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Search Results: 1 - 10 of 200607 matches for " Alicia N. Massa "
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The Transcriptome of the Reference Potato Genome Solanum tuberosum Group Phureja Clone DM1-3 516R44
Alicia N. Massa, Kevin L. Childs, Haining Lin, Glenn J. Bryan, Giovanni Giuliano, C. Robin Buell
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0026801
Abstract: Advances in molecular breeding in potato have been limited by its complex biological system, which includes vegetative propagation, autotetraploidy, and extreme heterozygosity. The availability of the potato genome and accompanying gene complement with corresponding gene structure, location, and functional annotation are powerful resources for understanding this complex plant and advancing molecular breeding efforts. Here, we report a reference for the potato transcriptome using 32 tissues and growth conditions from the doubled monoploid Solanum tuberosum Group Phureja clone DM1-3 516R44 for which a genome sequence is available. Analysis of greater than 550 million RNA-Seq reads permitted the detection and quantification of expression levels of over 22,000 genes. Hierarchical clustering and principal component analyses captured the biological variability that accounts for gene expression differences among tissues suggesting tissue-specific gene expression, and genes with tissue or condition restricted expression. Using gene co-expression network analysis, we identified 18 gene modules that represent tissue-specific transcriptional networks of major potato organs and developmental stages. This information provides a powerful resource for potato research as well as studies on other members of the Solanaceae family.
Integration of Two Diploid Potato Linkage Maps with the Potato Genome Sequence
Kimberly J. Felcher, Joseph J. Coombs, Alicia N. Massa, Candice N. Hansey, John P. Hamilton, Richard E. Veilleux, C. Robin Buell, David S. Douches
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0036347
Abstract: To facilitate genome-guided breeding in potato, we developed an 8303 Single Nucleotide Polymorphism (SNP) marker array using potato genome and transcriptome resources. To validate the Infinium 8303 Potato Array, we developed linkage maps from two diploid populations (DRH and D84) and compared these maps with the assembled potato genome sequence. Both populations used the doubled monoploid reference genotype DM1-3 516 R44 as the female parent but had different heterozygous diploid male parents (RH89-039-16 and 84SD22). Over 4,400 markers were mapped (1,960 in DRH and 2,454 in D84, 787 in common) resulting in map sizes of 965 (DRH) and 792 (D84) cM, covering 87% (DRH) and 88% (D84) of genome sequence length. Of the mapped markers, 33.5% were in candidate genes selected for the array, 4.5% were markers from existing genetic maps, and 61% were selected based on distribution across the genome. Markers with distorted segregation ratios occurred in blocks in both linkage maps, accounting for 4% (DRH) and 9% (D84) of mapped markers. Markers with distorted segregation ratios were unique to each population with blocks on chromosomes 9 and 12 in DRH and 3, 4, 6 and 8 in D84. Chromosome assignment of markers based on linkage mapping differed from sequence alignment with the Potato Genome Sequencing Consortium (PGSC) pseudomolecules for 1% of the mapped markers with some disconcordant markers attributable to paralogs. In total, 126 (DRH) and 226 (D84) mapped markers were not anchored to the pseudomolecules and provide new scaffold anchoring data to improve the potato genome assembly. The high degree of concordance between the linkage maps and the pseudomolecules demonstrates both the quality of the potato genome sequence and the functionality of the Infinium 8303 Potato Array. The broad genome coverage of the Infinium 8303 Potato Array compared to other marker sets will enable numerous downstream applications.
