The Experts below are selected from a list of 312 Experts worldwide ranked by ideXlab platform
Graziano Pesole - One of the best experts on this subject based on the ideXlab platform.
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Statistical assessment of discriminative features for protein-coding and non coding cross-species Conserved sequence elements.
BMC Bioinformatics, 2009Co-Authors: Teresa Maria Creanza, Flavio Mignone, Rosalia Maglietta, Nicola Ancona, Annarita D'addabbo, David S Horner, Graziano PesoleAbstract:Background The identification of protein coding elements in sets of mammalian Conserved elements is one of the major challenges in the current molecular biology research. Many features have been proposed for automatically distinguishing coding and non coding Conserved Sequences, making so necessary a systematic statistical assessment of their differences. A comprehensive study should be composed of an association study, i.e. a comparison of the distributions of the features in the two classes, and a prediction study in which the prediction accuracies of classifiers trained on single and groups of features are analyzed, conditionally to the compared species and to the sequence lengths.
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Genome-wide identification of coding and non-coding Conserved sequence tags in human and mouse genomes
BMC Genomics, 2008Co-Authors: Flavio Mignone, Giorgio Grillo, Anna Anselmo, Giorgio Maggi, Giacinto Donvito, Graziano PesoleAbstract:The accurate detection of genes and the identification of functional regions is still an open issue in the annotation of genomic Sequences. This problem affects new genomes but also those of very well studied organisms such as human and mouse where, despite the great efforts, the inventory of genes and regulatory regions is far from complete. Comparative genomics is an effective approach to address this problem. Unfortunately it is limited by the computational requirements needed to perform genome-wide comparisons and by the problem of discriminating between Conserved coding and non-coding Sequences. This discrimination is often based (thus dependent) on the availability of annotated proteins. In this paper we present the results of a comprehensive comparison of human and mouse genomes performed with a new high throughput grid-based system which allows the rapid detection of Conserved Sequences and accurate assessment of their coding potential. By detecting clusters of coding Conserved Sequences the system is also suitable to accurately identify potential gene loci. Following this analysis we created a collection of human-mouse Conserved sequence tags and carefully compared our results to reliable annotations in order to benchmark the reliability of our classifications. Strikingly we were able to detect several potential gene loci supported by EST Sequences but not corresponding to as yet annotated genes. Here we present a new system which allows comprehensive comparison of genomes to detect Conserved coding and non-coding Sequences and the identification of potential gene loci. Our system does not require the availability of any annotated sequence thus is suitable for the analysis of new or poorly annotated genomes.
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CSTminer: a web tool for the identification of coding and noncoding Conserved sequence tags through cross-species genome comparison.
Nucleic acids research, 2004Co-Authors: Tiziana Castrignanò, Giorgio Grillo, Flavio Mignone, Alessandro Canali, Sabino Liuni, Graziano PesoleAbstract:The identification and characterization of genome tracts that are highly Conserved across species during evolution may contribute significantly to the functional annotation of whole-genome Sequences. Indeed, such Sequences are likely to correspond to known or unknown coding exons or regulatory motifs. Here, we present a web server implementing a previously developed algorithm that, by comparing user-submitted genome Sequences, is able to identify statistically significant Conserved blocks and assess their coding or noncoding nature through the measure of a coding potential score. The web tool, available at http://www.caspur.it/CSTminer/, is dynamically interconnected with the Ensembl genome resources and produces a graphical output showing a map of detected Conserved Sequences and annotated gene features.
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Mammalian mitochondrial D-loop region structural analysis: identification of new Conserved Sequences and their functional and evolutionary implications.
Gene, 1997Co-Authors: E Sbisà, Graziano Pesole, F Tanzariello, A Reyes, C SacconeAbstract:This paper reports the first comprehensive analysis of Displacement loop (D-loop) region Sequences from ten different mammalian orders. It represents a systematic evolutionary study at the molecular level on regulatory homologous regions in organisms belonging to a well defined class, mammalia, which radiated about 150 million years ago (Mya). We have aligned and analyzed 26 complete D-loop region Sequences available in the literature and the fat dormouse sequence, recently determined in our laboratory. The novelty of our alignment consists of the extensive manual revision of the preliminary output obtained by computer program to optimize sequence similarity, particularly for the two peripheral domains displaying heterogeneity in length and the presence of repeated Sequences. The multialignment is available at the WWW site: http://www.ba.cnr.it/dloop.html. Our comparative study has allowed us to identify new Conserved sequence blocks present in all the species under consideration and events of insertion/deletion which have important implications in both functional and evolutionary aspects. In particular we have detected two blocks, about 60 bp long, extended termination associated Sequences (ETAS1 and ETAS2) Conserved in all the organisms considered. Evaluation against experimental work suggests a possible functional role of ETAS1 and ETAS2 in the regulation of replication and transcription and targeted experimental approaches. The analyses on Conserved sequence blocks (CSBs) clearly indicate that CSB1 is the only very essential element, common to all mammalian mt genomes, while CSB2 and CSB3 could be involved in different though related functions, probably species specific, and thus more linked to nuclear mitochondrial coevolutionary processes. Our hypothesis on the different functional implications of the Conserved elements, CSBs and TASs, reported so far as main regulatory signals, would explain the different conservation of these elements in evolution. Moreover the intra-order comparison of the D-loop regions highlights peculiar features useful to define the evolutionary dynamics of this region in closely related species.
