A Universal DNA Aptamer that Recognizes Spike Proteins of Diverse SARS-CoV-2 Variants of Concern

We report on a unique DNA aptamer, denoted MSA52, that displays universally high affinity for the spike proteins of wildtype SARS-CoV-2 as well as the Alpha, Beta, Gamma, Epsilon, Kappa, Delta and Omicron variants. Using an aptamer pool produced from round 13 of selection against the S1 domain of the wildtype spike protein, we carried out one-round SELEX experiments using five different trimeric spike proteins from variants, followed by high-throughput sequencing and sequence alignment analysis of aptamers that formed complexes with all proteins. A previously unidentified aptamer, MSA52, showed K_d values ranging from 2 to 10 nM for all variant spike proteins, and also bound similarly to variants not present in the reselection experiments. This aptamer also recognized pseudotyped lentiviruses (PL) expressing eight different spike proteins of SARS-CoV-2 with K_d values between 20 and 50 pM, and was integrated into a simple colorimetric assay for detection of multiple PL variants. This discovery provides evidence that aptamers can be generated with high affinity to multiple variants of a single protein, including emerging variants, making it well-suited for molecular recognition of rapidly evolving targets such as those found in SARS-CoV-2.     

New observations on scratch deformations of soda lime silica glass

In spite of the wealth of literature, the role of the scratching speed in affecting the material removal mechanism in soda lime silica (SLS) glass is yet to be comprehensively understood. Here we report the surface and sub‐surface deformation mechanisms of SLS glass scratched under three different normal loads of 5, 10 and 15 N at various speeds in the range of 100–1000 μm/s with a diamond indenter of ~ 200 μm tip radius. The results show that at any given applied normal load, the width, depth, wear volume of the scratch grooves and wear rate of the SLS glass decreased with an inverse power law dependence on the applied scratching speed. The surface damage also reduced with the increase in scratching speed. A new, simple model was developed to explain these observations. The significant contributions of the time of contact, the tensile stress behind the indenter and the shear stress active just underneath the indenter in governing the material removal mechanisms of the SLS glass were discussed.     

Magneto-thermo-elastic waves in an infinite perfectly conducting elastic solid with energy dissipation

The generalized thermo-elasticity theory, i.e., Green and Naghdi （G-N） Ⅲ theory, with energy dissipation （TEWED） is employed in the study of time-harmonic plane wave propagation in an unbounded, perfectly electrically conducting elastic medium subject to primary uniform magnetic field. A more general dispersion equation with com- plex coefficients is obtained for coupled magneto-thermo-elastic wave solved in complex domain by using the Leguerre＇s method. It reveals that the coupled magneto-thermoelastic wave corresponds to modified dilatational and thermal wave propagation with finite speeds modified by finite thermal wave speeds, thermo-elastic coupling, thermal diffusivity, and the external magnetic field. Numerical results for a copper-like material are presented.     

Effect of load in scratch experiments on soda lime silica glass

Today the technological applications of glass span from everyday life to many advanced areas. These advanced applications require very accurate grinding and polishing that involve controlled removal of glass to achieve micron or even sub-micron surface finish. The major bottleneck in this connection is that the material removal mechanisms during such processes are yet to be fully understood. Since grinding involves many single pass scratch processes happening simultaneously, to develop better understanding about the effect of the normal load in affecting the material removal mechanisms; a number of single pass scratch experiments were conducted on a commercially available soda lime silica glass as a function of various normal loads (2–15 N) at a constant scratch speed of 100 μm.s^? 1. The results showed that the tribological properties, the severity and the spatial density of damage evolution were sensitive to the applied normal loads and the resultant tensile as well as shear stresses. Extensive optical and scanning electron photomicrography of the surface and sub-surface deformation zones proved the existence of three distinct deformation zones in the immediate vicinity of the scratch grooves and led to the development of a qualitative model of the material removal mechanisms.     

Effect of scratching speed on deformation of soda–lime–silica glass

The grinding and polishing of a fundamentally brittle material like glass to an utmost precision level for ultra-sophisticated applications ranging from mobile devices to aerospace as well as space shuttle components to biomedical appliances pose a big challenge today. Looking simplistically, the grinding and polishing processes are basically material removal by multiple scratching at a given speed. Unfortunately however, the role of the scratching speed in affecting the material removal mechanism in soda–lime–silica (SLS) glass is yet to be comprehensively understood. Therefore, the present work explores the surface and subsurface deformation mechanisms of SLS glass scratched under a normal load of 5 N at various speeds in the range of 100–1000 μm?s^?1 with a diamond indenter of ～200 μm tip radius. The results show important roles of the time of contact, the tensile stress behind the indenter and the shear stress just beneath the indenter in governing the material removal mechanisms of the SLS glass.     

