COVID-19 pandemic: Insights into structure, function, and hACE2 receptor recognition by SARS-CoV-2.

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a newly emerging, highly transmissible, and pathogenic coronavirus in humans that has caused global public health emergencies and economic crises. To date, millions of infections and thousands of deaths have been reported worldwide, and the numbers continue to rise. Currently, there is no specific drug or vaccine against this deadly virus; therefore, there is a pressing need to understand the mechanism(s) through which this virus enters the host cell. Viral entry into the host cell is a multistep process in which SARS-CoV-2 utilizes the receptor-binding domain (RBD) of the spike (S) glycoprotein to recognize angiotensin-converting enzyme 2 (ACE2) receptors on the human cells; this initiates host-cell entry by promoting viral-host cell membrane fusion through large-scale conformational changes in the S protein. Receptor recognition and fusion are critical and essential steps of viral infections and are key determinants of the viral host range and cross-species transmission. In this review, we summarize the current knowledge on the origin and evolution of SARS-CoV-2 and the roles of key viral factors. We discuss the structure of RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 and its significance in drug discovery and explain the receptor recognition mechanisms of coronaviruses. Further, we provide a comparative analysis of the SARS-CoV and SARS-CoV-2 S proteins and their receptor-binding specificity and discuss the differences in their antigenicity based on biophysical and structural characteristics.

Spatial and seasonal variability in the water chemistry of Kabar Tal wetland (Ramsar site), Bihar, India: multivariate statistical techniques and GIS approach.

This study was performed to evaluate the spatial and temporal distribution of major ions in water samples of a newly designated Ramsar site, namely Kabar Tal (KT) wetland of Bihar. Samples were collected during summer, monsoon, and winter seasons. The analytical and GIS results show that concentration of electrical conductivity, chloride, and nitrate are higher in summer than monsoon and winter. However, the concentration of major cations such as sodium, potassium, calcium, and magnesium are higher in winter than monsoon and summer. In addition, major anions like sulphate and phosphate concentration is higher during monsoon than summer and winter. Multivariate statistical tool (discriminant analysis) results suggest that temperature, pH, electrical conductivity, sulphate, and potassium are the major parameters distinguishing the water quality in different seasons. The study confirms that seasonal variations are playing a major role in the hydrochemistry of KT wetland. Overall, this work outlines the approach towards proper conservation and utilization of wetlands and to assess the quality of surface water for determining its suitability for agricultural purposes. Overall, this work highlights the approach towards estimating the seasonal dynamics of chemical species in KT wetland and its suitability for irrigation purposes.

Siderophore-assisted cadmium hyperaccumulation in Bacillus subtilis.

Siderophores (Gk iron carriers) are low molecular weight secondary metabolites produced by bacteria, fungi, and plants that have strong binding affinity for iron. Owing to their iron-chelating ability, they are produced mainly when the organism faces iron scarcity. The present study empirically investigated the importance of applying hydroxamate siderophore extracted from Aspergillus nidulans to the cells of Bacillus subtilis for bioremediation of cadmium salt. This investigation deals with siderophore-mediated intracellular Cd accumulation by bacterial cells, growth estimation, biochemical assays like lipid peroxidation, total protein content, carbohydrate content, and iron content estimation. In silico docking and STRING analyses revealed specific interaction between Aspergillus siderophore and receptors present on B. subtilis. Estimation of intracellular Cd by atomic absorption spectroscopy showed more accumulation of Cd ions by B. subtilis in the presence of hydroxamate siderophore. This suggests a possibility of confiscating environmental Cd2+ by utilizing metal chelation property of siderophores and hence can lead to emerging bioremediation mechanisms for heavy metals. In silico studies support experimental investigation and suggest higher affinity of siderophore for Cd ions as compared with ferric ions.

Geochemical fractionation, bioavailability, and ascertaining ecological risk of phosphorus in surface and core sediments of mangroves, western coast of India.