Mark A. Lehrman - One of the best experts on this subject based on the ideXlab platform.
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Conserved Sequences in enzymes of the UDP-GlcNAc/MurNAc family are essential in hamster UDP-GlcNAc:dolichol-P GlcNAc-1-P transferase
Glycobiology, 1998Co-Authors: Anthony R. Dal Nogare, Ning Dan, Mark A. LehrmanAbstract:The UDP-GlcNAc/MurNAc family of eukaryotic and prokaryotic enzymes use UDP-GlcNAc or UDP-MurNAc-pentapeptide as donors, dolichol-P or polyprenol-P as acceptors, and generate sugar-P-P-polyisoprenols. A series of six Conserved Sequences, designated A through F and ranging from 5 to 13 amino acid residues, has been identified in this family. To determine whether these Conserved Sequences are required for enzyme function, various mutations were examined in hamster UDP-GlcNAc:dolichol-P GlcNAc-1-P transferase (GPT). Scramble mutations of Sequences B-F, generated by scrambling the residues within each sequence, demonstrated that each is important in GPT. While E and F scrambles appeared to prevent stable expression of GPT, scrambling of B-D resulted in GPT mutants that could be stably expressed and bound tunicamycin, but lacked enzymatic activity. Further, the C and D scramble mutants had an unexpected sorting defect. Replacement of Sequences B-F with prokaryotic counterparts from either the B.subtilis mraY or E.coli rfe genes also affected GPT by preventing expression of the mutant protein (B, F) or inhibiting its enzymatic activity (C-E). For the C-E replacements, no acquisition of acceptor activity for polyprenol-P, the fully unsaturated natural bacterial acceptor, was detected. These studies show that the Conserved Sequences of the UDP-GlcNAc/MurNAc family are important, and that the eukaryotic and prokaryotic counterparts are not freely interchangeable. Since several mutants were efficiently expressed and bound tunicamycin, yet lacked enzymatic activity, the data are consistent with these Sequences having a direct role in product formation.
Annette Martin - One of the best experts on this subject based on the ideXlab platform.
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Inhibition of Hepatitis C Virus Infection in Cell Culture by Small Interfering RNAs.
Molecular Therapy, 2007Co-Authors: Christophe Chevalier, Aure Saulnier, Yann Benureau, Dorian Fléchet, David Delgrange, Florence Colbère-garapin, Czeslaw Wychowski, Annette MartinAbstract:Hepatitis C virus (HCV) infection is a major cause of chronic liver disease and hepatocellular carcinoma, yet fully efficacious treatments are missing. In this study, we investigated RNA interference (RNAi), a specific gene silencing process mediated by small interfering RNA (siRNA) duplexes, as an antiviral strategy against HCV. Synthetic siRNAs were designed to target Conserved Sequences of the HCV 5' nontranslated region (NTR) located in a functional, stem-loop structured domain of the HCV internal ribosome entry site (IRES), which is crucial for initiation of polyprotein translation. Several siRNAs dramatically reduced or even abrogated the replication of selectable subgenomic HCV replicons upon cotransfection of human hepatoma cells with viral target and siRNAs, or upon transfection of cells supporting autonomous replication of HCV replicon with siRNAs. Importantly, three siRNAs also proved capable of strongly inhibiting virus production in cell culture. One siRNA, targeting a sequence that is highly Conserved across all genotypes and forms a critical pseudoknot structure involved in translation, was identified as the most promising therapeutic candidate. These results indicate that the HCV life cycle can be efficiently blocked by using properly-designed siRNAs that target functionally important, highly Conserved Sequences of the HCV IRES. This finding offers a novel approach towards developing IRES-based antiviral treatment for chronic HCV infections.Molecular Therapy (2007) 15 8, 1452-1462. doi:10.1038/sj.mt.6300186.
