Inter University Consortium for Supercomputing in Research

Rome, Italy

Inter University Consortium for Supercomputing in Research

Rome, Italy
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Cicconardi F.,University of Tuscia | Cicconardi F.,Inter University Consortium for Supercomputing in Research | Cicconardi F.,University of Rome La Sapienza | Chillemi G.,Inter University Consortium for Supercomputing in Research | And 5 more authors.
BMC Genomics | Year: 2013

Background: Copy number variations (CNVs) represent a significant source of genomic structural variation. Their length ranges from approximately one hundred to millions of base pair. Genome-wide screenings have clarified that CNVs are a ubiquitous phenomenon affecting essentially the whole genome. Although Bos taurus is one of the most important domestic animal species worldwide and one of the most studied ruminant models for metabolism, reproduction, and disease, relatively few studies have investigated CNVs in cattle and little is known about how CNVs contribute to normal phenotypic variation and to disease susceptibility in this species, compared to humans and other model organisms. Results: Here we characterize and compare CNV profiles in 2654 animals from five dairy and beef Bos taurus breeds, using the Illumina BovineSNP50 genotyping array (54001 SNP probes). In this study we applied the two most commonly used algorithms for CNV discovery (QuantiSNP and PennCNV) and identified 4830 unique candidate CNVs belonging to 326 regions. These regions overlap with 5789 known genes, 76.7% of which are significantly co-localized with segmental duplications (SD). Conclusions: This large scale screening significantly contributes to the enrichment of the Bos taurus CNV map, demonstrates the ubiquity, great diversity and complexity of this type of genomic variation and sets the basis for testing the influence of CNVs on Bos taurus complex functional and production traits. © 2013 Cicconardi et al; licensee BioMed Central Ltd.


Giampaoli S.,Foro Italico University of Rome | Chillemi G.,Inter University Consortium for Supercomputing in Research | Valeriani F.,Foro Italico University of Rome | Lazzaro D.,Foro Italico University of Rome | And 6 more authors.
New Biotechnology | Year: 2013

The analysis of human genetic variability can lead to the comprehension of medical issues and to the development of personalized therapeutic protocols. Single nucleotide polymorphisms, are the most common type of human genetic variation and have been associated to disease development and phenotype forecasting. The recent technologies for DNA sequencing and bioinformatic analysis are now giving the opportunity to develop new diagnostic and prevention approaches also through health promotion protocols. The genetic data management is at the same time underlining technical limitations and old ethical issues. © 2012 Elsevier B.V.


D'Angelo P.,University of Rome La Sapienza | Zitolo A.,University of Rome La Sapienza | Migliorati V.,University of Rome La Sapienza | Bodo E.,University of Rome La Sapienza | And 5 more authors.
Journal of Chemical Physics | Year: 2011

X-ray absorption spectroscopy (XAS) has been used to unveil the bromide ion local coordination structure in 1-alkyl-3-methylimidazolium bromide [C nmim]Br ionic liquids (ILs) with different alkyl chains. The XAS spectrum of 1-ethyl-3-methylimidazolium bromide has been found to be different from those of the other members of the series, from the butyl to the decyl derivatives, that have all identical XAS spectra. This result indicates that starting from 1-buthyl-3-methylimidazolium bromide the local molecular arrangement around the bromide anion is the same independently from the length of the alkyl chain, and that the imidazolium head groups in the liquid ILs with long alkyl chains assume locally the same orientation as in the [C 4mim]Br crystal. With this study we show that the XAS technique is an effective direct tool for unveiling the local structural arrangements around selected atoms in ILs. © 2011 American Institute of Physics.


Dangelo P.,University of Rome La Sapienza | Zitolo A.,University of Rome La Sapienza | Migliorati V.,University of Rome La Sapienza | Chillemi G.,Inter University Consortium for Supercomputing in Research | And 6 more authors.
Inorganic Chemistry | Year: 2011

A new set of ionic radii in aqueous solution has been derived for lanthanoid(III) cations starting from a very accurate experimental determination of the ion-water distances obtained from extended X-ray absorption fine structure (EXAFS) data. At variance with previous results, a very regular trend has been obtained, as expected for this series of elements. A general procedure to compute ionic radii in solution by combining the EXAFS technique and molecular dynamics (MD) structural data has been developed. This method can be applied to other ions allowing one to determine ionic radii in solution with an accuracy comparable to that of the Shannon crystal ionic radii. © 2011 American Chemical Society.


Migliorati V.,University of Rome La Sapienza | Mancini G.,Inter University Consortium for Supercomputing in Research | Chillemi G.,Inter University Consortium for Supercomputing in Research | Zitolo A.,University of Rome La Sapienza | Dangelo P.,University of Rome La Sapienza
Journal of Physical Chemistry A | Year: 2011

The effect of ions on the structure of liquid water is still not completely understood, despite extensive experimental and theoretical studies. A combined XANES and molecular dynamics investigation on diluted Zn2+ and Hg2+ aqueous solutions reveals that the influence of a single ion on the bonding pattern of water molecules is strongly dependent on the nature of the ion. While the structure of water is not altered by the presence of the Zn2+ ion, the Hg2+ cation has a strong impact on the hydrogen-bond network of water that extends beyond the first coordination shell. © 2011 American Chemical Society.


