1,721,049 research outputs found
Control of translation initiation and neuronal subcellular localisation of mRNAs by G-quadruplex structures
No full textThe translation of mRNA is a key regulatory step in control of gene expression. The primary sequence of an mRNA determines much of the regulation of translation, including the location of translation initiation. The efficiency of translation initiation is determined by the initiation codon and its context. Translation initiation occurs at the canonical initiation codon, AUG, or a less efficient near canonical non-AUG alternative initiation codon (AIC). The secondary structure of an mRNA impacts its translation, principally by inhibiting binding and/or migration of ribosomal subunits. Hairpins form by hydrogen bonding between Watson-Crick complementary base-pairs. Guanine-rich nucleotide sequences form planar tetrads via hydrogen bonds and stack as stable G-quadruplex structures. Much has been reported on the impact of hairpins in regulating translation and G-quadruplex structures are emerging as an important factor in the regulation of translation of some mRNAs.Two-pore potassium leak (K2P) channels set and maintain the resting membrane potential of cells, so precise regulation of K2P protein expression in cells is critical to cell behaviour and survival. The 5’ untranslated regions (5’ UTR) of K2P channels are poorly annotated in databases. This thesis details investigations of 5’ UTR primary sequence and secondary structure effects on the expression of K2P leak channels. We characterised an extension to the annotated 5’ UTR sequence of Task3 by 5’RACE. The extension is characterised by a 5’ terminal (GGN) repeat which we show forms a G-quadruplex structure and inhibits translation of Task 3. G-quadruplex formation was measured by circular dichroism and increased fluorescence of Mesoporphyrin IX dihydrochloride. RT-PCR of Task3-FLAG mRNA relative to ?-actin mRNA in polysome fractions of transfected HeLa cells suggests the inhibition of Task3 protein synthesis results from an inhibition of translation initiation due to the 5’-terminal G-quadruplex. Results suggest the inhibition of Task3 protein synthesis can be modulated by RNA-binding proteins. hnRNPA2 is shown to relieve translational inhibition, and the DEAH/RHA RNA helicases, DHX29, DHX30 and DHX36 differentially regulate translation from Task3 mRNA dependent on the presence of the 5’ terminal G-quadruplex. We also investigate the use of small ligands TMPyP4 and Hippuristanol in modulating expression of Task3 in a G-quadruplex-dependent manner.Task3 is expressed in neuronal cells and is predicted to be able to exert control over local membrane potential. The local translation of mRNAs has been demonstrated in a variety of cells. In neurons, local translation of some mRNAs at synapses have been shown in plastic changes. G-quadruplex structures have been shown to affect mRNA subcellular targeting and direct protein synthesis at the synapse. We describe detection of Task3-GFP mRNA by Fluorescence In Situ Hybridisation (FISH) in transfected primary cortical neurons. It was found for the first time that the 5’-terminal G-quadruplex in Task3 mRNA appears to mediate localisation of Task3-GFP mRNA to discrete neurite particles. The roles of G-quadruplex-interacting RNA binding proteins (RBPs), hnRNP A2 and Pur[alpha], in the trafficking of Task3 mRNA was investigated, however, the mechanism of neurite delivery of Task3 mRNA requires further research. Dysregulation of this mechanism would cause perturbations to individual synapse excitability and therefore contribute to neuronal behaviour.FXR2 is a paralog of the neuronal translation regulator RBP, Fragile X Mental Retardation Protein (FMRP). Ribosome profiling of mouse embryonic stem cells identified Fxr2 to be subject to alternative upstream translation initiation. Results here demonstrate the production of different N-terminal length isoforms of Fxr2 from alternative translation initiation, primarily from GUG codon, -219 from the annotated AUG initiation codon. Investigation of the 5’ UTR of Fxr2 revealed a high concentration of guanine residues. We show evidence supporting G-quadruplex structures within its 5’UTR. This is the first report of potential G-quadruplex mediated control of AIC usage in an mRNA.<br/
G-quadruplexes mediate local translation in neurons
No full textThere has recently been a huge increase in interest in the formation of stable G-quadruplex structures in mRNAs and their functional significance. In neurons, local translation of mRNA is essential for normal neuronal behaviour. It has been discovered that local translation of specific mRNAs encoding some of the best known synaptic proteins is dependent on the presence of a G-quadruplex. The recognition of G-quadruplexes in mRNAs, their transport as repressed complexes and the control of their translation at their subcellular destinations involves a diversity of proteins, including those associated with disease pathologies. This is an exciting field, with rapid improvements to our knowledge and understanding. Here, we discuss some of the recent work on how G-quadruplexes mediate local translation in neurons
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
Topological data analysis identifies molecular phenotypes of idiopathic pulmonary fibrosis
No full textBACKGROUND: Idiopathic pulmonary fibrosis (IPF) is a debilitating, progressive disease with a median survival time of 3-5 years. Diagnosis remains challenging and disease progression varies greatly, suggesting the possibility of distinct subphenotypes.METHODS AND RESULTS: We analysed publicly available peripheral blood mononuclear cell expression datasets for 219 IPF, 411 asthma, 362 tuberculosis, 151 healthy, 92 HIV and 83 other disease samples, totalling 1318 patients. We integrated the datasets and split them into train (n=871) and test (n=477) cohorts to investigate the utility of a machine learning model (support vector machine) for predicting IPF. A panel of 44 genes predicted IPF in a background of healthy, tuberculosis, HIV and asthma with an area under the curve of 0.9464, corresponding to a sensitivity of 0.865 and a specificity of 0.89. We then applied topological data analysis to investigate the possibility of subphenotypes within IPF. We identified five molecular subphenotypes of IPF, one of which corresponded to a phenotype enriched for death/transplant. The subphenotypes were molecularly characterised using bioinformatic and pathway analysis tools identifying distinct subphenotype features including one which suggests an extrapulmonary or systemic fibrotic disease.CONCLUSIONS: Integration of multiple datasets, from the same tissue, enabled the development of a model to accurately predict IPF using a panel of 44 genes. Furthermore, topological data analysis identified distinct subphenotypes of patients with IPF which were defined by differences in molecular pathobiology and clinical characteristics.</p
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