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Developmental Cell Oct 2023Proper localization of receptors for synaptic organizing factors is crucial for synapse formation. Wnt proteins promote synapse assembly through Frizzled (Fz) receptors....
Proper localization of receptors for synaptic organizing factors is crucial for synapse formation. Wnt proteins promote synapse assembly through Frizzled (Fz) receptors. In hippocampal neurons, the surface and synaptic localization of Fz5 is regulated by neuronal activity, but the mechanisms involved remain poorly understood. Here, we report that all Fz receptors can be post-translationally modified by S-acylation and that Fz5 is S-acylated on three C-terminal cysteines by zDHHC5. S-acylation is essential for Fz5 localization to the cell surface, axons, and presynaptic sites. Notably, S-acylation-deficient Fz5 is internalized faster, affecting its association with signalosome components at the cell surface. S-acylation-deficient Fz5 also fails to activate canonical and divergent canonical Wnt pathways. Fz5 S-acylation levels are regulated by the pattern of neuronal activity. In vivo studies demonstrate that S-acylation-deficient Fz5 expression fails to induce presynaptic assembly. Our studies show that S-acylation of Frizzled receptors is a mechanism controlling their localization and function.
Topics: Animals; Rodentia; Frizzled Receptors; Wnt Signaling Pathway; Hippocampus; Acylation
PubMed: 37557176
DOI: 10.1016/j.devcel.2023.07.012 -
Surfaces: a software to quantify and visualize interactions within and between proteins and ligands.Bioinformatics (Oxford, England) Oct 2023Computational methods for the quantification and visualization of the relative contribution of molecular interactions to the stability of biomolecular structures and...
SUMMARY
Computational methods for the quantification and visualization of the relative contribution of molecular interactions to the stability of biomolecular structures and complexes are fundamental to understand, modulate and engineer biological processes. Here, we present Surfaces, an easy to use, fast and customizable software for quantification and visualization of molecular interactions based on the calculation of surface areas in contact. Surfaces calculations shows equivalent or better correlations with experimental data as computationally expensive methods based on molecular dynamics.
AVAILABILITY AND IMPLEMENTATION
All scripts are available at https://github.com/NRGLab/Surfaces. Surface's documentation is available at https://surfaces-tutorial.readthedocs.io/en/latest/index.html.
Topics: Software; Proteins; Molecular Dynamics Simulation; Documentation; Ligands
PubMed: 37788107
DOI: 10.1093/bioinformatics/btad608 -
Nucleic Acids Research Jul 2012We recently proposed to classify proteins by their functional surfaces. Using the structural attributes of functional surfaces, we inferred the pairwise relationships of...
We recently proposed to classify proteins by their functional surfaces. Using the structural attributes of functional surfaces, we inferred the pairwise relationships of proteins and constructed an expandable database of protein surface classification (PSC). As the functional surface(s) of a protein is the local region where the protein performs its function, our classification may reflect the functional relationships among proteins. Currently, PSC contains a library of 1974 surface types that include 25,857 functional surfaces identified from 24,170 bound structures. The search tool in PSC empowers users to explore related surfaces that share similar local structures and core functions. Each functional surface is characterized by structural attributes, which are geometric, physicochemical or evolutionary features. The attributes have been normalized as descriptors and integrated to produce a profile for each functional surface in PSC. In addition, binding ligands are recorded for comparisons among homologs. PSC allows users to exploit related binding surfaces to reveal the changes in functionally important residues on homologs that have led to functional divergence during evolution. The substitutions at the key residues of a spatial pattern may determine the functional evolution of a protein. In PSC (http://pocket.uchicago.edu/psc/), a pool of changes in residues on similar functional surfaces is provided.
Topics: Alcohol Dehydrogenase; Cluster Analysis; Humans; Internet; Proteins; Software; Structural Homology, Protein; Surface Properties
PubMed: 22669905
DOI: 10.1093/nar/gks495 -
Frontiers in Psychology 2018Commercial saturation diving involves divers living and working in an enclosed atmosphere with elevated partial pressure of oxygen (ppO) for weeks. The divers must...
