2,508 research outputs found

    Universal Features in the Genome-level Evolution of Protein Domains

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    Protein domains are found on genomes with notable statistical distributions, which bear a high degree of similarity. Previous work has shown how these distributions can be accounted for by simple models, where the main ingredients are probabilities of duplication, innovation, and loss of domains. However, no one so far has addressed the issue that these distributions follow definite trends depending on protein-coding genome size only. We present a stochastic duplication/innovation model, falling in the class of so-called Chinese Restaurant Processes, able to explain this feature of the data. Using only two universal parameters, related to a minimal number of domains and to the relative weight of innovation to duplication, the model reproduces two important aspects: (a) the populations of domain classes (the sets, related to homology classes, containing realizations of the same domain in different proteins) follow common power-laws whose cutoff is dictated by genome size, and (b) the number of domain families is universal and markedly sublinear in genome size. An important ingredient of the model is that the innovation probability decreases with genome size. We propose the possibility to interpret this as a global constraint given by the cost of expanding an increasingly complex interactome. Finally, we introduce a variant of the model where the choice of a new domain relates to its occurrence in genomic data, and thus accounts for fold specificity. Both models have general quantitative agreement with data from hundreds of genomes, which indicates the coexistence of the well-known specificity of proteomes with robust self-organizing phenomena related to the basic evolutionary ``moves'' of duplication and innovation

    Perennial grasses as lignocellulosic feedstock for second-generation bioethanol production in Mediterranean environment.

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    In this paper the suitability of three perennial, herbaceous, lignocellulosic grasses ( Arundo donax , Saccharum spontaneous spp. aegyptiacum and Miscanthus x giganteus ) for the production of second-generation bioethanol in semi-arid Mediterranean environment was studied. Crops were established in spring 2002, supplying irrigation and nitrogen fertilization up to 2004/2005 growing season. Subsequently, crops were grown without any agronomic input and harvested annually. Data reported in this paper refers to 2008/2009 and 2009/2010 growing seasons. Aboveground dry matter (DM) yield was higher in Arundo (35.4±2.1 Mg ha –1 in 2009 and 32.2±1.9 Mg ha –1 in 2010 harvest) than in Saccharum (27.3±2.0 and 23.9±1.9 Mg ha –1 , respectively) and Miscanthus (19.6±2.8 and 17.2±1.6 Mg ha –1 , respectively). Structural polysaccharides of the raw material were higher in Miscanthus (63.4% w/w) followed by Saccharum (61.5% w/w) and Arundo (57.6% w/w). The same trend was identified for the cellulose content (41.0%, 36.8% and 34.6%, respectively). The highest values in the total hemicellulose complex were observed in Saccharum (24.7%), followed by Arundo (23.1%) and Miscanthus (22.4%). The composition of structural polysaccharides leads to a higher theoretical ethanol yield (TEY) from one dry ton of Miscanthus feedstock (kg DM Mg –1 ), followed by Saccharum and Arundo . On the other hand, the TEY per unit surface (Mg ha –1 ) was greater in Arundo than in Saccharum and Miscanthus . When compared to other lignocellulosic sources used in the second-generation bioethanol technology, such as agricultural residues, woody species and other herbaceous perennial crops, Arundo , Saccharum and Miscanthus showed a great potential in terms of TEY ha –1 . Given the high levels of biomass yield and composition of structural polysaccharides, the three species might be introduced into the Mediterranean cropping systems to supply lignocellulosic biomass for second-generation industrial plants or bio-refineries

    Computational approaches to shed light on molecular mechanisms in biological processes

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    Computational approaches based on Molecular Dynamics simulations, Quantum Mechanical methods and 3D Quantitative Structure-Activity Relationships were employed by computational chemistry groups at the University of Milano-Bicocca to study biological processes at the molecular level. The paper reports the methodologies adopted and the results obtained on Aryl hydrocarbon Receptor and homologous PAS proteins mechanisms, the properties of prion protein peptides, the reaction pathway of hydrogenase and peroxidase enzymes and the defibrillogenic activity of tetracyclines. © Springer-Verlag 2007

    Validation of a model of the GAL regulatory system via robustness analysis of its bistability characteristics

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    In Saccharomyces cerevisiæ, structural bistability generates a bimodal expression of the galactose uptake genes (GAL) when exposed to low and high glucose concentrations. This indicates that yeast cells can decide between using either the limited amount of glucose or growing on galactose under changing environmental conditions. A crucial requirement for any plausible mechanistic model of this system is that it reproduces the robustness of the bistable response observed in vivo against inter-individual parametric variability and fluctuating environmental conditions
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