes revealed to be the best references. A common result regarding de novo assemblies is that Illumina paired-end reads of 100 nt in length assembled with OASES can provide reliable transcriptomes, while the contribution of longer reads is noticeable only when they complement a set of short, single-reads. Conclusions TransFlow can handle up to 181 different assembling strategies. Evaluation based on principal component analyses allows its self-adaptation to different sets of reads to provide a suitable transcriptome for each combination of reads and assemblers. As a result, each case study has its own behaviour, prioritises evaluation parameters, and gives an objective and automated way for detecting the best transcriptome within a pool of them. Sequencing data type and quantity (preferably several hundred millions of 2×100 nt or longer), assemblers (OASES for Illumina, MIRA4 and EULER-SR reconciled with CAP3 for Roche/454) and strategy (preferably scaffolding with OASES, and probably merging with Roche/454 when available) arise as the most impacting factors.
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- 2018
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9. Decoding Neuromuscular Disorders Using Phenotypic Clusters Obtained From Co-Occurrence Networks
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Elena Díaz-Santiago, M. Gonzalo Claros, Raquel Yahyaoui, Yolanda de Diego-Otero, Rocío Calvo, Janet Hoenicka, Francesc Palau, Juan A. G. Ranea, and James R. Perkins
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neuromuscular disorders ,rare disease ,phenotype ,network analysis ,cluster ,co-occurrence analysis ,Biology (General) ,QH301-705.5 - Abstract
Neuromuscular disorders (NMDs) represent an important subset of rare diseases associated with elevated morbidity and mortality whose diagnosis can take years. Here we present a novel approach using systems biology to produce functionally-coherent phenotype clusters that provide insight into the cellular functions and phenotypic patterns underlying NMDs, using the Human Phenotype Ontology as a common framework. Gene and phenotype information was obtained for 424 NMDs in OMIM and 126 NMDs in Orphanet, and 335 and 216 phenotypes were identified as typical for NMDs, respectively. ‘Elevated serum creatine kinase’ was the most specific to NMDs, in agreement with the clinical test of elevated serum creatinine kinase that is conducted on NMD patients. The approach to obtain co-occurring NMD phenotypes was validated based on co-mention in PubMed abstracts. A total of 231 (OMIM) and 150 (Orphanet) clusters of highly connected co-occurrent NMD phenotypes were obtained. In parallel, a tripartite network based on phenotypes, diseases and genes was used to associate NMD phenotypes with functions, an approach also validated by literature co-mention, with KEGG pathways showing proportionally higher overlap than Gene Ontology and Reactome. Phenotype-function pairs were crossed with the co-occurrent NMD phenotype clusters to obtain 40 (OMIM) and 72 (Orphanet) functionally coherent phenotype clusters. As expected, many of these overlapped with known diseases and confirmed existing knowledge. Other clusters revealed interesting new findings, indicating informative phenotypes for differential diagnosis, providing deeper knowledge of NMDs, and pointing towards specific cell dysfunction caused by pleiotropic genes. This work is an example of reproducible research that i) can help better understand NMDs and support their diagnosis by providing a new tool that exploits existing information to obtain novel clusters of functionally-related phenotypes, and ii) takes us another step towards personalised medicine for NMDs.
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- 2021
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10. De novo assembly and functional annotation of Citrus aurantifolia transcriptome from Candidatus Liberibacter asiaticus infected and non-infected trees
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Ángela Paulina Arce-Leal, Rocío Bautista, Edgar A. Rodríguez-Negrete, Miguel Ángel Manzanilla-Ramírez, José Joaquín Velázquez-Monreal, Jesús Méndez-Lozano, Eduardo R. Bejarano, Araceli G. Castillo, M. Gonzalo Claros, and Norma Elena Leyva-López
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Computer applications to medicine. Medical informatics ,R858-859.7 ,Science (General) ,Q1-390 - Abstract
Mexican lime (Citrus aurantifolia) belongs to the Rutaceae family and nowadays is one of the major commercial citrus crops in different countries. In Mexico, Mexican lime production is impaired by Huanglongbing (HLB) disease associated to Candidatus Liberibacter asiaticus (CLas) bacteria. To date, transcriptomic studies of CLas-Citrus interaction, have been performed mainly in sweet citrus models at symptomatic (early) stage where pleiotropic responses could mask important, pathogen-driven host modulation as well as, host antibacterial responses. Additionally, well-assembled reference transcriptomes for acid limes including C. aurantifolia are not available. The development of improved transcriptomic resources for CLas-citrus pathosystem, including both asymptomatic (early) and symptomatic (late) stages, could accelerate the understanding of the disease. Here, we provide the first transcriptomic analysis from healthy and HLB-infected C. aurantifolia leaves at both asymptomatic and symptomatic stages, using a RNA-seq approach in the Illumina NexSeq500 platform. The construction of the assembled transcriptome was conducted using the predesigned workflow Transflow and a total of 41,522 tentative transcripts (TTs) obtained. These C. aurantifolia TTs were functionally annotated using TAIR10 and UniProtKB databases. All raw reads were deposited in the NCBI SRA with accession numbers SRR10353556, SRR10353558, SRR10353560 and SRR10353562. Overall, this dataset adds new transcriptomic valuable tools for future breeding programs, will allow the design of novel diagnostic molecular markers, and will be an essential tool for studying the HLB disease. Keywords: Citrus aurantifolia, Huanglongbing, Candidatus Liberibacter asiaticus, Infection early and late stages, RNA-Seq, Transcriptome assembly
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- 2020
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11. Biomarker potential of repetitive-element transcriptome in lung cancer
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Macarena Arroyo, Rocío Bautista, Rafael Larrosa, Manuel Ángel Cobo, and M. Gonzalo Claros
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Repetitive element ,Lung cancer ,Differential expression ,Biomarker ,Transcriptome ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Since repetitive elements (REs) account for nearly 53% of the human genome, profiling its transcription after an oncogenic change might help in the search for new biomarkers. Lung cancer was selected as target since it is the most frequent cause of cancer death. A bioinformatic workflow based on well-established bioinformatic tools (such as RepEnrich, RepBase, SAMTools, edgeR and DESeq2) has been developed to identify differentially expressed RNAs from REs. It was trained and tested with public RNA-seq data from matched sequencing of tumour and healthy lung tissues from the same patient to reveal differential expression within the RE transcriptome. Healthy lung tissues express a specific set of REs whose expression, after an oncogenic process, is strictly and specifically changed. Discrete sets of differentially expressed REs were found for lung adenocarcinoma, for small-cell lung cancer, and for both cancers. Differential expression affects more HERV-than LINE-derived REs and seems biased towards down-regulation in cancer cells. REs behaving consistently in all patients were tested in a different patient cohort to validate the proposed biomarkers. Down-regulation of AluYg6 and LTR18B was confirmed as potential lung cancer biomarkers, while up-regulation of HERVK11D-Int is specific for lung adenocarcinoma and up-regulation of UCON88 is specific for small cell lung cancer. Hence, the study of RE transcriptome might be considered another research target in cancer, making REs a promising source of lung cancer biomarkers.
