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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 -
Pathogens (Basel, Switzerland) Jul 2023Bacterial adhesion is the first step in the formation of surface biofilms. The number of bacteria that bind to a surface from the solution depends on how many bacteria...
Bacterial adhesion is the first step in the formation of surface biofilms. The number of bacteria that bind to a surface from the solution depends on how many bacteria can reach the surface (bacterial transport) and the strength of interactions between bacterial adhesins and surface receptors (adhesivity). By using microfluidic channels and video microscopy as well as computational simulations, we investigated how the interplay between bacterial transport and adhesivity affects the number of the common human pathogen that bind to heterogeneous surfaces with different receptor densities. We determined that gravitational sedimentation causes bacteria to concentrate at the lower surface over time as fluid moves over a non-adhesive region, so bacteria preferentially adhere to adhesive regions on the lower, inflow-proximal areas that are downstream of non-adhesive regions within the entered compartments. Also, initial bacterial attachment to an adhesive region of a heterogeneous lower surface may be inhibited by shear due to mass transport effects alone rather than shear forces per se, because higher shear washes out the sedimented bacteria. We also provide a conceptual framework and theory that predict the impact of sedimentation on adhesion between and within adhesive regions in flow, where bacteria would likely bind both in vitro and in vivo, and how to normalize the bacterial binding level under experimental set-ups based on the flow compartment configuration.
PubMed: 37513788
DOI: 10.3390/pathogens12070941 -
ACS Omega Dec 2023Biofilm formation is a multistep process that requires initial contact between a bacterial cell and a surface substrate. Recent work has shown that nanoscale topologies...
Biofilm formation is a multistep process that requires initial contact between a bacterial cell and a surface substrate. Recent work has shown that nanoscale topologies impact bacterial cell viability; however, less is understood about how nanoscale surface properties impact other aspects of bacterial behavior. In this study, we examine the adhesive, viability, morphology, and colonization behavior of the bacterium on 21 plasma-etched polymeric surfaces. Although we predicted that specific nanoscale surface structures of the surface would control specific aspects of bacterial behavior, we observed no correlation between any bacterial response or surface structures/properties. Instead, it appears that the surface composition of the polymer plays the most significant role in controlling and determining a bacterial response to a substrate, although changes to a polymeric surface via plasma etching alter initial bacteria colonization and morphology.
PubMed: 38144076
DOI: 10.1021/acsomega.3c04747 -
International Journal of Molecular... Aug 2023The influence of nanoscale surface topography on protein adsorption is highly important for numerous applications in medicine and technology. Herein, ferritin adsorption...
The influence of nanoscale surface topography on protein adsorption is highly important for numerous applications in medicine and technology. Herein, ferritin adsorption at flat and nanofaceted, single-crystalline AlO surfaces is investigated using atomic force microscopy and X-ray photoelectron spectroscopy. The nanofaceted surfaces are generated by the thermal annealing of AlO wafers at temperatures above 1000 °C, which leads to the formation of faceted saw-tooth-like surface topographies with periodicities of about 160 nm and amplitudes of about 15 nm. Ferritin adsorption at these nanofaceted surfaces is notably suppressed compared to the flat surface at a concentration of 10 mg/mL, which is attributed to lower adsorption affinities of the newly formed facets. Consequently, adsorption is restricted mostly to the pattern grooves, where the proteins can maximize their contact area with the surface. However, this effect depends on the protein concentration, with an inverse trend being observed at 30 mg/mL. Furthermore, different ferritin adsorption behavior is observed at topographically similar nanofacet patterns fabricated at different annealing temperatures and attributed to different step and kink densities. These results demonstrate that while protein adsorption at solid surfaces can be notably affected by nanofacet patterns, fine-tuning protein adsorption in this way requires the precise control of facet properties.
