1,721,007 research outputs found
C. elegans as a model to identify and functionally characterize novel genes causing RASopathies and other developmental diseases
Full text linkRASopathies are a family of syndromes affecting development and growth, sharing RAS signaling
dysregulation as pathogenetic mechanism. Past work of our group and others have significantly
contributed to our understanding of the molecular causes of these diseases. However, a large
fraction of RASopathy cases remains unexplained molecularly. Here, I used the nematode C.
elegans to reveal novel molecular mechanisms underlying RASopathies, as well as to identify new
candidate genes for these group of developmental disorders. C. elegans is an excellent model to
study RASopathies since the RAS-MAPK pathway is well conserved in worms, where it plays a
crucial role in vulval development.
Based on a gene candidacy approach, we identified two germline mutations in RRAS, a gene
encoding a small monomeric GTPase controlling cell adhesion, spreading and migration,
underlying a rare and atypical form of Noonan syndrome (NS), the most common RASopathy. We
also identified somatic RRAS mutations in 2 cases of non-syndromic juvenile myelomonocytic
leukaemia (JMML), a childhood myeloproliferative/myelodysplastic disease caused by upregulated
RAS signaling. Two of the three identified mutations affected known oncogenic hotspots of RAS
genes and conferred variably enhanced RRAS function and stimulus-dependent MAPK activation.
Expression of an RRAS mutant homolog in C. elegans enhanced RAS signaling causing a
multivulva (Muv) phenotype, and engendered protruding vulva (Pvl), a phenotype previously linked
to the RASopathy-causing SHOC2S2G mutant. These findings provided evidence of a functional link
between RRAS and MAPK signaling and reveal an unpredicted role of enhanced RRAS function in
human disease.
Epistatic analyses performed on C. elegans transgenic lines allowed us to establish that the
RASopathy-causing SHOC2 and RRAS mutants belong to the same pathway. Within this signaling
network, both RAS-1/RRAS and RAS-2/MRAS are downstream to constitutively active SHOC2,
with the former being epistatic to the latter. By using a reverse genetic approach based on RNA
interference experiments, we demonstrated that the Muv phenotype was completely mediated by
LET-60/RAS, while the Pvl phenotype was modulated by the RHO-family small GTPases CDC-42
and RAC1. We then confirmed these results in fibroblasts derived from patients with Mazzanti
syndrome (NS with loose anagen hair) and transfected cell lines. In these models, we observed
constitutive RAC1 activation and aberrant lamellipodia formation in cells expressing SHOC2S2G
compared to wild-type cells.
These results suggested RHO GTPases as excellent candidate genes to be mutated in
RASopathies. To explore this hypothesis, mutation scanning of RAC1, RAC2 and CDC42 genes was
performed in RASopathy patients by targeted resequencing and identified seven different
germline CDC42 mutations in 11 unrelated subjects with a variable phenotype partially overlapping
NS and predisposing to thrombocytopenia. In vitro biochemical characterization demonstrated a
variable impact of the mutations on GTPase activity and defective binding to WASP. In vitro and in
vivo (C. elegans) functional characterization of these mutants allowed to define their impact on cell
migration and proliferation, as well as on vulval induction and morphogenesis. A first class of
mutations was shown to have an hypomorphic effect on processes mediating cell polarized
migration, with no effect on the RAS-MAPK signaling, while a second class of mutations had a
gain-of-function effect on both cell migration/proliferation and LET-60/RAS-mediated vulval
induction. Overall, our data highlighted the possible contribution of dysregulated signaling
controlling cell spreading and migration to certain features of RASopathies, such as lymphedema,
cardiac defects and lymphocytes infiltration in non-hematopoietic tissues in case of JMML
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
Assessment of a high fat diet on transcriptomic and epigenomic profiles of Immortalized Human Endometrial Stromal Cells
No full textInfertility is a multifactorial pathological condition affecting approximately 10–15% of couples, especially in industrialized regions that could be influenced by many factors, such as improper eating habits. Diet, including hypercaloric nutrition due to a high fat diet (HFD), could promote an increment in endometrial epigenetic modifications and dysfunction improving the risk of infertility. Thereby, the aim of the project is to study in vitro the effect of an excessive intake of non-esterified fatty acids, mimicking the HFD lifestyle, on transcriptomic and epigenomic signatures of Immortalized Human Endometrial Stromal Cells (HESC) (Abmgood). Thus, the Affymetrix Microarray platform will be put into use to investigate gene and microRNA (miRNA) expression using the GeneChip Scanner 3000Dx v2. Moreover, for methylome analysis, NGS Illumina platforms will be used and processed by the NextSeq 550 and MiSeq detection systems. So far, the first part of the PhD course focused mainly on the study of the literature for the choice of the HESC cell line and on apprehending the main molecular biology techniques useful for its future development. The methods learned include: the validation of protocols for manual extraction of DNA and total RNA, including miRNAs, from single cell as well as pooled cells with consequent quantization of nucleic acids; the validation of bisulfite conversion/cleanup of converted DNA and PCR amplification for methylation analysis protocols for pyrosequencing, and of reverse transcription and Real-Time protocols (qRT-PCR) for target analysis of gene expression and miRNAs both by SYBR and TaqMan array panels. All the experiments were performed on different in vitro models. Therefore, the next step will be to extend the acquired knowledge and perform all the experiments through omics investigations to have a deeper knowledge from a molecular point of view that might help clarify the multifaceted elements of infertility and potentially curative treatments
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
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