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- 2019
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12. Regulatory role of microRNA in mesenteric lymph nodes after Salmonella Typhimurium infection
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Juber Herrera-Uribe, Sara Zaldívar-López, Carmen Aguilar, Cristina Luque, Rocío Bautista, Ana Carvajal, M. Gonzalo Claros, and Juan J. Garrido
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Veterinary medicine ,SF600-1100 - Abstract
Abstract Salmonellosis is a gastrointestinal disease caused by non-typhoidal Salmonella serovars such as Salmonella Typhimurium. This pathology is a zoonosis, and food animals with subclinical infection constitute a vast reservoir for disease. After intestinal colonization, Salmonella Typhimurium reaches mesenteric lymph nodes (MLN), where infection is controlled avoiding systemic spread. Although the molecular basis of this infection has been extensively studied, little is known about how microRNA (miRNA) regulate the expression of proteins involved in the Salmonella-host interaction. Using small RNA-seq, we examined expression profiles of MLN 2 days after infection with Salmonella Typhimurium, and we found 110 dysregulated miRNA. Among them, we found upregulated miR-21, miR-155, miR-150, and miR-221, as well as downregulated miR-143 and miR-125, all of them previously linked to other bacterial infections. Integration with proteomic data revealed 30 miRNA potentially regulating the expression of 15 proteins involved in biological functions such as cell death and survival, inflammatory response and antigenic presentation. The inflammatory response was found increased via upregulation of miRNA such as miR-21 and miR-155. Downregulation of miR-125a/b, miR-148 and miR-1 were identified as potential regulators of MHC-class I components PSMB8, HSP90B1 and PDIA3, respectively. Furthermore, we confirmed that miR-125a is a direct target of immunoproteasome component PSMB8. Since we also found miR-130 downregulation, which is associated with upregulation of HSPA8, we suggest induction of both MHC-I and MHC-II antigen presentation pathways. In conclusion, our study identifies miRNA that could regulate critical networks for antigenic presentation, inflammatory response and cytoskeletal rearrangements.
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- 2018
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13. S-nitroso- and nitro- proteomes in the olive (Olea europaea L.) pollen. Predictive versus experimental data by nano-LC-MS
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Rosario Carmona, MarÃa José Jimenez-Quesada, Elena Lima-Cabello, José Ãngel Traverso, Antonio Jesús Castro, M. Gonzalo Claros, and Juan de Dios Alché
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Computer applications to medicine. Medical informatics ,R858-859.7 ,Science (General) ,Q1-390 - Abstract
The data presented here are related to the research article entitled âGeneration of nitric oxide by olive (Olea europaea L.) pollen during in vitro germination and assessment of the S-nitroso- and nitro-proteomes by computational predictive methodsâ doi:10.1016/j.niox.2017.06.005 (Jimenez-Quesada et al., 2017) [1]. Predicted cysteine S-nitrosylation and Tyr-nitration sites in proteins derived from a de novo assembled and annotated pollen transcriptome from olive tree (Olea europaea L.) were obtained after using well-established predictive tools in silico. Predictions were performed using both default and highly restrictive thresholds. Numerous gene products identified with these characteristics are listed here. An experimental validation of the data, consisting in nano-LC-MS (Liquid Chromatography-Mass Spectrometry) determination of olive pollen proteins after immunoprecipitation with antibodies to anti-S-nitrosoCys and anti-3-NT (NitroTyrosine) allowed identification of numerous proteins subjected to these two post-translational modifications, which are listed here together with information regarding their cross-presence among the predictions. Keywords: Immunoprecipitation, Proteome, S-nitrosylation, Transcriptome, Tyrosine nitration
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- 2017
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14. Automated identification of reference genes based on RNA-seq data
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Rosario Carmona, Macarena Arroyo, María José Jiménez-Quesada, Pedro Seoane, Adoración Zafra, Rafael Larrosa, Juan de Dios Alché, and M. Gonzalo Claros
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Reference genes ,Normalization ,Real-time PCR ,Quantitative PCR ,Olive (Olea europaea L.) ,Cancer ,Medical technology ,R855-855.5 - Abstract
Abstract Background Gene expression analyses demand appropriate reference genes (RGs) for normalization, in order to obtain reliable assessments. Ideally, RG expression levels should remain constant in all cells, tissues or experimental conditions under study. Housekeeping genes traditionally fulfilled this requirement, but they have been reported to be less invariant than expected; therefore, RGs should be tested and validated for every particular situation. Microarray data have been used to propose new RGs, but only a limited set of model species and conditions are available; on the contrary, RNA-seq experiments are more and more frequent and constitute a new source of candidate RGs. Results An automated workflow based on mapped NGS reads has been constructed to obtain highly and invariantly expressed RGs based on a normalized expression in reads per mapped million and the coefficient of variation. This workflow has been tested with Roche/454 reads from reproductive tissues of olive tree (Olea europaea L.), as well as with Illumina paired-end reads from two different accessions of Arabidopsis thaliana and three different human cancers (prostate, small-cell cancer lung and lung adenocarcinoma). Candidate RGs have been proposed for each species and many of them have been previously reported as RGs in literature. Experimental validation of significant RGs in olive tree is provided to support the algorithm. Conclusion Regardless sequencing technology, number of replicates, and library sizes, when RNA-seq experiments are designed and performed, the same datasets can be analyzed with our workflow to extract suitable RGs for subsequent PCR validation. Moreover, different subset of experimental conditions can provide different suitable RGs.
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- 2017
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15. TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens strain Pdp11
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Pedro Seoane, Silvana T. Tapia-Paniagua, Rocío Bautista, Elena Alcaide, Consuelo Esteve, Eduardo Martínez-Manzanares, M. Carmen Balebona, M. Gonzalo Claros, and Miguel A. Moriñigo
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Probiotics ,Cultured fish ,Synteny ,Workflow ,Bioinformatics ,Shewanella putrefaciens ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Probiotic microorganisms are of great interest in clinical, livestock and aquaculture. Knowledge of the genomic basis of probiotic characteristics can be a useful tool to understand why some strains can be pathogenic while others are probiotic in the same species. An automatized workflow called TarSynFlow (Targeted Synteny Workflow) has been then developed to compare finished or draft bacterial genomes based on a set of proteins. When used to analyze the finished genome of the probiotic strain Pdp11 of Shewanella putrefaciens and genome drafts from seven known non-probiotic strains of the same species obtained in this work, 15 genes were found exclusive of Pdp11. Their presence was confirmed by PCR using Pdp11-specific primers. Functional inspection of the 15 genes allowed us to hypothesize that Pdp11 underwent genome rearrangements spurred by plasmids and mobile elements. As a result, Pdp11 presents specific proteins for gut colonization, bile salt resistance and gut pathogen adhesion inhibition, which can explain some probiotic features of Pdp11.
