Toward a multilevel representation of protein molecules: comparative approaches to the aggregation/folding propensity problem

This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free standardized microenvironment. The hardness of the problem comes from the superposition between the driving forces of intra- and inter-molecule interactions and it is mirrored by the evidences of shift from folding to aggregation phenotypes by single-point mutations [10]. Here we apply several state-of-the-art classification methods coming from the field of structural pattern recognition, with the aim to compare different representations of the same proteins gathered from the Niwa et al. data base; such representations include sequences and labeled (contact) graphs enriched with chemico-physical attributes. By this comparison, we are able to identify also some interesting general properties of proteins. Notably, (i) we suggest a threshold around 250 residues discriminating "easily foldable" from "hardly foldable" molecules consistent with other independent experiments, and (ii) we highlight the relevance of contact graph spectra for folding behavior discrimination and characterization of the E. coli solubility data. The soundness of the experimental results presented in this paper is proved by the statistically relevant relationships discovered among the chemico-physical description of proteins and the developed cost matrix of substitution used in the various discrimination systems.Comment: 17 pages, 3 figures, 46 reference

A generative model for protein contact networks

In this paper we present a generative model for protein contact networks. The soundness of the proposed model is investigated by focusing primarily on mesoscopic properties elaborated from the spectra of the graph Laplacian. To complement the analysis, we study also classical topological descriptors, such as statistics of the shortest paths and the important feature of modularity. Our experiments show that the proposed model results in a considerable improvement with respect to two suitably chosen generative mechanisms, mimicking with better approximation real protein contact networks in terms of diffusion properties elaborated from the Laplacian spectra. However, as well as the other considered models, it does not reproduce with sufficient accuracy the shortest paths structure. To compensate this drawback, we designed a second step involving a targeted edge reconfiguration process. The ensemble of reconfigured networks denotes improvements that are statistically significant. As a byproduct of our study, we demonstrate that modularity, a well-known property of proteins, does not entirely explain the actual network architecture characterizing protein contact networks. In fact, we conclude that modularity, intended as a quantification of an underlying community structure, should be considered as an emergent property of the structural organization of proteins. Interestingly, such a property is suitably optimized in protein contact networks together with the feature of path efficiency.Comment: 18 pages, 67 reference

Multifractal Characterization of Protein Contact Networks

The multifractal detrended fluctuation analysis of time series is able to reveal the presence of long-range correlations and, at the same time, to characterize the self-similarity of the series. The rich information derivable from the characteristic exponents and the multifractal spectrum can be further analyzed to discover important insights about the underlying dynamical process. In this paper, we employ multifractal analysis techniques in the study of protein contact networks. To this end, initially a network is mapped to three different time series, each of which is generated by a stationary unbiased random walk. To capture the peculiarities of the networks at different levels, we accordingly consider three observables at each vertex: the degree, the clustering coefficient, and the closeness centrality. To compare the results with suitable references, we consider also instances of three well-known network models and two typical time series with pure monofractal and multifractal properties. The first result of notable interest is that time series associated to proteins contact networks exhibit long-range correlations (strong persistence), which are consistent with signals in-between the typical monofractal and multifractal behavior. Successively, a suitable embedding of the multifractal spectra allows to focus on ensemble properties, which in turn gives us the possibility to make further observations regarding the considered networks. In particular, we highlight the different role that small and large fluctuations of the considered observables play in the characterization of the network topology

Analysis of heat kernel highlights the strongly modular and heat-preserving structure of proteins

In this paper, we study the structure and dynamical properties of protein contact networks with respect to other biological networks, together with simulated archetypal models acting as probes. We consider both classical topological descriptors, such as the modularity and statistics of the shortest paths, and different interpretations in terms of diffusion provided by the discrete heat kernel, which is elaborated from the normalized graph Laplacians. A principal component analysis shows high discrimination among the network types, either by considering the topological and heat kernel based vector characterizations. Furthermore, a canonical correlation analysis demonstrates the strong agreement among those two characterizations, providing thus an important justification in terms of interpretability for the heat kernel. Finally, and most importantly, the focused analysis of the heat kernel provides a way to yield insights on the fact that proteins have to satisfy specific structural design constraints that the other considered networks do not need to obey. Notably, the heat trace decay of an ensemble of varying-size proteins denotes subdiffusion, a peculiar property of proteins

Secondo contributo alla conoscenza della flora esotica dell'Arcipelago Toscano, Italia

Si presenta qui un secondo contributo per la realizzazione di una Checklist della flora esotica dell'Arcipelago Toscano. Per ogni taxon sono riportati lo status di naturalizzazione, sia per ciascuna isola che per l'intero Arcipelago, e i dati relativi alla distribuzione locale. Delle 31 specie elencate, 18 risultano nuove per il territorio dell'Arcipelago Toscano, tra le quali 4 nuove per l'intera Toscana; le restanti sono nuove per una o più isole

Snow Observations from Space: an Approach to Map Snow Cover from Three Decades of Landsat Imagery Across Switzerland

Snow accumulation is one of the most important forms of water storage. The natural cycle of water is being increasingly influenced by climate change and will continue to change in the future. To understand the evolution of snow cover and to perfect its accurate detection UN Environment/GRID-Geneva and the University of Geneva have developed a Snow Detection tool called Snow Observations from Space for the Swiss Data Cube. The Snow Detection tool uses the C Function of Mask to identify snow pixels and then subsequently produces a normalized detection raster. Through further development, this tool will reach its full potential as an accurate method of detecting snow cover change for Switzerland

Importance of Gamete Quality in Ecotoxicological Application: Natural versus Bred Population in Paracentrotus lividus

Several approaches have been tested to respond to the depletion of wild stocks, from the production of seeds to the setting up of closed echinoculture systems, starting with fertilization of eggs with the consequent development to adult sea urchins. Hence, in the last years, our research group has focused on the assessment of a feasible and sustainable strategy aimed to ensure a rapid and effective gonadal growth of healthy gametes in recirculating aquaculture system (RAS) to employ in ecotoxicological application. In order to compare the health of obtained gametes with wild populations, the effectiveness of diets was evaluated with different biological parameters, such as fertilization and embryo-development test, and with histological analysis of gonads to appraise the stage of maturation. Moreover, the information regarding different breeding conditions of adults and genetic variability should be combined with the analysis of larval settlement and its requirements, demonstrating the importance of these parameters for the possible closure of the echinoculture cycle in RAS. Results achieved so far in terms of gonadal development and health of gametes have provided evidence of success in overcoming natural gaps between reproductive events in natural populations and an efficient and standardize breeding condition in RAS