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Digital.CSIC. Repositorio Institucional del CSIC
Dataset

PORQUE A ALGUNAS PERSONAS LES AFECTA MÁS EL CORONAVIRUS

  • Casado, Marta
  • Pérez-Tur, Jordi
  • Planas, Anna M.
  • CSIC - Instituto de Biomedicina de Valencia (IBV)
6º Vídeo de Divulgación Científica de la serie: "Un virus, mil preguntas" creada por Marta Casado y el Instituto de Biomedicina de Valencia: "Porque a algunas personas les afecta más el coronavirus" 7,26 min. Guion y realización: Aprende con DANIO, En este video os explicamos el proyecto que lleva a cabo el Dr. Jordi Pérez-Tur director de la Unidad de Genética Molecular del Instituto de Biomedicina de Valencia en colaboración con la Dra. Anna Planas Obradors del Instituto de Investigaciones Biomédicas de Barcelona y más investigadores nacionales e internacionales para intentar comprender las causas de que las personas respondamos de manera diferente al virus Sars-Cov2, Fundación General CSIC, Programa Cuenta la Ciencia., Peer reviewed

Proyecto: //
DOI: http://hdl.handle.net/10261/269377
Digital.CSIC. Repositorio Institucional del CSIC
HANDLE: http://hdl.handle.net/10261/269377
Digital.CSIC. Repositorio Institucional del CSIC
PMID: http://hdl.handle.net/10261/269377
Digital.CSIC. Repositorio Institucional del CSIC
Ver en: http://hdl.handle.net/10261/269377
Digital.CSIC. Repositorio Institucional del CSIC

Digital.CSIC. Repositorio Institucional del CSIC
Dataset

BUSCANDO AL CORONAVIRUS EN AGUAS RESIDUALES

  • Casado, Marta
  • Sánchez Moragas, Gloria
  • Allende, Ana
  • CSIC - Instituto de Biomedicina de Valencia (IBV)
7º Vídeo de Divulgación Científica de la serie: "Un virus, mil preguntas" creada por Marta Casado y el Instituto de Biomedicina de Valencia: "Buscando al coronavirus en aguas residuales" 4,13 min. Guion y realización: Aprende con DANIO, La vigilancia microbiológica en aguas residuales puede utilizarse como indicador epidemiológico para la detección de la circulación del virus en la población. Las experiencias previas en la utilización de esta herramienta han demostrado su sensibilidad, incluso cuando la prevalencia de la COVID-19 presenta niveles bajos en la población. Se introducie el proyecto liderado por la Dra. Gloria Sánchez del IATA-Valencia y la Dra. Ana Allende del CEBAS-Murcia, que detectan SARS-CoV-2 en aguas residuales como alerta temprana de la infección, Fundación General CSIC, Programa Cuenta la Ciencia., No

Proyecto: //
DOI: http://hdl.handle.net/10261/269429
Digital.CSIC. Repositorio Institucional del CSIC
HANDLE: http://hdl.handle.net/10261/269429
Digital.CSIC. Repositorio Institucional del CSIC
PMID: http://hdl.handle.net/10261/269429
Digital.CSIC. Repositorio Institucional del CSIC
Ver en: http://hdl.handle.net/10261/269429
Digital.CSIC. Repositorio Institucional del CSIC

Digital.CSIC. Repositorio Institucional del CSIC
Dataset

DATA FROM: DYNAMIC ANTAGONISM BETWEEN PHYTOCHROMES AND PIF-FAMILY BHLHS INDUCES SELECTIVE RECIPROCAL RESPONSES TO LIGHT AND SHADE IN A RAPIDLY RESPONSIVE TRANSCRIPTIONAL NETWORK IN ARABIDOPSIS

  • Leivar, Pablo
  • Tepperman, James
  • Cohn, Megan M.
  • Monte, Elena
  • Al-Sady, Bassem
  • Erickson, Erika
  • Quail, Peter H.
Plants respond to shade-modulated light-signals, via the phytochrome (phy) system, by adaptive changes, collectively termed the shade avoidance syndrome (SAS). To examine the roles of the Phy-Interacting bHLH Factors, PIF1, 3, 4 and 5, in relaying this information to the transcriptional network, we compared the genome-wide expression profiles of wild-type and quadruple pif (pifq) mutants in response to shade. The data identify a subset of genes, enriched in transcription-factor-encoding loci, that respond rapidly (within 1 h), in a PIF-dependent manner, to the shade signal, and that contain promoter-located G-box-sequence motifs (CACGTG), known to be preferred PIF binding sites. These genes are thus potential direct targets of phy-PIF signaling that function in the primary transcriptional circuitry controlling downstream response-elaboration. A second subset of PIF-dependent, early-response genes, lacking G-box motifs, are enriched for auxin-responsive loci, suggestive of being indirect targets of phy-PIF signaling involved in the rapid cell-expansion known to be induced by shade. A meta-analysis comparing deetiolation- and shade-responsive transcriptomes identifies a further subset of G-box-containing genes that reciprocally display rapid repression and induction in response to light and shade signals at the inception of deetiolation and shade-avoidance, respectively. Collectively, these data define a core set of transcriptional and hormonal (auxin, cytokinin) processes that appear to be dynamically poised to react rapidly to changes in the light environment via perturbations in the mutually antagonistic actions of the phys and PIFs. Data from comparative analysis of the quadruple pifq and all triple pif-mutant combinations in response to light and shade, confirm that the PIF-quartet members act with overlapping redundancy on seedling morphogenesis and transcriptional regulation, but that the individual PIFs contribute differentially to these responses., Peer reviewed