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- 2019
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16. Gene Expression Profile of Mexican Lime (Citrus aurantifolia) Trees in Response to Huanglongbing Disease caused by Candidatus Liberibacter asiaticus
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Ángela Paulina Arce-Leal, Rocío Bautista, Edgar Antonio Rodríguez-Negrete, Miguel Ángel Manzanilla-Ramírez, José Joaquín Velázquez-Monreal, María Elena Santos-Cervantes, Jesús Méndez-Lozano, Carmen R. Beuzón, Eduardo R. Bejarano, Araceli G. Castillo, M. Gonzalo Claros, and Norma Elena Leyva-López
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HLB ,Candidatus Liberibacter asiaticus (CLas) ,transcriptomics ,tolerant citrus species ,Mexican lime ,Biology (General) ,QH301-705.5 - Abstract
Nowadays, Huanglongbing (HLB) disease, associated with Candidatus Liberibacter asiaticus (CLas), seriously affects citriculture worldwide, and no cure is currently available. Transcriptomic analysis of host–pathogen interaction is the first step to understand the molecular landscape of a disease. Previous works have reported the transcriptome profiling in response to HLB in different susceptible citrus species; however, similar studies in tolerant citrus species, including Mexican lime, are limited. In this work, we have obtained an RNA-seq-based differential expression profile of Mexican lime plants challenged against CLas infection, at both asymptomatic and symptomatic stages. Typical HLB-responsive differentially expressed genes (DEGs) are involved in photosynthesis, secondary metabolism, and phytohormone homeostasis. Enrichment of DEGs associated with biotic response showed that genes related to cell wall, secondary metabolism, transcription factors, signaling, and redox reactions could play a role in the tolerance of Mexican lime against CLas infection. Interestingly, despite some concordance observed between transcriptional responses of different tolerant citrus species, a subset of DEGs appeared to be species-specific. Our data highlights the importance of studying the host response during HLB disease using as model tolerant citrus species, in order to design new and opportune diagnostic and management methods.
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- 2020
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17. Characterization of Iodine-Related Molecular Processes in the Marine Microalga Tisochrysis lutea (Haptophyta)
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Laura Hernández Javier, Hicham Benzekri, Marta Gut, M. Gonzalo Claros, Stefanie van Bergeijk, José Pedro Cañavate, and Manuel Manchado
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hydrogen peroxide ,iodide ,Tisochrysis lutea ,peroxidase ,deiodinase ,gene expression ,Science ,General. Including nature conservation, geographical distribution ,QH1-199.5 - Abstract
Iodine metabolism is essential for the antioxidant defense of marine algae and in the biogeochemical cycle of iodine. Moreover, some microalgae can synthetize thyroid hormone-like compounds that are essential to sustain food webs. However, knowledge regarding iodine-related molecular processes in microalgae is still scarce. In this study, a de novo transcriptome of Tisochrysis lutea cultured under high iodide concentrations (5 mM) was assembled using both long and short reads. A database termed IsochrysisDB was established to host all genomic information. Gene expression analyses during microalgal growth showed that most of the antioxidant- (aryl, ccp, perox, sod1, sod2, sod3, apx3, ahp1) and iodide-specific deiodinase (dio) genes increased their mRNA abundance progressively until the stationary phase to cope with oxidative stress. Moreover, the increase of dio mRNA abundance in aging cultures indicated that this enzyme was also involved in senescence. Cell treatments with iodide modified the expression of perox whereas treatments with iodate changed the transcript levels of gpx1 and ccp. To test the dependence of perox on iodide, microalgae cells were treated with hydrogen peroxide (H2O2) either in presence or absence of iodide observing that several genes related to reactive oxygen species (ROS) deactivation (perox, gpx1, apx2, apx3, ahp1, ahp2, sod1, sod3, and aryl) were transcriptionally activated although with some temporal differences. However, only the expression of perox was dependent on iodide levels indicating this enzyme, acquired by horizontal gene transfer (HGT), could act as a haloperoxidase. All these data indicate that T. lutea activates coordinately the expression of antioxidant genes to cope with oxidative stress. The identification of a phase-regulated deiodinase and a novel haloperoxidase provide new clues about the origin and evolution of thyroid signaling and the antioxidant role of iodine in the marine environment.
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- 2018
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18. Identification and Functional Annotation of Genes Differentially Expressed in the Reproductive Tissues of the Olive Tree (Olea europaea L.) through the Generation of Subtractive Libraries
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Adoración Zafra, Rosario Carmona, José A. Traverso, John T. Hancock, Maria H. S. Goldman, M. Gonzalo Claros, Simon J. Hiscock, and Juan D. Alche
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gynoecium ,leaf ,olive ,pollen ,self-incompatibility ,SSH ,Plant culture ,SB1-1110 - Abstract
The olive tree is a crop of high socio-economical importance in the Mediterranean area. Sexual reproduction in this plant is an essential process, which determines the yield. Successful fertilization is mainly favored and sometimes needed of the presence of pollen grains from a different cultivar as the olive seizes a self-incompatibility system allegedly determined of the sporophytic type. The purpose of the present study was to identify key gene products involved in the function of olive pollen and pistil, in order to help elucidate the events and signaling processes, which happen during the courtship, pollen grain germination, and fertilization in olive. The use of subtractive SSH libraries constructed using, on the one hand one specific stage of the pistil development with germinating pollen grains, and on the other hand mature pollen grains may help to reveal the specific transcripts involved in the cited events. Such libraries have also been created by subtracting vegetative mRNAs (from leaves), in order to identify reproductive sequences only. A variety of transcripts have been identified in the mature pollen grains and in the pistil at the receptive stage. Among them, those related to defense, transport and oxidative metabolism are highlighted mainly in the pistil libraries where transcripts related to stress, and response to biotic and abiotic stimulus have a prominent position. Extensive lists containing information as regard to the specific transcripts determined for each stage and tissue are provided, as well as functional classifications of these gene products. Such lists were faced up to two recent datasets obtained in olive after transcriptomic and genomic approaches. The sequences and the differential expression level of the SSH-transcripts identified here, highly matched the transcriptomic information. Moreover, the unique presence of a representative number of these transcripts has been validated by means of qPCR approaches. The construction of SSH libraries using pistil and pollen, considering the high interaction between male-female counterparts, allowed the identification of transcripts with important roles in stigma physiology. The functions of many of the transcripts obtained are intimately related, and most of them are of pivotal importance in defense, pollen-stigma interaction and signaling.
- Published
- 2017
- Full Text
- View/download PDF
19. Micro-Variations from RNA-seq Experiments for Non-model Organisms.
- Author
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Elena Espinosa, Macarena Arroyo, Rafael Larrosa, Manuel Manchado, M. Gonzalo Claros, and Rocío Bautista
- Published
- 2020
- Full Text
- View/download PDF
20. Structural and Functional Features of Glutathione Reductase Transcripts from Olive (Olea europaea L.) Seeds.
- Author
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Elena Lima-Cabello, Isabel Martínez-Beas, Estefanía García-Quirós, Rosario Carmona, M. Gonzalo Claros, Jose Carlos Jimenez-Lopez, and Juan de Dios Alché
- Published
- 2019
- Full Text
- View/download PDF
21. Expression Change Correlations Between Transposons and Their Adjacent Genes in Lung Cancers Reveal a Genomic Location Dependence and Highlights Cancer-Significant Genes.
