Search results for "interaction [dark matter]"
showing 10 items of 363 documents
Exploring the Human-Nipah Virus Protein-Protein Interactome
2017
ABSTRACT Nipah virus is an emerging, highly pathogenic, zoonotic virus of the Paramyxoviridae family. Human transmission occurs by close contact with infected animals, the consumption of contaminated food, or, occasionally, via other infected individuals. Currently, we lack therapeutic or prophylactic treatments for Nipah virus. To develop these agents we must now improve our understanding of the host-virus interactions that underpin a productive infection. This aim led us to perform the present work, in which we identified 101 human-Nipah virus protein-protein interactions (PPIs), most of which (88) are novel. This data set provides a comprehensive view of the host complexes that are manip…
ceRNA Network Regulation of TGF-β, WNT, FOXO, Hedgehog Pathways in the Pharynx of Ciona robusta
2021
The transforming growth factor-β (TGF-β) family of cytokines performs a multifunctional signaling, which is integrated and coordinated in a signaling network that involves other pathways, such as Wintless, Forkhead box-O (FOXO) and Hedgehog and regulates pivotal functions related to cell fate in all tissues. In the hematopoietic system, TGF-β signaling controls a wide spectrum of biological processes, from immune system homeostasis to the quiescence and self-renewal of hematopoietic stem cells (HSCs). Recently an important role in post-transcription regulation has been attributed to two type of ncRNAs: microRNAs and pseudogenes. Ciona robusta, due to its philogenetic position close to verte…
Identification and structural characterization of LytU, a unique peptidoglycan endopeptidase from the lysostaphin family
2017
AbstractWe introduce LytU, a short member of the lysostaphin family of zinc-dependent pentaglycine endopeptidases. It is a potential antimicrobial agent for S. aureus infections and its gene transcription is highly upregulated upon antibiotic treatments along with other genes involved in cell wall synthesis. We found this enzyme to be responsible for the opening of the cell wall peptidoglycan layer during cell divisions in S. aureus. LytU is anchored in the plasma membrane with the active part residing in the periplasmic space. It has a unique Ile/Lys insertion at position 151 that resides in the catalytic site-neighbouring loop and is vital for the enzymatic activity but not affecting the …
Dynamics of a Protein Interaction Network Associated to the Aggregation of polyQ-Expanded Ataxin-1
2020
Background: Several experimental models of polyglutamine (polyQ) diseases have been previously developed that are useful for studying disease progression in the primarily affected central nervous system. However, there is a missing link between cellular and animal models that would indicate the molecular defects occurring in neurons and are responsible for the disease phenotype in vivo. Methods: Here, we used a computational approach to identify dysregulated pathways shared by an in vitro and an in vivo model of ATXN1(Q82) protein aggregation, the mutant protein that causes the neurodegenerative polyQ disease spinocerebellar ataxia type-1 (SCA1). Results: A set of common dysregulated pathwa…
Visualizing Human Protein‐Protein Interactions and Subcellular Localizations on Cell Images Through CellMap
2020
Visualizing protein data remains a challenging and stimulating task. Useful and intuitive visualization tools may help advance biomolecular and medical research; unintuitive tools may bar important breakthroughs. This protocol describes two use cases for the CellMap (http://cellmap.protein.properties) web tool. The tool allows researchers to visualize human protein-protein interaction data constrained by protein subcellular localizations. In the simplest form, proteins are visualized on cell images that also show protein-protein interactions (PPIs) through lines (edges) connecting the proteins across the compartments. At a glance, this simultaneously highlights spatial constraints that prot…
(Im)Politeness and interactions in Dialogic Literary Gatherings
2016
Abstract This article examines the interactions that occur in Dialogic Literary Gatherings (DLG), a cultural activity in which low literate adults read and debate classic literature. To respect the principle of egalitarian dialogue, participants agree on how to communicate and reflect on their communicative patterns. We analyse the actual interactional behaviour of participants and the pragmatic traits that evidence how this principle is implemented by identifying dialogic and power interactions in connection to (Im)politeness. This study shows the influence of the situated genre (DLG) over status in the prevalence of politeness and how the participants use polite mitigation strategies that…
Force Field for Water over Pt(111): Development, Assessment, and Comparison
2018
Metal/water interfaces are key in many natural and industrial processes, such as corrosion, atmospheric, or environmental chemistry. Even today, the only practical approach to simulate large interfaces between a metal and water is to perform force-field simulations. In this work, we propose a novel force field, GAL17, to describe the interaction of water and a Pt(111) surface. GAL17 builds on three terms: (i) a standard Lennard-Jones potential for the bonding interaction between the surface and water, (ii) a Gaussian term to improve the surface corrugation, and (iii) two terms describing the angular dependence of the interaction energy. The 12 parameters of this force field are fitted again…
Multisensory texture exploration at the tip of the pen
2016
A tool for the multisensory stylus-based exploration of virtual textures was used to investigate how different feedback modalities (static or dynamically deformed images, vibration, sound) affect exploratory gestures. To this end, we ran an experiment where participants had to steer a path with the stylus through a curved corridor on the surface of a graphic tablet/display, and we measured steering time, dispersion of trajectories, and applied force. Despite the variety of subjective impressions elicited by the different feedback conditions, we found that only nonvisual feedback induced significant variations in trajectories and an increase in movement time. In a post-experiment, using a pa…
Small Residues Inhibit Homo-Dimerization of the Human Carbonic Anhydrase XII Transmembrane Domain
2021
Amino acids with small side chains and motifs of small residues in a distance of four are rather abundant in human single-span transmembrane helices. While interaction of such helices appears to be common, the role of the small residues in mediating and/or stabilizing transmembrane helix oligomers remains mostly elusive. Yet, the mere existence of (small)xxx(small) motifs in transmembrane helices is frequently used to model dimeric TM helix structures. The single transmembrane helix of the human carbonic anhydrases XII contains a large number of amino acids with small side chains, and critical involvement of these small amino acids in dimerization of the transmembrane domain has been sugges…
Synthesis and Physical Stability of Novel Au-Ag@SiO<SUB>2</SUB> Alloy Nanoparticles
2012
The present study describes the synthesis of nanoparticles of silver-gold alloys and with their electrokinetic and spectroscopic characterisation. The synthesis was made in two steps. In the first step silver nanoparticles coated with silica (Ag@SiO2) were synthesised using a novel method assisted by laser ablation. The second step consisted on the introduction of KAuCl4 in the colloidal solution of Ag@ SiO2 nanoparticles in order to obtain silica-coated silver-gold alloy nanoparticles. The changes of colour and mean diameter of Ag@SiO2 nanoparticles caused by the introduction of the gold salt were found dependent on its concentration. Upon increasing (KAuCl4) the diameter of nanoparticles …