Kinetic analysis of RNA cleavage by coronavirus Nsp15 endonuclease: Evidence for acid-base catalysis and substrate-dependent metal ion activation.

Understanding the functional properties of severe acute respiratory syndrome coronavirus 2 nonstructural proteins is essential for defining their roles in the viral life cycle, developing improved therapeutics and diagnostics, and countering future variants. Coronavirus nonstructural protein Nsp15 is a hexameric U-specific endonuclease whose functions, substrate specificity, mechanism, and dynamics are not fully defined. Previous studies report that Nsp15 requires Mn2+ ions for optimal activity; however, the effects of divalent ions on Nsp15 reaction kinetics have not been investigated in detail. Here, we analyzed the single- and multiple-turnover kinetics for model ssRNA substrates. Our data confirm that divalent ions are dispensable for catalysis and show that Mn2+ activates Nsp15 cleavage of two different ssRNA oligonucleotide substrates but not a dinucleotide. Biphasic kinetics of ssRNA substrates demonstrates that Mn2+ stabilizes alternative enzyme states that have faster substrate cleavage on the enzyme. However, we did not detect Mn2+-induced conformational changes using CD and fluorescence spectroscopy. The pH-rate profiles in the presence and absence of Mn2+ reveal active-site ionizable groups with similar pKas of ca. 4.8 to 5.2. An Rp stereoisomer phosphorothioate modification at the scissile phosphate had minimal effect on catalysis supporting a mechanism involving an anionic transition state. However, the Sp stereoisomer is inactive because of weak binding, consistent with models that position the nonbridging phosphoryl oxygen deep in the active site. Together, these data demonstrate that Nsp15 employs a conventional acid-base catalytic mechanism passing through an anionic transition state, and that divalent ion activation is substrate dependent.

In silico EsxG EsxH rational epitope selection: Candidate epitopes for vaccine design against pulmonary tuberculosis.

Rational design of new vaccines against pulmonary tuberculosis is imperative. Early secreted antigens (Esx) G and H are involved in metal uptake, drug resistance, and immune response evasion. These characteristics make it an ideal target for rational vaccine development. The aim of this study is to show the rational design of epitope-based peptide vaccines by using bioinformatics and structural vaccinology tools. A total of 4.15 µs of Molecular Dynamics simulations were carried out to describe the behavior in solution of heterodimer, single epitopes, and epitopes loaded into MHC-II complexes. In order to predict T and B cell epitopes for antigenic activation, bioinformatic tools were used. Hence, we propose three epitopes with the potential to design pulmonary tuberculosis vaccines. The possible use of the proposed epitopes includes subunit vaccines, as a booster in BCG vaccination to improve its immune response, as well as the generation of antibodies that interfere with the Mycobacterium tuberculosis homeostasis, affecting its survival.

A rabbit model of tracheal collapse for optimal self-expanding metal stents.

Investigating the characteristics of tracheas can help the understanding of diseases related to the trachea, particularly tracheal collapse (TC) in dogs. This study aimed to compare the mechanical properties of tracheas from New Zealand White (NZW) rabbits and dogs and to introduce a method for inducing a model of TC in the normal trachea. Tracheal samples were obtained from NZW rabbit cadavers (n=5) weighing 3.62-3.92 kg and from dog cadavers (n=5) weighing 2.97-3.28 kg. Three live NZW rabbits weighing 3.5-4.0 kg were used to establish the model. The radial forces of both sample sets were measured using a digital force gauge and statistically compared. Subsequently, TC was surgically induced in three female NZW rabbits by physically weakening their tracheal cartilage under general anesthesia. Their clinical signs were monitored for 3 months, and radiographic examinations were performed monthly for 3 months. The mean radial forces of the two sample sets were comparable (P>0.05). The clinical signs, radiographic examinations, and macroscopic examinations were all comparable to those of dogs with TC. The cadaveric study between the rabbits and dogs demonstrated that the surgically induced rabbit model of TC is an excellent candidate for the experimental study of dogs with TC. This study also provides a reference of tracheal radial force values to enable selection of appropriate mesh types and wire diameters of self-expanding metal stents.