Single nucleotide polymorphism discovery in elite north american potato germplasm
John P Hamilton, Candice N Hansey, Brett R Whitty, Kevin Stoffel, Alicia N Massa, Allen Van Deynze, Walter S De Jong, David S Douches, C Robin Buell
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-302
Abstract: To identify a large number of Single Nucleotide Polymorphisms (SNPs) in elite potato germplasm, we sequenced normalized cDNA prepared from three commercial potato cultivars: 'Atlantic', 'Premier Russet' and 'Snowden'. For each cultivar, we generated 2 Gb of sequence which was assembled into a representative transcriptome of ~28-29 Mb for each cultivar. Using the Maq SNP filter that filters read depth, density, and quality, 575,340 SNPs were identified within these three cultivars. In parallel, 2,358 SNPs were identified within existing Sanger sequences for three additional cultivars, 'Bintje', 'Kennebec', and 'Shepody'. Using a stringent set of filters in conjunction with the potato reference genome, we identified 69,011 high confidence SNPs from these six cultivars for use in genotyping with the Infinium platform. Ninety-six of these SNPs were used with a BeadXpress assay to assess allelic diversity in a germplasm panel of 248 lines; 82 of the SNPs proved sufficiently informative for subsequent analyses. Within diverse North American germplasm, the chip processing market class was most distinct, clearly separated from all other market classes. The round white and russet market classes both include fresh market and processing cultivars. Nevertheless, the russet and round white market classes are more distant from each other than processing are from fresh market types within these two groups.The genotype data generated in this study, albeit limited in number, has revealed distinct relationships among the market classes of potato. The SNPs identified in this study will enable high-throughput genotyping of germplasm and populations, which in turn will enable more efficient marker-assisted breeding efforts in potato.The most widely cultivated potato species, Solanum tuberosum Group Tuberosum, is an autotetraploid (2n = 4x = 48) and the world's third most important food crop in overall production, after rice and wheat [1]. Potato improvement is constrained by numerous ch
Insular Organization of Gene Space in Grass Genomes
Andrea Gottlieb, Hans-Georg Müller, Alicia N. Massa, Humphrey Wanjugi, Karin R. Deal, Frank M. You, Xiangyang Xu, Yong Q. Gu, Ming-Cheng Luo, Olin D. Anderson, Agnes P. Chan, Pablo Rabinowicz, Katrien M. Devos, Jan Dvorak
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0054101
Abstract: Wheat and maize genes were hypothesized to be clustered into islands but the hypothesis was not statistically tested. The hypothesis is statistically tested here in four grass species differing in genome size, Brachypodium distachyon, Oryza sativa, Sorghum bicolor, and Aegilops tauschii. Density functions obtained under a model where gene locations follow a homogeneous Poisson process and thus are not clustered are compared with a model-free situation quantified through a non-parametric density estimate. A simple homogeneous Poisson model for gene locations is not rejected for the small O. sativa and B. distachyon genomes, indicating that genes are distributed largely uniformly in those species, but is rejected for the larger S. bicolor and Ae. tauschii genomes, providing evidence for clustering of genes into islands. It is proposed to call the gene islands “gene insulae” to distinguish them from other types of gene clustering that have been proposed. An average S. bicolor and Ae. tauschii insula is estimated to contain 3.7 and 3.9 genes with an average intergenic distance within an insula of 2.1 and 16.5 kb, respectively. Inter-insular distances are greater than 8 and 81 kb and average 15.1 and 205 kb, in S. bicolor and Ae. tauschii, respectively. A greater gene density observed in the distal regions of the Ae. tauschii chromosomes is shown to be primarily caused by shortening of inter-insular distances. The comparison of the four grass genomes suggests that gene locations are largely a function of a homogeneous Poisson process in small genomes. Nonrandom insertions of LTR retroelements during genome expansion creates gene insulae, which become less dense and further apart with the increase in genome size. High concordance in relative lengths of orthologous intergenic distances among the investigated genomes including the maize genome suggests functional constraints on gene distribution in the grass genomes.
