340 research outputs found

    The emergence and fate of horizontally acquired genes in Escherichia coli

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    Bacterial species, and even strains within species, can vary greatly in their gene contents and metabolic capabilities. We examine the evolution of this diversity by assessing the distribution and ancestry of each gene in 13 sequenced isolates of Escherichia coli and Shigella. We focus on the emergence and demise of two specific classes of genes, ORFans (genes with no homologs in present databases) and HOPs (genes with distant homologs), since these genes, in contrast to most conserved ancestral sequences, are known to be a major source of the novel features in each strain. We find that the rates of gain and loss of these genes vary greatly among strains as well as through time, and that ORFans and HOPs show very different behavior with respect to their emergence and demise. Although HOPs, which mostly represent gene acquisitions from other bacteria, originate more frequently, ORFans are much more likely to persist. This difference suggests that many adaptive traits are conferred by completely novel genes that do not originate in other bacterial genomes. With respect to the demise of these acquired genes, we find that strains of Shigella lose genes, both by disruption events and by complete removal, at accelerated rates

    The impact of mechanical shear on membrane flux and energy demand

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    The use of forced mechanical shear for both disc membranes (rotating and vibrating disc filtration, RDF and VDF respectively) and hollow fibres (vibrating HF membranes, VHFM) is reviewed. These systems have been extensively studied and, in the case of the disc membranes, have reached commercialisation and proven effective in achieving transmembrane pressure (TMP) control for various challenging feed waters. The effects of operating conditions, namely shear rate as enhanced by rotation and vibration speed and TMP, and feed water quality on the filtration flux and specific energy consumption are quantified as part of the review. A new relationship is revealed between the two empirical constants governing the classical relationship between membrane flux and shear rate, and a mathematical correlation proposed accordingly. A study of available information on energy reveals that operation at lower shear rates (i.e. rotation or vibration speeds) and more conservative fluxes leads to lower specific energy demands in kWh m−3 permeate, albeit with a larger required membrane area

    Managing Sustainability Projects for Social Impact from a Corporate Social Responsibility Perspective

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    Initiatives in Corporate Social Responsibility (CSR) can contribute to many programs for sustainable development. The Middle East and North Africa (MENA) region is considered to have been slower to change in CSR than have other Western developed countries. The purpose of this research is to explore examples in the United Arab Emirates (UAE) of how project initiatives in CSR and sustainable development can facilitate heightened awareness, engagement, and execution of action for sustainability. This research utilizes qualitative case study methods analysing a United Nations (UN) supported annual youth engagement program focused on implementation of sustainable development projects in the UAE. The varying degrees of project complexity and “programmification” of sustainability activities in the UAE reveals a more systematic and mature stage of CSR and sustainable development projects and programs than is reported in the literature. The application of project management to organize, implement, align, and monitor sustainability-centred programs provides knowledge relevant to the UAE and other countries interested in the strategic management of change. The study demonstrates the application and value of project management for implementing sustainable development initiatives and highlights the collaborative contribution of corporate and governmental stakeholders to project management in organizations. An important area for future research on sustainable development in the MENA region is to study corporate and public sector partnerships in CSR projects and sustainability programs

    Measuring the three-dimensional shear from simulation data, with applications to weak gravitational lensing

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    We have developed a new three-dimensional algorithm, based on the standard P3^3M method, for computing deflections due to weak gravitational lensing. We compare the results of this method with those of the two-dimensional planar approach, and rigorously outline the conditions under which the two approaches are equivalent. Our new algorithm uses a Fast Fourier Transform convolution method for speed, and has a variable softening feature to provide a realistic interpretation of the large-scale structure in a simulation. The output values of the code are compared with those from the Ewald summation method, which we describe and develop in detail. With an optimal choice of the high frequency filtering in the Fourier convolution, the maximum errors, when using only a single particle, are about 7 per cent, with an rms error less than 2 per cent. For ensembles of particles, used in typical NN-body simulations, the rms errors are typically 0.3 per cent. We describe how the output from the algorithm can be used to generate distributions of magnification, source ellipticity, shear and convergence for large-scale structure.Comment: 22 pages, latex, 11 figure

    A connection between stress and development in the multicelular prokaryote Streptomyces coelicolor

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    Morphological changes leading to aerial mycelium formation and sporulation in the mycelial bacterium Streptomyces coelicolor rely on establishing distinct patterns of gene expression in separate regions of the colony. sH was identified previously as one of three paralogous sigma factors associated with stress responses in S. coelicolor. Here, we show that sigH and the upstream gene prsH (encoding a putative antisigma factor of sH) form an operon transcribed from two developmentally regulated promoters, sigHp1 and sigHp2. While sigHp1 activity is confined to the early phase of growth, transcription of sigHp2 is dramatically induced at the time of aerial hyphae formation. Localization of sigHp2 activity using a transcriptional fusion to the green fluorescent protein reporter gene (sigHp2–egfp) showed that sigHp2 transcription is spatially restricted to sporulating aerial hyphae in wild-type S. coelicolor. However, analysis of mutants unable to form aerial hyphae (bld mutants) showed that sigHp2 transcription and sH protein levels are dramatically upregulated in a bldD mutant, and that the sigHp2–egfp fusion was expressed ectopically in the substrate mycelium in the bldD background. Finally, a protein possessing sigHp2 promoter-binding activity was purified to homogeneity from crude mycelial extracts of S. coelicolor and shown to be BldD. The BldD binding site in the sigHp2 promoter was defined by DNase I footprinting. These data show that expression of sH is subject to temporal and spatial regulation during colony development, that this tissue-specific regulation is mediated directly by the developmental transcription factor BldD and suggest that stress and developmental programmes may be intimately connected in Streptomyces morphogenesis

