Mostrando recursos 1 - 12 de 12

  1. A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery

    Moazzzam Jazi, Maryam; Seyedi, Seyed M.; Ebrahimie, Esmaeil; Ebrahimi, Mansour; De Moro, Gianluca; Botanga, Christopher
    Background Pistachio (Pistacia vera L.) is one of the most important commercial nut crops worldwide. It is a salt-tolerant and long-lived tree, with the largest cultivation area in Iran. Climate change and subsequent increased soil salt content have adversely affected the pistachio yield in recent years. However, the lack of genomic/global transcriptomic sequences on P. vera impedes comprehensive researches at the molecular level. Hence, whole transcriptome sequencing is required to gain insight into functional genes and pathways in response to salt stress. Results RNA sequencing of a pooled sample representing 24 different tissues of two pistachio cultivars with contrasting salinity...

  2. rdml: A Mathematica package for parsing and importing Real-Time qPCR data

    Magno, Ramiro; Duarte, Isabel; Andrade, Raquel P.; Palmeirim, Isabel
    Objective The purpose and objective of the research presented is to provide a package for easy importing of Real-Time PCR data markup language (RDML) data to Mathematica. Results Real-Time qPCR is the most widely used experimental method for the accurate quantification of gene expression. To enable the straightforward archiving and sharing of qPCR data and its associated experimental information, an XML-based data standard was developed—the Real-Time PCR data markup language (RDML)—devised by the RDML consortium. Here, we present rdml, a package to parse and import RDML data into Mathematica, allowing the quick loading and extraction of relevant data,...

  3. Intraspecific genetic lineages of a marine mussel show behavioural divergence and spatial segregation over a tropical/subtropical biogeographic transition

    Zardi, Gerardo I.; Nicastro, K. R.; McQuaid, C. D.; Castilho, Rita; Costa, Joana; Serrão, Ester A.; Pearson, Gareth A.
    Background: Intraspecific variability is seen as a central component of biodiversity. We investigated genetic differentiation, contemporary patterns of demographic connectivity and intraspecific variation of adaptive behavioural traits in two lineages of an intertidal mussel (Perna perna) across a tropical/subtropical biogeographic transition. Results: Microsatellite analyses revealed clear genetic differentiation between western (temperate) and eastern (subtropical/tropical) populations, confirming divergence previously detected with mitochondrial (COI) and nuclear (ITS) markers. Gene flow between regions was predominantly east-to-west and was only moderate, with higher heterozygote deficiency where the two lineages co-occur. This can be explained by differential selection and/or oceanographic dynamics acting as a barrier to...

  4. Characterization of the cork oak transcriptome dynamics during acorn development

    Miguel, Andreia; de Vega-Bartol, José; Marum, Liliana; Chaves, Inês; Santo, Tatiana; Leitão, José; Varela, Maria C.; Miguel, Célia M.
    Background: Cork oak (Quercus suber L.) has a natural distribution across western Mediterranean regions and is a keystone forest tree species in these ecosystems. The fruiting phase is especially critical for its regeneration but the molecular mechanisms underlying the biochemical and physiological changes during cork oak acorn development are poorly understood. In this study, the transcriptome of the cork oak acorn, including the seed, was characterized in five stages of development, from early development to acorn maturation, to identify the dominant processes in each stage and reveal transcripts with important functions in gene expression regulation and response to water. Results: A...

  5. Polymorphic microsatellite markers in the brown seaweed Fucus vesiculosus

    Candeias, R.; Casado-Amezúa, Pilar; Pearson, Gareth A.; Serrão, Ester; Teixeira, Sara
    Background: Fucus vesiculosus is a brown seaweed dominant on temperate rocky shores of the northern hemisphere and, is typically distributed in the mid-upper intertidal zone. It is an external fertilizer that reproduces sexually, providing an excellent model to address conflicting theories related to mating systems and sexual selection. Microsatellite markers have been reported for several Fucus species, however the genomic libraries from where these markers have been isolated, have originated from two or more species pooled together (F. vesiculosus and F. serratus in one library; F. vesiculosus, F. serratus and Ascophyllum nodosum in a second library), or when the genomic...

  6. A novel phosphatidylinositol 3-kinase (PI3K) inhibitor directs a potent FOXO-dependent, p53-independent cell cycle arrest phenotype characterized by the differential induction of a subset of FOXO-regulated genes

    Hill, Richard; Kalathur, Ravi K. R.; Callejas, Sergio; Colaço, Laura; Brandão, Ricardo; Serelde, Beatriz; Cebriá, Antonio; Blanco-Aparicio, Carmen; Pastor, Joaquín; Futschik, Matthias; Dopazo, Ana; Link, Wolfgang
    Introduction: The activation of the phosphoinositide 3-kinase (PI3K)/AKT signalling pathway is one the most frequent genetic events in breast cancer, consequently the development of PI3K inhibitors has attracted much attention. Here we evaluate the effect of PI3K inhibition on global gene expression in breast cancer cells. Methods: We used a range of methodologies that include in silico compound analysis, in vitro kinase assays, cell invasion assays, proliferation assays, genome-wide transcription studies (Agilent Technologies full genome arrays), gene set enrichment analysis, quantitative real-time PCR, immunoblotting in addition to chromatin immunoprecipitation. Results: We defined the physico-chemical and the biological properties of ETP-45658, a novel...