Phosphorus (P), a crucial macronutrient, is essential in the maintenance of ecosystem productivity and the biogeochemical processes of other biogenic substances found in marine settings. The aim of the present study is to quantify the different geochemical fractions, bioavailability, and ecological risk of phosphorus in surface and core sediment of mangroves, Gulf of Kachchh (GoK). To better understand the P dynamics, sequential chemical extraction techniques were used to study sediment P pool distribution such as exchangeable P; Fe-bound P; authigenic P; detrital P; and organic P. The total sedimentary P ranged from 539.51 to 7217.24 mg/kg in pre-monsoon and 487.04 to 7180.26 mg/kg in post-monsoon, and was primarily composed of inorganic P. Authigenic P and Fe-bound P were the dominant fractions of P in surface and core sediments, exhibiting a significant long-term P reservoir. Sources such as riverine inputs, industrial and sewage discharge, aquaculture farms, and seaport operations all have an impact on the P dynamics in GoK. Furthermore, organic matter, pH, ORP, and diagenetic processes in sedimentary environment have influenced P retention and release. FeBD:Fe-P ratio indicates the presence of Fe matrices, having strong adsorption potential for P, with the availability of a surplus of Fe(III) (oxy)hydroxides serving as a significant P pool, governing the P dynamics. The P enrichment index (PEI) showed that sediments were highly impacted by anthropogenic P and could cause a high ecological risk. Bioavailable phosphorus (BAP) suggests the availability of an ample amount of bioavailable P fractions (average of 49.70% post-monsoon and 44.64% post-monsoon) in surface sediments. Sites 3, 13, 14, 20, 21, and 26 exhibited considerably higher BAP. Core 1 comprised significantly higher BAP (60.52%). Thus, sediments of GoK could act as a source of P to the overlying water if released from sediments.

Trace metal fractionation in the Pichavaram mangrove-estuarine sediments in southeast India after the tsunami of 2004.

The geochemistry of coastal sediments of southern India was altered after the tsunami in 2004. A five-step sequential extraction procedure was applied to assess the effects of tsunami on mobility and redistribution of selected elements (Cd, Cr, Cu, Fe, Mn, Ni, Pb, and Zn). Ten surface sediments and three cores were analyzed for different metal fractions (exchangeable, carbonate, reduced, oxidized, and residual). Total metal concentrations increased in mangrove sediments after the tsunami, but their spatial distribution did not show significant variation (except Mn). The sediments were mixed by the tsunami, and there was lack of variation in metal concentrations in different fractions with depth (except Pb and Mn). High concentrations of Pb and Zn occurred in the oxide fractions, whereas Cu, Cr, Cd, and Ni were high in the organic and sulfide-rich fractions. Metals in the residual fraction (lattice bound) had the highest concentration suggesting their non-availability and limited biological uptake in the system. Most of the metals (except Mn) do not constitute a risk based on the different geochemical indices.

Differential responses of hydrochemical factors and LULC changes on the spatial and temporal hydrogeochemistry of the eco-sensitive Baraila wetland, Bihar, India.

