1,721,116 research outputs found
The human interaction network mediated by Src Homology-3 domains: enriching the viral-host interactomes with interactions mediated by Src Homology-3 domains
Full text linkLe interazioni fisiche e funzionali che avvengono fra le proteine all’interno della cellula hanno un ruolo essenziale nella regolazione di molti processi cellulari. La capacità delle proteine di formare complessi funzionali è in parte supportata da famiglie di domini proteici conservati, specializzati nel mediare interazioni con brevi motivi peptidici lineari. Un ruolo cruciale nei processi biologici che richiedono l’assemblaggio coordinato di complessi multi proteici è svolto da una sottofamiglia di motivi proteici, caratterizzati da un’elevata frequenza dell’amminoacido prolina, che mediano il riconoscimento e l’interazione con proteine contenenti particolari moduli proteici, come i domini Src Homology-3 (SH3), specializzati nel riconoscere specifici motivi ricchi in prolina.
Per descrivere l’insieme delle interazioni definito dai domini di riconoscimento a sequenze ricche in prolina nel proteoma umano è stato utilizzato una variante dell’approccio WISE (Whole Interactome Scanning Experiment) in cui i peptidi pre-sintetizzati sono stati stampati ad alta densità su una superficie di vetro. Con questo metodo abbiamo testato la capacità di legame di 90 domini SH3 umani su un insieme di circa 9600 peptidi ricchi in prolina immobilizzati su una superficie di vetro (microarray di peptidi).
Per verificare la qualità delle interazioni ottenute sono stati effettuati alcuni saggi di pull down in cui il dominio SH3 in fusione alla proteina GST è stato usato per precipitare lo specifico interattore predetto dai microarray di peptidi da estratti proteici di linee cellulari umane; questi saggi confermano più del 90% delle interazioni peptide-dominio.
Alcune di queste interazioni sono state testate anche tramite esperimenti di phage display in cui una libreria di fago filamentoso M13, che espone sulla superficie capsidica dei nonameri di sequenza casuali fusi al gene della proteina pVIII, è stata utilizzata per arricchire i fagi che espongono delle sequenze specifiche per alcuni domini SH3.
Il tasso di peptidi falsi positivi, che vengono selezionati negli esperimenti di microarray, è stato verificato con esperimenti di “SPOT synthesis” in cui i peptidi positivi di alcuni domini SH3 sono stati sintetizzati a bassa densità su membrane di cellulosa e successivamente testati per la loro capacità di legare il dominio SH3 specifico fuso alla proteina GST.
Questi quattro approcci sperimentali ci hanno permesso di determinare la specificità e la promiscuità dei domini che legano regioni ricche in prolina e di descrivere il loro network d’interazioni proteiche. Le interazioni predette tramite questo approccio sono state collezionate in un apposito database chiamato PepspotDB (http://mint.bio.uniroma2.it/PepspotDB/), una risorsa bioinformatica sviluppata nel nostro laboratorio per raccogliere e analizzare grandi quantità di dati provenienti da esperimenti di questo tipo.
Durante il loro ciclo riproduttivo i virus utilizzano strategie che coinvolgono e perturbano la rete delle interazioni proteiche della cellula ospite. La caratterizzazione della rete delle interazioni proteiche della cellula umana che viene alterata in seguito all’infezione virale, quindi, è un obbiettivo importate che potrebbe contribuire a delucidare i meccanismi biologici fondamentali del ciclo virale e ad identificare nuove strategie terapeutiche.
A questo scopo nel nostro laboratorio è stato sviluppato un database, VirusMint, che colleziona la maggior parte delle interazioni tra proteine virali e umane pubblicate in letteratura. Sebbene i domini SH3 appartengano ad una classe di moduli di interazione proteica ubiquitaria e abbondante, VirusMint contiene un esiguo numero di interazioni mediate da questa classe di domini. Per superare questa limitazione abbiamo applicato l’approccio WISE per identificare nuove interazioni tra 15 SH3 umani e i peptidi ricchi in prolina di due virus oncogenici, HPV (Human papillomavirus type 16) e Ad12 (Human adenovirus A type 12). Gli esperimenti hanno identificato 114 nuovi potenziali interazioni tra i domini SH3 umani in esame e le regioni ricche in prolina dei due proteomi virali in esame.Protein-protein interactions play an essential role in the regulation of most cellular processes. The ability of proteins to form functional complexes is in part supported by families of conserved protein domains that are specialized in mediating interactions with relatively short linear peptide motifs. An important subclass of these motifs, those that are characterized by the high proline content, play a pivotal role in biological processes requiring the coordinated assembly of multi-protein complexes. This is achieved via interaction with proteins containing modules such as Src Homology-3 (SH3) that are specialized in recognizing specific proline rich patterns. To characterize the interactome defined by poly-proline binding domains we have used a variant of the WISE (Whole Interactome Scanning Experiment) approach where pre-synthesized, naturally occurring, peptides are arrayed at high density on a glass surface.
By this method we have tested a collection of 90 SH3 domains for their binding to a set of 9600 poly-proline containing peptides immobilized on a glass chip.
To evaluate the quality of the obtained dataset, we performed a series of pull down experiments. The results validated more than 90% of the peptide-domain interactions.
The protein-peptide interactions were also assayed with a library of M13 filamentous phages in which the gene for the VIII coat protein is fused to random 9-mer peptides. In order to evaluate the false positive rate of our experiments we carried out SPOT synthesis assays in which the peptides interacting with some SH3 domains were re-synthesized and probed with the protein fusions.
Peptide chips, pull down assays, SPOT synthesis and phage display experiments allowed us to determine the specificity and promiscuity of proline-rich binding domains and to map their interaction network. All the predicted interactions were collected and stored in the PepspotDB (http://mint.bio.uniroma2.it/PepspotDB/), a bioinformatic resource developed in our lab for this purpose.
Many viral pathogenic strategies involve targeting and perturbing host protein interactions. The characterization of the host protein sub-networks disturbed by invading viruses is a major goal of viral research and may contribute to reveal fundamental biological mechanisms and to identify new therapeutic strategies. To assist in this approach we have developed a database, VirusMINT, that stores in a structured format most of the published interactions between the viral and the host proteome. Although SH3 are the most ubiquitous and abundant class of protein binding modules, VirusMINT contains only a few interactions mediated by this domain class. To overcome this limitation we have applied the WISE (Whole Interactome Scanning Experiment) approach to identify interactions between 15 human SH3 domains and viral proline-rich peptides of two oncogenic viruses, HPV (Human papillomavirus type 16) and Ad12 (Human adenovirus A type 12). This approach identified 114 new potential interactions between the human SH3 domains and proline rich regions of the two viral proteomes
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
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
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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