2,851 research outputs found
L’archivio dell’Istituto di Toppo Wassermann
No full textIl volume ripercorre la storia di palazzo Toppo Wassermann, tesoro artistico e architettonico di Udine e del Friuli. Residenza prima dei nobili di Polcenigo, che lo costruirono nei primi anni del Settecento, poi dei Garzolini, che lo acquistarono nel 1790 e ne furono proprietari per tutto l’Ottocento, il palazzo attraversa gli epocali cambiamenti che segnano la società friulana tra l’ultimo secolo dell’età veneta e i primi decenni dell’annessione al Regno d’Italia. Nel corso del Novecento la sua storia è legata invece all’Istituto di Toppo Wassermann, luogo di formazione e istruzione per intere generazioni. Palazzo Polcenigo, Garzolini, Toppo Wassermann è ora sede della Scuola superiore dell’Università degli studi di Udine
L’archivio dell’Istituto di Toppo Wassermann
No full textIl volume ripercorre la storia di palazzo Toppo Wassermann, tesoro artistico e architettonico di Udine e del Friuli. Residenza prima dei nobili di Polcenigo, che lo costruirono nei primi anni del Settecento, poi dei Garzolini, che lo acquistarono nel 1790 e ne furono proprietari per tutto l’Ottocento, il palazzo attraversa gli epocali cambiamenti che segnano la società friulana tra l’ultimo secolo dell’età veneta e i primi decenni dell’annessione al Regno d’Italia. Nel corso del Novecento la sua storia è legata invece all’Istituto di Toppo Wassermann, luogo di formazione e istruzione per intere generazioni. Palazzo Polcenigo, Garzolini, Toppo Wassermann è ora sede della Scuola superiore dell’Università degli studi di Udine
Organochalcogen peroxidase mimetics as potential drugs: a long story of a promise still unfulfilled
No full textOrganochalcogen compounds have attracted the interest of a multitude of studies to design potential therapeutic agents mimicking the peroxidase activity of selenium-based glutathione peroxidases (GPx's). Starting from the pioneering ebselen, various compounds have been synthesized over the years, which may be traced in three major classes of molecules: cyclic selenenyl amides, diaryl diselenides, and aromatic or aliphatic monoselenides. These compounds share common features and determinants needed to exert an efficient GPx-like activity, such as polarizing groups in close proximity to selenium and steric effects. Nonetheless, the reactivity of selenium, and tellurium as well, poses serious problems for the predictability of the biological effects of these compounds in vivo when used as potential drugs. These molecules, indeed, interfere with thiols of redox-regulated proteins and enzymes, leading to unexpected biological effects. The various chemical aspects of the reaction mechanism of peroxidase mimetics are surveyed here, focusing on experimental evidence and quantum mechanics calculations of organochalcogen representatives of the various classes
Large-scale prediction of protein structure and function from sequence
No full textThe identification of novel drug targets from genomic data involves the large-scale analysis of many protein sequences. Methods for automated structure and function prediction are an essential tool for this purpose. In this review we concentrate on the recent developments in the field of protein structure prediction and how these can be used to gain hints about the function of proteins. The current state-of-the-art is highlighted through recent community-wide experiments aimed at comparing different approaches. For structure prediction this allows the identification of key improvements to increase the crucial sequence to structure alignment needed for accurate models. Function prediction is a rapidly maturing field that is still being benchmarked. Definitions for protein function are presented and available methods, mostly concentrating on functional site descriptors and structural motifs, presented
QPARSE: searching for long-looped or multimeric G-quadruplexes potentially distinctive and druggable
No full textMOTIVATION: G-quadruplexes (G4s) are non-canonical nucleic acid conformations that are widespread in all kingdoms of life and are emerging as important regulators both in RNA and DNA. Recently, two new higher-order architectures have been reported: adjacent interacting G4s, and G4s with stable long loops forming stem-loop structures. As there are no specialized tools to identify these conformations, we developed QPARSE. RESULTS: QPARSE can exhaustively search for degenerate potential quadruplex-forming sequences (PQSs) containing bulges and/or mismatches at genomic level, as well as either multimeric or long-looped PQS (MPQS and LLPQS respectively). While its assessment vs. known reference datasets is comparable with the state-of-the-art, what is more interesting is its performance in the identification of MPQS and LLPQS that present algorithms are not designed to search for. We report a comprehensive analysis of MPQS in human gene promoters and the analysis of LLPQS on three experimentally validated case studies from HIV-1, BCL2, and hTERT. AVAILABILITY: QPARSE is freely accessible on the web at http://www.medcomp.medicina.unipd.it/qparse/index or downloadable from github as a python 2.7 program https://github.com/B3rse/qparse. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online