Electrochemical Sensing of Favipiravir with an Innovative Water-Dispersible Molecularly Imprinted Polymer Based on the Bimetallic Metal-Organic Framework: Comparison of Morphological Effects.

Molecularly imprinted polymers (MIPs) are widely used as modifiers in electrochemical sensors due to their high sensitivity and promise of inexpensive mass manufacturing. Here, we propose and demonstrate a novel MIP-sensor that can measure the electrochemical activity of favipiravir (FAV) as an antiviral drug, thereby enabling quantification of the concentration of FAV in biological and river water samples and in real-time. MOF nanoparticles' application with various shapes to determine FAV at nanomolar concentrations was described. Two different MOF nanoparticle shapes (dodecahedron and sheets) were systematically compared to evaluate the electrochemical performance of FAV. After carefully examining two different morphologies of MIP-Co-Ni@MOF, the nanosheet form showed a higher performance and efficiency than the nanododecahedron. When MIP-Co/Ni@MOF-based and NIP-Co/Ni@MOF electrodes (nanosheets) were used instead, the minimum target concentrations detected were 7.5 × 10-11 (MIP-Co-Ni@MOF) and 8.17 × 10-9 M (NIP-Co-Ni@MOF), respectively. This is a significant improvement (>102), which is assigned to the large active surface area and high fraction of surface atoms, increasing the amount of greater analyte adsorption during binding. Therefore, water-dispersible MIP-Co-Ni@MOF nanosheets were successfully applied for trace-level determination of FAV in biological and water samples. Our findings seem to provide useful guidance in the molecularly imprinted polymer design of MOF-based materials to help establish quantitative rules in designing MOF-based sensors for point of care (POC) systems.

Metal-induced oxidative stress and human plasma protein oxidation after SARS-CoV-2 infection.

Pathogenesis of COVID-19 by SARS-CoV-2 resulted in a global pandemic and public health emergency in 2020. Viral infection can induce oxidative stress through reactive oxygen species (ROS). Inflammation and environmental stress are major sources of oxidative stress after infection. Micronutrients such as iron, copper, zinc, and manganese play various roles in human tissues and their imbalance in blood can impact immune responses against pathogens including SARS CoV-2. We hypothesized that alteration of free metal ions during infection and metal-catalyzed oxidation plays a critical role towards pathogenesis after infection. We analyzed convalescent and hospitalized COVID-19 patient plasma using orthogonal analytical techniques to determine redox active metal concentrations, overall protein oxidation, oxidative modifications, and protein levels via proteomics to understand the consequences of metal-induced oxidative stress in COVID-19 plasma proteins. Metal analysis using ICP-MS showed significantly greater concentrations of copper in COVID-19 plasma compared to healthy controls. We demonstrate significantly greater total protein carbonylation, other oxidative modifications, and deamidation of plasma proteins in COVID-19 plasma compared to healthy controls. Proteomics analysis showed that levels of redox active proteins including hemoglobulin were elevated in COVID-19 plasma. Molecular modeling concurred with potential interactions between iron binding proteins and SARS CoV-2 surface proteins. Overall, increased levels of redox active metals and protein oxidation indicate that oxidative stress-induced protein oxidation in COVID-19 may be a consequence of the interactions of SARS-CoV-2 proteins with host cell metal binding proteins resulting in altered cellular homeostasis.

Modular Metal-Quinone Networks with Tunable Architecture and Functionality.

Nanostructured materials with tunable structures and functionality are of interest in diverse areas. Herein, metal ions are coordinated with quinones through metal-acetylacetone coordination bonds to generate a class of structurally tunable, universally adhesive, hydrophilic, and pH-degradable materials. A library of metal-quinone networks (MQNs) is produced from five model quinone ligands paired with nine metal ions, leading to the assembly of particles, tubes, capsules, and films. Importantly, MQNs show bidirectional pH-responsive disassembly in acidic and alkaline solutions, where the quinone ligands mediate the disassembly kinetics, enabling temporal and spatial control over the release of multiple components using multilayered MQNs. Leveraging this tunable release and the inherent medicinal properties of quinones, MQN prodrugs with a high drug loading (>89 wt %) are engineered using doxorubicin for anti-cancer therapy and shikonin for the inhibition of the main protease in the SARS-CoV-2 virus.

