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Automated FingerPrint Background removal: FPB
Simone Scalabrin, Michele Morgante, Alberto Policriti
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-127
Abstract: At the moment, the only tools available for such a task are GenoProfiler and its descendant FPMiner. The large variation in the quality of fingerprints that is usually present in large fingerprinting projects represents a major difficulty in the correct removal of background peaks that has only been partially addressed by the methods so far adopted that all require a long manual optimization of parameters. Thus, we implemented a new data-independent tool, FPB (FingerPrint Background removal), suitable for large scale projects as well as mapping of few clones.FPB is freely available at http://www.appliedgenomics.org/tools.php webcite. FPB was used to remove the background from all fingerprints of three grapevine physical map projects. The first project consists of about 50,000 fingerprints, the second one consists of about 70,000 fingerprints, and the third one consists of about 45,000 fingerprints. In all cases a successful assembly was built.The construction of a whole-genome physical map [1-6] has been an essential component of numerous genome projects initiated since the inception of the Human Genome Project [7]. Its usefulness has been proved for whole-genome shotgun projects as a post-assembly validation and recently it has also been used in the assembly step to constrain on BACs positions [8].High-throughput fingerprinting can produce thousands of BAC clone fingerprints per day. Hence automatic editing of corresponding files can be extremely useful.From now on the description of the process will be based on fingerprints produced on Applied Biosystems Instruments (ABI) automated DNA sequencers, but the method can be applied to any kind of fingerprint as long as similar input is provided. Moreover, the following terms will be used interchangeably since they correspond to the same entity: fragment, band, and peak.Fingerprint data is stored in electrochromatograms, i.e. fsa files, output by GeneMapper, ABI sequencer software. Each peak represents a fragment with a
An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis
Cristian Del Fabbro, Simone Scalabrin, Michele Morgante, Federico M. Giorgi
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0085024
Abstract: Next Generation Sequencing is having an extremely strong impact in biological and medical research and diagnostics, with applications ranging from gene expression quantification to genotyping and genome reconstruction. Sequencing data is often provided as raw reads which are processed prior to analysis 1 of the most used preprocessing procedures is read trimming, which aims at removing low quality portions while preserving the longest high quality part of a NGS read. In the current work, we evaluate nine different trimming algorithms in four datasets and three common NGS-based applications (RNA-Seq, SNP calling and genome assembly). Trimming is shown to increase the quality and reliability of the analysis, with concurrent gains in terms of execution time and computational resources needed.
Historical Introgression of the Downy Mildew Resistance Gene Rpv12 from the Asian Species Vitis amurensis into Grapevine Varieties
Silvia Venuti, Dario Copetti, Serena Foria, Luigi Falginella, Sarolta Hoffmann, Diana Bellin, Petar Cindri?, Pál Kozma, Simone Scalabrin, Michele Morgante, Raffaele Testolin, Gabriele Di Gaspero
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0061228
Abstract: The Amur grape (Vitis amurensis Rupr.) thrives naturally in cool climates of Northeast Asia. Resistance against the introduced pathogen Plasmopara viticola is common among wild ecotypes that were propagated from Manchuria into Chinese vineyards or collected by Soviet botanists in Siberia, and used for the introgression of resistance into wine grapes (Vitis vinifera L.). A QTL analysis revealed a dominant gene Rpv12 that explained 79% of the phenotypic variance for downy mildew resistance and was inherited independently of other resistance genes. A Mendelian component of resistance–a hypersensitive response in leaves challenged with P. viticola–was mapped in an interval of 0.2 cM containing an array of coiled-coil NB-LRR genes on chromosome 14. We sequenced 10-kb genic regions in the Rpv12+ haplotype and identified polymorphisms in 12 varieties of V. vinifera using next-generation sequencing. The combination of two SNPs in single-copy genes flanking the NB-LRR cluster distinguished the resistant haplotype from all others found in 200 accessions of V. vinifera, V. amurensis, and V. amurensis x V. vinifera crosses. The Rpv12+ haplotype is shared by 15 varieties, the most ancestral of which are the century-old ‘Zarja severa’ and ‘Michurinets’. Before this knowledge, the chromosome segment around Rpv12+ became introgressed, shortened, and pyramided with another downy mildew resistance gene from North American grapevines (Rpv3) only by phenotypic selection. Rpv12+ has an additive effect with Rpv3+ to protect vines against natural infections, and confers foliar resistance to strains that are virulent on Rpv3+ plants.