Flavio Mignone - One of the best experts on this subject based on the ideXlab platform.
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Statistical assessment of discriminative features for protein-coding and non coding cross-species Conserved sequence elements.
BMC Bioinformatics, 2009Co-Authors: Teresa Maria Creanza, Flavio Mignone, Rosalia Maglietta, Nicola Ancona, Annarita D'addabbo, David S Horner, Graziano PesoleAbstract:Background The identification of protein coding elements in sets of mammalian Conserved elements is one of the major challenges in the current molecular biology research. Many features have been proposed for automatically distinguishing coding and non coding Conserved Sequences, making so necessary a systematic statistical assessment of their differences. A comprehensive study should be composed of an association study, i.e. a comparison of the distributions of the features in the two classes, and a prediction study in which the prediction accuracies of classifiers trained on single and groups of features are analyzed, conditionally to the compared species and to the sequence lengths.
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Genome-wide identification of coding and non-coding Conserved sequence tags in human and mouse genomes
BMC Genomics, 2008Co-Authors: Flavio Mignone, Giorgio Grillo, Anna Anselmo, Giorgio Maggi, Giacinto Donvito, Graziano PesoleAbstract:The accurate detection of genes and the identification of functional regions is still an open issue in the annotation of genomic Sequences. This problem affects new genomes but also those of very well studied organisms such as human and mouse where, despite the great efforts, the inventory of genes and regulatory regions is far from complete. Comparative genomics is an effective approach to address this problem. Unfortunately it is limited by the computational requirements needed to perform genome-wide comparisons and by the problem of discriminating between Conserved coding and non-coding Sequences. This discrimination is often based (thus dependent) on the availability of annotated proteins. In this paper we present the results of a comprehensive comparison of human and mouse genomes performed with a new high throughput grid-based system which allows the rapid detection of Conserved Sequences and accurate assessment of their coding potential. By detecting clusters of coding Conserved Sequences the system is also suitable to accurately identify potential gene loci. Following this analysis we created a collection of human-mouse Conserved sequence tags and carefully compared our results to reliable annotations in order to benchmark the reliability of our classifications. Strikingly we were able to detect several potential gene loci supported by EST Sequences but not corresponding to as yet annotated genes. Here we present a new system which allows comprehensive comparison of genomes to detect Conserved coding and non-coding Sequences and the identification of potential gene loci. Our system does not require the availability of any annotated sequence thus is suitable for the analysis of new or poorly annotated genomes.
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CSTminer: a web tool for the identification of coding and noncoding Conserved sequence tags through cross-species genome comparison.
Nucleic acids research, 2004Co-Authors: Tiziana Castrignanò, Giorgio Grillo, Flavio Mignone, Alessandro Canali, Sabino Liuni, Graziano PesoleAbstract:The identification and characterization of genome tracts that are highly Conserved across species during evolution may contribute significantly to the functional annotation of whole-genome Sequences. Indeed, such Sequences are likely to correspond to known or unknown coding exons or regulatory motifs. Here, we present a web server implementing a previously developed algorithm that, by comparing user-submitted genome Sequences, is able to identify statistically significant Conserved blocks and assess their coding or noncoding nature through the measure of a coding potential score. The web tool, available at http://www.caspur.it/CSTminer/, is dynamically interconnected with the Ensembl genome resources and produces a graphical output showing a map of detected Conserved Sequences and annotated gene features.
Jesus Torres-flores - One of the best experts on this subject based on the ideXlab platform.
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Inhibition of dengue virus infection by small interfering RNAs that target highly Conserved Sequences in the NS4B or NS5 coding regions.
Archives of virology, 2018Co-Authors: Paula M Villegas, Elizabeth Ortega, Lourdes Villa-tanaca, Blanca L. Barrón, Jesus Torres-floresAbstract:Dengue fever is one of the most common viral infections in the world. Although a vaccine against dengue virus (DENV) has been approved in several countries, this disease is still considered a public health priority worldwide. The ability of three small interfering RNAs (FG-siRNAs) targeting Conserved Sequences in the NS4B and NS5 regions of the DENV genome to inhibit DENV replication was tested in vitro in both Vero and C6/36 cells. The FG-siRNAs were effective against DENV-1, -3, and -4, but not DENV-2. A fourth siRNA specifically targeting the NS5 region of the DENV-2 genome (SG-siRNA) was designed and tested against two different DENV-2 strains, showing high levels of inhibition in both mammalian and insect cells.