COVID-19 lockdown-driven changes in the Ganga River ecosystem in response to human perturbations.

We examined 10 subsurface water, 5 benthic water and 19 sediment (02 cm) samples along a 518 km of the middle segment of the Ganga River to assess the possible improvements that resulted from the industrial shutdown during the COVID-19 pandemic. The sites included the main stem river, tributary confluences, and two point sources, one of which releases metal-rich effluents and the other flushes municipal sewage. We found significant declines in the carbon, nutrient and metal concentrations in both the water and sediment. Even the most polluted zones did not show hypoxia (dissolve oxygen; DO < 2.0 mg L-1) that had been observed in the previous year. Despite a significant decline in carbon and nitrogen as substrates, the activities of extracellular enzymes (EEs), such as ß-D-glucosidase, FDAase and protease in sediment (0-2 cm depth), increased significantly (p < 0.05) in response to the declining metal concentrations resulting from the industrial shutdown. We found strong negative correlations between EE activity and the concentrations of metal pollutants measured in 2019, but the correlations between these variables appeared poor in 2020 (lockdown period). Also, we found large variances (low stability coefficients) during the period of strong anthropogenic effects (2019). The study indicates that industrial sources are important contributors of metal pollution in the Ganga River and has relevance exploring river ecosystem recovery windows for management decisions.

Reducing disease and death from Artisanal and Small-Scale Mining (ASM) - the urgent need for responsible mining in the context of growing global demand for minerals and metals for climate change mitigation.

Artisanal and small-scale mining (ASM) takes place under extreme conditions with a lack of occupational health and safety. As the demand for metals is increasing due in part to their extensive use in 'green technologies' for climate change mitigation, the negative environmental and occupational consequences of mining practices are disproportionately felt in low- and middle-income countries. The Collegium Ramazzini statement on ASM presents updated information on its neglected health hazards that include multiple toxic hazards, most notably mercury, lead, cyanide, arsenic, cadmium, and cobalt, as well as physical hazards, most notably airborne dust and noise, and the high risk of infectious diseases. These hazards affect both miners and mining communities as working and living spaces are rarely separated. The impact on children and women is often severe, including hazardous exposures during the child-bearing age and pregnancies, and the risk of child labor. We suggest strategies for the mitigation of these hazards and classify those according to primordial, primary, secondary, and tertiary prevention. Further, we identify knowledge gaps and issue recommendations for international, national, and local governments, metal purchasers, and employers are given. With this statement, the Collegium Ramazzini calls for the extension of efforts to minimize all hazards that confront ASM miners and their families.

Large-Scale Functionalized Metasurface-Based SARS-CoV-2 Detection and Quantification.

Plasmonic metasurfaces consist of metal-dielectric interfaces that are excitable at background and leakage resonant modes. The sharp and plasmonic excitation profile of metal-free electrons on metasurfaces at the nanoscale can be used for practical applications in diverse fields, including optoelectronics, energy harvesting, and biosensing. Currently, Fano resonant metasurface fabrication processes for biosensor applications are costly, need clean room access, and involve limited small-scale surface areas that are not easy for accurate sample placement. Here, we leverage the large-scale active area with uniform surface patterns present on optical disc-based metasurfaces as a cost-effective method to excite asymmetric plasmonic modes, enabling tunable optical Fano resonance interfacing with a microfluidic channel for multiple target detection in the visible wavelength range. We engineered plasmonic metasurfaces for biosensing through efficient layer-by-layer surface functionalization toward real-time measurement of target binding at the molecular scale. Further, we demonstrated the quantitative detection of antibodies, proteins, and the whole viral particles of SARS-CoV-2 with a high sensitivity and specificity, even distinguishing it from similar RNA viruses such as influenza and MERS. This cost-effective plasmonic metasurface platform offers a small-scale light-manipulation system, presenting considerable potential for fast, real-time detection of SARS-CoV-2 and pathogens in resource-limited settings.

