1,721,001 research outputs found
THE PRESENT AND THE FUTURE OF COLLAGEN VI GENES ANALYSIS: OVERVIEW OF CELLULAR MODELS, GENOME AND TRANSCRIPTOME STUDIES
No full textIl collagene VI è una proteina della matrice extracellulare che forma un reticolo di microfilamenti nel muscolo scheletrico ed in altri organi. Le mutazioni dei geni del collagene VI causano, nell'uomo, principalmente due malattie genetiche: la miopatia di Bethlem e la distrofia muscolare congenita di Ullrich. Come centro di riferimento nazionale per le neuropatie muscolari, in 12 anni, abbiamo raccolto una casistica di 245 pazienti, indagati a livello genomico e trascrittomico, al fine di catalogare e caratterizzare le mutazioni nei tre geni del collagene VI. La casistica a livello nazionale si è dimostrata sovrapponibile a quella presente in letteratura sia per frequenza di mutazione e fenotipo, sia per tipo di mutazioni riscontrate.
Considerata l’importanza di indagare il trascritto in generale nelle patologie neuromuscolari e, nello specifico, nei disordini del collagene VI, in questo lavoro abbiamo paragonato due differenti metodiche: RNA sequencing (RNAseq) e FluiCol6 micro-fluidic exome array. Il sequenziamento dell’RNA si è rivelato il miglior strumento da utilizzare, in parallelo con l’analisi genomica, nella diagnosi delle patologie del collagene VI. Al contrario, la micro-fluidic card FluiCol6 ha fornito diversi falsi positivi e si è dimostrata inefficace nell’identificare la mutazione di splicing del controllo positivo.
Ad oggi manca un modello cellulare che riproduca fedelmente e in modo completo il fenotipo patologico, indotto dal deficit di collagene VI. A tale scopo si è scelto di studiare e validare le cellule staminali di origine urinaria, rivelatesi un buon modello in vitro per lo studio della Distrofia muscolare di Duchenne. I primi risultati ottenuti hanno fornito buone aspettative; le cellule staminali urinarie infatti mostrano lo stesso pattern di espressione, per i geni del collagene VI e relative isoforme, dei fibroblasti. Inoltre, i primi esperimenti di immunoistochimica rivelano la presenza della proteina nella matrice extracellulare anche se, la completa caratterizzazione proteica non è ancora conclusa. I modelli cellulari per il collagene VI, utilizzati solitamente in diagnostica e ricerca sono i fibroblasti e i mioblasti isolati da biopsie cutanee e muscolari, rispettivamente. Ottenere questi due tipi cellulari richiede l’utilizzo di metodiche invasive perciò, se le USCs si rivelassero un modello cellulare alternativo agli attuali sistemi si avrebbe la possibilità di ottenere linee cellulari in modo semplice, poco costoso, ripetibile e ben accettato dai pazienti, soprattutto da quelli in età pediatrica.Collagen VI-related myopathies are a group of rare inherited genetic disorders with varying degree of clinical severity, caused by mutations in the Collagen type VI genes: COL6A1, COL6A2, and COL6A3.
As a national reference center for diagnosis of neuromuscular disorders, 245 patients were analyzed in the Medical Genetics Unit over a 12-year period (2006-2018). The aim of this thesis is to provide a nationwide study of patients with COLVI phenotype and an overview of COL6 genes variants. The detection of mutations in collagen VI genes remains the gold standard for diagnosis, but traditional diagnostic tools do not completely achieve this goal. Next generation sequencing panel offers the ability to efficiently and cost-effectively screening all exons of the three COL6A genes. However, it is known the importance of studying transcriptome to enhance the diagnostic rate and to study the mutation functional consequence, therefore confirming their pathogenicity. In our results, the RNA-seq was shown to be the innovative strategy to explore RNA profile of COL6 genes in patients.