    The Qatar Biobank: background and methods

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    Background: The Qatar Biobank aims to collect extensive lifestyle, clinical, and biological information from up to 60,000 men and women Qatari nationals and long-term residents (individuals living in the country for ≥15 years) aged ≥18 years (approximately one-fifth of all Qatari citizens), to follow up these same individuals over the long term to record any subsequent disease, and hence to study the causes and progression of disease, and disease burden, in the Qatari population. Methods: Between the 11th-December-2012 and 20th-February-2014, 1209 participants were recruited into the pilot study of the Qatar Biobank. At recruitment, extensive phenotype information was collected from each participant, including information/measurements of socio-demographic factors, prevalent health conditions, diet, lifestyle, anthropometry, body composition, bone health, cognitive function, grip strength, retinal imaging, total body dual energy X-ray absorptiometry, and measurements of cardiovascular and respiratory function. Blood, urine, and saliva were collected and stored for future research use. A panel of 66 clinical biomarkers was routinely measured on fresh blood samples in all participants. Rates of recruitment are to be progressively increased in the coming period and the recruitment base widened to achieve a cohort of consented individuals broadly representative of the eligible Qatari population. In addition, it is planned to add additional measures in sub-samples of the cohort, including Magnetic Resonance Imaging (MRI) of the brain, heart and abdomen. Results: The mean time for collection of the extensive phenotypic information and biological samples from each participant at the baseline recruitment visit was 179 min. The 1209 pilot study participants (506 men and 703 women) were aged between 28–80 years (median 39 years); 899 (74.4 %) were Qatari nationals and 310 (25.6 %) were long-term residents. Approximately two-thirds of pilot participants were educated to graduate level or above. Conclusions: The pilot has proven that recruitment of volunteers into the Qatar Biobank project with intensive baseline measurements of behavioural, physical, and clinical characteristics is well accepted and logistically feasible. Qatar Biobank will provide a powerful resource to investigate the major determinants of ill-health and well-being in Qatar, providing valuable insights into the current and future public health burden that faces the country.Qatar Foundation for Education, Science and Community Development and the Supreme Council of Healt

    Discovering study-specific gene regulatory networks

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    This article has been made available through the Brunel Open Access Publishing Fund.Microarrays are commonly used in biology because of their ability to simultaneously measure thousands of genes under different conditions. Due to their structure, typically containing a high amount of variables but far fewer samples, scalable network analysis techniques are often employed. In particular, consensus approaches have been recently used that combine multiple microarray studies in order to find networks that are more robust. The purpose of this paper, however, is to combine multiple microarray studies to automatically identify subnetworks that are distinctive to specific experimental conditions rather than common to them all. To better understand key regulatory mechanisms and how they change under different conditions, we derive unique networks from multiple independent networks built using glasso which goes beyond standard correlations. This involves calculating cluster prediction accuracies to detect the most predictive genes for a specific set of conditions. We differentiate between accuracies calculated using cross-validation within a selected cluster of studies (the intra prediction accuracy) and those calculated on a set of independent studies belonging to different study clusters (inter prediction accuracy). Finally, we compare our method's results to related state-of-the art techniques. We explore how the proposed pipeline performs on both synthetic data and real data (wheat and Fusarium). Our results show that subnetworks can be identified reliably that are specific to subsets of studies and that these networks reflect key mechanisms that are fundamental to the experimental conditions in each of those subsets

    PAHs in the Halo of NGC 5529

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    We present sensitive ISO λ6.7μ\lambda 6.7 \mum observations of the edge-on galaxy, NGC 5529, finding an extensive MIR halo around NGC 5529. The emission is dominated by PAHs in this band. The PAH halo has an exponential scale height of 3.7 kpc but can still be detected as far as 10\approx 10 kpc from the plane to the limits of the high dynamic range (1770/1) data. This is the most extensive PAH halo yet detected in a normal galaxy. This halo shows substructure and the PAHs likely originate from some type of disk outflow. PAHs are long-lived in a halo environment and therefore continuous replenishment from the disk is not required (unless halo PAHs are also being destroyed or removed), consistent with the current low SFR of the galaxy. The PAHs correlate spatially with halo Hα\alpha emission, previously observed by Miller & Veilleux (2003); both components are likely excited/ionized by in-disk photons that are leaking into the halo. The presence of halo gas may be related to the environment of NGC 5529 which contains at least 17 galaxies in a small group of which NGC 5529 is the dominant member. Of these, we have identified two new companions from the SDSS.Comment: 16 pages, 5 gif figures, accepted for publication in A&A, For pdf with higher quality figures, see http://www.astro.queensu.ca/~irwi
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