Spectro-electrochemical, fluorometric and biothermodynamic evaluation of pharmacologically active morpholine scaffold single crystal ligand and its metal(II) complexes: A comparative study on in-vitro and in-silico screening towards DNA/BSA/SARS-CoV-19.

A novel series of metal(II) complexes (1-5) [MII(L)2]{Where M = Cu (1), Co (2), Mn (3), Ni (4) and Zn (5)} constructed from 2-(4-morpholinobenzylideneamino)phenol Schiff base ligand (HL) in a 1:2 M ratio and the spectral and analytical results put forward square planar geometry. Spectro-electrochemical, hydrodynamic, gel electrophoresis, and DNA binding/cleavage results for all the compounds demonstrate that complex (1) had excellent DNA binding/cleavage properties compared to other compounds. The observation also suggests that test compounds could intercalate with DNA, and the biothermodynamic property more strongly supports the stabilizing of the double helix DNA with the complexes. BSA binding constant results show that complex (1) exposes the best binding property via a static mode, which is further confirmed by FRET calculations. The DFT calculations and docking results for all compounds towards DNA, BSA and SARS-CoV-19 main protease (3CLPro), reveal the binding energies were in the range of -7.8 to -9.4, -6.6 to -10.2 and - 6.1 - -8.2 kcal/mol for all test compounds respectively. In this case, complexes showed favorable binding energies compared to free ligand, which stimulates further studies aimed at validating the predicted activity as well as contributing to tackling the current and future viral pandemics. The in-vitro antioxidant, antimicrobial, and anticancer results for all compounds revealed that copper complex (1) has better activity compared to others. This might result in an effective anticancer drug for future research, which is especially promising since the observed experimental results for all cases were in close agreement with the theoretical calculations.

[Concentration Variation and Source Analysis of Metal Elements in PM2.5 During COVID-19 Control in Suzhou].

To study the variation in concentration and source analysis of metal elements during COVID-19 control in Suzhou, a multi-metal online monitor was used to determine hourly online data of 14 metal elements from December 1, 2019 to March 31, 2020. This study analyzed variation in concentration and source analysis of metal elements using a PMF model before, during, and after shutdown during COVID-19 control. The results showed that the concentrations of Cr, Mn, Zn, and Fe during shutdown decreased the most, by 87.6%, 85.6%, 78.3%, and 72.2%, respectively, compared with those before shutdown. The concentrations of Mn, Cr, Zn, and Fe after shutdown increased the most, by 227.0%, 215.4%, 147.4%, and 113.4%, respectively, compared with those of the previous stage. The diurnal variation in K differed at three stages. Zn showed a single peak shape at three stages, but the peak width and peak time were different. Unlike the concentrations, the diurnal variations in Fe, Mn, Pb, Se, and Hg were not significantly changed. The daily variation characteristics of Ca, Ba, Cu, As, Cr, and Ni during and after shutdown were significantly different from those before shutdown. The results of source analysis by the PMF model showed that metal elements mainly came from dust, motor vehicle, coal burning, industrial smelting, and mixed-combustion sources. Among them, the concentration of industrial smelting sources changed greatly, with the concentration decreasing by 89.0% during shutdown and increasing by 358.0% after shutdown.

Theory for nanoscale curvature induced enhanced inactivation kinetics of SARS-CoV-2.

We develop a novel theory for the nanomorphology dependent outer sphere heterogeneous electron transfer (ET) rate constant () based on an energy level alignment approach. is modelled through the activation free energy, which is a product of the water monolayer covered metal work function (WF) and the fractional electronic charge exchanged at the transition state (attained through the alignment of the metal Fermi and HOMO/LUMO energy levels of the electroactive species). The theory shows that is an exponentially increasing and decreasing function of the mean curvature in concave and convex nanomorphologies, respectively, for electroactive species or proteins involving their HOMO energy. For the specific spike protein of SARS-CoV-2, we have estimated the half lifetime (t1/2) and degree of inactivation as a function of the metal WF, nanostructure mean curvature, spike protein HOMO energy, and the environmental temperature (T). By varying the metal from Ag to Au, t1/2 is reduced from 7 h to 4 min, respectively. The reduction in the copper nanoparticle size from 50 to 5 nm increases the degree of inactivation from 60 to 99.6% (with a reduction factor of 10 in t1/2). Similarly, the increase in T from 10 °C to 65 °C causes a 100 times lowering of the t1/2 and t99.9% of SARS-CoV-2 on Cu metal. The theory predicts that involving the HOMO energy level of a protein follows the surface nanostructure shape dependent order as follows: spherical nanoparticle > cylindrical nanorod > cylindrical nanopore > spherical nanocavity, while the opposite trend is observed in the case of the LUMO energy level participation. Finally, the theory shows agreement with the reported experimental data of the degree of inactivation of SARS-CoV-2 on Ag and Cu nanoparticles.

