83 research outputs found

    Influence of offshore oil and gas structures on seascape ecological connectivity.

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    Offshore platforms, subsea pipelines, wells and related fixed structures supporting the oil and gas (O&G) industry are prevalent in oceans across the globe, with many approaching the end of their operational life and requiring decommissioning. Although structures can possess high ecological diversity and productivity, information on how they interact with broader ecological processes remains unclear. Here, we review the current state of knowledge on the role of O&G infrastructure in maintaining, altering or enhancing ecological connectivity with natural marine habitats. There is a paucity of studies on the subject with only 33 papers specifically targeting connectivity and O&G structures, although other studies provide important related information. Evidence for O&G structures facilitating vertical and horizontal seascape connectivity exists for larvae and mobile adult invertebrates, fish and megafauna; including threatened and commercially important species. The degree to which these structures represent a beneficial or detrimental net impact remains unclear, is complex and ultimately needs more research to determine the extent to which natural connectivity networks are conserved, enhanced or disrupted. We discuss the potential impacts of different decommissioning approaches on seascape connectivity and identify, through expert elicitation, critical knowledge gaps that, if addressed, may further inform decision making for the life cycle of O&G infrastructure, with relevance for other industries (e.g. renewables). The most highly ranked critical knowledge gap was a need to understand how O&G structures modify and influence the movement patterns of mobile species and dispersal stages of sessile marine species. Understanding how different decommissioning options affect species survival and movement was also highly ranked, as was understanding the extent to which O&G structures contribute to extending species distributions by providing rest stops, foraging habitat, and stepping stones. These questions could be addressed with further dedicated studies of animal movement in relation to structures using telemetry, molecular techniques and movement models. Our review and these priority questions provide a roadmap for advancing research needed to support evidence-based decision making for decommissioning O&G infrastructure

    Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer

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    Endocrine therapy resistance frequently develops in estrogen receptor positive (ER+) breast cancer, but the underlying molecular mechanisms are largely unknown. Here, we show that 3-dimensional (3D) chromatin interactions both within and between topologically associating domains (TADs) frequently change in ER+ endocrine-resistant breast cancer cells and that the differential interactions are enriched for resistance-associated genetic variants at CTCF-bound anchors. Ectopic chromatin interactions are preferentially enriched at active enhancers and promoters and ER binding sites, and are associated with altered expression of ER-regulated genes, consistent with dynamic remodelling of ER pathways accompanying the development of endocrine resistance. We observe that loss of 3D chromatin interactions often occurs coincidently with hypermethylation and loss of ER binding. Alterations in active A and inactive B chromosomal compartments are also associated with decreased ER binding and atypical interactions and gene expression. Together, our results suggest that 3D epigenome remodelling is a key mechanism underlying endocrine resistance in ER+ breast cancer

    Weighted coefficients to measure agreement among several sets of ranks emphasizing top and bottom ranks at the same time

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    In this paper, two new weighted coefficients of agreement to measure the concordance among several (more than two) sets of ranks, putting more weight in the lower and upper ranks simultaneously, are presented. These new coefficients, the signed Klotz and the signed Mood, generalize the correspondent rank-order coefficients to measure the agreement between two sets of ranks previously proposed by the authors [1]. Under the null hypothesis of no agreement or no association among the rankings, the asymptotic distribution of these new coefficients was derived. To illustrate the worth of these measures, an example is presented to compare them with the Kendall’s coefficient and the van der Waerden correlation coefficient.info:eu-repo/semantics/publishedVersio

    Resistance to Meloidogyne incognita, Meloidogyne javanica and Pratylenchus brachyurus in sunflower cultivars adapted to the tropical region of Brazil.

