44 research outputs found

    Data management and data analysis in the large European projects GEHA (GEnetics of Healthy Aging) and NU-AGE (NUtrition and AGEing): a bioinformatic approach

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    The aging process is characterized by the progressive fitness decline experienced at all the levels of physiological organization, from single molecules up to the whole organism. Studies confirmed inflammaging, a chronic low-level inflammation, as a deeply intertwined partner of the aging process, which may provide the “common soil” upon which age-related diseases develop and flourish. Thus, albeit inflammation per se represents a physiological process, it can rapidly become detrimental if it goes out of control causing an excess of local and systemic inflammatory response, a striking risk factor for the elderly population. Developing interventions to counteract the establishment of this state is thus a top priority. Diet, among other factors, represents a good candidate to regulate inflammation. Building on top of this consideration, the EU project NU-AGE is now trying to assess if a Mediterranean diet, fortified for the elderly population needs, may help in modulating inflammaging. To do so, NU-AGE enrolled a total of 1250 subjects, half of which followed a 1-year long diet, and characterized them by mean of the most advanced –omics and non –omics analyses. The aim of this thesis was the development of a solid data management pipeline able to efficiently cope with the results of these assays, which are now flowing inside a centralized database, ready to be used to test the most disparate scientific hypotheses. At the same time, the work hereby described encompasses the data analysis of the GEHA project, which was focused on identifying the genetic determinants of longevity, with a particular focus on developing and applying a method for detecting epistatic interactions in human mtDNA. Eventually, in an effort to propel the adoption of NGS technologies in everyday pipeline, we developed a NGS variant calling pipeline devoted to solve all the sequencing-related issues of the mtDNA

    Greenhouse gas emissions from the grassy outdoor run of organic broilers

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    Nitrous oxide (N<sub>2</sub>O), methane (CH<sub>4</sub>) and carbon dioxide (CO<sub>2</sub>) fluxes over the grassy outdoor run of organically grown broilers were monitored using static chambers over two production batches in contrasted seasons. Measured N<sub>2</sub>O and CH<sub>4</sub> fluxes were extremely variable in time and space for both batches, with fluxes ranging from a small uptake by soil to large emissions peaks, the latter of which always occurred in the chambers located closest to the broiler house. In general, fluxes decreased with increasing distance to the broiler house, demonstrating that the foraging of broilers and the amount of excreted nutrients (carbon, nitrogen) largely control the spatial variability of emissions. Spatial integration by kriging methods was carried out to provide representative fluxes on the outdoor run for each measurement day. Mechanistic relationships between plot-scale estimates and environmental conditions (soil temperature and water content) were calibrated in order to fill gaps between measurement days. Flux integration over the year 2010 showed that around 3 ± 1 kg N<sub>2</sub>O-N ha<sup>−1</sup> were emitted on the outdoor run, equivalent to 0.9% of outdoor N excretion and substantially lower than the IPCC default emission factor of 2%. By contrast, the outdoor run was found to be a net CH<sub>4</sub> sink of about −0.56 kg CH<sub>4</sub>-C ha<sup>−1</sup>, though this sink compensated less than 1.5% (in CO<sub>2</sub> equivalents) of N<sub>2</sub>O emissions. The net greenhouse gas (GHG) budget of the outdoor run is explored, based on measured GHG fluxes and short-term (1.5 yr) variations in soil organic carbon

    Pai Hsien-yung, Crystal Boys and Taipei's Memories : View from 'Metropolis Spaces' of the 1970s(Summaries : International Symposium "People's Transportation and Cultural Diversity in East Asia")

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    Genetic signatures from the Paleolithic inhabitants of Eurasia can be traced from the early divergent mitochondrial DNA lineages still present in contemporary human populations. Previous studies already suggested a pre-Neolithic diffusion of mitochondrial haplogroup HV*(xH,V) lineages, a relatively rare class of mtDNA types that includes parallel branches mainly distributed across Europe and West Asia with a certain degree of structure. Up till now, variation within haplogroup HV was addressed mainly by analyzing sequence data from the mtDNA control region, except for specific sub-branches, such as HV4 or the widely distributed haplogroups H and V. In this study, we present a revised HV topology based on full mtDNA genome data, and we include a comprehensive dataset consisting of 316 complete mtDNA sequences including 60 new samples from the Italian peninsula, a previously underrepresented geographic area. We highlight points of instability in the particular topology of this haplogroup, reconstructed with BEAST-generated trees and networks. We also confirm a major lineage expansion that probably followed the Late Glacial Maximum and preceded Neolithic population movements. We finally observe that Italy harbors a reservoir of mtDNA diversity, with deep-rooting HV lineages often related to sequences present in the Caucasus and the Middle East. The resulting hypothesis of a glacial refugium in Southern Italy has implications for the understanding of late Paleolithic population movements and is discussed within the archaeological cultural shifts occurred over the entire continent

    All-sky Medium Energy Gamma-ray Observatory: Exploring the Extreme Multimessenger Universe

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    The All-sky Medium Energy Gamma-ray Observatory (AMEGO) is a probe class mission concept that will provide essential contributions to multimessenger astrophysics in the late 2020s and beyond. AMEGO combines high sensitivity in the 200 keV to 10 GeV energy range with a wide field of view, good spectral resolution, and polarization sensitivity. Therefore, AMEGO is key in the study of multimessenger astrophysical objects that have unique signatures in the gamma-ray regime, such as neutron star mergers, supernovae, and flaring active galactic nuclei. The order-of-magnitude improvement compared to previous MeV missions also enables discoveries of a wide range of phenomena whose energy output peaks in the relatively unexplored medium-energy gamma-ray band

    Multiplexed systems of microsatellite markers for genetic analysis of mahogany, Swietenia macrophylla king (meliaceae), a threatened neotropical timber species

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    Mahogany (Swietenia macrophylla King [Meliaceae]) is the most valuable hardwood species in the neotropics. Its conservation status has been the subject of increasing concern due to overexploitation and habitat destruction. In this work we report the development and characterization of 10 highly variable microsatellite loci for S. macrophylla. Twenty-nine percent of the 126 sequenced mahogany clones yielded useful microsatellite loci. Three highthroughput genotyping systems were developed based on polymerase chain reaction (PCR) multiplexing of these mahogany loci. We identified a total of 158 alleles in 121 adult individuals of S. macrophylla, with an average of 15.8 alleles (range 11-25) per locus. All loci showed Mendelian inheritance in open-pollinated half-sib families. The mean expected heterozygosity was 0.84 and the mean observed heterozygosity was 0.73. The combined probability of identity-the probability that two individuals selected at random from a population would have identica genotypes-was 7.0 × 10-15, and combined probability of paternity exclusion was 0.999998 overall loci. These microsatellite loci permit precise estimates of parameters such as gene flow, mating system, and paternity, thus providing important insights into the population genetics and conservation of S. macrophylla
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