Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models

RNA is a unique biomolecule that is involved in a variety of fundamental biological functions, all of which depend solely on its structure and dynamics. Since the experimental determination of crystal RNA structures is laborious, computational 3D structure prediction methods are experiencing an ongoing and thriving development. Such methods can lead to many models; thus, it is necessary to build comparisons and extract common structural motifs for further medical or biological studies. Here, we introduce a computational pipeline dedicated to reference-free high-throughput comparative analysis of 3D RNA structures. We show its application in the RNA-Puzzles challenge, in which five participating groups attempted to predict the three-dimensional structures of 5′- and 3′-untranslated regions (UTRs) of the SARS-CoV-2 genome. We report the results of this puzzle and discuss the structural motifs obtained from the analysis. All simulated models and tools incorporated into the pipeline are open to scientific and academic use.     

Compact Wideband Meandered Slotted Multi Frequency Microstrip Antenna

A compact wideband multi frequency microstrip antenna for wireless communication is proposed in this paper. The antenna is designed by introducing meandered slot on the patch and a pair of spur lines along the triangular notch on the finite ground plane. The overall size of the fabricated antenna is very small and low profile as the total dimension is 20?×?16 mm². The proposed antenna operates at 3.7 GHz, 4.27 GHz and 5.1 GHz which may be suitable for WiMAX and WLAN applications. In addition with multi frequency operation a wide bandwidth (VSWR?≤?2) has been achieved from 6 to 13.7 GHz i.e. 78.2% bandwidth of center frequency, which is suitable for X-band communication and ITU band applications. The meandered slot on the patch causes multi frequency operation of the antenna with 60% compactness and the spur line along with triangular notch on finite ground plane cause bandwidth enhancement.

     

Zinc oxide nanorod mediated visible light photoinactivation of model microbes in water

The inactivation of model microbes in aqueous matrix by visible light photocatalysis as mediated by ZnO nanorods was investigated. ZnO nanorods were grown on glass substrate following a hydrothermal route and employed in the inactivation of gram-negative Escherichia coli and gram-positive Bacillus subtilis in MilliQ water. The concentration of Zn(2+) ions in the aqueous matrix, bacterial cell membrane damage, and DNA degradation at post-exposure were also studied. The inactivation efficiencies for both organisms under light conditions were about two times higher than under dark conditions across the cell concentrations assayed. Anomalies in supernatant Zn(2+) concentration were observed under both conditions as compared to control treatments, while cell membrane damage and DNA degradation were observed only under light conditions. Inactivation under dark conditions was hence attributed to the bactericidal effect of Zn(2+) ions, while inactivation under light conditions was due to the combined effects of Zn(2+) ions and photocatalytically mediated electron injection. The reduction of pathogenic bacterial densities by the photocatalytically active ZnO nanorods in the presence of visible light implies potential ex situ application in water decontamination at ambient conditions under sunlight.     

Cytogenetic and genotoxic effects of zinc oxide nanoparticles on root cells of Allium cepa

Increasing use of zinc oxide nanoparticles (ZnO NP) in consumer products may enhance its release into the environment. Phytotoxicity study is important to understand its possible environmental impact. Allium cepa (Onion bulb) is the best model organism to study genetic toxicology of nanoparticles. Here we have reported cytogenetic and genotoxic effects of ZnO NPs on the root cells of A. cepa. The effects of ZnO NPs on the mitotic index (MI), micronuclei index (MN index), chromosomal aberration index, and lipid peroxidation were determined through the hydroponic culturing of A. cepa. A. cepa roots were treated with the dispersions of ZnO NPs at four different concentrations (25, 50, 75, and 100 μg ml(-1)). With the increasing concentrations of ZnO NPs MI decreased with the increase of pycnotic cells, on the other hand MN and chromosomal aberration index increased. The frequency of micronucleated cells was higher in ZnO NPs treated cells as compared to control (deionized distilled water). The number of cells in each mitotic phase changed upon ZnO NPs treatment. The effect of ZnO NPs on lipid peroxidation as examined by measuring TBARS concentration was evident at all the concentrations compared to bulk ZnO. The TEM image showed internalization of ZnO NPs like particles. SEM image of treated A. cepa demonstrated that the internalized nanoparticles agglomerated depending on the physico-chemical environment inside the cell. Our results demonstrated that ZnO NPs can be a clastogenic/genotoxic and cytotoxic agent. In conclusion, the A. cepa cytogenetic test can be used for the genotoxicity monitoring of novel nanomaterials like ZnO NPs, which is used in many consumer products.     