  7. Thermal plasticity of the miRNA transcriptome during Senegalese sole development

    Campos, C.; Sundaram, Arvind Y. M.; Valente, Luisa M. P.; Conceição, L. E. C.; Engrola, S.; Fernandes, Jorge M. O.
    Several miRNAs are known to control myogenesis in vertebrates. Some of them are specifically expressed in muscle while others have a broader tissue expression but are still involved in establishing the muscle phenotype. In teleosts, water temperature markedly affects embryonic development and larval growth. It has been previously shown that higher embryonic temperatures promoted faster development and increased size of Senegalese sole (Solea senegalensis) larvae relatively to a lower temperature. The role of miRNAs in thermal-plasticity of growth is hitherto unknown. Hence, we have used high-throughput SOLiD sequencing to determine potential changes in the miRNA transcriptome in Senegalese sole embryos...

  8. A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing

    Pereira-Leal, José B.; Abreu, Isabel A.; Alabaça, Cláudia S.; Almeida, Maria H.; Almeida, Paulo; Almeida, Tânia; Amorim, Maria I.; Araújo, Susana; Azevedo, Herlânder; Badia, Aleix; Batista, Dora; Bohn, Andreas; Capote, Tiago; Carrasquinho, Isabel; Chaves, Inês; Coelho, A. C.; Costa, Maria M. R.; Costa, Rita; Cravador, A.; Egas, Conceição; Faro, Carlos; Fortes, Ana M.; Fortunato, Ana S.; Gaspar, Maria J.; Gonçalves, Sónia; Graça, José; Horta, M.; Inácio, Vera; Leitão, José; Lino-Neto, Teresa; Marum, Liliana; Matos, José; Mendonça, Diogo; Miguel, Andreia; Miguel, Célia M.; Morais-Cecílio, Leonor; Neves, Isabel; Nóbrega, Filomena; Oliveira, Maria M.; Oliveira, Rute; Pais, Maria S.; Paiva, Jorge A.; Paulo, Octávio S.; Pinheiro, Miguel; Raimundo, João A. P.; Ramalho, J. C.; Ribeiro, Ana I.; Ribeiro, Teresa; Rocheta, Margarida; Rodrigues, Ana I.; Rodrigues, José C.; Saibo, Nelson J. M.; Santo, Tatiana E.; Santos, Ana M.; Sá-Pereira, Paula; Sebastiana, Mónica; Simões, Fernanda; Sobral, Rómulo S.; Tavares, Rui; Teixeira, Rita; Varela, Carolina; Veloso, Maria M.; Ricardo, Cândido P. P.
    Background: Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing...

  9. Transthoracic echocardiography reference values in juvenile and adult 129/Sv mice

    Vinhas, Maurícia; Araújo, Ana Carolina; Ribeiro, Sónia; Rosário, Luís Brás; Belo, José António
    Background In the recent years, the use of Doppler-echocardiography has become a standard non-invasive technique in the analysis of cardiac malformations in genetically modified mice. Therefore, normal values have to be established for the most commonly used inbred strains in whose genetic background those mutations are generated. Here we provide reference values for transthoracic echocardiography measurements in juvenile (3 weeks) and adult (8 weeks) 129/Sv mice. Methods Echocardiographic measurements were performed using B-mode, M-mode and Doppler-mode in 15 juvenile (3 weeks) and 15 adult (8 weeks) mice, during isoflurane anesthesia. M-mode measurements variability of left ventricle (LV) was determined. Results Several echocardiographic measurements significantly...

  10. Shift happens: trailing edge contraction associated with recent warming trends threatens a distinct genetic lineage in the marine macroalga Fucus vesiculosus

    Nicastro, K. R.; Zardi, G. I.; Teixeira, Sara; Neiva, J.; Serrão, Ester; Pearson, G. A.
    Significant effects of recent global climate change have already been observed in a variety of ecosystems, with evidence for shifts in species ranges, but rarely have such consequences been related to the changes in the species genetic pool. The stretch of Atlantic coast between North Africa and North Iberia is ideal for studying the relationship between species distribution and climate change as it includes the distributional limits of a considerable number of both cold- and warm-water species. We compared temporal changes in distribution of the canopy-forming alga Fucus vesiculosus with historical sea surface temperature (SST) patterns to draw links between range...

  11. Huntington's Disease and its therapeutic target genes: a global functional profile based on the HD Research Crossroads database

    Kalathur, Ravi K. R.; Hernández-Prieto, Miguel A; Futschik, Matthias
    Huntington’s disease (HD) is a fatal progressive neurodegenerative disorder caused by the expansion of the polyglutamine repeat region in the huntingtin gene. Although the disease is triggered by the mutation of a single gene, intensive research has linked numerous other genes to its pathogenesis. To obtain a systematic overview of these genes, which may serve as therapeutic targets, CHDI Foundation has recently established the HD Research Crossroads database. With currently over 800 cataloged genes, this web-based resource constitutes the most extensive curation of genes relevant to HD. It provides us with an unprecedented opportunity to survey molecular mechanisms involved in...

  12. Fine-scale genetic breaks driven by historical rangedynamics and ongoing density-barrier effects in theestuarine seaweed Fucus ceranoides L.

    Neiva, J.; Pearson, G. A.; Valero, M.; Serrão, Ester
    Factors promoting the emergence of sharp phylogeographic breaks include restricted dispersal, habitat discontinuity, physical barriers, disruptive selection, mating incompatibility, genetic surfing and secondary contact. Disentangling the role of each in any particular system can be difficult, especially when species are evenly distributed across transition zones and dispersal barriers are not evident. The estuarine seaweed Fucus ceranoides provides a good example of highly differentiated populations along its most persistent distributional range at the present rear edge of the species distribution, in NW Iberia. Intrinsic dispersal restrictions are obvious in this species, but have not prevented F. ceranoides from vastly expanding its...

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