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Search Results: 1 - 10 of 704 matches for " Ignazio Carbone "
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The evolutionary history of Cytochrome P450 genes in four filamentous Ascomycetes
Jixin Deng, Ignazio Carbone, Ralph A Dean
BMC Evolutionary Biology , 2007, DOI: 10.1186/1471-2148-7-30
Abstract: A total of 376 P450 genes were assigned to 168 families according to standard nomenclature. On average, only 1 to 2 genes per family were in each genome. To resolve conflicting results between different clustering analyses and standard family designation, a higher order relationship was formulated. 376 genes were clustered into 115 clans. Subsequently a novel approach based on parsimony was developed to build the evolutionary models. Based on these analyses, a core of 30 distinct clans of P450s was defined. The core clans experienced contraction in all four fungal lineages while new clans expanded in all with exception of NC. MG experienced more genes and clans gains compared to the other fungi. Parsimonious analyses unanimously supported one species topology for the four fungi.The four studied fungi exhibit unprecedented diversity in their P450omes in terms of coding sequence, intron-exon structures and genome locations, suggesting a complicated evolutionary history of P450s in filamentous Ascomycetes. Clan classification and a novel strategy were developed to study evolutionary history. Contraction of core clans and expansion of novel clans were identified. The exception was the NC lineage, which exhibited pure P450 gene loss.Fungi comprise a large and diverse kingdom of organisms. It is estimated that as many as 1.5 million species exist in the planet today [1,2]. Most described fungi grow by producing long, multi-celled hyphae, and are known as filamentous fungi. Filamentous fungi occupy a wide range of ecological niches with diverse life histories and physiological processes. Many live as saprotrophs decomposing and absorbing nutrients from dead materials while others have evolved the ability to be pathogens deriving their nutrients from living or dying hosts. Taking advantage of available genome sequences to explore the evolution of important gene families may help shed light on the processes that have allowed fungi to exploit diverse habitats.The P450-contain
Evidence that the Human Pathogenic Fungus Cryptococcus neoformans var. grubii May Have Evolved in Africa
Anastasia P. Litvintseva,Ignazio Carbone,Jenny Rossouw,Rameshwari Thakur,Nelesh P. Govender,Thomas G. Mitchell
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0019688
Abstract: Most of the species of fungi that cause disease in mammals, including Cryptococcus neoformans var. grubii (serotype A), are exogenous and non-contagious. Cryptococcus neoformans var. grubii is associated worldwide with avian and arboreal habitats. This airborne, opportunistic pathogen is profoundly neurotropic and the leading cause of fungal meningitis. Patients with HIV/AIDS have been ravaged by cryptococcosis – an estimated one million new cases occur each year, and mortality approaches 50%. Using phylogenetic and population genetic analyses, we present evidence that C. neoformans var. grubii may have evolved from a diverse population in southern Africa. Our ecological studies support the hypothesis that a few of these strains acquired a new environmental reservoir, the excreta of feral pigeons (Columba livia), and were globally dispersed by the migration of birds and humans. This investigation also discovered a novel arboreal reservoir for highly diverse strains of C. neoformans var. grubii that are restricted to southern Africa, the mopane tree (Colophospermum mopane). This finding may have significant public health implications because these primal strains have optimal potential for evolution and because mopane trees contribute to the local economy as a source of timber, folkloric remedies and the edible mopane worm.