Proyecto: //
DOI: http://hdl.handle.net/10261/269511
Digital.CSIC. Repositorio Institucional del CSIC
HANDLE: http://hdl.handle.net/10261/269511
Digital.CSIC. Repositorio Institucional del CSIC
PMID: http://hdl.handle.net/10261/269511
Digital.CSIC. Repositorio Institucional del CSIC
Ver en: http://hdl.handle.net/10261/269511
Digital.CSIC. Repositorio Institucional del CSIC

Digital.CSIC. Repositorio Institucional del CSIC
Dataset

RADAR_ON_RAIA GPRS DRIFTING BUOYS, ATLANTIC OCEAN - RÍA DE VIGO (NW IBERIA) - SEP. 2021 - SEP. 2021

  • Gilcoto, Miguel
  • Martínez Fernández, Adrián
  • Redondo, W.
  • Villacieros-Robineau, Nicolás
This item is made of 2 files: the dataset in netcdf format, a Readme.txt file including a small description of the computed variables, and 3 figures representing the buoy and the two experiments. Dataset contributed to the Project RADAR ON RAIA (0461_RADAR ON RAIA_1_E).-- Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0), readme files for more detail information, GPS fixes of the drifts of manufactured buoys (GPRS) under Radar On Raia Project. These bouys were used in two short experiments (< 1 day) in September 2021 in order to validate the data collected by the HF Radar of RAIA_Vigo system. http://radaronraia.eu/, Funding for this study was provided by the European Union through EP-INTERREG V-A España-Portugal (POCTEP) program (RADAR ON RAIA, 0461_RADAR ON RAIA_1_E), No

Proyecto: //
DOI: http://hdl.handle.net/10261/269565
Digital.CSIC. Repositorio Institucional del CSIC
HANDLE: http://hdl.handle.net/10261/269565
Digital.CSIC. Repositorio Institucional del CSIC
PMID: http://hdl.handle.net/10261/269565
Digital.CSIC. Repositorio Institucional del CSIC
Ver en: http://hdl.handle.net/10261/269565
Digital.CSIC. Repositorio Institucional del CSIC

Digital.CSIC. Repositorio Institucional del CSIC
Dataset

RADAR_ON_RAIA SPOT DRIFTING BUOYS, ATLANTIC OCEAN (NW IBERIA) - SEP. 2020 - AUG. 2021

  • Gilcoto, Miguel
  • Martínez Fernández, Adrián
  • Redondo, W.
  • Villacieros-Robineau, Nicolás
This item is made of 2 files: the dataset in netcdf format, a Readme.txt file including a small description of the computed variables, and 4 figures representing the buoy and the three experiments. Dataset contributed to the Project RADAR ON RAIA (0461_RADAR ON RAIA_1_E).-- Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0), readme files for more detail information, GPS fixes of the drifts of manufracted buoys (SPOT) under Radar On Raia Project. This bouys were used in three experiments between Sep. 2020 and Aug. 2021 in order to validate the data collected by the HFR of RAIA_NW_Iberian system. http://radaronraia.eu, Funding for this study was provided by the European Union through EP-INTERREG V-A España-Portugal (POCTEP) program (RADAR ON RAIA, 0461_RADAR ON RAIA_1_E), No

Proyecto: //
DOI: http://hdl.handle.net/10261/269569
Digital.CSIC. Repositorio Institucional del CSIC
HANDLE: http://hdl.handle.net/10261/269569
Digital.CSIC. Repositorio Institucional del CSIC
PMID: http://hdl.handle.net/10261/269569
Digital.CSIC. Repositorio Institucional del CSIC
Ver en: http://hdl.handle.net/10261/269569
Digital.CSIC. Repositorio Institucional del CSIC