Topics: Ferritins; Adsorption; Medicine; Microscopy, Atomic Force; Photoelectron Spectroscopy
PubMed: 37628990
DOI: 10.3390/ijms241612808 -
Heliyon Jun 2024This review comprehensively surveys the latest advancements in surface modification of pure magnesium (Mg) in recent years, with a focus on various cost-effective... (Review)
Review
This review comprehensively surveys the latest advancements in surface modification of pure magnesium (Mg) in recent years, with a focus on various cost-effective procedures, comparative analyses, and assessments of outcomes, addressing the merits and drawbacks of pure Mg and its alloys. Diverse economically feasible methods for surface modification, such as hydrothermal processes and ultrasonic micro-arc oxidation (UMAO), are discussed, emphasizing their exceptional performance in enhancing surface properties. The attention is directed towards the biocompatibility and corrosion resistance of pure Mg, underscoring the remarkable efficacy of techniques such as Ca-deficientca-deficient hydroxyapatite (CDHA)/MgF bi-layer coating and UMAO coating in electrochemical processes. These methods open up novel avenues for the application of pure Mg in medical implants. Emphasis is placed on the significance of adhering to the principles of reinforcing the foundation and addressing the source. The advocacy is for a judicious approach to corrosion protection on high-purity Mg surfaces, aiming to optimize the overall mechanical performance. Lastly, a call is made for future in-depth investigations into areas such as composite coatings and the biodegradation mechanisms of pure Mg surfaces, aiming to propel the field towards more sustainable and innovative developments.
PubMed: 38845950
DOI: 10.1016/j.heliyon.2024.e31703 -
Journal of Dentistry Nov 2023To explore the variability of tooth wear progression at the surface-, tooth- and patient-level over a period of three years three years using in vivo 3D-measurements of...
Inter- and intra-variability in tooth wear progression at surface-, tooth- and patient-level over a period of three years: A cohort study: Inter- and intra-variation in tooth wear progression.
OBJECTIVE
To explore the variability of tooth wear progression at the surface-, tooth- and patient-level over a period of three years three years using in vivo 3D-measurements of full dentitions amongst patients with moderate to severe tooth wear and without demand for restorative rehabilitation.
METHODS
Fifty-five eligible patients with moderate to severe tooth wear had intra-oral scans taken using either the 3 M True Definition Intraoral Scanner or the 3 M Lava Chairside Oral Scanner. The maximum height loss (µm) per cusp/incisal/palatal surface at unrestored surfaces was measured using the 3D Wear Analysis (3DWA)-protocol with Geomagic Qualify, resulting in sixty-four measurements per dentition. Data was visualized using box plots. Correlation was calculated between tooth wear progression rates of different tooth types and surfaces.
RESULTS
Thirty patients with scans at intake and after three years were included (38 ± 8 years, 77% M, 23% F). Mean observation time was 3.1 ± 0.2 years. Surface measurements (N = 1,615) showed a high deviation and a high number of outliers at all surfaces, indicating large variability amongst the surfaces, tooth types and patients with tooth wear progression rates. Correlations between regions were very low: anterior-molar region -0.219, anterior-premolar region 0.116 and premolar-molar region 0.113. Correlations between the surfaces of molars were also low (between 0.190 and 0.565).
CONCLUSIONS
In a group of patients with moderate to severe tooth wear, large differences in wear progression were found within and amongst patients. Tooth wear progression is therefore highly individualized and can be very localized.
CLINICAL SIGNIFICANCE
This study confirms the necessity of individual management of patients with moderate to severe tooth wear. Effective monitoring of tooth wear is important when deciding the timing and need for restorative intervention.
CLINICAL TRIAL REGISTRATION NUMBER
NCT04790110.
Topics: Humans; Cohort Studies; Tooth Wear; Tooth Attrition; Molar; Bicuspid
PubMed: 37683799
DOI: 10.1016/j.jdent.2023.104693 -
Environmental Science & Technology Dec 2023The use of household bleach cleaning products results in emissions of highly oxidative gaseous species, such as hypochlorous acid (HOCl) and chlorine (Cl). These species...
Gas-Phase and Surface-Initiated Reactions of Household Bleach and Terpene-Containing Cleaning Products Yield Chlorination and Oxidation Products Adsorbed onto Indoor Relevant Surfaces.
The use of household bleach cleaning products results in emissions of highly oxidative gaseous species, such as hypochlorous acid (HOCl) and chlorine (Cl). These species readily react with volatile organic compounds (VOCs), such as limonene, one of the most abundant compounds found in indoor enviroments. In this study, reactions of HOCl/Cl with limonene in the gas phase and on indoor relevant surfaces were investigated. Using an environmental Teflon chamber, we show that silica (SiO), a proxy for window glass, and rutile (TiO), a component of paint and self-cleaning surfaces, act as a reservoir for adsorption of gas-phase products formed between HOCl/Cl and limonene. Furthermore, high-resolution mass spectrometry (HRMS) shows that the gas-phase reaction products of HOCl/Cl and limonene readily adsorb on both SiO and TiO. Surface-mediated reactions can also occur, leading to the formation of new chlorine- and oxygen-containing products. Transmission Fourier-transform infrared (FTIR) spectroscopy of adsorption and desorption of bleach and terpene oxidation products indicates that these chlorine- and oxygen-containing products strongly adsorb on both SiO and TiO surfaces for days, providing potential sources of human exposure and sinks for additional heterogeneous reactions.