Freshwater scarcity, deterioration and associated water management remain to be one of the most challenging aspects of high-population density economies especially in subtropical/tropical regions. The present research deals with hydrogeochemical analysis of the eco-sensitive Baraila wetland and possible sources of anthropogenic pollution. The hydrochemical characterization was performed in GIS environment, considering meteorologically induced parameters and spatial variability. Temporal variations were assessed through different seasons, namely pre-monsoon, monsoon and post-monsoon with the help of multivariate statistics. The changes in water depth across the seasons showed significant hydrochemical variations in the vertical profile of the wetland apart from thermal demarcation. Seasonal variations in the hydrogeochemistry were induced by multiple physicochemical parameters, geochemical processes, geomorphology of the surrounding area and land use and land cover (LULC) changes. The pre-post flooding changes revealed that aquatic vegetation was increased by 15.36% whereas a major decrease in water bodies (- 73.2%) occurred. Dissolved oxygen (DO), pH, temperature and carbonates are fundamental towards establishing wetland's water chemistry. The water type is primarily of Ca-HCO3 type, mostly derived from rock-water interactions and cation exchange processes. Irrigational quality of water was assessed through multiple indices (sodium adsorption ratio (SAR), %Na, residual sodium carbonate (RSC), magnesium hazard (MH) and total hardness (TH)) and plots. The heavy aquatic vegetation abundance and eutrophication because of agricultural run-off is currently the major issue with the Baraila wetland and may be playing a simultaneous role in regulating the water chemistry to a large extent apart from other geochemical processes. The hydrogeochemical interactions between sediment and overlying water have created distinct effects on biota and land use/land cover changes. Their role in the landscape is prominent in this respect and may be utilized for environmental management, eco-tourism and employment boost. Serious lack of hydrogeochemical studies in this important floodplain wetland and its rapid deterioration deems it necessary to focus on the comprehensive research and wetland management options for its conservation and sustainable usage in future.

Metal speciation studies in the aquifer sediments of Semria Ojhapatti, Bhojpur District, Bihar.

The pollution of aquifer sediments by heavy metals has assumed serious concern due to their toxicity and accumulative behavior. Changes in environmental conditions can strongly influence the behavior of both essential and toxic elements by altering the forms in which they occur and therefore quantification of the different forms of metal is more meaningful than total metal concentrations. In this study, fractionation of metal ions in aquifer sediments of Semria Ojhapatti area, Bhojpur district, Bihar has been studied to determine the ecotoxic potential of metal ions. The investigations suggest that iron, copper, and arsenic have a tendency to remain associated in the following order residual > reducible > acid-soluble > oxidizable; manganese and zinc have tendency to be associated as residual > acid-soluble > reducible > oxidizable. The risk assessment code reveals that manganese and zinc occur in significant concentration in acid-soluble fraction and therefore comes under the high risk category and can easily enter the food chain. Most of the iron, copper, and arsenic occur as immobile fraction (i.e. residual) followed by its presence in reducible fraction and would pose threat to the water quality due to changing redox conditions. The metal enrichment factor in the study area shows moderate to significant metal enrichment in the aquifer sediments which may pose a real threat in near future. The geo-accumulation index of metals also shows that the metals lie in the range of strongly contaminated (for iron at shallow depths) to moderately contaminated to uncontaminated values.

Bioavailability and risk assessment of trace metals in sediments of a high-altitude eutrophic lake, Ooty, Tamil Nadu, India.

Ooty lake, in the southern part of India, has raised huge concern about the role of metals in a lake due to increasing anthropogenic activities. Present study is aimed at understanding fate of trace metals in a lake's sediment. Sixteen sediment samples collected from bottom of the lake at various locations during March 2017 were analysed for trace metals cobalt, chromium, copper, iron, lead, manganese, nickel and zinc. Fe and Mn dominate total metal concentration followed by Ni and Cr. A high concentration of Cr, Cu, Ni and Zn in residual fraction indicates weathering as the source for these metals. A significant concentration of metals in exchangeable, reducible and oxidisable fraction indicates adsorbtion/chelation of these metals with oxides and organic matter due to change in oxic state. Geo-accumulation index for metals show unpolluted to moderate nature of sediments at all sampling locations. Moderate to significant enrichment factor of Cr, Ni and Zn indicates influence of anthropogenic sources. Co, Pb and Zn show a high amount of bioavailability for aquatic life. Other metals (Cr, Ni, Fe and Mn) show scarce to moderate bioavailability. On the other hand, a global contamination factor denotes moderate to high metal contamination of sediments in the entire lake. Statistical analysis of metals shows good inter-element correlation among metals Fe, Cr, Ni, Co, Cu and Zn indicating natural source. Influence of domestic sewage and recreational activities as the main/additional source is revealed by negative loading of Pb and Zn in principal component analysis. The present study, in essence, has identified rock weathering, as a major source of trace meals in the sediments of Ooty lake entering through stream and surface runoff from an adjacent forest area. The study has also identified high bioavailability of Pb and Zn, which is derived through the recreational activities (boating) causing permanent adverse impact.