Digital.CSIC. Repositorio Institucional del CSIC
Dataset

LOS LINFOCITOS VAN A CLASE: LAS VACUNAS

  • Casado, Marta
  • Esteban, Mariano
  • García Arriaza, Juan
  • CSIC - Instituto de Biomedicina de Valencia (IBV)
8º Vídeo de Divulgación Científica de la serie: "Un virus, mil preguntas" creada por Marta Casado y el Instituto de Biomedicina de Valencia: "Los linfocitos van a clase: las vacunas" 8,13 min. Guion y realización: Aprende con DANIO, En este nuevo vídeo de la serie vamos a explicar qué es una vacuna, porqué son importantes en el contexto de la pandemia, y se discutirá la estrategia de la vacuna diseñada por el equipo de los Dres. Mariano Esteban y Juan García Arriaza., Fundación General CSIC, Programa Cuenta la Ciencia., Peer reviewed

Proyecto: //
DOI: http://hdl.handle.net/10261/269606
Digital.CSIC. Repositorio Institucional del CSIC
HANDLE: http://hdl.handle.net/10261/269606
Digital.CSIC. Repositorio Institucional del CSIC
PMID: http://hdl.handle.net/10261/269606
Digital.CSIC. Repositorio Institucional del CSIC
Ver en: http://hdl.handle.net/10261/269606
Digital.CSIC. Repositorio Institucional del CSIC

Digital.CSIC. Repositorio Institucional del CSIC
Dataset

DATA FROM: GENOME DATA FROM A 16TH CENTURY PIG ILLUMINATE MODERN BREED RELATIONSHIPS

  • Pérez-Enciso, Miguel
Ancient DNA (aDNA) provides direct evidence of historical events that have modeled the genome of modern individuals. In livestock, resolving the differences between the effects of initial domestication and of subsequent modern breeding is not straight forward without aDNA data. Here, we have obtained shotgun genome sequence data from a sixteenth century pig from Northeastern Spain (Montsoriu castle), the ancient pig was obtained from an extremely well-preserved and diverse assemblage. In addition, we provide the sequence of three new modern genomes from an Iberian pig, Spanish wild boar and a Guatemalan Creole pig. Comparison with both mitochondrial and autosomal genome data shows that the ancient pig is closely related to extant Iberian pigs and to European wild boar. Although the ancient sample was clearly domestic, admixture with wild boar also occurred, according to the D-statistics. The close relationship between Iberian, European wild boar and the ancient pig confirms that Asian introgression in modern Iberian pigs has not existed or has been negligible. In contrast, the Guatemalan Creole pig clusters apart from the Iberian pig genome, likely due to introgression from international breeds., Peer reviewed

Proyecto: //
DOI: http://hdl.handle.net/10261/269613
Digital.CSIC. Repositorio Institucional del CSIC
HANDLE: http://hdl.handle.net/10261/269613
Digital.CSIC. Repositorio Institucional del CSIC
PMID: http://hdl.handle.net/10261/269613
Digital.CSIC. Repositorio Institucional del CSIC
Ver en: http://hdl.handle.net/10261/269613
Digital.CSIC. Repositorio Institucional del CSIC

Digital.CSIC. Repositorio Institucional del CSIC
Dataset

DATA FROM: ANALYSIS OF THE PORCINE APOA2 GENE EXPRESSION IN LIVER, POLYMORPHISMS IDENTIFICATION AND ASSOCIATION WITH FATTY ACID COMPOSITION TRAITS

  • Ballester, María
  • Revilla, Manuel
  • Puig-Oliveras, Anna
  • Marchesi, J.A.P.
  • Castelló, Anna
  • Corominas, Jordi
  • Fernández, Ana Isabel
  • Folch, Josep María
Usage Notes Porcine APOA2 gene expression in liver Data from Analysis of the porcine APOA2 gene expression in liver, polymorphisms identification and association with fatty acid composition traits. Contains SNP genotypes for GWAS and eGWAS studies, mRNA expression of APOA2 in liver, and fatty acid composition in backfat and muscle, APOA2 is a protein implicated in triglyceride, fatty acid and glucose metabolism. In pigs, the APOA2 gene is located on pig chromosome 4 (SSC4) in a QTL region affecting fatty acid composition, fatness and growth traits. In this study, we evaluated APOA2 as a candidate gene for meat quality traits in an Iberian × Landrace backcross population. The APOA2:c.131T>A polymorphism, located in exon 3 of APOA2 and determining a missense mutation, was associated with the percentage of hexadecenoic acid [C16:1(n–9)], linoleic acid [C18:2(n–6)], α-linolenic acid [C18:3(n–3)], dihomo-gamma-linolenic acid [C20:3(n–6)] and polyunsaturated fatty acids (PUFAs) in backfat. Furthermore, this SNP was associated with the global mRNA expression levels of APOA2 in liver and was used as a marker to determine allelic expression imbalance by pyrosequencing. We determined an overexpression of the T allele in heterozygous samples with a mean ratio of 2.8 (T/A), observing a high variability in the allelic expression among individuals. This result suggests that complex regulatory mechanisms, beyond a single polymorphism (e.g. epigenetic effects or multiple cis-acting polymorphisms), may be regulating APOA2 gene expression., Peer reviewed