Commercial saturation diving involves divers living and working in an enclosed atmosphere with elevated partial pressure of oxygen (ppO) for weeks. The divers must acclimatize to these conditions during compression, and for up to 28 days until decompression is completed. During decompression, the ppO and ambient pressure are gradually decreased; then the divers must acclimatize again to breathing normal air in atmospheric pressure when they arrive at surface. We investigated 51 saturation divers' subjective evaluation of the saturation and post-decompression phase via questionnaires and individual interviews. The questions were about decompression headaches and fatigue; and time before recovering to a pre-saturation state. Twenty-two (44%) of the divers who responded declared having headaches; near surface (44%) or after surfacing (56%). 71% reported post-saturation fatigue after their last saturation, 82% of them described it as typical and systematic after each saturation. Recovery was reported to normally take from 1 to 10 days. The fatigue and headaches observed are compatible with divers' acclimatization to the changes in ppO levels during saturation and decompression. They appear to be reversible post- decompression.
PubMed: 30692957
DOI: 10.3389/fpsyg.2018.02774 -
Angewandte Chemie (International Ed. in... Oct 2021Gathering information on the atomic nature of reactive sites and trap states is key to fine tuning catalysis and suppressing deleterious surface voltage losses in...
Gathering information on the atomic nature of reactive sites and trap states is key to fine tuning catalysis and suppressing deleterious surface voltage losses in photoelectrochemical technologies. Here, spectroelectrochemical and computational methods were combined to investigate a model photocathode from the promising chalcopyrite family: CuIn Ga S . We found that voltage losses are linked to traps induced by surface Ga and In vacancies, whereas operando Raman spectroscopy revealed that catalysis occurred at Ga, In, and S sites. This study allows establishing a bridge between the chalcopyrite's performance and its surface's chemistry, where avoiding formation of Ga and In vacancies is crucial for achieving high activity.
PubMed: 34428331
DOI: 10.1002/anie.202108994 -
Micromachines Mar 2023The controlled and efficient formation of oxygen vacancies on the surface of metal oxide semiconductors is required for their use in gas sensors. This work addresses the...
The controlled and efficient formation of oxygen vacancies on the surface of metal oxide semiconductors is required for their use in gas sensors. This work addresses the gas-sensing behaviour of tin oxide (SnO) nanoparticles for nitrogen oxide (NO), NH, CO, and HS detection at various temperatures. Synthesis of SnO powder and deposition of SnO film is conducted using sol-gel and spin-coating methods, respectively, as these methods are cost-effective and easy to handle. The structural, morphological, and optoelectrical properties of nanocrystalline SnO films were studied using XRD, SEM, and UV-visible characterizations. The gas sensitivity of the film was tested by a two-probe resistivity measurement device, showing a better response for the NO and outstanding low-concentration detection capacity (down to 0.5 ppm). The anomalous relationship between specific surface area and gas-sensing performance indicates the SnO surface's higher oxygen vacancies. The sensor depicts a high sensitivity at 2 ppm for NO with response and recovery times of 184 s and 432 s, respectively, at room temperature. The result demonstrates that oxygen vacancies can significantly improve the gas-sensing capability of metal oxide semiconductors.
PubMed: 37420962
DOI: 10.3390/mi14040728 -
Paediatrics & Child Health Jun 2012With concerns increasing around childhood obesity and inactivity, playgrounds offer a chance for children to be active. But playgrounds also have risks, with injuries...
With concerns increasing around childhood obesity and inactivity, playgrounds offer a chance for children to be active. But playgrounds also have risks, with injuries from falls being the most common. Research has shown that playground injuries can be reduced by lowering the heights of play equipment and using soft, deep surfaces to cushion falls. The Canadian Standards Association has published voluntary standards for playgrounds to address these risks for several years. Parents can further reduce injury risks by following simple playground strategies. This statement outlines the burden of playground injuries. It also provides parents and health care providers with opportunities to reduce injury incidence and severity through education and advocacy, and to implement evidence-informed safety standards and safer play strategies in local playgrounds. This document replaces a previous Canadian Paediatric Society position statement published in 2002.