A Unique Mutation in a MYB Gene Cosegregates with the Nectarine Phenotype in Peach
Elisa Vendramin, Giorgio Pea, Luca Dondini, Igor Pacheco, Maria Teresa Dettori, Laura Gazza, Simone Scalabrin, Francesco Strozzi, Stefano Tartarini, Daniele Bassi, Ignazio Verde, Laura Rossini
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0090574
Abstract: Nectarines play a key role in peach industry; the fuzzless skin has implications for consumer acceptance. The peach/nectarine (G/g) trait was described as monogenic and previously mapped on chromosome 5. Here, the position of the G locus was delimited within a 1.1 cM interval (635 kb) based on linkage analysis of an F2 progeny from the cross ‘Contender’ (C, peach) x ‘Ambra’ (A, nectarine). Careful inspection of the genes annotated in the corresponding genomic sequence (Peach v1.0), coupled with variant discovery, led to the identification of MYB gene PpeMYB25 as a candidate for trichome formation on fruit skin. Analysis of genomic re-sequencing data from five peach/nectarine accessions pointed to the insertion of a LTR retroelement in exon 3 of the PpeMYB25 gene as the cause of the recessive glabrous phenotype. A functional marker (indelG) developed on the LTR insertion cosegregated with the trait in the CxA F2 progeny and was validated on a broad panel of genotypes, including all known putative donors of the nectarine trait. This marker was shown to efficiently discriminate between peach and nectarine plants, indicating that a unique mutational event gave rise to the nectarine trait and providing a useful diagnostic tool for early seedling selection in peach breeding programs.
Rede Edunet
Scalabrin Maria Elisa
Educa??o & Sociedade , 1997,
Angela Maria Scalabrin Coutinho
Poiésis , 2011,
Abstract: This article has as its subject the social action of babies in the context of the nursery. It is based on the idea that the body is a central category in this action and is placed at the interaction between two main areas: the children’s education and the Sociology of Childhood. To investigate the social action in the nursery, it was chosen the development of an ethnographic study among a group of babies and the professionals that attended them in a nursery in Braga-Portugal. The gathering of data was made by participating observations recorded on a field diary and on video, which allowed a very fruitful approach to the children’s everyday experiences. In this article the choice is to discuss the idea of social action by deepening the analysis from the body, understood as a component of social action.
A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance
Marco Moroldo, Sophie Paillard, Raffaella Marconi, Legeai Fabrice, Aurelie Canaguier, Corinne Cruaud, Veronique De Berardinis, Cecile Guichard, Veronique Brunaud, Isabelle Le Clainche, Simone Scalabrin, Raffaele Testolin, Gabriele Di Gaspero, Michele Morgante, Anne-Francoise Adam-Blondon
BMC Plant Biology , 2008, DOI: 10.1186/1471-2229-8-66
Abstract: The physical map included 29,727 BAC clones assembled into 1,770 contigs, spanning 715,684 kbp, and corresponding to 1.5-fold the genome size. Map inflation was due to high heterozygosity, which caused either the separation of allelic BACs in two different contigs, or local mis-assembly in contigs containing BACs from the two haplotypes. Genetic markers anchored 395 contigs or 255,476 kbp to chromosomes. The fully automated assembly and anchorage procedures were validated by BAC-by-BAC blast of the end sequences against the grape genome sequence, unveiling 7.3% of chimerical contigs. The distribution across the physical map of candidate genes for non-host and host resistance, and for defence signalling pathways was then studied. NBS-LRR and RLK genes for host resistance were found in 424 contigs, 133 of them (32%) were assigned to chromosomes, on which they are mostly organised in clusters. Non-host and defence signalling genes were found in 99 contigs dispersed without a discernable pattern across the genome.Despite some limitations that interfere with the correct assembly of heterozygous clones into contigs, the 'Cabernet Sauvignon' physical map is a useful and reliable intermediary step between a genetic map and the genome sequence. This tool was successfully exploited for a quick mapping of complex families of genes, and it strengthened previous clues of co-localisation of major NBS-LRR clusters and disease resistance loci in grapevine.Physical maps built from large-insert BAC clones and anchored to linkage maps assist sequence assembly in whole genome shotgun (WGS) sequencing projects [1], enable positional cloning of genes/QTLs and structural studies on gene families [2,3], and facilitate the isolation of homologous genes from model plants in heterozygous or polyploid species [4].In plants, physical maps have been constructed for Arabidopsis thaliana [5], sorghum [6], rice [7], soybean [8], apple [9], black cottonwood [10], and grapevine [11]. Strategies based
Physical mapping in highly heterozygous genomes: a physical contig map of the Pinot Noir grapevine cultivar
Simone Scalabrin, Michela Troggio, Marco Moroldo, Massimo Pindo, Nicoletta Felice, Giuseppina Coppola, Giacomo Prete, Giulia Malacarne, Raffaella Marconi, Giorgia Faes, Irena Jurman, Stella Grando, Taco Jesse, Cinzia Segala, Giorgio Valle, Alberto Policriti, Paolo Fontana, Michele Morgante, Riccardo Velasco
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-204