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    The continuous soybean-maize crop succession in the tropical region of Brazil has led to significant increases in the population size of root-knot (Meloidogyne incognita and M. javanica ) and root-lesion nematodes (Pratylenchus brachyurus), which make soils unsuitable for soybean cropping. A greenhouse study was conducted to identify sunflower genotypes adapted to the tropical region of Brazil and that are resistant to M. incognita, M. javanica and/or P. brachyurus . Two experiments for each nematode were conducted in a completely randomized design with six replicates. Gall index was calculated from visual scores (0?5) of gall intensity on roots for the root-knot nematode. Initial and final population density and reproduction factor were also measured for each nematode. Sunflower genotypes varied in resistance to the nematodes. Sunflower hybrids BRS 321 and BRS 323 were resistant to M. javanica and P. brachyurus and exhibited low gall index for M. incognita . The cultivars are good alternatives to using in the succession of soybean in nematode-infested areas of the tropical regions of Brazil. No sunflower genotype was identified as resistant to M. incognita and thus sunflower cropping is not indicated in areas infested with this nematode

    Estrogen-induced chromatin decondensation and nuclear re-organization linked to regional epigenetic regulation in breast cancer

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    BACKGROUND: Epigenetic changes are being increasingly recognized as a prominent feature of cancer. This occurs not only at individual genes, but also over larger chromosomal domains. To investigate this, we set out to identify large chromosomal domains of epigenetic dysregulation in breast cancers. RESULTS: We identify large regions of coordinate down-regulation of gene expression, and other regions of coordinate activation, in breast cancers and show that these regions are linked to tumor subtype. In particular we show that a group of coordinately regulated regions are expressed in luminal, estrogen-receptor positive breast tumors and cell lines. For one of these regions of coordinate gene activation, we show that regional epigenetic regulation is accompanied by visible unfolding of large-scale chromatin structure and a repositioning of the region within the nucleus. In MCF7 cells, we show that this depends on the presence of estrogen. CONCLUSIONS: Our data suggest that the liganded estrogen receptor is linked to long-range changes in higher-order chromatin organization and epigenetic dysregulation in cancer. This may suggest that as well as drugs targeting histone modifications, it will be valuable to investigate the inhibition of protein complexes involved in chromatin folding in cancer cells. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0719-9) contains supplementary material, which is available to authorized users

    Large conserved domains of low DNA methylation maintained by 5-hydroxymethycytosine and Dnmt3a

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    Gains and losses in DNA methylation are prominent features of mammalian cell types. To gain insight into the mechanisms that promote shifts in DNA methylation and contribute to changes in cell fate, including malignant transformation, we performed genome-wide mapping of 5-methylcytosine and 5-hydroxymethylcytosine in purified mouse hematopoietic stem cells. We discovered extended regions of low methylation (canyons) that span conserved domains frequently containing transcription factors and are distinct from CpG islands and shores. About half of the genes in these methylation canyons are coated with repressive histone marks, whereas the remainder are covered by activating histone marks and are highly expressed in hematopoietic stem cells (HSCs). Canyon borders are demarked by 5-hydroxymethylcytosine and become eroded in the absence of DNA methyltransferase 3a (Dnmt3a). Genes dysregulated in human leukemias are enriched for canyon-associated genes. The new epigenetic landscape we describe may provide a mechanism for the regulation of hematopoiesis and may contribute to leukemia development. © 2014 Nature America, Inc.close585

    Native-plant hosts of Meloidogyne spp. from Western Paraná, Brazil

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    The present study was focused on the parasitism of Meloidogyne species on the roots of native nursery plants from the Atlantic forest. Native plants were selected from a commercial nursery in Western Paraná, searching for the natural infection of Meloidogyne. Also, the seeds of native plants were cultivated in sterile soil and inoculated with M. incognita. In both the experiments, the number of galls and number of eggs and J2 per root, allied to the reproduction factor of M. incognita on each inoculated plant were assessed. Natural infection by M. javanica was found on Cordia ecalyculata, Citharexyllum myrianthum and Aspidosperma subincanum and by M. incognita on Croton urucurana, Lonchocarpus muehlbergianus, Tabebuia impetiginosa and T. serratifolia. Meloidogyne incognita induced galls formation on Genipa americana, Schinus terebinthifolius and Rollinia mucosa after inoculation, which suggested that those plants could host this nematode in natural biomes. Nursery soil should be disinfested before seeding the native forest plants for reforestation purpose
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