NeSSie: a tool for the identification of approximate DNA sequence symmetries
No full textNon-B DNA conformations play an important role in genomic rearrangements, structural three-dimensional organization and gene regulation. Many non-B DNA structures show symmetrical properties as palindromes and mirrors that can form hairpins, cruciform structures or triplexes. A comprehensive tool, capable to perform a fast genome wide search for exact and degenerate symmetrical patterns, is needed for further investigating nucleotide tracts potentially forming non-B DNA structures
Mass spectrometry data analysis in the proteomics era
No full textWith the advent of whole genome sequencing, large-scale proteomics has rapidly come to dominate the post-genomic age. As such, tandem mass spectrometry has emerged as the most promising and powerful technique in this area but analysis of raw spectra remains one of the principle bottlenecks to making effective use of the technology. Analytical approaches for identifying proteins from MS/MS data fall into two categories: comparing measured fragment spectra to theoretical spectra from sequence databases and de novo peptide sequencing. Available methods still have weaknesses, highlighting the need for new powerful algorithms that are able to exploit the enormous volume of data generated by proteomic experiments. Recent efforts have also been directed towards the identification of post-translational modifications, biomarker discovery and quantitative proteomics. Overall, the intended goal of this review is to give as thorough as possible an overview of state-of-the-art approaches and tools developed to analyze tandem mass spectra in different fields and discuss future directions aimed at overcoming the limits of present methods
Matching up Phosphosites to Kinases: A Survey of Available Predictive Programs
No full textOver the past few years, research in phosphoproteomic has assisted a tremendous revolution thanks to instrumental technologies advances in mass spectrometry combined with innovative experimental strategies. This has allowed the identification of thousands of high confidence phosphosites. Presently, almost 60000 non-redundant phosphosites have been identified from similar to 10000 non-redundant proteins and about 80% of these phosphosites have been identified from high throughput experiments in the last six years. The vast majority of phosphosites are still functionally uncharacterized and the kinases responsible of their generation are almost unknown.
Several computational approaches have been developed to link kinase families with putative substrates and although these are powerful tools, they are not commonly used.
Here we discuss about the present approaches and tools developed for predicting the functional link between the kinases and their substrates
A Comparison of Thiol Peroxidase Mechanisms
No full textThiol peroxidases comprise glutathione peroxidases (GPx) and peroxiredoxins (Prx). The enzymes of both families reduce hydroperoxides with thiols by enzyme-substitution mechanisms. H(2)O(2) and organic hydroperoxides are reduced by all thiol peroxidases, most efficiently by SecGPxs, whereas fast peroxynitrite reduction is more common in Prxs. Reduction of lipid hydroperoxides is the domain of monomeric GPx4-type enzymes and of some Prxs. The catalysis starts with oxidation of an active-site selenocysteine (U(P)) or cysteine (C(P)). Activation of Cys (Sec) for hydroperoxide reduction in the GPx family is achieved by a typical tetrad composed of Cys (Sec), Asn, Gln, and Trp, whereas a triad of Cys Thr (or Ser) and Arg is the signature of Prx. In many of the CysGPxs and Prxs, a second Cys (C(R)) is required. In these 2-CysGPxs and 2-CysPrxs, the C(P) oxidized to a sulfenic acid forms an intra-or intermolecular disulfide (typical 2-CysPrx) with C(R), before a stepwise regeneration of ground-state enzyme by redoxin-type proteins can proceed. In SecGPxs and sporadically in Prxs, GSH is used as the reductant. Diversity combined with structural variability predestines thiol peroxidases for redox regulation via ROOH sensing and direct or indirect transduction of oxidant signals to specific protein targets. Antioxid. Redox Signal. 15, 763-780
Applications of next-generation sequencing technologies to diagnostic virology.
No full textNovel DNA sequencing techniques, referred to as "next-generation" sequencing (NGS), provide high speed and throughput that can produce an enormous volume of sequences with many possible applications in research and diagnostic settings. In this article, we provide an overview of the many applications of NGS in diagnostic virology. NGS techniques have been used for high-throughput whole viral genome sequencing, such as sequencing of new influenza viruses, for detection of viral genome variability and evolution within the host, such as investigation of human immunodeficiency virus and human hepatitis C virus quasispecies, and monitoring of low-abundance antiviral drug-resistance mutations. NGS techniques have been applied to metagenomics-based strategies for the detection of unexpected disease-associated viruses and for the discovery of novel human viruses, including cancer-related viruses. Finally, the human virome in healthy and disease conditions has been described by NGS-based metagenomics
- …
