Evaluation of potential miRNA sponge effects of SARS genomes in human

: To date the coronavirus family is composed of seven different viruses which were commonly known as cold viruses until the appearance of the severe acute respiratory coronavirus (SARS-CoV) in 2002, the middle east respiratory syndrome coronavirus (MERS) in 2012 and the severe acute respiratory coronavirus 2 (SARS-CoV-2) which caused the COVID-19 global pandemic in 2019. Using bioinformatic approaches we tested the potential interactions of human miRNAs, expressed in pulmonary epithelial cells, with the available coronavirus genomes. Putative miRNA binding sites were then compared between pathogenic and non pathogenic virus groups. The pathogenic group shares 6 miRNA binding sites that can be potentially involved in the sequestration of miRNAs already known to be associated with deep vein thrombosis. We then analysed ∼100k SARS-CoV-2 variant genomes for their potential interaction with human miRNAs and this study highlighted a group of 97 miRNA binding sites which is present in all the analysed genomes. Among these, we identified 6 miRNA binding sites specific for SARS-CoV-2 and the other two pathogenic viruses whose down-regulation has been seen associated with deep vein thrombosis and cardiovascular diseases. Interestingly, one of these miRNAs, namely miR-20a-5p, whose expression decreases with advancing age, is involved in cytokine signaling, cell differentiation and/or proliferation. We hypothesize that depletion of poorly expressed miRNA could be related with disease severity

MitImpact 3: modeling the residue interaction network of the Respiratory Chain subunits

Numerous lines of evidence have shown that the interaction between the nuclear and mitochondrial genomes ensures the efficient functioning of the OXPHOS complexes, with substantial implications in bioenergetics, adaptation, and disease. Their interaction is a fascinating and complex trait of the eukaryotic cell that MitImpact explores with its third major release. MitImpact expands its collection of genomic, clinical, and functional annotations of all non-synonymous substitutions of the human mitochondrial genome with new information on putative Compensated Pathogenic Deviations and co-varying amino acid sites of the Respiratory Chain subunits. It further provides evidence of energetic and structural residue compensation by techniques of molecular dynamics simulation. MitImpact is freely accessible at http://mitimpact.css-mendel.it

Mechanisms of pathogenesis of missense mutations on the KDM6A-H3 interaction in type 2 Kabuki Syndrome

Mutations in genes encoding for histone methylation proteins are associated with several developmental disorders. Among them, KDM6A is the disease causative gene of type 2 Kabuki Syndrome, a rare multisystem disease. While nonsense mutations and short insertions/deletions are known to trigger pathogenic mechanisms, the functional effects of missense mutations are still uncharacterized. In this study, we demonstrate that a selected set of missense mutations significantly hamper the interaction between KDM6A and the histone H3, by modifying the dynamics of the linker domain, and then causing a loss of function effect

Phosfinder: a web server for the identification of phosphate-binding sites on protein structures

Phosfinder is a web server for the identification of phosphate binding sites in protein structures. Phosfinder uses a structural comparison algorithm to scan a query structure against a set of known 3D phosphate binding motifs. Whenever a structural similarity between the query protein and a phosphate binding motif is detected, the phosphate bound by the known motif is added to the protein structure thus representing a putative phosphate binding site. Predicted binding sites are then evaluated according to (i) their position with respect to the query protein solvent-excluded surface and (ii) the conservation of the binding residues in the protein family. The server accepts as input either the PDB code of the protein to be analyzed or a user-submitted structure in PDB format. All the search parameters are user modifiable. Phosfinder outputs a list of predicted binding sites with detailed information about their structural similarity with known phosphate binding motifs, and the conservation of the residues involved. A graphical applet allows the user to visualize the predicted binding sites on the query protein structure. The results on a set of 52 apo/holo structure pairs show that the performance of our method is largely unaffected by ligand-induced conformational changes. Phosfinder is available at http://phosfinder.bio.uniroma2.it

Thermal-mechanical behaviour of the hierarchical structure of human dental tissue

