1,720,974 research outputs found
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
Cellular stress positively regulates the expression of Myc promoter-Binding Protein-1 (MBP-1).
No full textDal trascrittoma all’interattoma di miRNA: identificazione sperimentale e bioinformatica delle interazioni funzionali miRNA:mRNA
No full textI miRNA, piccole molecole endogene di RNA non codificante, regolano l’espressione genica attraverso la degradazione dei messaggeri (mRNA) o l’inibizione della traduzione. I miRNA maturi interagiscono con le proteine del complesso RISC (RNA-induced silencing complex) tra cui le proteine Argonaute (Ago), capaci di legare direttamente i miRNA e di mediare la regolazione dell’espressione genica in seguito alla interazione del miRNA con il proprio mRNA target. Un singolo miRNA può legare diversi mRNA e ciascun mRNA può essere regolato da diversi miRNA. La maggior parte dei software di predizione oggi disponibili individuano i putativi target di singoli miRNA ignorando caratteristiche di tipo globale, come i livelli di espressione di mRNA e miRNA coespressi. Obiettivo del nostro lavoro è sviluppare un sistema per lo studio e la predizione delle interazioni funzionali miRNA:mRNA che tenga conto di tutti i miRNA e degli mRNA coespressi in una cellula in determinate condizioni. Allo scopo di misurare e mettere in relazione i livelli di espressione di mRNA e miRNA, abbiamo messo a punto una immunoprecipitazione ad alta efficienza del complesso RISC-Ago2 da estratti citoplasmatici della linea cellulare di tumore mammario MCF-7. I profili di espressione di mRNA e miRNA dei campioni ottenuti sono stati ricavati mediante microarray. Tale tecnica ci ha consentito di caratterizzare separatamente l’insieme di mRNA e miRNA legati e non legati ai complessi RISC. E’ stata inoltre utilizzata la centrifugazione su gradiente di densità per separare gli mRNA in fase di traduzione da quelli non tradotti e i miRNA associati a ciascuna di queste frazioni. Anche questi campioni saranno analizzati mediante microarray. L’analisi dei dati ottenuti ci consentirà di individuare tra tutti i miRNA ed gli mRNA espressi nella cellula quelli coinvolti nel processo di regolazione ed identificare le interazioni miRNA:mRNA che inducono un blocco della traduzione o la degradazione del messaggero target. Utilizzando i dati ottenuti ci proponiamo di mettere a punto un modello matematico per predire l’insieme delle interazioni funzionali tra i miRNA e i relativi target in qualsiasi condizione cellulare in cui siano noti i profili di espressione dei miRNA e degli mRNA
Statistical Validation of a Comprehensive Gene/miRNA Expression Profile Dataset for miRNA:mRNA Interaction Analysis
No full textStatistical validation of a comprehensive gene/miRNA expression profile dataset for miRNA:mRNA interctome analysis
No full textENO1/Hsp70 Interaction Domains: In Silico and In Vitro Insight for a Putative Therapeutic Target in Cancer
Full text linkAlpha-enolase (ENO1) is a multifunctional protein with oncogenic roles. First described as a glycolytic enzyme, the protein performs different functions according to its cellular localization, post-translational modifications, and binding partners. Cell surface-localized ENO1 serves as a plasminogen-binding receptor, and it has been detected in several cell types, including various tumor cells. The plasminogen system plays a crucial role in pathological events, such as tumor cell invasion and metastasis. We have previously demonstrated that the interaction of ENO1 with the multifunctional chaperone Hsp70 increases its surface localization and the migratory and invasive capacity of breast cancer cells, thus representing a novel potential target to counteract the metastatic potential of tumors. Here, we have used computational approaches to map the putative binding region of ENO1 to Hsp70 and predict the key anchoring amino acids, also called hot spots. In vitro coimmunoprecipitation experiments were then used to validate the in silico prediction of the protein-protein interaction. This work outcome will be further used as a guide for the design of potential ENO1/HSP70 inhibitors
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
The Kelch protein NS1-BP interacts with alpha-enolase/MBP-1 and is involved in c-Myc gene transcriptional control
No full textAlpha-enolase is a key glycolytic enzyme that plays a functional role in several physiological processes depending on the cellular localization. The enzyme is mainly localized in the cytoplasm whereas an alternative translated form, named MBP-1, is predominantly nuclear. The MBP-1 protein has been characterized as a c-Myc promoter binding protein that negatively controls transcription. In the present study, we identified the kelch protein NS1-BP as one of the alpha-enolase/MBP-1 partners by using a yeast two-hybrid screening. Although NS1-BP has been originally described as a protein mainly localized in the nucleus, we provide evidence that NS1-BP also interacts with actin in human cells, as reported for most kelch-containing proteins. Here we showed that alpha-enolase and MBP-1 associate with NS1-BP in vitro and in vivo by GST pull-down assays and coimmunoprecipitation experiments; subsequent immunofluorescent staining confirmed colocalization of the proteins within the cells. Furthermore, functional analyses performed by cotransfection assays revealed that NS1-BP enhances the inhibitory effect exerted by MBP-1 on c-Myc promoter. In mammalian cells, the overexpression of both proteins resulted in an increased repression of basal c-Myc transcription and consistently affected the steady state levels of endogenous c-Myc mRNA. These findings further support the distinct roles of alpha-enolase and its MBP-1 variant in maintaining cell homeostasis. Moreover, our data suggest a novel function for NS1-BP in the control of cell proliferation. © 2007 Elsevier B.V. All rights reserved
Detecting significant features in modeling microRNA-target interactions
Full text linkMicroRNAs (miRNAs) are small non-coding RNA molecules mediating the translational repression and degradation of target mRNAs in the cell. Mature miRNAs are used as a template by the RNA-induced silencing complex (RISC) to recognize the complementary mRNAs to be regulated. Up to 60% of human genes are putative targets of one or more miRNAs. Several prediction tools are available to suggest putative miRNA targets, however, only a small part of the interaction pairs has been validated by experimental approaches. The analysis of the expression profile of the RNA fraction immunoprecipitated (IP) with the RISC proteins is an established method to detect which genes are actually regulated by the RISC machinery. In fact, genes that result over-expressed in the IP sample with respect to the whole cell lysate RNA, are considered as involved in the RISC complex, then miRNA targets. Here, we aim to find the features useful to predict which genes are overexpressed in IP, i.e. miRNA targets, without actually performing the IP experiments. To this purpose, we compiled and analyzed a novel high throughput data set suitable to unravel the features involved in the miRNA regulatory activities. We analyzed IP samples obtained by the immunoprecipitation of two RISC proteins, AGO2 and GW182. The two proteins shows different behaviors, in terms of enriched genes and features characterizing the immunoprecipitated RNA fractio. Further analysis is needed to unravel the reason of such different behavior
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