To date, a disease cellular model for COL6-RD with the capacity to completely recapitulate the pathological phenotype in humans is yet to be established. Having this in mind, the use of Urine Stem cells (USCs) as a collagen VI cellular model was in this study developed and validated at the RNA level. Despite being a preliminary study defining whether USCs could be a good collagen VI cellular model, the data presented herein hold good promise. In contrast to skin and muscle biopsies, USCs can easily and non invasively be retrieved from urine samples. Hence, the collagen VI cellular model employing USCs with the ability to function equally well to the existing using fibroblasts could have many advantages. We propose these cells as COLVI disease in vitro model for functional studies, drug screening and validation
Method for implementing the design of synthetic nucleic acid molecules for gene therapies in rare diseases
No full textThe invention relates to methods that may be used to identify critical codons and design synthetic nucleic acid molecules of disease-causing genes. Synthetic nucleic acid sequences may be designed from a reference nucleic acid sequence, for example, to optimize heterologous expression of the nucleic acid sequence in a particular tissue of a host organism. Alternatively, synthetic nucleic acid sequences may be designed de novo to encode a desired polypeptide. Such synthetic nucleic acid sequences may be used for example in gene therapy or other therapeutic applications
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
Mediterranean Azadinium dexteroporum (Dinophyceae) produces six novel azaspiracids and azaspiracid-35: a structural study by a multi-platform mass spectrometry approach
Full text linkAzadinium dexteroporum is the first species of the genus described from the Mediterranean Sea and it produces different azaspiracids (AZA). The aims of this work were to characterize the toxin profile of the species and gain structural information on azaspiracids produced by the A. dexteroporum strain SZN-B848 isolated from the Gulf of Naples. Liquid chromatography-mass spectrometry (LC-MS) analyses were carried out on three MS systems having different ion source geometries (ESI, TurboIonSpray®, ESI ION MAX) and different MS analyzers operating either at unit resolution or at high resolution, namely a hybrid triple quadrupole-linear ion trap (Q-trap MS), a time of flight (TOF MS), and a hybrid linear ion trap Orbitrap XL fourier transform mass spectrometer (LTQ Orbitrap XL FTMS). As a combined result of these different analyses, A. dexteroporum showed to produce AZA-35, previously reported from A. spinosum, and six compounds that represent new additions to the AZA-group of toxins, including AZA-54 to AZA-58 and 3-epiAZA-7, a stereoisomer of the shellfish metabolite AZA-7. Based on the interpretation of fragmentation patterns, we propose that all these molecules, except AZA-55, have the same A to I ring system as AZA-1, with structural modifications all located in the carboxylic side chain. Considering that none of the azaspiracids being produced by the Mediterranean strain of A. dexteroporum is currently regulated by European food safety authorities, monitoring programmes of marine biotoxins in the Mediterranean area should take into account the occurrence of the new analogues to avoid an underestimation of the AZA-related risk for seafood consumers
Magmas, a novel over-expressed gene in Pituitary rat cell lines and in human pituitary adenomas: a new pituitary bio marker?
No full textPituitary tumors are mostly benign, being locally invasive in 5-35% of cases. Deregulation of several genes has been suggested as a possible alteration underlying the development and progression of pituitary tumors. Recently we have demonstrated that Magmas is over-expressed in a mouse ACTH-secreting pituitary adenoma cell line. Here we investigate by RT-QPCR the expression of Magmas in 4 rat pituitary adenoma cell lines: three growth hormone (GH) and prolactin (PRL)-secreting cells lines (GH1, GH3, and GH4C1) and one PRL-secreting cell line (MMQ). We found that Magmas is over-expressed in GH3 (2.2 fold) and MMQ (3.6 fold) cell lines, while GH1 and GH4C1 display Magmas expression levels similar to those detected in a pool of normal rat pituitaries. These results were confirmed by Western blot analysis that showed the same expression pattern found by RT-QPCR. Magmas mRNA expression was also assessed in 29 human pituitary tissues, including 19 nonfunctioning, 8 GH-secreting, 2 PRL-secreting, and one TSH-secreting pituitary adenoma, as well as in a pool of human normal pituitary mRNAs. We found that 24 out of 29 pituitary adenomas (82.7%) displayed a Magmas mRNA expression level >2-fold than that detected in a pool of human normal pituitaries (from 2 to 30-fold), in all types of pituitary adenomas, except for the TSH-secreting pituitary adenoma. Our results suggest that Magmas could be a novel tumor selective over-expressed gene and could be a novel molecular target to be studied in order to understand pituitary adenomas pathophysiology
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
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