- Author
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Macarena Arroyo, Rafael Larrosa, M. Gonzalo Claros, and Rocío Bautista
- Published
- 2019
- Full Text
- View/download PDF
22. De novo Transcriptome Assembly of Solea senegalensis v5.0 Using TransFlow.
- Author
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José Córdoba-Caballero, Pedro Seoane-Zonjic, Manuel Manchado, and M. Gonzalo Claros
- Published
- 2019
- Full Text
- View/download PDF
23. NearTrans Can Identify Correlated Expression Changes Between Retrotransposons and Surrounding Genes in Human Cancer.
- Author
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Rafael Larrosa, Macarena Arroyo, Rocío Bautista, Carmen María López-Rodríguez, and M. Gonzalo Claros
- Published
- 2018
- Full Text
- View/download PDF
24. Obtaining the Most Accurate de novo Transcriptomes for Non-model Organisms: The Case of Castanea sativa.
- Author
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Marina Espigares, Pedro Seoane, Rocío Bautista, Julia Quintana, Luis Gómez, and M. Gonzalo Claros
- Published
- 2017
- Full Text
- View/download PDF
25. Identification and in silico Analysis of Glutathione Reductase Transcripts Expressed in Olive (Olea europaea L.) Pollen and Pistil.
- Author
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Estefanía García-Quirós, Rosario Carmona, Adoración Zafra, M. Gonzalo Claros, and Juan de Dios Alché
- Published
- 2017
- Full Text
- View/download PDF
26. First draft genome assembly of the Argane tree ( Argania spinosa) [version 2; peer review: 2 approved]
- Author
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Slimane Khayi, Nour Elhouda Azza, Fatima Gaboun, Stacy Pirro, Oussama Badad, M. Gonzalo Claros, David A. Lightfoot, Turgay Unver, Bouchra Chaouni, Redouane Merrouch, Bouchra Rahim, Soumaya Essayeh, Matika Ganoudi, Rabha Abdelwahd, Ghizlane Diria, Meriem Alaoui Mdarhi, Mustapha Labhilili, Driss Iraqi, Jamila Mouhaddab, Hayat Sedrati, Majid Memari, Noureddine Hamamouch, Juan de Dios Alché, Noureddine Boukhatem, Rachid Mrabet, Rachid Dahan, Adelkhaleq Legssyer, Mohamed Khalfaoui, Mohamed Badraoui, Yves Van de Peer, Tatiana Tatusova, Abdelhamid El Mousadik, Rachid Mentag, and Hassan Ghazal
- Subjects
Research Article ,Articles ,Argane ,Argania spinosa ,Endemic ,Genome ,Assembly ,Morocco ,International Argane Genome Consortium - Abstract
Background: The Argane tree ( Argania spinosa L. Skeels) is an endemic tree of mid-western Morocco that plays an important socioeconomic and ecologic role for a dense human population in an arid zone. Several studies confirmed the importance of this species as a food and feed source and as a resource for both pharmaceutical and cosmetic compounds. Unfortunately, the argane tree ecosystem is facing significant threats from environmental changes (global warming, over-population) and over-exploitation. Limited research has been conducted, however, on argane tree genetics and genomics, which hinders its conservation and genetic improvement. Methods: Here, we present a draft genome assembly of A. spinosa. A reliable reference genome of A. spinosa was created using a hybrid de novo assembly approach combining short and long sequencing reads. Results: In total, 144 Gb Illumina HiSeq reads and 7.6 Gb PacBio reads were produced and assembled. The final draft genome comprises 75 327 scaffolds totaling 671 Mb with an N50 of 49 916 kb. The draft assembly is close to the genome size estimated by k-mers distribution and covers 89% of complete and 4.3 % of partial Arabidopsis orthologous groups in BUSCO. Conclusion: The A. spinosa genome will be useful for assessing biodiversity leading to efficient conservation of this endangered endemic tree. Furthermore, the genome may enable genome-assisted cultivar breeding, and provide a better understanding of important metabolic pathways and their underlying genes for both cosmetic and pharmacological.
- Published
- 2020
- Full Text
- View/download PDF
27. Automatic Workflow for the Identification of Constitutively-Expressed Genes Based on Mapped NGS Reads.
- Author
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Rosario Carmona, Pedro Seoane, Adoración Zafra, María José Jiménez-Quesada, Juan de Dios Alché, and M. Gonzalo Claros
- Published
- 2016
- Full Text
- View/download PDF
28. Transcriptome-Based Identification of a Seed Olive Legumin (11S Globulin). Characterization of Subunits, 3D Modelling and Molecular Assessment of Allergenicity.
- Author
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Adoración Zafra, José Carlos Jimenez-Lopez, Rosario Carmona, M. Gonzalo Claros, and Juan de Dios Alché
- Published
- 2016
- Full Text
- View/download PDF
29. Identification and in silico Analysis of NADPH Oxidase Homologues Involved in Allergy from an Olive Pollen Transcriptome.
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María José Jiménez-Quesada, Jose ángel Traverso, Adoración Zafra, Jose C. Jimenez-Lopez, Rosario Carmona, M. Gonzalo Claros, and Juan D. Alché
- Published
- 2015
- Full Text
- View/download PDF
30. DEgenes Hunter - A Self-customised Gene Expression Analysis Workflow for Non-model Organisms.
- Author
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Isabel González Gayte, Rocío Bautista Moreno, and M. Gonzalo Claros
- Published
- 2015
- Full Text
- View/download PDF
31. Bioinformatics Analyses to Separate Species Specific mRNAs from Unknown Sequences in de novo Assembled Transcriptomes.
- Author
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David Velasco, Pedro Seoane, and M. Gonzalo Claros
- Published
- 2015
- Full Text
- View/download PDF
32. 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
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Adoración Zafra, Rosario Carmona, Jose C. Jimenez-Lopez, Amada Pulido, M. Gonzalo Claros, and Juan D. Alché
- Published
- 2015
- Full Text
- View/download PDF
33. First draft genome assembly of the Argane tree ( Argania spinosa) [version 1; referees: 1 approved, 1 approved with reservations]
- Author
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Slimane Khayi, Nour Elhouda Azza, Fatima Gaboun, Stacy Pirro, Oussama Badad, M. Gonzalo Claros, David A. Lightfoot, Turgay Unver, Bouchra Chaouni, Redouane Merrouch, Bouchra Rahim, Soumaya Essayeh, Matika Ganoudi, Rabha Abdelwahd, Ghizlane Diria, Meriem Alaoui Mdarhi, Mustapha Labhilili, Driss Iraqi, Jamila Mouhaddab, Hayat Sedrati, Majid Memari, Noureddine Hamamouch, Juan de Dios Alché, Noureddine Boukhatem, Rachid Mrabet, Rachid Dahan, Adelkhaleq Legssyer, Mohamed Khalfaoui, Mohamed Badraoui, Yves Van de Peer, Tatiana Tatusova, Abdelhamid El Mousadik, Rachid Mentag, and Hassan Ghazal
- Subjects
Research Article ,Articles ,Argane ,Argania spinosa ,Endemic ,Genome ,Assembly ,Morocco ,International Argane Genome Consortium - Abstract
Background: The Argane tree ( Argania spinosa L. Skeels) is an endemic tree of southwestern Morocco that plays an important socioeconomic and ecologic role for a dense human population in an arid zone. Several studies confirmed the importance of this species as a food and feed source and as a resource for both pharmaceutical and cosmetic compounds. Unfortunately, the argane tree ecosystem is facing significant threats from environmental changes (global warming, over-population) and over-exploitation. Limited research has been conducted, however, on argane tree genetics and genomics, which hinders its conservation and genetic improvement. Methods: Here, we present a draft genome assembly of A. spinosa. A reliable reference genome of A. spinosa was created using a hybrid de novo assembly approach combining short and long sequencing reads. Results: In total, 144 Gb Illumina HiSeq reads and 7.2 Gb PacBio reads were produced and assembled. The final draft genome comprises 75 327 scaffolds totaling 671 Mb with an N50 of 49 916 kb. The draft assembly is close to the genome size estimated by k-mers distribution and covers 89% of complete and 4.3 % of partial Arabidopsis orthologous groups in BUSCO. Conclusion: The A. spinosa genome will be useful for assessing biodiversity leading to efficient conservation of this endangered endemic tree. Furthermore, the genome may enable genome-assisted cultivar breeding, and provide a better understanding of important metabolic pathways and their underlying genes for both cosmetic and pharmacological purposes.
