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Zambelli F.,University of Milan | Prazzoli G.M.,University of Milan | Pesole G.,CNR Institute of Biomembrane and Bioenergetics | Pesole G.,University of Bari | Pavesi G.,University of Milan
Nucleic Acids Research | Year: 2012

The regulation of transcription of eukaryotic genes is a very complex process, which involves interactions between transcription factors (TFs) and DNA, as well as other epigenetic factors like histone modifications, DNA methylation, and so on, which nowadays can be studied and characterized with techniques like ChIP-Seq. Cscan is a web resource that includes a large collection of genome-wide ChIP-Seq experiments performed on TFs, histone modifications, RNA polymerases and others. Enriched peak regions from the ChIP-Seq experiments are crossed with the genomic coordinates of a set of input genes, to identify which of the experiments present a statistically significant number of peaks within the input genes' loci. The input can be a cluster of co-expressed genes, or any other set of genes sharing a common regulatory profile. Users can thus single out which TFs are likely to be common regulators of the genes, and their respective correlations. Also, by examining results on promoter activation, transcription, histone modifications, polymerase binding and so on, users can investigate the effect of the TFs (activation or repression of transcription) as well as of the cell or tissue specificity of the genes' regulation and expression. The web interface is free for use, and there is no login requirement. Available at: http://www.beaconlab.it/cscan. © 2012 The Author(s). Source


D'Onorio De Meo P.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | D'Antonio M.,University of Bari | Griggio F.,University of Milan | Lupi R.,University of Milan | And 6 more authors.
Nucleic Acids Research | Year: 2012

The MITOchondrial genome database of metaZOAns (MitoZoa) is a public resource for comparative analyses of metazoan mitochondrial genomes (mtDNA) at both the sequence and genomic organizational levels. The main characteristics of the MitoZoa database are the careful revision of mtDNA entry annotations and the possibility of retrieving gene order and non-coding region (NCR) data in appropriate formats. The MitoZoa retrieval system enables basic and complex queries at various taxonomic levels using different search menus. MitoZoa 2.0 has been enhanced in several aspects, including: a re-annotation pipeline to check the correctness of protein-coding gene predictions; a standardized annotation of introns and of precursor ORFs whose functionality is post-transcriptionally recovered by RNA editing or programmed translational frameshifting; updates of taxon-related fields and a BLAST sequence similarity search tool. Database novelties and the definition of standard mtDNA annotation rules, together with the user-friendly retrieval system and the BLAST service, make MitoZoa a valuable resource for comparative and evolutionary analyses as well as a reference database to assist in the annotation of novel mtDNA sequences. MitoZoa is freely accessible at http://www.caspur.it/mitozoa. © The Author(s) 2011. Published by Oxford University Press. Source


de Bari L.,CNR Institute of Biomembrane and Bioenergetics | Valenti D.,CNR Institute of Biomembrane and Bioenergetics | Atlante A.,CNR Institute of Biomembrane and Bioenergetics | Passarella S.,University of Molise
FEBS Letters | Year: 2010

In order to ascertain whether and how mitochondria can produce hydrogen peroxide (H2O2) as a result of l-lactate addition, we monitored H2O2 generation in rat liver mitochondria and in submitochondrial fractions free of peroxisomal and cytosolic contamination. We found that H2O2 is produced independently on the respiratory chain with 1:1 stoichiometry with pyruvate, due to a putative flavine-dependent l-lactate oxidase restricted to the intermembrane space. The l-lactate oxidase reaction shows a hyperbolic dependence on l-lactate concentration and is inhibited by NAD+ in a competitive manner, being the enzyme different from the l-lactate dehydrogenase isoenzymes as shown by their pH profiles. © 2010 Federation of European Biochemical Societies. Source


De Bari L.,CNR Institute of Biomembrane and Bioenergetics | Moro L.,CNR Institute of Biomembrane and Bioenergetics | Passarella S.,University of Molise
FEBS Letters | Year: 2013

Although d-lactate metabolism has been shown to occur in a variety of mitochondria, the metabolic fate of d-lactate in cancer cells has never been investigated, as it is believed to be exported to the extracellular phase. We show that mitochondria from both cancer (PC-3) and normal (PNT1A) prostate cells can metabolize d-lactate in an energy competent manner. This is due to the mitochondrial d-lactate dehydrogenase, a membrane flavoprotein, the activity and protein level of which are higher in PC-3 than in PNT1A cells, as detected by both kinetic and immunological analysis. d-Lactate can enter prostate mitochondria and cause the export of newly synthesized malate in a carrier-mediated manner, with the rate of malate efflux from mitochondria twofold higher in cancer. © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. Source


Guaragnella N.,CNR Institute of Biomembrane and Bioenergetics | Passarella S.,University of Molise | Marra E.,CNR Institute of Biomembrane and Bioenergetics | Giannattasio S.,CNR Institute of Biomembrane and Bioenergetics
FEBS Letters | Year: 2010

To gain further insight into yeast acetic acid-induced programmed cell death (AA-PCD) we analyzed the effects of the antioxidant N-acetyl-l-cysteine (NAC) on cell viability, hydrogen peroxide (H2O2) production, DNA fragmentation, cytochrome c (cyt c) release and caspase-like activation in wild type (wt) and metacaspase and/or cyt c-lacking cells. We found that NAC prevents AA-PCD in wt cells, by scavenging H2O2 and by inhibiting both cyt c release and caspase-like activation. This shows the occurrence of a reactive oxygen species (ROS)-dependent AA-PCD. Contrarily no NAC dependent change in AA-PCD of mutant cells was detectable, showing that a ROS-independent AA-PCD can also occur. © 2010 Federation of European Biochemical Societies. Source

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