Ab Initio Insight into the Interaction of Metal-Decorated Fluorinated Carbon Fullerenes with Anti-COVID Drugs.

We theoretically investigated the adsorption of two common anti-COVID drugs, favipiravir and chloroquine, on fluorinated C60 fullerene, decorated with metal ions Cr3+, Fe2+, Fe3+, Ni2+. We focused on the effect of fluoridation on the interaction of fullerene with metal ions and drugs in an aqueous solution. We considered three model systems, C60, C60F2 and C60F48, and represented pristine, low-fluorinated and high-fluorinated fullerenes, respectively. Adsorption energies, deformation of fullerene and drug molecules, frontier molecular orbitals and vibrational spectra were investigated in detail. We found that different drugs and different ions interacted differently with fluorinated fullerenes. Cr3+ and Fe2+ ions lead to the defluorination of low-fluorinated fullerenes. Favipiravir also leads to their defluorination with the formation of HF molecules. Therefore, fluorinated fullerenes are not suitable for the delivery of favipiravir and similar drugs molecules. In contrast, we found that fluorine enhances the adsorption of Ni2+ and Fe3+ ions on fullerene and their activity to chloroquine. Ni2+-decorated fluorinated fullerenes were found to be stable and suitable carriers for the loading of chloroquine. Clear shifts of infrared, ultraviolet and visible spectra can provide control over the loading of chloroquine on Ni2+-doped fluorinated fullerenes.

Recent Advances in Metal-Based Antimicrobial Coatings for High-Touch Surfaces.

International interest in metal-based antimicrobial coatings to control the spread of bacteria, fungi, and viruses via high contact human touch surfaces are growing at an exponential rate. This interest recently reached an all-time high with the outbreak of the deadly COVID-19 disease, which has already claimed the lives of more than 5 million people worldwide. This global pandemic has highlighted the major role that antimicrobial coatings can play in controlling the spread of deadly viruses such as SARS-CoV-2 and scientists and engineers are now working harder than ever to develop the next generation of antimicrobial materials. This article begins with a review of three discrete microorganism-killing phenomena of contact-killing surfaces, nanoprotrusions, and superhydrophobic surfaces. The antimicrobial properties of metals such as copper (Cu), silver (Ag), and zinc (Zn) are reviewed along with the effects of combining them with titanium dioxide (TiO2) to create a binary or ternary contact-killing surface coatings. The self-cleaning and bacterial resistance of purely structural superhydrophobic surfaces and the potential of physical surface nanoprotrusions to damage microbial cells are then considered. The article then gives a detailed discussion on recent advances in attempting to combine these individual phenomena to create super-antimicrobial metal-based coatings with binary or ternary killing potential against a broad range of microorganisms, including SARS-CoV-2, for high-touch surface applications such as hand rails, door plates, and water fittings on public transport and in healthcare, care home and leisure settings as well as personal protective equipment commonly used in hospitals and in the current COVID-19 pandemic.

Questioning Established Theories and Treatment Methods Related to Iron and Other Metal Metabolic Changes, Affecting All Major Diseases and Billions of Patients.

The medical and scientific literature is dominated by highly cited historical theories and findings [...].

Impact persistence of stock market risks in commodity markets: Evidence from China.