- Published
- 2018
- Full Text
- View/download PDF
34. Detecting and correcting mis-assembled reads in contigs.
- Author
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Hicham Benzekri, Darío Guerrero-Fernández, Rocío Bautista, and M. Gonzalo Claros
- Published
- 2013
35. FQbin a compatible and optimized format for storing and managing sequence data.
- Author
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Darío Guerrero-Fernández, Rafael Larrosa, and M. Gonzalo Claros
- Published
- 2013
36. GENote v.β: A Web Tool Prototype for Annotation of Unfinished Sequences in Non-model Eukaryotes.
- Author
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Noé Fernández-Pozo, Darío Guerrero-Fernández, Rocío Bautista, Josefa Gómez-Maldonado, Concepción Avila, Francisco M. Cánovas, and M. Gonzalo Claros
- Published
- 2010
- Full Text
- View/download PDF
37. Intuitive Bioinformatics for Genomics Applications: Omega-Brigid Workflow Framework.
- Author
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David Díaz, Sergio Gálvez, Juan Falgueras, Juan Antonio Caballero, Pilar Hernández, M. Gonzalo Claros, and Gabriel Dorado
- Published
- 2009
- Full Text
- View/download PDF
38. On Selecting the Best Pre-processing Method for Affymetrix Genechips.
- Author
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J. P. Florido, Héctor Pomares, Ignacio Rojas, José C. Calvo, José M. Urquiza, and M. Gonzalo Claros
- Published
- 2009
- Full Text
- View/download PDF
39. Robust gene signatures from microarray data using genetic algorithms enriched with biological pathway keywords.
- Author
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Rafael Marcos Luque Baena, Daniel Urda, M. Gonzalo Claros, Leonardo Franco, and José M. Jerez
- Published
- 2014
- Full Text
- View/download PDF
40. A Web Tool to Discover Full-Length Sequences - Full-Lengther.
- Author
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Antonio J. Lara, Guillermo Pérez-Trabado, David P. Villalobos, Sara Díaz-Moreno, Francisco R. Cantón, and M. Gonzalo Claros
- Published
- 2008
- Full Text
- View/download PDF
41. SeqTrim - A Validation and Trimming Tool for All Purpose Sequence Reads.
- Author
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Juan Falgueras, Antonio J. Lara, Francisco R. Cantón, Guillermo Pérez-Trabado, and M. Gonzalo Claros
- Published
- 2008
- Full Text
- View/download PDF
42. Construction of miRNA-mRNA networks for the identification of lung cancer biomarkers in liquid biopsies
- Author
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Elena Espinosa Garcia, Macarena Arroyo Varela, Rafael Larrosa Jimenez, Josefa Gomez-Maldonado, Manuel Angel Cobo Dols, M. Gonzalo Claros, and Rocio Bautista Moreno
- Subjects
Cancer Research ,High-throughput sequencing ,Lung Neoplasms ,Liquid Biopsy ,General Medicine ,Biomarker ,Gene Expression Regulation, Neoplastic ,MicroRNAs ,Oncology ,Biomarkers, Tumor ,Humans ,RNA, Messenger ,Lung cancer ,RNA-seq ,Lung ,miRNA - Abstract
Lung cancer (LC) is the most common cause of cancer death worldwide mostly due to the low survival rate: 75% of cases are identified in advanced stages. In this study, the list of useful biomarkers to make an early diagnosis using liquid biopsies was expanded. A total of 30 samples of LC were analyzed to define potential miRNA biomarkers in liquid biopsies for LC. The biomarkers have been identified in interaction networks miRNA–mRNA. The potential biomarkers have been then validated in large cohorts. A total of 15 candidate miRNAs, that regulate the repression of 30 mRNAs, have been identified as a specific functional interaction network for squamous carcinoma, while the specific functional interaction network of adenocarcinoma consists of four candidate miRNAs that seem to handle the repression of five mRNA. Inspection of expression levels in larger cohorts validates the usefulness of the 11 candidates as biomarkers in liquid biopsies. The 11 candidate miRNAs found could be utilized to form diagnostic predictive biomarkers for LC in liquid biopsies.
- Published
- 2022
43. Salmonella Typhimurium induces genome-wide expression and phosphorylation changes that modulate immune response, intracellular survival and vesicle transport in infected neutrophils
- Author
-
Sara Zaldívar-López, Juber Herrera-Uribe, Rocío Bautista, Ángeles Jiménez, Ángela Moreno, M. Gonzalo Claros, and Juan J. Garrido
- Subjects
Immunology ,Developmental Biology - Abstract
Salmonella Typhimurium is a food-borne pathogen that causes salmonellosis. When in contact with the host, neutrophils are rapidly recruited to act as first line of defense. To better understand the pathogenesis of this infection, we used an in vitro model of neutrophil infection to perform dual RNA-sequencing (both host and pathogen). In addition, and given that many pathogens interfere with kinase-mediated phosphorylation in host signaling, we performed a phosphoproteomic analysis. The immune response was overall diminished in infected neutrophils, mainly JAK/STAT and toll-like receptor signaling pathways. We found decreased expression of proinflammatory cytokine receptor genes and predicted downregulation of the mitogen-activated protein (MAPK) signaling pathway. Also, Salmonella infection inhibited interferons I and II signaling pathways by upregulation of SOCS3 and subsequent downregulation of STAT1 and STAT2. Additionally, phosphorylation of PSMC2 and PSMC4, proteasome regulatory proteins, was decreased in infected neutrophils. Cell viability and survival was increased by p53 signaling, cell cycle arrest and NFkB-proteasome pathways activation. Combined analysis of RNA-seq and phosphoproteomics also revealed inhibited vesicle transport mechanisms mediated by dynein/dynactin and exocyst complexes, involved in ER-to-Golgi transport and centripetal movement of lysosomes and endosomes. Among the overexpressed virulence genes from Salmonella we found potential effectors responsible of these dysregulations, such as spiC, sopD2, sifA or pipB2, all of them involved in intracellular replication. Our results suggest that Salmonella induces (through overexpression of virulence factors) transcriptional and phosphorylation changes that increases neutrophil survival and shuts down immune response to minimize host response, and impairing intracellular vesicle transport likely to keep nutrients for replication and Salmonella-containing vacuole formation and maintenance.