Human dental tissues are fascinating nano-structured hierarchical materials that combine organic and mineral phases in an intricate and ingenious way to obtain remarkable combinations of mechanical strength, thermal endurance, wear resistance and chemical stability. Attempts to imitate and emulate this performance have been made since time immemorial, in order to provide replacement (e.g. in dental prosthodontics) or to develop artificial materials with similar characteristics (e.g. light armour). The key objectives of the present project are to understand the structure-property relationships that underlie the integrity of natural materials, human dental tissues in particular, and the multi-scale architecture of mineralized tissues and its evolution under thermal treatment and mechanical loading. The final objective is to derive ideas for designing and manufacturing novel artificial materials serving biomimetic purposes. The objectives are achieved using the combination of a range of characterization techniques, with particular attention paid to the synchrotron X-ray scattering (Small- and Wide-Angle X-ray Scattering, SAXS and WAXS) and imaging techniques (Micro Computed Tomography), as well as microscopy techniques such as Environmental Scanning Electron Microscopy (ESEM), Transmission Electron Microscopy (TEM) and Atomic Force Microscopy (AFM). Mechanical properties were characterized by nanoindentation and photoelasticity; and thermal analysis was carried out via thermogravimetric analysis (TGA). Experimental observations were critically examined and matched by advanced numerical simulation of the tissue under thermal-mechanical loading. SAXS and WAXS provided the initial basis for elucidating the structure-property relationships in human dentine and enamel through in situ experimentation. Four principal types of experiment were used to examine the thermal and mechanical behaviour of the hierarchical structure of human dental tissue and contributed to the Chapters of this thesis: (i) In situ elastic strain evolution under loading within the hydroxyapatite (HAp) in both dentine and enamel. An improved multi-scale Eshelby inclusion model was proposed taking into account the two-level hierarchical structure, and was validated against the experimental strain evaluation data. The achieved agreement indicates that the multi-scale model accurately reflects the structural arrangement of human dental tissue and its response to applied forces. (ii) The morphology of the dentine-enamel junction (DEJ) was examined by a range of techniques, including X-ray imaging and diffraction. The transition of mechanical properties across the DEJ was evaluated by the high resolution mapping and in situ compression measurement, followed by a brief description of the thermal behaviour of DEJ. The results show that DEJ is a narrow band of material with graded structure and mechanical properties, rather than a discrete interface. (iii) Further investigation regarding the thermo-mechanical structure-property relationships in human dental tissues was carried out by nanoindentation mapping of the nano-mechanical properties in ex situ thermally treated dental tissues. (iv) In order to understand the details of the thermal behaviour, in situ heat treatment was carried out on both human dental tissues and synthetic HAp crystallites. For the first time the in situ ultrastructural alteration of natural and synthetic HAp crystallites was captured in these experiments. The results presented in this thesis contribute to the fundamental understanding of the structure-property integrity mechanisms of natural materials, human dental tissues in particular. These results were reported in several first author publications in peer-reviewed journals, conference proceedings, and a book chapter.</p

Estudo Comparativo entre Densidade Básica e Penetração do Pilodyn em Espécies/Procedências de Pinus Centro-Americanos em três locais dos Cerrados.

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Nucleos: a web server for the identification of nucleotide binding sites in protein structures

Nucleos is a web server for the identification of nucleotide-binding sites in protein structures. Nucleos compares the structure of a query protein against a set of known template 3D binding sites representing nucleotide modules, namely the nucleobase, carbohydrate and phosphate. Structural features, clustering and conservation are used to filter and score the predictions. The predicted nucleotide modules are then joined to build whole nucleotide-binding sites, which are ranked by their score. The server takes as input either the PDB code of the query protein structure or a user-submitted structure in PDB format. The output of Nucleos is composed of ranked lists of predicted nucleotide-binding sites divided by nucleotide type (e.g. ATP-like). For each ranked prediction, Nucleos provides detailed information about the score, the template structure and the structural match for each nucleotide module composing the nucleotide-binding site. The predictions on the query structure and the template-binding sites can be viewed directly on the web through a graphical applet. In 98% of the cases, the modules composing correct predictions belong to proteins with no homology relationship between each other, meaning that the identification of brand-new nucleotide-binding sites is possible using information from non-homologous proteins. Nucleos is available at http://nucleos.bio.uniroma2.it/nucleos/

Nucleos: a web server for the identification of nucleotide-binding sites in protein structures

Nucleos is a web server for the identification of nucleotide-binding sites in protein structures. Nucleos compares the structure of a query protein against a set of known template 3D binding sites representing nucleotide modules, namely the nucleobase, carbohydrate and phosphate. Structural features, clustering and conservation are used to filter and score the predictions. The predicted nucleotide modules are then joined to build whole nucleotide-binding sites, which are ranked by their score. The server takes as input either the PDB code of the query protein structure or a user-submitted structure in PDB format. The output of Nucleos is composed of ranked lists of predicted nucleotide-binding sites divided by nucleotide type (e.g. ATP-like). For each ranked prediction, Nucleos provides detailed information about the score, the template structure and the structural match for each nucleotide module composing the nucleotide-binding site. The predictions on the query structure and the template-binding sites can be viewed directly on the web through a graphical applet. In 98% of the cases, the modules composing correct predictions belong to proteins with no homology relationship between each other, meaning that the identification of brand-new nucleotide-binding sites is possible using information from non-homologous proteins. Nucleos is available at http://nucleos.bio.uniroma2.it/nucleos/

Discovering sequence and structure landscapes in RNA interaction motifs

RNA molecules are able to bind proteins, DNA and other small or long RNAs using information at primary, secondary or tertiary structure level. Recent techniques that use cross-linking and immunoprecipitation of RNAs can detect these interactions and, if followed by high-throughput sequencing, molecules can be analysed to find recurrent elements shared by interactors, such as sequence and/or structure motifs. Many tools are able to find sequence motifs from lists of target RNAs, while others focus on structure using different approaches to find specific interaction elements. In this work, we make a systematic analysis of RBP-RNA and RNA-RNA datasets to better characterize the interaction landscape with information about multi-motifs on the same RNAs. To achieve this goal, we updated our BEAM algorithm to combine both sequence and structure information to create pairs of patterns that model motifs of interaction. This algorithm was applied to several RNA binding proteins and ncRNAs interactors, confirming already known motifs and discovering new ones. This landscape analysis on interaction variability reflects the diversity of target recognition and underlines that often both primary and secondary structure are involved in molecular recognition