1,720,977 research outputs found
Characterization of molecular bases of Myhre syndrome
Full text linkMyhre syndrome (MYHRS, MIM 139210) is a rare developmental disorder first described in 1981, for which about 50 cases are currently reported. Clinical features of MHYRS include typical facial gestalt (short palpebral fissures and philtrum, mid-face hypoplasia, prognathism, narrow mouth), thickened skin, joint limitation, muscular pseudohypertrophy, mild-to-moderate intellectual deficiency and hearing loss.
Our group (Caputo et al., 2012) and others (Le Goff et al., 2011a) identified SMAD4 (MIM 600993) as the gene mutated in MYHRS using Whole Exome Sequencing approach. Three different de novo missense changes involving Isoleucine 500 (p.Ile500Thr, p.Ile500Val and p.Ile500Met) within the evolutionary conserved MAD homology 2 domain of SMAD4 were detected in 19 patients.
SMAD4 plays a pivotal role in signal transduction of the transforming growth factor beta (TGFβ) superfamily cytokines, which exerts an important role from early embryogenesis to adulthood by mediating transcriptional activation of target genes involved in different cellular processes (such as cell division, differentiation, migration, and programmed cell death). SMAD4 has been established as a tumor suppressor gene, since loss-of-function mutations are known to cause two familiar cancer-prone diseases (juvenile polyposis syndrome (JPS, MIM 174900) and Juvenile polyposis/hereditary hemorrhagic telangiectasia (JPHT, MIM 175050), Gallione et al., 2004; Gallione et al., 2010), and occur in different types of carcinomas (pancreas, gastrointestinal tract and skin).
The main purpose of this thesis was the investigation of the molecular bases of Myhre syndrome through functional and in silico approaches. Molecular studies and assays on cell cultures were performed in order to characterize MYHRS causative variants.
Firstly, different cellular and biochemical assays were performed, in order to assess MYHRS Ile500 mutations functional impact on SMAD4 protein expression, localization, and on cell proliferation. Western blot analysis of MYHRS fibroblasts and HeLa SMAD4-mutated transfected cells, showed an increased endogenous and ectopic expression of the protein, respectively. Immunofluorescence analysis by confocal laser scanning microscopy of MYHRS fibroblasts disclosed an extra-nuclear accumulation of MYHRS-mutated SMAD4 in patient fibroblasts after 2.5 and 5 hours of TGFβ stimulation. Growth curve of MYHRS-mutated fibroblasts, as well as BrdU incorporation assay on MYHRS fibroblasts and 3T3 transfected cells, demonstrated a reduction in the proliferation levels of both patient and SMAD4-mutated overexpressing cells.
Moreover, we collected a cohort of cases with clinical features fitting MYHRS. Molecular screening of SMAD4 coding sequence in these patients identified a novel missense change affecting Arginine 496 (p.Arg496Cys) in three cases. In silico structural analysis, performed in collaboration with Tor Vergata University, suggested that conformational changes promoted by replacement of Arg496 impact the stability of the SMAD heterotrimer and/or proper SMAD4 ubiquitination (Caputo et al., 2014). Since the triplet coding for the Arginine at position 496 encompassed a CpG dinucleotide, we preliminarily investigated the methylation status of the cytosine at nucleotide c.1486, through digestion assays of genomic DNA from leukocytes of control subjects with Hpy99I methylation sensitive restriction enzyme which confirmed that c.1486 C>T mutation localized in a methylated CpG dinucleotide.
Finally, the investigation of the parental germline origin of MYHRS mutations was performed. Cloning of genomic fragments encompassing SMAD4 causative mutation and intronic polymorphic site for 11 informative MYHRS cases and segregation analysis demonstrated the paternal germline origin of Myhre pathogenic variants in all these patients, in line with the well-known gender bias in the origin of point mutations.
In conclusion, our functional data confirm increased expression of Ile500-mutated SMAD4 in MYHRS affected cells and point out a loss of function effect of MYHRS mutations on fibroblasts proliferation, a mechanism activated by TGFβ signaling. Furthermore, the identification of a new mutation causing this syndrome (c.1486 C>T; p.Arg496Cys), which encompass an amino acid close to Ile500 residue, suggests the impairment of ubiquitination and/or transcription complex stability as the probable outcome of this variant, highlighting the need of further investigations on possible different effect of MYHRS mutations on TGFβ signaling and gene transcription. Finally, the exclusive paternal origin of MYHRS variants in our 11 informative patients expand the number of point mutations causing dominant disorders which display a paternal bias in origin, and lead us to speculate on possibly other mechanisms which could produce a positive selection on MYHRS mutations in male testes
Exploring non-coding genetic variability in ACE2: Functional annotation and in vitro validation of regulatory variants
No full textThe surge in human whole-genome sequencing data has facilitated the study of non-coding region variations, yet understanding their biological significance remains a challenge. We used a computational workflow to assess the regulatory potential of non-coding variants, with a particular focus on the Angiotensin Converting Enzyme 2 (ACE2) gene. This gene is crucial in physiological processes and serves as the entry point for severe acute respiratory syndrome coronavirus 2 (SARSCoV-2), the virus causing coronavirus disease 19 (COVID-19). In our analysis, using data from the gnomAD population database and functional annotation, we identified 17 significant Single Nucleotide Variants (SNVs) in ACE2, particularly in its enhancers, promoters, and 3’ untranslated regions (UTRs). We found preliminary evidence supporting the regulatory impact of some of these variants on ACE2 expression. Our detailed examination of two SNVs, rs147718775 and rs140394675, in the ACE2 promoter revealed that these co-occurring SNVs, when mutated, significantly enhance promoter activity, suggesting a possible increase in specific ACE2 isoform expression. This method proves effective in identifying and interpreting impactful non-coding variants, aiding in further studies and enhancing understanding of molecular bases of monogenic and complex traits
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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