- Published
- 2023
44. QuasiFlow: a bioinformatic tool for genetic variability analysis from next generation sequencing data
- Author
-
Pedro Seoane, Luis Díaz-Martínez, Enrique Viguera, M. Gonzalo Claros, Ana Grande-Pérez, Junta de Andalucía, European Commission, Universidad de Málaga, Seoane, Pedro, Díaz-Martínez, Luis, Viguera, Enrique, Claros, Gonzalo M., Grande-Pérez, Ana, Seoane, Pedro [0000-0002-3020-1415], Díaz-Martínez, Luis [0000-0002-7659-4349], Viguera, Enrique [0000-0001-5475-3807], Claros, Gonzalo M. [/0000-0002-0112-3550], and Grande-Pérez, Ana [0000-0002-2821-062X]
- Abstract
Populations of RNA and ssDNA viruses within their hosts contain a heterogeneous collection of variant genomes known as quasispecies. Large variability in mitochondrial DNA has also been found within the same organism, drawing an interesting parallel between the two situations. The advent of next-generation sequencing technologies facilitated studying genetic variation, but many open-source bioinformatic tools have to be combined in a non-trivial approach. Here it is presented QuasiFlow, a workflow based on well-stablished software that extracts reliable mutations and recombinations, even at low frequencies (~10-4), provided that at least 250 million nucleotides are analysed. Accurate prediction of mutations and recombinations has been demonstrated with synthetic reads and with in vitro rolling-circle amplification of a plant geminivirus. An in-depth analysis of viral quasispecies was performed and QuasiFlow revealed the coexistence in the plant of three virus genomes and distinct recombinations between some of them. Human mitochondrial variants were also investigated and high level of heteroplasmy (75%) was confirmed, and the relation between low-frequency heteroplasmy (0.1- 0.2%) and some human diseases, regardless of sex, was established. Hence, we propose that QuasiFlow may find use with known and emerging viruses to reveal evolutionary jumps and co-infections, with mitochondrial DNA to detect relevant heteroplasmy would otherwise be elusive, or even in other population studies such as those considering single cell sequencing., This work was supported by Consejería de Economía, Innovación y Ciencia, Junta de Andalucía with assistance from the European Regional Development Fund (ERDF) and the European Social Fund (ESF) [grant to Research Groups BIO-264 and BIO-267; P10594 -CVI- 6561 and UMA18-FEDERJA178 to A.G.-P., E.V.M; UMA20-FEDERJA-029 to MGC; and a predoctoral fellowship to L.D.-M. A.G-P. acknowledges support of Plan Propio de Investigación y Transferencia of the University of Málaga. Open access charges was funded by University of Málaga. The authors also thankfully acknowledge the computer resources and the technical support provided by the Plataforma Andaluza de Bioinformática of the University of Málaga.
- Published
- 2022
45. MOWServ: a web client for integration of bioinformatic resources.
- Author
-
Sergio Ramírez, Antonio Muñoz-Merida, Tor Johan Mikael Karlsson, Maximiliano García, Antonio J. Pérez-Pulido, M. Gonzalo Claros, and Oswaldo Trelles
- Published
- 2010
- Full Text
- View/download PDF
46. Chromosome anchoring in Senegalese sole (Solea senegalensis) reveals sex-associated markers and genome rearrangements in flatfish
- Author
-
M. Gonzalo Claros, Concha Berbel, Manuel Manchado, Juan F. Martinez-Blanch, Jèssica Gómez-Garrido, Israel Guerrero-Cózar, Pierre-Alexandre Gagnaire, Tyler Alioto, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Guerrero-Cózar, Israel, Gómez-Garrido, Jèssica, Berbel, Concha, Martinez-Blanch, Juan F., Alioto, Tyler, Claros, M. Gonzalo, Gagnaire, Pierre-Alexandre, Manchado, Manuel, [Guerrero-Cózar,I, Berbel,C, Manchado,M] IFAPA Centro El Toruño, Junta de Andalucía, Puerto de Santa María, Cádiz, Spain. [Gomez-Garrido,J, Alioto,T] CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. [Martinez-Blanch,JF] Biopolis S.L.-ADM, Parc Cientifc Universidad De Valencia, Paterna, Spain. [Alioto,T] Universitat Pompeu Fabra (UPF), Barcelona, Spain. [Claros,MG] Department of Molecular Biology and Biochemistry, Universidad de Málaga, Málaga, Spain. [Claros,MG] CIBER de Enfermedades Raras (CIBERER), Málaga, Spain. [Claros,MG] Institute of Biomedical Research in Málaga (IBIMA), IBIMA-RARE, Málaga, Spain. [Claros,MG] Instituto de Hortofruticultura Subtropical Y Mediterránea (IHSM-UMA-CSIC), Málaga, Spain. [Gagnaire,PA] ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France. [Manchado,M] Crecimiento Azul, Centro IFAPA El Toruño, Unidad Asociada al CSIC, El Puerto de Santa María, Spain., and This study was funded by project RTA2017-00054-C03-01 and RTA2017-00054-C03-funded from MCIU/AEI/FEDER, UE and cofunded 80% by Programa Operativo FEDER de Andalucía 2014-2020, project PP.AVA.AVA201601.9 SOLEALGAE. Moreover, the study has received funding from EU H2020 research and innovation program under grant agreement 817992 ERANET-BLUEBIO COFUND project PCI2020-111994 BestBrood/AEI/10.13039/501100011033. IGC is funded by a predoctoral fellowship from INIA. This work would not have been possible without the computer resources and the technical support provided by the Plataforma Andaluza de Bioinformática of the University of Málaga and CNAG. We acknowledge the support of the Spanish Ministry of Science, Innovation and Universities to the EMBL partnership, the Centro de Excelencia Severo Ochoa and the CERCA Programme/Generalitat de Catalunya, the Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III, Generalitat de Catalunya through Departament de Salut and Departament d’Empresa i Coneixement and co-fnancing with funds from the European Regional Development Fund by the Spanish Ministry of Science and Innovation corresponding to the Programa Operativo FEDER Plurirregional de España (POPE) 2014-2020 and by the Secretaria d’Universitats i Recerca, Departament d’Empresa i Coneixe ment of the Generalitat de Catalunya corresponding to the Programa Operatiu FEDER de Catalunya 2014-20.
