Repetitive DNA in eukaryotic genomes Biscotti, Maria Assunta; Olmo, Ettore; Heslop-Harrison, J. S. (Pat)
Chromosome research,
09/2015, Letnik:
23, Številka:
3
Journal Article
Recenzirano
Repetitive DNA—sequence motifs repeated hundreds or thousands of times in the genome—makes up the major proportion of all the nuclear DNA in most eukaryotic genomes. However, the significance of ...repetitive DNA in the genome is not completely understood, and it has been considered to have both structural and functional roles, or perhaps even no essential role. High-throughput DNA sequencing reveals huge numbers of repetitive sequences. Most bioinformatic studies focus on low-copy DNA including genes, and hence, the analyses collapse repeats in assemblies presenting only one or a few copies, often masking out and ignoring them in both DNA and RNA read data. Chromosomal studies are proving vital to examine the distribution and evolution of sequences because of the challenges of analysis of sequence data. Many questions are open about the origin, evolutionary mode and functions that repetitive sequences might have in the genome. Some, the satellite DNAs, are present in long arrays of similar motifs at a small number of sites, while others, particularly the transposable elements (DNA transposons and retrotranposons), are dispersed over regions of the genome; in both cases, sequence motifs may be located at relatively specific chromosome domains such as centromeres or subtelomeric regions. Here, we overview a range of works involving detailed characterization of the nature of all types of repetitive sequences, in particular their organization, abundance, chromosome localization, variation in sequence within and between chromosomes, and, importantly, the investigation of their transcription or expression activity. Comparison of the nature and locations of sequences between more, and less, related species is providing extensive information about their evolution and amplification. Some repetitive sequences are extremely well conserved between species, while others are among the most variable, defining differences between even closely relative species. These data suggest contrasting modes of evolution of repetitive DNA of different types, including selfish sequences that propagate themselves and may even be transferred horizontally between species rather than by descent, through to sequences that have a tendency to amplification because of their sequence motifs, to those that have structural significance because of their bulk rather than precise sequence. Functional consequences of repeats include generation of variability by movement and insertion in the genome (giving useful genetic markers), the definition of centromeres, expression under stress conditions and regulation of gene expression via RNA moieties. Molecular cytogenetics and bioinformatic studies in a comparative context are now enabling understanding of the nature and behaviour of this major genomic component.
Subfossil pollen and plant macrofossil data derived from
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C-dated sediment profiles can provide quantitative information on glacial and interglacial climates. The data allow climate variables ...related to growing-season warmth, winter cold, and plant-available moisture to be reconstructed. Continental-scale reconstructions have been made for the mid-Holocene (MH, around 6 ka) and Last Glacial Maximum (LGM, around 21 ka), allowing comparison with palaeoclimate simulations currently being carried out as part of the fifth Assessment Report (AR5) of the Intergovernmental Panel on Climate Change. The synthesis of the available MH and LGM climate reconstructions and their uncertainties, obtained using modern-analogue, regression and model-inversion techniques, is presented for four temperature variables and two moisture variables. Reconstructions of the same variables based on surface-pollen assemblages are shown to be accurate and unbiased. Reconstructed LGM and MH climate anomaly patterns are coherent, consistent between variables, and robust with respect to the choice of technique. They support a conceptual model of the controls of Late Quaternary climate change whereby the first-order effects of orbital variations and greenhouse forcing on the seasonal cycle of temperature are predictably modified by responses of the atmospheric circulation and surface energy balance.
Managing for Stakeholders: Survival, Reputation, and Success,the culmination of twenty years of research, interviews, and observations in the workplace, makes a major new contribution to management ...thinking and practice. Current ways of thinking about business and stakeholder management usually ask the Value Allocation Question: How should we distribute the burdens and benefits of corporate activities among stakeholders?Managing for Stakeholders,however, helps leaders develop a mindset that instead asks the Value Creation Question: How can we create as much value as possible for all of our stakeholders?
Business is about how customers, suppliers, employees, financiers (stockholders, bondholders, banks, etc.), communities, the media, and managers interact and create value. World-renowned management scholar R. Edward Freeman and his coauthors outline ten concrete principles and seven practical techniques for managing stakeholder relationships in order to ensure a firm's survival, reputation, and success.Managing for Stakeholdersis a revolutionary book that will change not only how managers do business but also how they recognize and evaluate business opportunities that would otherwise be invisible.
Most, if not all, green plant (Virdiplantae) species including angiosperms and ferns are polyploids themselves or have ancient polyploid or whole genome duplication signatures in their genomes. ...Polyploids are not only restricted to our major crop species such as wheat, maize, potato and the brassicas, but also occur frequently in wild species and natural habitats. Polyploidy has thus been viewed as a major driver in evolution, and its influence on genome and chromosome evolution has been at the centre of many investigations. Mechanistic models of the newly structured genomes are being developed that incorporate aspects of sequence evolution or turnover (low-copy genes and regulatory sequences, as well as repetitive DNAs), modification of gene functions, the re-establishment of control of genes with multiple copies, and often meiotic chromosome pairing, recombination and restoration of fertility.