Studies on interfacial interactions of TiO2 nanoparticles with bacterial cells under light and dark conditions

The probable underlying mechanism(s) of bacterial cell–TiO₂ nanoparticles (TiO₂ NPs) interaction in the absence of photo-irradiation has been less studied since most of the prior cytotoxicity studies focused on irradiated TiO₂. The present study draws attention to the possible role of cell surface–TiO₂ NP interactions under dark conditions, through an array of spectroscopic and microscopic investigations. A dominant freshwater bacterial isolate, Bacillus licheniformis, which interacted with environmentally relevant concentrations of TiO₂ NPs (1 μg/mL), was analysed and compared under both light and dark conditions. Aggregation of cells upon NP interaction and adsorption of NPs onto the cell membrane was evident from the scanning electron micrographs under both light and dark conditions. The FT–IR and FT–Raman spectra suggested stress response of bacterial cells by elevated protein and polysaccharide content in the cell–NP interaction. The Xray photoelectron spectroscopic data substantiated the reduction of titanium from Ti(IV) to Ti(III) species which might have contributed to the redox interactions on the cell surface under light as well as dark conditions. The internalization of NPs in the cytoplasm were obvious from the transmission electron micrographs. The consequent cell death/damage was confirmed through fluorescence spectroscopy and microscopy. To conclude, the current study established the substantial role of interfacial interactions in cytotoxicity of the TiO₂ NPs irrespective of the irradiation conditions.     

Hydrothermal growth of ZnO nanostructures

One-dimensional nanostructures exhibit interesting electronic and optical properties due to their low dimensionality leading to quantum confinement effects. ZnO has received lot of attention as a nanostructured material because of unique properties rendering it suitable for various applications. Amongst the different methods of synthesis of ZnO nanostructures, the hydrothermal method is attractive for its simplicity and environment friendly conditions. This review summarizes the conditions leading to the growth of different ZnO nanostructures using hydrothermal technique. Doping of ZnO nanostructures through hydrothermal method are also highlighted.     

Zinc stannate nanostructures: hydrothermal synthesis

Nanostructured binary semiconducting metal oxides have received much attention in the last decade owing to their unique properties rendering them suitable for a wide range of applications. In the quest to further improve the physical and chemical properties, an interest in ternary complex oxides has become noticeable in recent times. Zinc stannate or zinc tin oxide (ZTO) is a class of ternary oxides that are known for their stable properties under extreme conditions, higher electron mobility compared to its binary counterparts and other interesting optical properties. The material is thus ideal for applications from solar cells and sensors to photocatalysts. Among the different methods of synthesizing ZTO nanostructures, the hydrothermal method is an attractive green process that is carried out at low temperatures. In this review, we summarize the conditions leading to the growth of different ZTO nanostructures using the hydrothermal method and delve into a few of its applications reported in the literature.     

Photocatalytic paper using zinc oxide nanorods

Zinc oxide (ZnO) nanorods were grown on a paper support prepared from soft wood pulp. The photocatalytic activity of a sheet of paper with ZnO nanorods embedded in its porous matrix has been studied. ZnO nanorods were firmly attached to cellulose fibers and the photocatalytic paper samples were reused several times with nominal decrease in efficiency. Photodegradation of up to 93% was observed for methylene blue in the presence of paper filled with ZnO nanorods upon irradiation with visible light at 963 Wm^–2 for 120 min. Under similar conditions, photodegradation of approximately 35% was observed for methyl orange. Antibacterial tests revealed that the photocatalytic paper inhibits the growth of Escherichia coli under room lighting conditions.     

Electromagnetic band gap coupled tri-notched miniaturized ultra-wideband antenna loaded with slot and parasitic strip

An electromagnetic band gap (EBG) coupled miniaturized tri-notched printed ultra-wideband (UWB) monopole microstrip antenna having dimensions of 22 mm × 26 mm × 1.6 mm loaded with a slot in radiating patch and a parasitic strip in the ground plane has been presented. The proposed structure incorporates a square-shaped metallic radiating patch with a square EBG structure adjacent to the microstrip feed line, a U-shaped meandered slot over the radiating element, and a U-shaped parasitic resonator at the ground plane beneath the radiating element, to reject the C-band satellite downlink (3.7 to 4.2 GHz), WLAN frequency band (5.15 to 5.85 GHz), and X-band satellite downlink (7.25 to 7.75 GHz) frequency bands, respectively. The designed antenna operates in the frequency range from 3 to 11.1 GHz, with an impedance bandwidth of 8.1 GHz and a percentage bandwidth of 114%. Modification steps incorporating into the reference antenna to achieve the desired design objectives have been discussed, along with parametric studies. The proposed design has been simulated using Ansys HFSS, and measurement has been taken using standard measurement technique and compared with the simulated results.