- Subjects
Male ,Genetic Linkage ,Genome-wide association study ,Genome ,0302 clinical medicine ,Organisms::Eukaryota::Animals [Medical Subject Headings] ,Diferenciación sexual ,Ligamiento genético ,Genetics ,Gene Rearrangement ,0303 health sciences ,Multidisciplinary ,Contig ,Organisms::Eukaryota::Animals::Chordata::Vertebrates::Fishes::Flatfishes [Medical Subject Headings] ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,Genomics ,Penetrance ,Repeticiones de microsatélite ,Fatfish ,Phenomena and Processes::Genetic Phenomena::Genetic Structures::Base Sequence::Repetitive Sequences, Nucleic Acid::Tandem Repeat Sequences::Microsatellite Repeats [Medical Subject Headings] ,Flatfishes ,Medicine ,Sex ,Female ,Heterogametic sex ,Phenomena and Processes::Genetic Phenomena::Genetic Processes::Sex Determination Processes [Medical Subject Headings] ,Science ,Check Tags::Male [Medical Subject Headings] ,Locus (genetics) ,Biology ,Chromosome ,Article ,Phenomena and Processes::Genetic Phenomena::Genetic Structures::Genome [Medical Subject Headings] ,03 medical and health sciences ,Genetic linkage ,Phenomena and Processes::Genetic Phenomena::Genetic Linkage [Medical Subject Headings] ,Phenomena and Processes::Genetic Phenomena::Genetic Processes::Gene Rearrangement [Medical Subject Headings] ,Animals ,Genoma ,030304 developmental biology ,Animal breeding ,Cromosomas ,Sex Determination Processes ,[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics ,Genes ,Check Tags::Female [Medical Subject Headings] ,030217 neurology & neurosurgery ,Genome-Wide Association Study ,Microsatellite Repeats - Abstract
The integration of physical and high-density genetic maps is a very useful approach to achieve chromosome-level genome assemblies. Here, the genome of a male Senegalese sole (Solea senegalensis) was de novo assembled and the contigs were anchored to a high-quality genetic map for chromosome-level scaffolding. Hybrid assembled genome was 609.3 Mb long and contained 3403 contigs with a N50 of 513 kb. The linkage map was constructed using 16,287 informative SNPs derived from ddRAD sequencing in 327 sole individuals from five families. Markers were assigned to 21 linkage groups with an average number of 21.9 markers per megabase. The anchoring of the physical to the genetic map positioned 1563 contigs into 21 pseudo-chromosomes covering 548.6 Mb. Comparison of genetic and physical distances indicated that the average genome-wide recombination rate was 0.23 cM/Mb and the female-to-male ratio 1.49 (female map length: 2,698.4 cM, male: 2,036.6 cM). Genomic recombination landscapes were different between sexes with crossovers mainly concentrated toward the telomeres in males while they were more uniformly distributed in females. A GWAS analysis using seven families identified 30 significant sex-associated SNP markers located in linkage group 18. The follicle-stimulating hormone receptor appeared as the most promising locus associated with sex within a region with very low recombination rates. An incomplete penetrance of sex markers with males as the heterogametic sex was determined. An interspecific comparison with other Pleuronectiformes genomes identified a high sequence similarity between homologous chromosomes, and several chromosomal rearrangements including a lineage-specific Robertsonian fusion in S. senegalensis. This study was funded by project RTA2017-00054-C03-01 and RTA2017-00054-C03-funded from MCIU/AEI/FEDER, UE and cofunded 80% by Programa Operativo FEDER de Andalucía 2014-2020, project PP.AVA.AVA201601.9 SOLEALGAE. Moreover, the study has received funding from EU H2020 research and innovation program under grant agreement 817992 ERANET-BLUEBIO COFUND project PCI2020-111994 BestBrood/AEI/10.13039/501100011033. IGC is funded by a predoctoral fellowship from INIA. This work would not have been possible without the computer resources and the technical support provided by the Plataforma Andaluza de Bioinformática of the University of Málaga and CNAG.
- Published
- 2021
47. Differential expression analysis of lncRNA in different types of lung cancer
- Author
-
Rafael Larrosa Jiménez, M. Gonzalo Claros Díaz, Esperanza Salcedo Lobera, Lorena Aguilera Cobos, Macarena Arroyo Varela, and Rocío Bautista Moreno
- Subjects
Differential expression analysis ,business.industry ,Cancer research ,Medicine ,business ,Lung cancer ,medicine.disease - Published
- 2021
48. Nitric oxide-dependent regulation of sweet pepper fruit ripening
- Author
-
Salvador González-Gordo, Rocío Bautista, Francisco J. Corpas, Amanda Cañas, José M. Palma, M. Gonzalo Claros, Junta de Andalucía, European Commission, and Ministerio de Economía y Competitividad (España)
- Subjects
0106 biological sciences ,0301 basic medicine ,Physiology ,Lipid peroxidation ,fruit ripening ,Plant Science ,Nitric Oxide ,fatty acids ,01 natural sciences ,Transcriptomes ,Nitric oxide ,03 medical and health sciences ,chemistry.chemical_compound ,pepper ,Pepper ,RNA-Seq ,Proline ,Food science ,Fatty acids ,proline ,biology ,food and beverages ,lipid peroxidation ,Ripening ,Lipid metabolism ,Glutathione ,Fruit ripening ,Research Papers ,030104 developmental biology ,Proline, RNA-Seq ,chemistry ,Fruit ,biology.protein ,Ascorbate peroxidase ,Capsicum ,transcriptome ,Signal Transduction ,010606 plant biology & botany ,Peroxidase - Abstract
Ripening is a complex physiological process that involves changes in reactive nitrogen and oxygen species that govern the shelf-life and quality of fruits. Nitric oxide (NO)-dependent changes in the sweet pepper fruit transcriptome were determined by treating fruits at the initial breaking point stage with NO gas. Fruits were also harvested at the immature (green) and ripe (red) stages. Fruit ripening in the absence of NO resulted in changes in the abundance of 8805 transcripts whose function could be identified. Among these, functional clusters associated with reactive oxygen/nitrogen species and lipid metabolism were significantly modified. NO treatment resulted in the differential expression of 498 genes framed within these functional categories. Biochemical analysis revealed that NO treatment resulted in changes in fatty acid profiling, glutathione and proline contents, and the extent of lipid peroxidation, as well as increases in the activity of ascorbate peroxidase and lipoxygenase. These data provide supporting evidence for the crucial role of NO in the ripening of pepper fruit., The work of FJC and JMP is supported by a European Regional Development Fund-cofinanced grant from the Ministry of Economy and Competitiveness (AGL2015-65104-P) and Junta de Andalucia (group BIO192), Spain. SGG acknowledges a ‘Formacion de Personal Investigador’ contract from the Ministry of Economy and Competitiveness. The provision of pepper fruits by Syngenta Seeds Ltd (El Ejido, Almeria, Spain) is acknowledged. GC-MS analyses were done at the Instrumental Technical Services of the Estacion Experimental del Zaidin (CSIC) and special thanks are given to Dr Rafael Nunez-Gomez. The valuable technical assistance of Mrs Maria J. Campos and Mr Carmelo Ruiz-Torres is deeply acknowledged. The authors also gratefully acknowledge the computer resources and technical support provided by the Plataforma Andaluza de Bioinformatica of the University of Malaga.