Gene duplication, modularity and adaptation in the evolution of the aflatoxin gene cluster
Ignazio Carbone, Jorge H Ramirez-Prado, Judy L Jakobek, Bruce W Horn
BMC Evolutionary Biology , 2007, DOI: 10.1186/1471-2148-7-111
Abstract: To elucidate the mechanisms that have driven formation of these clusters, we performed systematic searches of aflatoxin cluster homologs across five Aspergillus genomes. We found a high level of gene duplication and identified seven modules consisting of highly correlated gene pairs (aflA/aflB, aflR/aflS, aflX/aflY, aflF/aflE, aflT/aflQ, aflC/aflW, and aflG/aflL). With the exception of A. nomius, contrasts of mean Ka/Ks values across all cluster genes showed significant differences in selective pressure between section Flavi and non-section Flavi species. A. nomius mean Ka/Ks values were more similar to partial clusters in A. fumigatus and A. terreus. Overall, mean Ka/Ks values were significantly higher for section Flavi than for non-section Flavi species.Our results implicate several genomic mechanisms in the evolution of ST, OMST and AF cluster genes. Gene modules may arise from duplications of a single gene, whereby the function of the pre-duplication gene is retained in the copy (aflF/aflE) or the copies may partition the ancestral function (aflA/aflB). In some gene modules, the duplicated copy may simply augment/supplement a specific pathway function (aflR/aflS and aflX/aflY) or the duplicated copy may evolve a completely new function (aflT/aflQ and aflC/aflW). Gene modules that are contiguous in one species and noncontiguous in others point to possible rearrangements of cluster genes in the evolution of these species. Significantly higher mean Ka/Ks values in section Flavi compared to non-section Flavi species indicate increased positive selection acting in the evolution of genes in OMST and AF gene clusters.Filamentous fungi produce a wide variety of economically important secondary metabolites (extrolites). An extrolite is any outwardly directed chemical compound that is excreted or accumulated in the cell wall of a living organism [1]. Many of these extrolite compounds are beneficial, such as antibiotics, food grade pigments, enzymes, vitamins, lipids, and
Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens
Amy J Powell, Gavin C Conant, Douglas E Brown, Ignazio Carbone, Ralph A Dean
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-147
Abstract: To determine if patterns of gene duplication differed between pathogens and non-pathogens, we identified gene families across nine euascomycete and two basidiomycete species. Gene family size distributions were fit to power laws to compare gene duplication trends in pathogens versus non-pathogens. Fungal phytopathogens showed globally altered patterns of gene duplication, as indicated by differences in gene family size distribution. We also identified sixteen examples of gene family expansion and five instances of gene family contraction in pathogenic lineages. Expanded gene families included those predicted to be important in melanin biosynthesis, host cell wall degradation and transport functions. Contracted families included those encoding genes involved in toxin production, genes with oxidoreductase activity, as well as subunits of the vacuolar ATPase complex. Surveys of the functional distribution of gene duplicates indicated that pathogens show enrichment for gene duplicates associated with receptor and hydrolase activities, while euascomycete pathogens appeared to have not only these differences, but also significantly more duplicates associated with regulatory and carbohydrate binding functions.Differences in the overall levels of gene duplication in phytopathogenic species versus non-pathogenic relatives implicate gene inventory flux as an important virulence-associated process in fungi. We hypothesize that the observed patterns of gene duplicate enrichment, gene family expansion and contraction reflect adaptation within pathogenic life histories. These adaptations were likely shaped by ancient, as well as contemporary, intimate associations with monocot hosts.Change in gene inventory in pathogenic genomes is an important evolutionary signal. Previous studies have documented the relationship between virulence and differential gene gain and/or loss in bacteria and viruses [1-8]. However, this phenomenon remains unexamined at a genomic scale in fungal pathoge
GT-Miner: a graph-theoretic data miner, viewer, and model processor
Douglas E. Brown,Amy J. Powell,Ignazio Carbone,Ralph A. Dean
Bioinformation , 2008,
Abstract: Inexpensive computational power combined with high-throughput experimental platforms has created a wealth of biological information requiring analytical tools and techniques for interpretation. Graph-theoretic concepts and tools have provided an important foundation for information visualization, integration, and analysis of datasets, but they have often been relegated to background analysis tasks. GT-Miner is designed for visual data analysis and mining operations, interacts with other software, including databases, and works with diverse data types. It facilitates a discovery-oriented approach to data mining wherein exploration of alterations of the data and variations of the visualization is encouraged. The user is presented with a basic iterative process, consisting of loading, visualizing, transforming, and then storing the resultant information. Complex analyses are built-up through repeated iterations and user interactions. The iterative process is optimized by automatic layout following transformations and by maintaining a current selection set of interest for elements modified by the transformations. Multiple visualizations are supported including hierarchical, spring, and force-directed self-organizing layouts. Graphs can be transformed with an extensible set of algorithms or manually with an integral visual editor. GT-Miner is intended to allow easier access to visual data mining for the non-expert.