PubMed: 23730171
DOI: No ID Found -
Medicina (Kaunas, Lithuania) Oct 2022The antimicrobial efficacy of a nonthermal atmospheric-pressure plasma jet (NAPPJ) on dental impression materials was investigated. Type 3 polyvinyl siloxane was used...
The antimicrobial efficacy of a nonthermal atmospheric-pressure plasma jet (NAPPJ) on dental impression materials was investigated. Type 3 polyvinyl siloxane was used as the impression material, and air and nitrogen NAPPJ were applied. The antibacterial effect of the NAPPJ was measured using the number of colony-forming units (CFUs) and scanning electron microscopy (SEM) images of . Surface chemical characteristics of the impression material were examined using X-ray photoelectron spectroscopy (XPS) and contact angle measurement. Additionally, physical properties were analyzed through surface roughness measurement, detail reproduction, and strain-in-compression test. Compared with the control group, the plasma treatment group showed ruptured bacteria membranes, destroyed bacteria structures, a significant reduction in the number of CFUs, and a significantly reduced contact angle. Further, XPS analysis showed that their surface was significantly richer in hydroxyl groups. The surface roughness, detail reproduction, and strain-in-compression results indicated no significant differences between the plasma treatment and control groups. NAPPJ treatment could remove bacteria from polyvinyl siloxane dental impression materials without changing the surface's physical properties. Therefore, it is considered a promising method for disinfection.
Topics: Humans; Plasma Gases; Surface Properties; Materials Testing; Dental Impression Materials
PubMed: 36363513
DOI: 10.3390/medicina58111556 -
PloS One 2023Species Distribution Models often include spatial effects which may improve prediction at unsampled locations and reduce Type I errors when identifying environmental...
Species Distribution Models often include spatial effects which may improve prediction at unsampled locations and reduce Type I errors when identifying environmental drivers. In some cases ecologists try to ecologically interpret the spatial patterns displayed by the spatial effect. However, spatial autocorrelation may be driven by many different unaccounted drivers, which complicates the ecological interpretation of fitted spatial effects. This study aims to provide a practical demonstration that spatial effects are able to smooth the effect of multiple unaccounted drivers. To do so we use a simulation study that fit model-based spatial models using both geostatistics and 2D smoothing splines. Results show that fitted spatial effects resemble the sum of the unaccounted covariate surface(s) in each model.
Topics: Computer Simulation; Spatial Analysis
PubMed: 37253039
DOI: 10.1371/journal.pone.0285463 -
Frontiers in Bioengineering and... 2022Corneal injury inevitably leads to disruption of the ocular surface microenvironment, which is closely associated with delayed epithelial cell repair and the development...
Corneal injury inevitably leads to disruption of the ocular surface microenvironment, which is closely associated with delayed epithelial cell repair and the development of infection. Recently, drug-loaded therapeutic contact lenses have emerged as a new approach to treating corneal injury due to their advantages of relieving pain, promoting corneal repair, and preventing infection. However, few therapeutic contact lenses could modulate the ocular surface's inflammation and oxidative stress microenvironment. To address this, in this study, we covalently immobilized multifunctional baicalin (BCL), a flavon molecular with anti-inflammatory, anti-oxidative stress, and antibacterial capabilities, onto the surface of the contact lens. The BCL-modified contact lens showed excellent optical properties, powerful antibacterial properties, and non-toxicity to endothelial cells. Furthermore, the BCL-modified contact lens could significantly modulate the ocular surface microenvironment, including inhibition of macrophage aggregation and resistance to epithelium damage caused by oxidative stress. In animal models, BCL-modified corneal contact lens effectively promoted corneal epithelial cells repair. These excellent properties suggested that multifunctional BCL molecules had great application potential in the surface engineering of ophthalmic medical materials.
PubMed: 35309981
DOI: 10.3389/fbioe.2022.855022