- Published
- 2019
49. TransFlow: a modular framework for assembling and assessing accurate de novo transcriptomes in non-model organisms
- Author
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Rosario Carmona, Enrico Cretazzo, Josefina Bota, Juan de Dios Alché, Álvaro Polonio, Luis Gómez, Pedro Seoane, M. Gonzalo Claros, Marina Espigares, Alejandro Pérez-García, Julia Quintana, European Commission, Junta de Andalucía, and Consejo Superior de Investigaciones Científicas (España)
- Subjects
0301 basic medicine ,Computer science ,ved/biology.organism_classification_rank.species ,Computational biology ,Assembling ,lcsh:Computer applications to medicine. Medical informatics ,Biochemistry ,Genome ,Transcriptomes ,Workflow ,Set (abstract data type) ,Transcriptome ,03 medical and health sciences ,Structural Biology ,Model organism ,Molecular Biology ,Base Pairing ,lcsh:QH301-705.5 ,Selection (genetic algorithm) ,Principal Component Analysis ,PCA ,Non-model organism ,business.industry ,ved/biology ,Sequence Analysis, RNA ,Applied Mathematics ,Research ,Gene Expression Profiling ,Fungi ,Reproducibility of Results ,pipeline ,Modular design ,Plants ,Computer Science Applications ,030104 developmental biology ,lcsh:Biology (General) ,Pyrosequencing ,lcsh:R858-859.7 ,DNA microarray ,business ,Software - Abstract
[Background]: The advances in high-throughput sequencing technologies are allowing more and more de novo assembling of transcriptomes from many new organisms. Some degree of automation and evaluation is required to warrant reproducibility, repetitivity and the selection of the best possible transcriptome. Workflows and pipelines are becoming an absolute requirement for such a purpose, but the issue of assembling evaluation for de novo transcriptomes in organisms lacking a sequenced genome remains unsolved. An automated, reproducible and flexible framework called TransFlow to accomplish this task is described., [Results]: TransFlow with its five independent modules was designed to build different workflows depending on the nature of the original reads. This architecture enables different combinations of Illumina and Roche/454 sequencing data, and can be extended to other sequencing platforms. Its capabilities are illustrated with the selection of reliable plant reference transcriptomes and the assembling six transcriptomes (three case studies for grapevine leaves, olive tree pollen, and chestnut stem, and other three for haustorium, epiphytic structures and their combination for the phytopathogenic fungus Podosphaera xanthii). Arabidopsis and poplar transcriptomes revealed to be the best references. A common result regarding de novo assemblies is that Illumina paired-end reads of 100 nt in length assembled with OASES can provide reliable transcriptomes, while the contribution of longer reads is noticeable only when they complement a set of short, single-reads., [Conclusions]:TransFlow can handle up to 181 different assembling strategies. Evaluation based on principal component analyses allows its self-adaptation to different sets of reads to provide a suitable transcriptome for each combination of reads and assemblers. As a result, each case study has its own behaviour, prioritises evaluation parameters, and gives an objective and automated way for detecting the best transcriptome within a pool of them. Sequencing data type and quantity (preferably several hundred millions of 2×100 nt or longer), assemblers (OASES for Illumina, MIRA4 and EULER-SR reconciled with CAP3 for Roche/454) and strategy (preferably scaffolding with OASES, and probably merging with Roche/454 when available) arise as the most impacting factors., This work was supported by co-funding by the European Union through the European Regional Development Fund (ERDF) 2014-2020 “Programa Operativo de Crecimiento Inteligente” together with Spanish AEI “Agencia Estatal de Investigación” (BFU2016-77243-P, RTC-2015-4181-2, RTC-2016-4824-2, AGL2013-41939-R and AGL2016-76216-C2-1-R), AEI-INIA (RTA2013-00023-C02 and RTA2013-00068-C03), and Junta de Andalucía (P2011-CVI-7487), as well as CSIC grant 201540E065. PS received a postdoctoral fellowship from Junta de Andalucía linked to grant P10-CVI-6075. Publication costs were funded by the mentioned RTA2013-00068-C03 grant.
- Published
- 2018
50. Insights into ROS-dependent signalling underlying transcriptomic plant responses to the herbicide 2,4-D
- Author
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M. Ángeles Peláez-Vico, María C. Romero-Puertas, M. Gonzalo Claros, Jose de Leon, Rocío Bautista, Laura Carmen Terrón-Camero, Luisa M. Sandalio, María Rodríguez-Serrano, Aurelio Gómez-Cadenas, Diana M. Pazmiño, Ministerio de Ciencia, Innovación y Universidades (España), and European Commission
- Subjects
Physiology ,Arabidopsis ,Plant Science ,Mitochondrion ,Biology ,Protein degradation ,Transcriptomes ,Ubiquitin ,Auxin ,Peroxisomes ,Acyl-CoA oxidase ,chemistry.chemical_classification ,Herbicides ,fungi ,food and beverages ,Peroxisome ,Ubiquitin ligase ,Cell biology ,Acyl‐CoA oxidase ,Proteasome ,chemistry ,biology.protein ,2,4-Dichlorophenoxyacetic Acid ,Transcriptome ,Reactive oxygen species ,Signal Transduction - Abstract
The synthetic auxin 2,4¿dichlorophenoxyacetic acid (2,4¿D) functions as an agro-nomic weed control herbicide. High concentrations of 2,4¿D induce plant growthdefects, particularly leaf epinasty and stem curvature. Although the 2,4¿D triggeredreactive oxygen species (ROS) production, little is known about its signalling. In thisstudy, by using a null mutant in peroxisomal acyl CoA oxidase 1 (acx1¿2), we iden-tified acyl¿coenzyme A oxidase 1 (ACX1) as one of the main sources of ROS pro-duction and, in part, also causing the epinastic phenotype following 2,4¿Dapplication. Transcriptomic analyses of wild type (WT) plants after treatment with2,4¿D revealed a ROS¿related peroxisomal footprint in early plant responses, whileother organelles, such as mitochondria and chloroplasts, are involved in later re-sponses. Interestingly, a group of 2,4¿D¿responsive ACX1¿dependent transcriptspreviously associated with epinasty is related to auxin biosynthesis, metabolism, andsignalling. We found that the auxin receptor auxin signalling F¿box 3 (AFB3), acomponent of Skp, Cullin, F¿box containing complex (SCF) (ASK¿cullin¿F¿box) E3ubiquitin ligase complexes, which mediates auxin/indole acetic acid (AUX/IAA)degradation by the 26S proteasome, acts downstream of ACX1 and is involved in theepinastic phenotype induced by 2,4¿D. We also found that protein degradationassociated with ubiquitin E3¿RING and E3¿SCF¿FBOX in ACX1¿dependent signallingin plant responses to 2,4¿D is significantly regulated over longer treatment periods, This study was funded by the Spanish Ministry of Science, Innovation and Universities (MCIU), the State Research Agency (AEI) and FEDER grant PGC2018-098372-B-I00. MAP-V was supported by MCIU Research Personnel Training (FPI) grant BES-2016-076518.
- Published
- 2021
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