The risk spillover among financial markets has been noticeably investigated in a burgeoning number of literature. Given those doctrines, we scrutinize the impact persistence of volatility spillover and illiquidity spillover of Chinese commodity markets in this paper. Based on the sample from 2010 to 2020, we reveal that there is a cross-market spillover of volatility and illiquidity in China and also, interactions between volatility and illiquidity in different financial markets are pronounced. More importantly, we demonstrate that different commodity markets have different responsiveness to stock market shocks, which embeds their market characteristics. Specifically, we discover that the majority of the traders in gold market might be hedger and therefore gold market is more sensitive to stock market illiquidity shock and thus the shock impact in persistent. On the other hand, agricultural markets like corn and soybean markets might be dominated by investors and thus those markets respond to the stock market volatility shocks and the shock impact in persistent over 10 periods given the first period of risk shock happening. In fact, different Chinese commodity markets' responsiveness towards Chinese stock market risk shocks indicates the stock market risk impact persistence in Chinese commodity markets. This result can help policymakers to understand the policy propagation effect according to this risk spillover channel and risk impact persistence mechanism in China.

Degradation of contaminants in plasma technology: An overview.

The information of plasma technologies applications for environmental clean-up on treating and degrading metals, metalloids, dyes, biomass, antibiotics, pesticides, volatile organic compounds (VOCs), bacteria, virus and fungi is compiled and organized in the review article. Different reactor configurations of plasma technology have been applied for reactive species generation, responsible for the pollutants removal, hydrogen and methane production and microorganism inactivation. Therefore, in this review article, the reactive species from discharge plasma are presented here to provide the insight into the environmental applications. The combinations of plasma technology with flux agent and photocatalytic are also given in this review paper associated with the setup of the plasma system on the removal process of metals, VOCs, and microorganisms. Furthermore, the potential of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) inactivation via plasma technology is also described in this review paper. Detailed information of plasma parameter configuration is given to support the influence of the critical process in the plasma system to deal with contaminants.

Metal leaching from antimicrobial cloth face masks intended to slow the spread of COVID-19.

Global health organizations recommend the use of cloth face coverings to slow the spread of COVID-19. Seemingly overnight, companies whose primary business is in no way related to healthcare or personal protective equipment-from mattresses manufacturers to big box stores-transitioned into the "mask business." Many companies advertise antimicrobial masks containing silver, copper, or other antimicrobials. Often, the techniques used to load such antimicrobials onto mask fibers are undisclosed, and the potential for metal leaching from these masks is yet unknown. We exposed nine so-called "antimicrobial" face masks (and one 100% cotton control mask) to deionized water, laundry detergent, and artificial saliva to quantify the leachable silver and copper that may occur during mask washing and wearing. Leaching varied widely across manufacturer, metal, and leaching solution, but in some cases was as high as 100% of the metals contained in the as-received mask after 1 h of exposure.

Metal-Bound Methisazone; Novel Drugs Targeting Prophylaxis and Treatment of SARS-CoV-2, a Molecular Docking Study.

SARS-CoV-2 currently lacks effective first-line drug treatment. We present promising data from in silico docking studies of new Methisazone compounds (modified with calcium, Ca; iron, Fe; magnesium, Mg; manganese, Mn; or zinc, Zn) designed to bind more strongly to key proteins involved in replication of SARS-CoV-2. In this in silico molecular docking study, we investigated the inhibiting role of Methisazone and the modified drugs against SARS-CoV-2 proteins: ribonucleic acid (RNA)-dependent RNA polymerase (RdRp), spike protein, papain-like protease (PlPr), and main protease (MPro). We found that the highest binding interactions were found with the spike protein (6VYB), with the highest overall binding being observed with Mn-bound Methisazone at -8.3 kcal/mol, followed by Zn and Ca at -8.0 kcal/mol, and Fe and Mg at -7.9 kcal/mol. We also found that the metal-modified Methisazone had higher affinity for PlPr and MPro. In addition, we identified multiple binding pockets that could be singly or multiply occupied on all proteins tested. The best binding energy was with Mn-Methisazone versus spike protein, and the largest cumulative increases in binding energies were found with PlPr. We suggest that further studies are warranted to identify whether these compounds may be effective for treatment and/or prophylaxis.