1,721,059 research outputs found
Quantitative predictions of protein interactions with long noncoding RNAs
No full textLong noncoding RNAs (lncRNAs, which comprise 68% of the human transcriptome with average length of 1,000 nt) interact with various RNA-binding proteins (RBPs) to mediate cellular functions. Here we introduce Global Score as a tool to predict protein interactions with lncRNAs (http://service.tartaglialab.com/new_submission/globalscore). We used enhanced CLIP (eCLIP) to test the binding of the lncRNA Xist to the RBPs HnrnpK (Global Score of 0.99), Ptbp1 (0.99), Lbr (0.79), HnrnpU (Saf-A) (0.66), Spen (Sharp) (0.59) and negative control Dkc1 (0.01). Global Score prediction correlates with the eCLIP binding profile (Pearson correlation = 0.93). As for the binding sites, Spen and HnrnpK, Ptbp1, and Lbr interact respectively with Xist A, B, and E repeats and adjacent regions, while HnrnpU binds across the whole transcript, and Dkc1 does not interact with Xist
Blind Date: Pastoralists meet agribusiness in the Senegal River Delta
No full textThis thesis analyses a case study on territorial transformations induced by the private lease of a natural reserve situated in the Senegal River Delta Region. It aims to question mainstream discourses about large-scale land acquisitions that portray stakeholders as homogeneous entities, i.e. the “state”, the “company”, the “local community”, bestowing them with static features and prearranged power relations. Against these arguments, the theoretical proposal is to look at the land acquisition through the relational approach to territory and territoriality of Claude Raffestins’, by integrating it with the Sandra Evers’ analytical tool of Zones of Intermediality. ‘zones of intermediality’ has been used as analytical tool to grasp stakeholders’ discourses and positionalities that slip away by macro narratives. Therefore, this study analyses variations in stakeholders’ positioning, their interconnections and the divergent responses of groups of farmer, pastoralist and agro-pastoralist to a new top-down project of territory. Moreover, it aims to show how grounded analysis on large-scale land acquisitions can disentangle the simplistic discourses of “global threats to vulnerable local territories”, by pointing out the distinctiveness of places in attracting and/or mediating transnational dynamics of resource accumulation. I argue that by analysing power-embedded mediation patterns and discursive practices, the Zones of Intermediality could enhance the capacity of Raffestin’s territoriality approach in capturing territorial ideas and practices of everyday life.Questa tesi tratta uno studio di caso sulle trasformazioni territoriali indotte dalla concessione ad un privato di parte di una riserva naturale nel Delta del fiume Senegal. Lo studio desidera mettere in questione il discorso dominante sulle acquisizioni di terra su larga scala che rappresenta gli attori come unità omogenee. Così facendo “lo stato”, “la compagnia” e la “comunità locale” ad esempio vengono resi soggetti statici e caratterizzati da rapporti di potere predeterminati. In contrapposizione a questi argomenti, la proposta teorica alla base di questo lavoro è di guardare alle acquisizioni di terra su larga scala attraverso l’approccio relazionale al territorio e alla territorialità di Claude Raffestin, integrandolo con lo strumento analitico delle Zones of Intermediality di Sandra Evers. Zones of Intermediality viene qui usato per analizzare i repertori discorsivi e le razionalità territoriali che possono sfuggire da grandi narrazioni. Quindi questo studio analizza le variazioni nel posizionamento degli attori, le loro interconnessioni e le risposte divergenti di gruppi di contadini, pastori ed agro-pastori ad un progetto di territorio imposto dall’alto. Inoltre la tesi vuole dimostrare come lo studio delle acquisizioni di terra su larga scala a livello micro permetta di decostruire le narrazioni semplicistiche che parlano di “minacce globali a territori locali” mettendo in luce il valore delle complessità locali nell’attrarre o mediare le dinamiche transnazionali di accumulazione delle risorse. Sostengo che Zones of Intermediality, analizzando le dinamiche di mediazione intrinseche al potere e le pratiche discorsive, possa ampliare la capacità del modello di Raffestin nel cogliere le idee e le pratiche territoriali della quotidianità
Land grab, cooperazione internazionale e geografia: Riflessioni per la ricerca e l’azione
Full text linkNowadays many rural territories, not only in the Global South, have been targeted by large scale land acquisitions. The article highlights the