Internet Districts in Italy: Is Proximity an Antidote against Weak Broadband Competition?  [PDF]
Alessio D’Ignazio, Emanuele Giovannetti
Modern Economy (ME) , 2011, DOI: 10.4236/me.2011.23044
Abstract: We study the effects of proximity in the interconnections between Internet providers participating at the three main Italian Internet Exchange Points. We find that geographical proximity plays a role in driving Internet Providers’ interconnection, positively affecting the likelihood of an agreement. This suggests the existence of localized positive externalities in the form of mutual knowledge and reputation, one of the cited drivers underlying the formation of districts in non high-tech industries. We interpret these results as resulting from the necessity for cooperation in interconnection between smaller providers facing the weak competitiveness of the highly concentrated Italian broadband access market.
Time and Space in J. G. Ballard's Chronopolis Il tempo e lo spazio in Chronopolis di J. G. Ballard
Ignazio Sanna
Between , 2011,
Abstract: Time and space are two of the main features in Ballard’s fiction. They are also the main topic in this short story. In Chronopolis the measurement of time is forbidden. When the story’s main character, Newman, discovers the existence of clocks, he decides to defy the law to restore the previous condition. In doing so he moves from the city he used to live in to the old forsaken city. So, he moves both in time and space. He pursues the utopia of liberating time, and man, from the Orwellian prohibition of dealing with linear time. But he fails eventually, being imprisoned for having tried to break free from the State control of time. His crossing of the symbolic border between the new and the old city is a passage from a static, present time to a flowing linear time, not limited to the present. But the old Chronopolis in a sense has become a non-place, while the new one has been deprived of time, thus being characterized by non-time. Since these notions are represented by the terms, respectively, utopia and uchronia, ultimately this means a disappearing of Chronopolis on an imaginary Cartesian graph displaying it. Time and space are two of the main features in Ballard’s fiction. They are also the main topic in this short story. In Chronopolis the measurement of time is forbidden. When the story’s main character, Newman, discovers the existence of clocks, he decides to defy the law to restore the previous condition. In doing so he moves from the city he used to live in to the old forsaken city. So, he moves both in time and space. He pursues the utopia of liberating time, and man, from the Orwellian prohibition of dealing with linear time. But he fails eventually, being imprisoned for having tried to break free from the State control of time. His crossing of the symbolic border between the new and the old city is a passage from a static, present time to a flowing linear time, not limited to the present. But the old Chronopolis in a sense has become a non-place, while the new one has been deprived of time, thus being characterized by non-time. Since these notions are represented by the terms, respectively, utopia and uchronia, ultimately this means a disappearing of Chronopolis on an imaginary Cartesian graph displaying it.
Prima sessione - Politiche pubbliche per la sostenibilità
Ignazio Musu
Aestimum , 2002,
Abstract:
Welfare systems, ageing and work: an OECD perspective
Ignazio Visco
PSL Quarterly Review , 2000,
Abstract: This paper examines the scale of the demographic problem facing OECD economies and the labour market trends among older workers, considering the macroeconomic implications of welfare provision for ageing on living standards and fiscal balances. The nature and the scale of incentives for early retirement are then discussed, concluding that welfare systems in OECD countries will come under increasing pressure as the share of public pension payments on total welfare outlays could rise dramatically over the coming decades. The paper illustrates some of the recent OECD recommendations for responding to the challenges posed by ageing societies in the context of diverse social welfare systems and concludes that policies are urgently needed in a number of countries to pursue two fundamental objectives: increasing the average number of years individuals spend active in the labour force and raising the sources of provision for an adequate retirement income.
Paying for pensions: how important is economic growth?
Ignazio Visco
PSL Quarterly Review , 2001,
Abstract: This paper focuses on the scope for a higher level of output and faster productivitygrowth to ease future fiscal pressures stemming from demographic developments in OECD countries over the next fifty years. After concluding that, without substantial reforms, pressure on government spending linked to ageing populations (both onpensions and health expenditures), will in general result in significant increases in expenditures to GDP ratios, the paper examines how these pressures might be redressed. Responses which focus on achieving an increase in the average number of years individuals spend active in the labour force and raising the level as well as widening the sources of individual provision of retirement income are recommended. Increasing output (through lower structural unemployment and higher female and elderly workers' participation rates) and its rate of growth (through gains in productivity) are seen as offering a complementary, though limited, response.
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