1,720,959 research outputs found
Insights into SARS-CoV-2: Exploring Protein Dynamics and RNA Functionality for future Therapeutic Strategies
No full textThe main goal of this thesis is to thoroughly understand the structural and dynamic properties of key biomolecular components of SARS-CoV-2 with the aim of developing pan- coronavirus methods. For this reason, the thesis divided into two parts: a protein-oriented exploration and a genetic-material-focused analysis.
The protein-oriented approach delves deep into the immunoreactive, dynamic, and structural characteristics of SARS-CoV-2 Spike protein and its variants. By investigating these intricate details, we aim to unravel pivotal insights that transcend individual variants, ultimately leading us to identify fundamental patterns applicable to a broader range of viral agents. This understanding serves as a basis to devising adaptable strategies capable of addressing both present and future pandemics.
On the other hand, the genetic approach deepens the possibility of targeting secondary structures of the virus RNA other than the classical ones, the G-quadruplexes (G4).
Through the synergy of these two distinct yet interlinked approaches, this thesis aims to construct a comprehensive framework for addressing the challenges posed by viral mechanisms. By combining knowledge from the world of proteins and genetics, we aspire to build a general computational strategy for the study of the fine mechanisms regulating viral-host interactions and viral life regulation
Selective light-up of dimeric G-quadruplex forming aptamers for efficient VEGF165 detection
No full textTo develop efficient anticancer theranostic systems, we studied the interaction between a cyanine dye, analogue of thiazole orange (named CyOH), and two G-quadruplex-forming aptamers, V7t1 and 3R02, recognizing the Vascular Endothelial Growth Factor 165 (VEGF165) - an angiogenic protein overexpressed in cancer cells, responsible for the rapid growth and metastases of solid tumours. We demonstrated, by exploiting different biophysical techniques - i.e. gel electrophoresis, circular dichroism (CD), UV-vis and fluorescence spectroscopy - that this cyanine interacted with both aptamers giving a marked fluorescence light-up only when bound to their dimeric forms. Interestingly, both oligonucleotides recognized VEGF165 with higher affinity when adopting dimeric G-quadruplexes, largely prevalent over their monomeric forms in pseudo-physiological conditions. Notably, the fluorescence light-up produced by the probe was maintained when the dimeric aptamer-CyOH complexes bound to the target protein. These complexes, tested on MCF-7 cancer cells using non-tumorigenic MCF-10A cells as control, were effectively internalized in cells and colocalized with a fluorescently-labelled anti-VEGF-A antibody, allowing both recognition and detection of the target. Our experiments showed that the studied systems are promising tools for anticancer theranostic strategies, combining the therapeutic potential of the G4-forming anti-VEGF aptamers with the diagnostic efficacy of the cyanine selective fluorescence light-up
Exploiting Folding and Degradation Machineries To Target Undruggable Proteins: What Can a Computational Approach Tell Us?
No full textAdvances in genomics and proteomics have unveiled an ever-growing number of key proteins and provided mechanistic insights into the genesis of pathologies. This wealth of data showed that changes in expression levels of specific proteins, mutations, and post-translational modifications can result in (often subtle) perturbations of functional protein-protein interaction networks, which ultimately determine disease phenotypes. Although many such validated pathogenic proteins have emerged as ideal drug targets, there are also several that escape traditional pharmacological regulation; these proteins have thus been labeled as undruggable. Challenges posed by undruggable targets call for new sorts of molecular intervention. One fascinating solution is to perturb a pathogenic protein's expression levels, rather than blocking its activities. In this Concept Paper, we will discuss chemical interventions aimed at recruiting undruggable proteins to the Ubiquitin Proteasome System, or aimed at disrupting protein-protein interactions in the chaperone-mediated cellular folding machinery: both kinds of intervention lead to a decrease in the amount of active pathogenic protein expressed. Specifically, we will discuss the role of computational strategies in understanding the molecular determinants characterizing the function of synthetic molecules typically designed for either types of intervention. Finally, we will provide our perspectives and views on current limitations and possibilities to expand the scope of rational approaches to the design of chemical regulators of protein levels
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
Design and Test of Molecules that Interfere with the Recognition Mechanisms between the SARS-CoV-2 Spike Protein and Its Host Cell Receptors
No full text: The disruptive impact of the COVID-19 pandemic has led the scientific community to undertake an unprecedented effort to characterize viral infection mechanisms. Among these, interactions between the viral glycosylated Spike and the human receptors ACE2 and TMPRSS2 are key to allowing virus invasion. Here, we report and test a fully rational methodology to design molecules that are capable of perturbing the interactions between these critical players in SARS-CoV-2 pathogenicity. To this end, we computationally identify substructures on the fully glycosylated Spike protein that are not intramolecularly optimized and are thus prone to being stabilized by forming complexes with ACE2 and TMPRSS2. With the aim of competing with the Spike-mediated cell entry mechanisms, we have engineered the predicted putative interaction regions in the form of peptide mimics that could compete with Spike for interaction with ACE2 and/or TMPRSS2. Experimental models of viral entry demonstrate that the designed molecules are able to interfere with viral entry into ACE2/TMPRSS2 expressing cells, while they have no effects on the entry of control viral particles that do not harbor the Spike protein or on the entry of Spike-presenting viral particles into cells that do not display its receptors on their surface
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