Topics: Humans; Hypochlorous Acid; Limonene; Chlorine; Halogenation; Silicon Dioxide; Terpenes; Gases; Oxygen; Air Pollution, Indoor
PubMed: 38010858
DOI: 10.1021/acs.est.3c06656 -
ACS Applied Materials & Interfaces Aug 2023Quantifying the crystallographic phases present at a surface is an important challenge in fields such as functional materials and surface science. X-ray photoelectron...
Quantifying the crystallographic phases present at a surface is an important challenge in fields such as functional materials and surface science. X-ray photoelectron spectroscopy (XPS) is routinely employed in surface characterization to identify and quantify chemical species through core line analysis. Valence band (VB) spectra contain characteristic but complex features that provide information on the electronic density of states (DoS) and thus can be understood theoretically using density functional theory (DFT). Here, we present a method of fitting experimental photoemission spectra with DFT models for quantitative analysis of heterogeneous systems, specifically mapping the anatase to rutile ratio across the surface of mixed-phase TiO thin films. The results were correlated with mapped photocatalytic activity measured using a resazurin-based smart ink. This method allows large-scale functional and surface composition mapping in heterogeneous systems and demonstrates the unique insights gained from DFT-simulated spectra on the electronic structure origins of complex VB spectral features.
PubMed: 37552034
DOI: 10.1021/acsami.3c06638 -
International Journal of Molecular... Oct 2023The exact mechanisms by which implant surface properties govern osseointegration are incompletely understood. To gain insights into this process, we examined alterations...
The exact mechanisms by which implant surface properties govern osseointegration are incompletely understood. To gain insights into this process, we examined alterations in protein and blood recruitment around screw implants with different surface topographies and wettability using a computational fluid dynamics (CFD) model. Compared with a smooth surface, a microrough implant surface reduced protein infiltration from the outer zone to the implant thread and interface zones by over two-fold. However, the microrough implant surface slowed blood flow in the interface zone by four-fold. As a result, compared with the smooth surface, the microrough surface doubled the protein recruitment/retention index, defined as the mass of proteins present in the area per unit time. Converting implant surfaces from hydrophobic to superhydrophilic increased the mass of protein infiltration 2-3 times and slowed down blood flow by up to two-fold in the implant vicinity for both smooth and microrough surfaces. The protein recruitment/retention index was highest at the implant interface when the implant surface was superhydrophilic and microrough. Thus, this study demonstrates distinct control of the mass and speed of protein and blood flow through implant surface topography, wettability, and their combination, significantly altering the efficiency of protein recruitment. Although microrough surfaces showed both positive and negative impacts on protein recruitment over smooth surfaces, superhydrophilicity was consistently positive regardless of surface topography.
Topics: Hydrodynamics; Wettability; Osseointegration; Surface Properties; Prostheses and Implants; Titanium; Dental Implants
PubMed: 37958605
DOI: 10.3390/ijms242115618 -
Microorganisms Aug 2023The COVID-19 pandemic highlighted the limitations in scientific and engineering understanding of applying germicidal UV to surfaces. This study combines surface...
The COVID-19 pandemic highlighted the limitations in scientific and engineering understanding of applying germicidal UV to surfaces. This study combines surface characterization, viral retention, and the related UV dose response to evaluate the effectiveness of UV as a viral inactivation technology on five surfaces: aluminum, ceramic, Formica laminate, PTFE and stainless steel. Images of each surface were determined using SEM (Scanning Electron Microscopy), which produced a detailed characterization of the surfaces at a nanometer scale. From the SEM images, the surface porosity of each material was calculated. Through further analysis, it was determined that surface porosity, surface roughness, contact angle, and zeta potential correlate to viral retention on the material. The imaging revealed that the aluminum surface, after repeated treatment, is highly oxidized, increasing surface area and surface porosity. These interactions are important as they prevent the recovery of MS-2 without exposure to UV. The dose response curve for PTFE was steeper than ceramic, Formica laminate and stainless steel, as inactivation to the detection limit was achieved at 25 mJ/cm. These findings are consistent with well-established literature indicating UV reflectivity of PTFE is maximized. Statistical testing reinforced that the efficacy of UV for surface inactivation varies by surface type.
PubMed: 37764001
DOI: 10.3390/microorganisms11092157