Pedro Duque

Mr. Pedro Duque


Research Focus & Metrics

Academic Career Length

9Years (2018-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

View All Publications
18 June 2019 in BMC Ecology and Evolution
Verified
Journal Article
Open access
PDF file
SHSílvia F. Henriques
Sílvia F. Henriques
PDPedro Duque
Pedro Duque
HLHugo López-Fernández
Hugo López-Fernández
NVNoé Vázquez
Noé Vázquez
Florentino Fdez-RiverolaFlorentino Fdez-Riverola
Florentino Fdez-Riverola
Jorge VieiraJorge Vieira
Jorge Vieira
L-ascorbate (Vitamin C) is an important antioxidant and co-factor in eukaryotic cells, and in mammals it is indispensable for brain development and cognitive function. Vertebrates usually become L-ascorbate auxothrophs when the last enzyme of the synthetic pathway, an L-gulonolactone oxidase (GULO), is lost. Since Protostomes were until recently thought not to have a GULO gene, they were considered to be auxothrophs for Vitamin C. By performing phylogenetic analyses with tens of non-Bilateria and Protostomian genomes, it is shown, that a GULO gene is present in the non-Bilateria Placozoa, Myxozoa (here reported for the first time) and Anthozoa groups, and in Protostomians, in the Araneae family, the Gastropoda class, the Acari subclass (here reported for the first time), and the Priapulida, Annelida (here reported for the first time) and Brachiopoda phyla lineages. GULO is an old gene that predates the separation of Animals and Fungi, although it could be much older. We also show that within Protostomes, GULO has been lost multiple times in large taxonomic groups, namely the Pancrustacea, Nematoda, Platyhelminthes and Bivalvia groups, a pattern similar to that reported for Vertebrate species. Nevertheless, we show that Drosophila melanogaster seems to be capable of synthesizing L-ascorbate, likely through an alternative pathway, as recently reported for Caenorhabditis elegans. Non-Bilaterian and Protostomians seem to be able to synthesize Vitamin C either through the conventional animal pathway or an alternative pathway, but in this animal group, not being able to synthesize L-ascorbate seems to be the exception rather than the rule.

25 November 2020 in IEEE/ACM Transactions on Computational Biology and Bioinformatics
Verified
Journal Article
Closed access
HLHugo López-Fernández
Hugo López-Fernández
PDPedro Duque
Pedro Duque
NVNoé Vázquez
Noé Vázquez
Florentino Fdez-RiverolaFlorentino Fdez-Riverola
Florentino Fdez-Riverola
MRMiguel Reboiro-Jato
Miguel Reboiro-Jato
Jorge VieiraJorge Vieira
Jorge Vieira
SEDA (SEquence DAtaset builder) is a multiplatform desktop application for the manipulation of FASTA files containing DNA or protein sequences. The convenient graphical user interface gives access to a collection of simple (filtering, sorting, or file reformatting, among others) and advanced (BLAST searching, protein domain annotation, gene annotation, and sequence alignment) utilities not present in similar applications, which eases the work of life science researchers working with DNA and/or protein sequences, especially those who have no programming skills. This paper presents general guidelines on how to build efficient data handling protocols using SEDA, as well as practical examples on how to prepare high-quality datasets for single gene phylogenetic studies, the characterization of protein families, or phylogenomic studies. The user-friendliness of SEDA also relies on two important features: (i) the availability of easy-to-install distributable versions and installers of SEDA, including a Docker image for Linux, and (ii) the facility with which users can manage large datasets. SEDA is open-source, with GNU General Public License v3.0 license, and publicly available at GitHub (https://github.com/sing-group/seda). SEDA installers and documentation are available at https://www.sing-group.org/seda/