Migliorati V.,University of Rome La Sapienza | Chillemi G.,Inter University Consortium for Supercomputing in Research | Dangelo P.,University of Rome La Sapienza
Inorganic Chemistry | Year: 2011

The solvation properties of the Zn2+ ion in methanol solution have been investigated using a combined approach based on molecular dynamics (MD) simulations and extended X-ray absorption fine structure (EXAFS) experimental results. The quantum mechanical potential energy surface for the interaction of the Zn2+ ion with a methanol molecule has been calculated taking into account the effect of bulk solvent by the polarizable continuum model (PCM). The effective Zn-methanol interactions have been fitted by suitable analytical potentials, and have been utilized in the MD simulation to obtain the structural properties of the solution. The reliability of the whole procedure has been assessed by comparing the theoretical structural results with the EXAFS experimental data. The structural parameters of the first solvation shells issuing from the MD simulations provide an effective complement to the EXAFS experiments. © 2011 American Chemical Society.


Migliorati V.,University of Rome La Sapienza | Zitolo A.,University of Rome La Sapienza | Chillemi G.,Inter University Consortium for Supercomputing in Research | D'Angelo P.,University of Rome La Sapienza
ChemPlusChem | Year: 2012

A quantitative analysis of the X-ray absorption near-edge structure (XANES) spectra of the Zn 2+ ion in methanol and aqueous solution has been carried out starting from the microscopic description of the systems derived from molecular dynamics (MD) simulations. The different sensitivity of XANES towards the second-shell solvent molecules in the two solvents has been highlighted: in methanol solution, the Zn 2+ second solvation shell was found to provide a negligible contribution to the XANES spectrum, and it has been possible to reproduce the experimental data using a single coordination sphere in the calculation. Conversely, a reliable reproduction of the experimental spectrum of Zn 2+ in aqueous solution could be obtained only by including the second-shell water molecules in the calculation. The combination of MD and XANES was found to be essential to evaluate the contribution of the ion second solvation shell to the XANES spectra of a metal ion in organic solvents. © 2012 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.


Migliorati V.,University of Rome La Sapienza | Mancini G.,Inter University Consortium for Supercomputing in Research | Mancini G.,Normal School of Pisa | Tatoli S.,University of Rome La Sapienza | And 5 more authors.
Inorganic Chemistry | Year: 2013

The structure and dynamics of water in ionic solutions at high pressure have been investigated using a combined approach based on extended X-ray absorption fine structure (EXAFS) spectroscopy and Molecular Dynamics (MD) simulations. Modification of the hydration properties of the Zn2+ ion induced by a pressure increase from ambient condition up to ∼6.4 GPa has been revealed and accurately analyzed. With increasing pressure the first hydration shell of the Zn2+ ion has been found to retain an octahedral symmetry with a shortening of the Zn-O distance up to 0.09 Å and an increased width associated with thermal motion, as compared to the ambient condition hydration complex. A very interesting picture of the dynamic behavior of the first hydration shell has emerged from the analysis of the simulations: up to 2.5 GPa no exchange events between first and second shell water molecules occurred, while above this pressure value several exchange events take place in the solution following an associative interchange mechanism. This result can be explained by the very high compression and packing of the solvent which force second shell water molecules to enter the Zn 2+ first hydration shell. MD simulations indicate a strong pressure effect also on the structure of the second coordination shell which is compressed and becomes more disordered and less structured with increasing pressure. The water mobility and the ion diffusion coefficient have been found to increase in the high density conditions, as a consequence of the rupture of the hydrogen bond network caused by pressure. © 2012 American Chemical Society.


Zitolo A.,University of Rome La Sapienza | Chillemi G.,Inter University Consortium for Supercomputing in Research | D'Angelo P.,University of Rome La Sapienza
Inorganic Chemistry | Year: 2012

The solvation structure of Cu 2+ in methanol (MeOH) and dimethyl sulfoxide (DMSO) has been determined by studying both the extended X-ray absorption fine structure (EXAFS) and the X-ray absorption near-edge structure (XANES) regions of the K-edge absorption spectra. The EXAFS technique has been found to provide a very accurate determination of the next-neighbor coordination distances, but it is inconclusive in the determination of the coordination numbers and polyhedral environment. Conversely, quantitative analysis of the XANES spectra unambiguously shows the presence of an average 5-fold coordination in both the MeOH and DMSO solution, ruling out the usually proposed octahedral Jahn-Teller distorted geometry. The EXAFS and XANES techniques provide coherent values of the Cu-O first-shell distances that are coincident in the two solvents. This investigation shows that the combined analysis of the EXAFS and XANES data allows a reliable determination of the structural properties of electrolyte solutions, which is very difficult to achieve with other experimental techniques. © 2012 American Chemical Society.

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