Road Accident Mediation in Córdoba: in the crossroad of fields, strategies, and positions
Agustín Vélez Massa
O?ati Socio-Legal Series , 2012,
Abstract: Court-related mediations have become commonplace in many legal systems around the globe. In this research I will focus in road accident mediations taking place in a public mediation center in Córdoba (Argentina), where mediation is mandatory for an important range of cases. Throughout the thesis I attempt to grasp the set of practices that take place in those mediations; which have mediators, lawyers and parties as main actors. To endeavour to do this, I will rely on the concepts and ideas developed by Pierre Bourdieu. I intend to analyse the strategies, positions, habitus, and capitals of mediators, insurance companies (and their lawyers) and plaintiffs (and their lawyers). I attempt to show how road accident mediation constitutes a particular field, with its own illusio, which rules are continuously under struggle. The interconnections among the different agents are highlighted as well as the opportunities and constraints their position imposes above their practices. DOWNLOAD THIS PAPER FROM SSRN: http://ssrn.com/abstract=1997457
La "Frontera" Bonaerense en el siglo XVIII un espacio políticamente concertado: fuertes, vecinos, milicias y autoridades civiles-militares
Néspolo,Eugenia Alicia;
Mundo agrario , 2006,
Abstract: this work's objective is to argue that the bonaerense border is defined as a politically concerted space. for this we analyse the defensive actions practiced to determine that the material building resources and the military effectives were insufficient to protect the region. by the contrary, its shown that the militia service was essential to protect the space and was constitutive of vicinity conditions that made possible that some militia-neighbours could have access to authority. local powers that were on movement from the urban space, the lujan village, to the border areas. to argue this we show the knowledge from the militia service and the defensive structure -web- that was organized in the jurisdiction of buenos aires during the first half of xviiith century.
ESCRITURA, IMAGEN Y POLíTICA EN DOS POETAS ARGENTINAS: ALFONSINA STORNI Y ALICIA GENOVESE
Salomone,Alicia N;
Atenea (Concepción) , 2009, DOI: 10.4067/S0718-04622009000100008
Abstract: this paper revises comparatively two poetic texts of two argentine women writers of the 20th century: ?danzón porte?o? (1938) by alfonsina storni (1892-1938) and the group of poems puentes (2000) by alicia genovese (1953). the analysis takes into account the following aspects: on the one hand, the representation of buenos aires in two moments of acute social crisis and, on the other hand, the feminine identification of the poetic subjects. finally, we look at the intertextual links that the texts establish with other artistic spheres, especially with art and music. the hypothesis we set forward claims that in their urban flow, both works configure feminine subjects that are critically situated in relation to their surroundings, from a socio-political point of view as well as a sexual-generic one, and that in this discourse the reflection on the aesthetic and ethical implications of the practice of art and literature are central features.
?Dilemas?: metodológicos y éticos en la investigación antropológica en Servicios de salud
Barber,Nélida Alicia;
Av?? , 2009,
Abstract: in this paper we examine some particularities of anthropological research in hospitality institutions, on the basis of fieldwork carries out in hospitals of the metropolitan and suburban areas of buenos aires. on one side, we focus on the institutional requirements for allowing access to the hospital and, on the other side, on the emotional and ethical commitments of researchers. in what concern to the former, we discuss the problematic arising from procuring authorization from the ethical research committee of the hospital to conduct a research in these premises. on the other hand, we discuss some ethic problems and dilemmas and we analyze the methodological and theoretical implications of such issues.
Procesos de tradicionalización en el carnaval de Buenos Aires
Martín,Alicia;
Cuadernos de la Facultad de Humanidades y Ciencias Sociales. Universidad Nacional de Jujuy , 2009,
Abstract: in this paper we analyze the impact of carnival folk re-creation in buenos aires city, when new agents (local government, market, professional artists), traditionalized folk plays and contextualized them according with present times. at the very moment the practices of the old carnival groups, called murgas o centro-murgas, transformed their organizations forms, also was the aesthetics of carnival ways. the production and reproduction conditions of carnival feast and ?murgas? were modified in the last 20 years by their inclusion in the public cultural policies agenda. these topics establish a social space in wich all involved agents contend their own traditions and projects.
MACROECONOMíA, DESARROLLO Y GéNERO
Girón,Alicia;
Revista de Economía Institucional , 2006,
Abstract: this article establishes a relationship between the consensus of washington and gender inequality. it considers several important points: the reforms and the social impact; development and gender; for who is the structural process; gender budgets and the millennium objectives; and the employment program. it concludes that public policies today are very far to reach the millennium objectives. it is necessary to establish a development alternative agenda.
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