importance of geographical research in dealing with the above-mentioned phenomenon. Indeed, geographic critical analysis and its resulting
responses can provide a better understanding and thus represent valuable tools to envisage other possible territorial patterns. The ambiguities and
controversies of land grab will be examined by stressing on the several contradictions in the relation between international development coopera-
tion and land grab, and the geographic and transcalar character of the phenomenon. Finally, the article concludes by considering the challenges
of geographical knowledge and of academic positioning in the strain between a geography ‘for the prince’ and an ‘antagonistic’ geography
Discovery of protein-RNA networks
No full textCoding and non-coding RNAs associate with proteins to perform important functions in the cell. Protein-RNA complexes are essential components of the ribosomal and spliceosomal machinery; they are involved in epigenetic regulation and form non-membrane-bound aggregates known as granules. Despite the functional importance of ribonucleoprotein interactions, the precise mechanisms of macromolecular recognition are still poorly understood. Here, we present the latest developments in experimental and computational investigation of protein-RNA interactions. We compare performances of different algorithms and discuss how predictive models allow the large-scale investigation of ribonucleoprotein associations. Specifically, we focus on approaches to decipher mechanisms regulating the activity of transcripts in protein networks. Finally, the catRAPID omics express method is introduced for the analysis of protein-RNA expression networks
omiXcore: a web server for prediction of protein interactions with large RNA
Get PDFSUMMARY: Here we introduce omiXcore, a server for calculations of protein binding to large RNAs (> 500 nucleotides). Our webserver allows (i) use of both protein and RNA sequences without size restriction, (ii) pre-compiled library for exploration of human long intergenic RNAs interactions and (iii) prediction of binding sites. RESULTS: omiXcore was trained and tested on enhanced UV Cross-Linking and ImmunoPrecipitation data. The method discriminates interacting and non-interacting protein-RNA pairs and identifies RNA binding sites with Areas under the ROC curve > 0.80, which suggests that the tool is particularly useful to prioritize candidates for further experimental validation.
AVAILABILITY AND IMPLEMENTATION: omiXcore is freely accessed on the web at http://service.tartaglialab.com/grant_submission/omixcore. CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.We acknowledge support of the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’ and the CERCA Programme / Generalitat de Catalunya. This work was supported by the European Union Seventh Framework Programme [FP7/2007-13], European Research Council RIBOMYLOME_309545 (Gian Gaetano Tartaglia) and Spanish Ministry of Economy and Competitiveness BFU2014-5505-P (Gian Gaetano Tartaglia
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Neurodegeneration and cancer: where the disorder prevails
Full text linkIt has been reported that genes up-regulated in cancer are often down-regulated in neurodegenerative disorders and vice versa. The fact that apparently unrelated diseases share functional pathways suggests a link between their etiopathogenesis and the properties of molecules involved. Are there specific features that explain the exclusive association of proteins with either cancer or neurodegeneration? We performed a large-scale analysis of physico-chemical properties to understand what characteristics differentiate classes of diseases. We found that structural disorder significantly distinguishes proteins up-regulated in neurodegenerative diseases from those linked to cancer. We also observed high correlation between structural disorder and age of onset in Frontotemporal Dementia, Parkinson's and Alzheimer's diseases, which strongly supports the role of protein unfolding in neurodegenerative processes.The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013), through the European Research Council, under grant
agreement RIBOMYLOME_309545 (Gian Gaetano Tartaglia), and from the Fundació La Marató de TV3 (20142731). We also acknowledge support from AGAUR (2014 SGR00685) and the Spanish Ministry of Economy and Competitiveness (BFU2014-55054-P), ‘Centro de Excelencia Severo Ochoa 2013-2017′ (SEV-2012-0208
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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