Proyecto: //
DOI: http://hdl.handle.net/10261/269620
Digital.CSIC. Repositorio Institucional del CSIC
HANDLE: http://hdl.handle.net/10261/269620
Digital.CSIC. Repositorio Institucional del CSIC
PMID: http://hdl.handle.net/10261/269620
Digital.CSIC. Repositorio Institucional del CSIC
Ver en: http://hdl.handle.net/10261/269620
Digital.CSIC. Repositorio Institucional del CSIC

Digital.CSIC. Repositorio Institucional del CSIC
Dataset

DATA FROM: GENOME-WIDE SNP DATA UNVEILS THE GLOBALIZATION OF DOMESTICATED PIGS

  • Yang, Bin
  • Cui, Leilei
  • Pérez-Enciso, Miguel
  • Traspov, Aleksei
  • Crooijmans, Richard P. M. A.
  • Zinovieva, Natalia
  • Schook, Lawrence B.
  • Archibald, Alan L.
  • Gatphayak, Kesinee
  • Knorr, Christophe
  • Triantafyllidis, Alex
  • Alexandri, Panoraia
  • Semiadi, Gono
  • Hanotte, Olivier
  • Dias, Deodália
  • Dovč, Peter
  • Uimari, Pekka
  • Iacolina, Laura
  • Scandura, Massimo
  • Groenen, Martien A. M.
  • Huang, Lusheng
  • Megens, Hendrik-Jan
Usage Notes: Description_data_GSE_Global_pigs Table describing the samples. Note that the submitted data includes a few animals that were removed from the paper due to additional constraints applied in the review process. GSE_global_pigs.map PLINK MAP file, describing the SNPs used. GSE_global_pigs.ped Genotype data used in PLINK PED file format., [Background]: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection., [Results]: A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection., [Conclusions]: Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation., Peer reviewed

Proyecto: //
DOI: http://hdl.handle.net/10261/269720
Digital.CSIC. Repositorio Institucional del CSIC
HANDLE: http://hdl.handle.net/10261/269720
Digital.CSIC. Repositorio Institucional del CSIC
PMID: http://hdl.handle.net/10261/269720
Digital.CSIC. Repositorio Institucional del CSIC
Ver en: http://hdl.handle.net/10261/269720
Digital.CSIC. Repositorio Institucional del CSIC

Digital.CSIC. Repositorio Institucional del CSIC
Dataset

A COMPREHENSIVE PHYLOGENOMIC PLATFORM FOR EXPLORING THE ANGIOSPERM TREE OF LIFE

  • Baker, William J.
  • Bailey, Paul
  • Barber, Vanessa
  • Barker, Abigail
  • Bellot, Sidonie
  • Bishop, David
  • Botigue, Laura
  • Brewer, Grace
  • Carruthers, Tom
  • Clarkson, James
  • Cook, Jeffrey
  • Cowan, Robyn
  • Dodsworth, Steven
  • Epitawalage, Niroshini
  • Françoso, Elaine
  • Gallego, Berta
  • Johnson, Matthew
  • Kim, Jan
  • Leempoel, Kevin
  • Maurin, Olivier
  • McGinnie, Catherine
  • Pokorny, Lisa
  • Roy, Shyamali
  • Stone, Malcolm
  • Toledo, Eduardo
  • Wickett, Norman
  • Zuntini, Alexandre
  • Eiserhardt, Wolf
  • Kersey, Paul
  • Leitch, Ilia
  • Forest, Félix
Software https://treeoflife.kew.org https://github.com/RBGKew/KewTreeOfLife, The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this paper are to (i) document our methods, (ii) describe our first data release and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic dataset for angiosperms to date, comprising 3,099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96%) and 2,333 genera (17%). A “first pass” angiosperm tree of life was inferred from the data, which totalled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated dataset, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone towards a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardised nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections., Calleva Foundation. Sackler Trust. Garfield Weston Foundation, Peer reviewed

Proyecto: //
DOI: http://hdl.handle.net/10261/269729
Digital.CSIC. Repositorio Institucional del CSIC
HANDLE: http://hdl.handle.net/10261/269729
Digital.CSIC. Repositorio Institucional del CSIC
PMID: http://hdl.handle.net/10261/269729
Digital.CSIC. Repositorio Institucional del CSIC
Ver en: http://hdl.handle.net/10261/269729
Digital.CSIC. Repositorio Institucional del CSIC

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