World-wide interest in how green plants have evolved under different conditions - whether in small, isolated populations, or globally - suggests that gaining further insight into the contribution of polyploidy to plant speciation and adaptation to environmental changes is greatly needed. Forward-looking research and modelling, based on cytogenetics, expression studies, and genomics or genome sequencing analyses, discussed in this Special Issue of the Annals of Botany, consider how new polyploids behave and the pathways available for genome evolution. They address fundamental questions about the advantages and disadvantages of polyploidy, the consequences for evolution and speciation, and applied questions regarding the spread of polyploids in the environment and challenges in breeding and exploitation of wild relatives through introgression or resynthesis of polyploids.
Chromosome number, genome size, repetitive DNA sequences, genes and regulatory sequences and their expression evolve following polyploidy - generating diversity and possible novel traits and enabling species diversification. There is the potential for ever more polyploids in natural, managed and disturbed environments under changing climates and new stresses.
T cell dysfunction contributes to tumor immune escape in patients with cancer and is particularly severe amidst glioblastoma (GBM). Among other defects, T cell lymphopenia is characteristic, yet ...often attributed to treatment. We reveal that even treatment-naïve subjects and mice with GBM can harbor AIDS-level CD4 counts, as well as contracted, T cell-deficient lymphoid organs. Missing naïve T cells are instead found sequestered in large numbers in the bone marrow. This phenomenon characterizes not only GBM but a variety of other cancers, although only when tumors are introduced into the intracranial compartment. T cell sequestration is accompanied by tumor-imposed loss of S1P1 from the T cell surface and is reversible upon precluding S1P1 internalization. In murine models of GBM, hindering S1P1 internalization and reversing sequestration licenses T cell-activating therapies that were previously ineffective. Sequestration of T cells in bone marrow is therefore a tumor-adaptive mode of T cell dysfunction, whose reversal may constitute a promising immunotherapeutic adjunct.
Polymers based on olefins have wide commercial applicability. However, they are made from non-renewable resources and are characterised by difficulty in disposal where recycle and re-use is not ...feasible. Poly-β-hydroxybutyric acid (PHB) provides one example of a polymer made from renewable resources. Before motivating its widespread use, the advantages of a renewable polymer must be weighed against the environmental aspects of its production. Previous studies relating the environmental impacts of petroleum-based and bio-plastics have centred on the impact categories of global warming and fossil fuel depletion. Cradle-to-grave studies report equivalent or reduced global warming impacts, in comparison to equivalent polyolefin processes. This stems from a perceived CO
2 neutral status of the renewable resource. Indeed, no previous work has reported the results of a life cycle assessment (LCA) giving the environmental impacts in all major categories. This study investigates a cradle-to-gate LCA of PHB production taking into account net CO
2 generation and all major impact categories. It compares the findings with similar studies of polypropylene (PP) and polyethylene (PE). It is found that, in all of the life cycle categories, PHB is superior to PP. Energy requirements are slightly lower than previously observed and significantly lower than those for polyolefin production. PE impacts are lower than PHB values in acidification and eutrophication.
This paper argues that the notion of value has been overly simplified and narrowed to focus on economic returns. Stakeholder theory provides an appropriate lens for considering a more complex ...perspective of the value that stakeholders seek as well as new ways to measure it. We develop a four-factor perspective for defining value that includes, but extends beyond, the economic value stakeholders seek. To highlight its distinctiveness, we compare this perspective to three other popular performance perspectives. Recommendations are made regarding performance measurement for both academic researchers and practitioners. The stakeholder perspective on value offered in this paper draws attention to those factors that are most closely associated with building more value for stakeholders, and in so doing, allows academics to better measure it and enhances managerial ability to create it.
Accelerated glacier melt and the loss of perennial snowfields have been associated with increased warming in polar regions, at rates up to four times faster than the rest of the world, thereby ...reinforcing the critical need for improved models (and predictions) of glacier melt. An essential requirement for such models is an improved understanding of the sensible heat fluxes over glaciers. Since their complexity makes them difficult to model, and direct measurements of sensible turbulent heat fluxes over real glaciers are both rare and impractical, the present work involves simultaneous hot-wire anemometry and cold-wire thermometry measurements of two components of velocity and temperature above a melting glacier model in a series of wind-tunnel experiments. Both single- and multi-variable statistics were used to compare the turbulent velocity field measured over melting ice with that of a similar flow in the absence of ice. The results demonstrate that the ice's presence reduces the magnitude of the Reynolds stresses and vertical velocity variance, but also increases the streamwise velocity variance. The transient evolution of temperature statistics throughout the melt process was also investigated and found to be similar when suitably non-dimensionalized. The velocity and temperature fields were furthermore evaluated at an equivalent non-dimensional time during the melt process, in which statistics of the temperature field, and joint statistics of the vertical velocity and temperature, were studied. The present work lays the foundation for future laboratory-scale replications of the flow above melting glaciers, and provides additional insight into turbulent heat transfer over melting ice.
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