Novel B,C-ring truncated deguelin derivatives reveals as potential inhibitors of cyclin D1 and cyclin E using molecular docking and molecular dynamic simulation

The overexpression of cyclin D1 and cyclin E due to their oncogenic potential and amplification has been associated with a higher mortality rate in many cancers. The deguelin is a natural compound, has shown promising anti-cancer activity by directly binding cyclin D1 and cyclin E and thus suppressing its function. The C7a atomic position of deguelin structure contains a proton that generates stabilized radical, as a result, decomposed deguelin reduces its structural stability and significantly decreases its biological activity. To design deguelin derivatives with the reduced potential side effect, series of B, C-ring truncated derivatives were investigated as cyclin D1 and cyclin E inhibitors. R-group-based enumeration was implemented in the deguelin scaffold using the R-group enumeration module of Schrödinger. Drug-Like filters like, REOS and PAINs series were applied to the enumerated compound library to remove compounds containing reactive functional groups. Further, screened compounds were docked within the ligand-binding cavity of cyclin D1 and cyclin E crystal structure, using Glide SP and XP protocol to obtain docking poses. Enrichment calculations were done using SchrÖdinger software, with 1000 decoy compounds (from DUD.E database) and 60 compounds (XP best poses) along with deguelin, to validate the docking protocol. The receiver operating characteristic (ROC) curve indicates R²?=?0.94 for cyclin D1 and R²?=?0.79 for cyclin E, suggesting that the docking protocol is valid. Besides, we explored molecular dynamics simulation to probe the binding stability of deguelin and its derivatives within the binding cavity of cyclin D1 and cyclin E structures which are associated with the cyclin D1 and cyclin E inhibitory mechanism.

Graphic abstract

     

Ultrasound-assisted enhanced and rapid uptake of anionic dyes from the binary system onto MnFe2O4/polyaniline nanocomposite at neutral pH

Remediation of toxic dyes from an aqua matrix using novel nanocomposites as adsorbent is an attractive yet challenging task, especially when the adsorption process needs to be operated at near-neutral solution pH. Recently, conducting polymer-based novel nanocomposites have been studied widely for environmental remediation because of their high distinctive surface area, mesoporous nature, easy synthesis process, availability of the low-cost monomer, and comprehensive range of functionality. This research deals with the fabrication and application of manganese ferrite and polyaniline nanocomposite (MnF-PANI-NC) for the ultrasound-assisted adsorption of methyl red (MR) and congo red (CR) dye from binary dye solution at neutral pH. The X-ray diffraction pattern of MnF-PANI-NC confirmed the successful impregnation of manganese ferrite onto polyaniline, and the field emission gun scanning electron microscopy and transmission electron microscopy images revealed the nanoscale formation of this composite. The saturation magnetization of ~20 emu/g endorses the easy magnetic separation of MnF-PANI-NC from dye solution. MnF-PANI-NC has revealed higher adsorptive affinity towards MR and CR dye concerning pure PANI and pure MnF nanoparticles at near-neutral solution pH. Assimilation of ultrasound wavse in this adsorption procedure improved the mass transfer rate significantly, and within 6 min of reaction more than 95% of MR and CR dye removal was achieved. Ultrasound waves also enhanced the equilibrium dye uptake efficiency (more than 95%) of MnF-PANI-NC compared to the adsorption reaction by overhead stirring (40–50%) and shaking (40–60%) for both MR and CR dyes. Kinetic modeling of the experimental data revealed accurate fitting of the pseudo-second-order model in association with intraparticle diffusion. Binary dye adsorption onto MnF-PANI-NC obeyed the Langmuir isotherm model accurately, and maximum adsorption capacities of 294.12 and 317.46 mg/g were observed for MR and CR dyes, respectively.     

Optimization for the improvement of power in equal volume of single chamber microbial fuel cell using dairy wastewater

Microbial fuel cells (MFCs) are a type of sustainable technology that may treat wastewater and generate power at the same time. Therefore, researchers are being challenged to design a technically feasible bio electrochemical system that generates environmentally friendly and renewable electricity from waste water. The current research examined at how MFC may be used to generate electricity while treating real dairy wastewater (RDW) with Pseudomonas aeruginosa-MTCC-7814. The experiments were carried out in fed-batch mode for 15 days in two 300 ml single chamber microbial fuel cells (SCMFCs) that were connected in series. During a fed batch investigation, three process parameters such as inoculum percentage, temperature, and pH were optimized. Inoculum percentage, temperature, and pH were found to be optimal at 5%, 37 °C, and 7.4, respectively and the highest open-circuit voltage was found to be 1025 mV. The COD removal efficiency and columbic efficiency (CE) were found to be 95.84% and 37.13% respectively. The optimized fed batch process yielded the maximum current density and power density of 313 mA/m² and 105 mW/m², respectively. Thus, this work successfully demonstrates that connecting single chamber microbial fuel cells (SCMFCs) in series is a viable technique for generating sustainable power utilizing Pseudomonas aeruginosa-MTCC-7814 from dairy wastewater.