23 March 2023 in APUNTES DEL CENES
Verified
Journal Article
Open access
PDF file
CRCarlos Andres Diaz Restrepo
Carlos Andres Diaz Restrepo
MPMonica Patiño
Monica Patiño
PDPedro Duque
Pedro Duque
LCLuis Salvador Cervantes Cervantes
Luis Salvador Cervantes Cervantes
ARAndrea Franco Rivera
Andrea Franco Rivera
Las pymes desempeñan un papel protagónico en la economía global, por eso su estudio despierta cada vez más el interés de la comunidad científica y académica. Este artículo explora el desarrollado de la investigación sobre el tema financiero, uno de los aspectos relevantes para el crecimiento y la competitividad de este tipo de organizaciones. Se efectúa un mapeo científico de la investigación acerca del desempeño financiero y pymes, a través de un rastreo de la producción científica registrada en las bases de datos Scopus y WoS. Se determinan las regiones, los autores, las instituciones y revistas más relevantes utilizando herramientas y técnicas bibliométricas; también se identifican los documentos más representativos del área y se clasifican empleando el esquema metafórico del árbol. Los resultados permitieron establecer los trabajos seminales y estructurales, al igual que las subáreas que emergen sobre el tema; estas últimas determinan, a su vez, las subáreas o corrientes en las que se enmarca la investigación. El país más relevante en este tópico es Indonesia, seguido de Australia y Sudáfrica; la publicación de mayor impacto es el Journal of Cleaner Production del Reino Unido, y el autor más relevante es Jain, Priyanka, de Delhi Technological University. Finalmente, se plantea una agenda para futuras investigaciones, entre ellas, los rendimientos financieros relacionados con la responsabilidad social corporativa, la innovación empresarial y el sostenimiento del medio ambiente.

3 December 2018 in Interdisciplinary Sciences: Computational Life Sciences
Verified
Journal Article
Closed access
PDF file
HLHugo López-Fernández
Hugo López-Fernández
PDPedro Duque
Pedro Duque
SHSílvia Henriques
Sílvia Henriques
NVNoé Vázquez
Noé Vázquez
Florentino Fdez-RiverolaFlorentino Fdez-Riverola
Florentino Fdez-Riverola
JVJorge Vieira
Jorge Vieira

21 October 2022 in Genes
Verified
Journal Article
Open access
PDF file
PDPedro Duque
Pedro Duque
CVCristina Vieira
Cristina Vieira
Jorge VieiraJorge Vieira
Jorge Vieira
Vitamin C (VC) is an essential nutrient required for the optimal function and development of many organisms. VC has been studied for many decades, and still today, the characterization of its functions is a dynamic scientific field, mainly because of its commercial and therapeutic applications. In this review, we discuss, in a comparative way, the increasing evidence for alternative VC synthesis pathways in insects and nematodes, and the potential of myo-inositol as a possible substrate for this metabolic process in metazoans. Methodological approaches that may be useful for the future characterization of the VC synthesis pathways of Caenorhabditis elegans and Drosophila melanogaster are here discussed. We also summarize the current distribution of the eukaryote aldonolactone oxidoreductases gene lineages, while highlighting the added value of studies on prokaryote species that are likely able to synthesize VC for both the characterization of novel VC synthesis pathways and inferences on the complex evolutionary history of such pathways. Such work may help improve the industrial production of VC.

8 July 2025 in Evolution Letters
Verified
Journal Article
Open access
EMEsra Durmaz Mitchell
Esra Durmaz Mitchell
EKEnvel Kerdaffrec
Envel Kerdaffrec
EHEwan Harney
Ewan Harney
TPTânia F Paulo
Tânia F Paulo
MVMarija Savic Veselinovic
Marija Savic Veselinovic
TFThomas Flatt
Thomas Flatt
A particularly well-studied evolutionary model is the vinegar fly Drosophila melanogaster, a cosmopolitan insect of ancestral southern-central African origin. Recent work suggests that it expanded out of Africa ∼9,000 years ago, and spread from the Middle East into Europe ∼1,800 years ago. During its global expansion, this human commensal adapted to novel climate zones and habitats. Despite much work on phenotypic differentiation and adaptation on several continents (especially North America and Australia), typically in the context of latitudinal clines, little is known about phenotypic divergence among European populations. Here, we sought to provide a continent-wide study of phenotypic differentiation among European populations of D. melanogaster. In a consortium-wide phenomics effort, we assayed 16 fitness-related traits on a panel of 173 isofemale lines from 9 European populations, with the majority of traits measured by several groups using semi-standardized protocols. For most fitness-related traits, we found significant differentiation among populations on a continental scale. Despite inevitable differences in assay conditions among labs, the reproducibility and hence robustness of our measurements were overall remarkably good. Several fitness components (e.g., viability, development time) exhibited significant latitudinal or longitudinal clines, and populations differed markedly in multivariate trait structure. Notably, populations experiencing higher humidity/rainfall and lower maximum temperature showed higher viability, fertility, starvation resistance, and lifespan at the expense of lower heat-shock survival, suggesting a pattern of local adaptation. Our results indicate that derived populations of this tropical fly have been shaped by pervasive spatially varying multivariate selection and adaptation to different climates on the European continent.