Abstract: We report on the first whole genome physical map of grapevine built using high information content fingerprinting of 49,104 BAC clones from the cultivar Pinot Noir. Pinot Noir, as most grape varieties, is highly heterozygous at the sequence level. This resulted in the two allelic haplotypes sometimes assembling into separate contigs that had to be accommodated in the map framework or in local expansions of contig maps. We performed computer simulations to assess the effects of increasing levels of sequence heterozygosity on BAC fingerprint assembly and showed that the experimental assembly results are in full agreement with the theoretical expectations, given the heterozygosity levels reported for grape. The map is anchored to a dense linkage map consisting of 994 markers. 436 contigs are anchored to the genetic map, covering 342 of the 475 Mb that make up the grape haploid genome.We have developed a resource that makes it possible to access the grapevine genome, opening the way to a new era both in grape genetics and breeding and in wine making. The effects of heterozygosity on the assembly have been analyzed and characterized by using several complementary approaches which could be easily transferred to the study of other genomes which present the same features.With a production of 67.1 millions tons obtained from 7.9 millions hectares in 2004, grapevine (Vitis vinifera L.) is by far the most important fruit tree crop in the world http://www.oiv.org webcite. In comparison to other fruit crops, it shows a particularly wide range of uses: fresh, dried, transformed in juice and obviously wine. At present, its importance goes beyond the economic level, being wine associated in many cases with national cultures and life style. Moreover, red wines are thought to provide health benefits thanks to secondary metabolites such as resveratrol, a strong antioxidant supposed to provide health benefits [1].Despite the obvious economic relevance, most of the grape cultivars grown
The role of the process/case in building democracy: for a new meaning of participatory democracys O papel do processo na constru o da democracia: para uma nova defini o da democracia participativa
Darci Guimar?es Ribeiro,Felipe Scalabrin
Scientia Iuris , 2009,
Abstract: Democracy is in crisis. We no longer feel represented, no longer is the people summoned in an authentic way; it is now a mere icon; it is now only a facet of what should be a whole. Now a new assumption is needed, based on enabling maximum development of individual guarantees and ensuring that the State fulfills its constitutionally established functions. It is the unrestricted participation that will characterize participatory democracy, together with broad access to the Judiciary Power – which comes in the scenario as a real democratic leader. In this way, as a means of inclusion for all citizens, the process/case takes a political role (beyond the law) as a device that allows the judge to assess the multiple interests that are hierarchically set by the society and, finally, to bring law to life, thus making democracy real. A democracia está em crise, n o mais nos sentimos representados, n o mais o povo é invocado de maneira autêntica, ora é mero ícone, ora é apenas faceta do que deveria ser um todo. Necessário um novo pressuposto, calcado em possibilitar o máximo desenvolvimento das garantias individuais e de assegurar que o Estado cumpra suas fun es constitucionalmente estabelecidas. é a participa o irrestrita que caracterizará a democracia participativa, mesclando-se com o amplo acesso ao Poder Judiciário – que surge no cenário democrático como autêntico protagonista. Nessa senda, como meio de inclus o de qualquer cidad o, o processo adquire relevo em seu aspecto político (para além do jurídico), como instrumento que possibilita ao juiz avaliar os múltiplos interesses hierarquizados pela sociedade e, por fim, dar vida ao direito, concretizando, assim, o pressuposto democrático.
Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm
Ignazio Verde, Nahla Bassil, Simone Scalabrin, Barbara Gilmore, Cynthia T. Lawley, Ksenija Gasic, Diego Micheletti, Umesh R. Rosyara, Federica Cattonaro, Elisa Vendramin, Dorrie Main, Valeria Aramini, Andrea L. Blas, Todd C. Mockler, Douglas W. Bryant, Larry Wilhelm, Michela Troggio, Bryon Sosinski, Maria José Aranzana, Pere Arús, Amy Iezzoni, Michele Morgante, Cameron Peace
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0035668
Abstract: Although a large number of single nucleotide polymorphism (SNP) markers covering the entire genome are needed to enable molecular breeding efforts such as genome wide association studies, fine mapping, genomic selection and marker-assisted selection in peach [Prunus persica (L.) Batsch] and related Prunus species, only a limited number of genetic markers, including simple sequence repeats (SSRs), have been available to date. To address this need, an international consortium (The International Peach SNP Consortium; IPSC) has pursued a coordinated effort to perform genome-scale SNP discovery in peach using next generation sequencing platforms to develop and characterize a high-throughput Illumina Infinium? SNP genotyping array platform. We performed whole genome re-sequencing of 56 peach breeding accessions using the Illumina and Roche/454 sequencing technologies. Polymorphism detection algorithms identified a total of 1,022,354 SNPs. Validation with the Illumina GoldenGate? assay was performed on a subset of the predicted SNPs, verifying ~75% of genic (exonic and intronic) SNPs, whereas only about a third of intergenic SNPs were verified. Conservative filtering was applied to arrive at a set of 8,144 SNPs that were included on the IPSC peach SNP array v1, distributed over all eight peach chromosomes with an average spacing of 26.7 kb between SNPs. Use of this platform to screen a total of 709 accessions of peach in two separate evaluation panels identified a total of 6,869 (84.3%) polymorphic SNPs. The almost 7,000 SNPs verified as polymorphic through extensive empirical evaluation represent an excellent source of markers for future studies in genetic relatedness, genetic mapping, and dissecting the genetic architecture of complex agricultural traits. The IPSC peach SNP array v1 is commercially available and we expect that it will be used worldwide for genetic studies in peach and related stone fruit and nut species.
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