Assessment of trace metal contamination in the core sediment of Ramsar wetland (Kabar Tal), Begusarai, Bihar (India).

The concentration of trace metals Mn, Pb, Ni, Zn, and Cu in the core sediment from Kabar Tal wetland was analyzed to understand the level of contamination in the vertical profile. Additionally, total organic carbon (TOC) and available phosphorus (AP) were also analyzed to infer the biogeochemistry of trace metals and the correlation that exists among them. Five core sediments were collected at the end of the monsoon season from different locations in the study area, representing diverse anthropogenic and agricultural activities. The average concentration of trace metals in sediments followed the order Mn > Pb > Ni > Zn > Cu. The trace metal concentration in the surface sediments was higher and decreased with depth in the vertical profile. Contamination factor (CF), geoaccumulation index (Igeo), enrichment factor (EF), and pollution load index (PLI) were used to evaluate sediment quality and the pollution status of the lake sediments. Cu, Zn, and Ni showed minor to moderate enrichment, and Pb showed a severe level of enrichment in all the core sediment samples. However, the sediment quality guidelines' index indicates that the sediments are moderately polluted with copper, zinc, and nickel and severely polluted with lead. There exists a strong positive correlation among Pb-Ni, Ni-AP, and AP-Pb, and a strong negative correlation among TOC-Ni, TOC-Pb, and TOC-AP for all the sediment samples. Additionally, the principal component analysis (PCA) and cluster analysis (CA) suggest that a good similarity exists among Pb, Ni, and Zn. The study indicates that trace metals in wetland sediments have originated from multiple anthropogenic sources like agricultural runoff (fertilizers), direct addition of solid wastes, discharge of untreated wastewater, and long-range transport from the oil refinery in the wetland.

Possible bioremediation of arsenic toxicity by isolating indigenous bacteria from the middle Gangetic plain of Bihar, India.

In middle Gangetic plain, high arsenic concentration is present in water, which causes a significant health risk. Total 48 morphologically distinct arsenite resistant bacteria were isolated from middle Gangetic plain. The minimum inhibitory concentration (MIC) values of arsenite varied widely in the range 1-15 mM of the isolates. On the basis of their MIC, two isolates, AK1 (KY569423) and AK9 (KY569424) were selected. The analysis of the 16S rRNA gene sequence of selected isolates revealed that they are belong to the genus Pseudomonas. The AgNO3 test based microplate method revealed that isolates, AK1 and AK9, have potential in transformation of arsenic species. Further, the presence of aoxR, aoxB and aoxC genes in the both isolated strain AK1 and AK9 was confirmed, which play an important role in arsenic bioremediation by arsenite oxidation. Isolated strains also showed heavy metal resistance against Cr(IV), Ni(II), Co(II), Pb(II), Cu(II), Hg(II), Ag(I) and Cd(II).

Assessment of metal enrichments in tsunamigenic sediments of Pichavaram mangroves, southeast coast of India.

The 26 December 2004-Tsunami has deposited sediments in the Pichavaram mangrove ecosystem, east coast of India. Ten surface and three core sediment samples were collected within thirty days of the event. High concentrations of Cd, Cu, Cr, Pb, and Ni were observed in the tsunamigenic sediments. With respect to Fe, Zn, and Mn, there was little variation as compared to pre-tsunami values. The geo-accumulation index was calculated in order to assess the contamination of heavy metals in the sediments. The sediments were extremely contaminated with respect to Cd and they showed moderate to strong contamination with respect to Cr, Pb and Ni. The study highlighted the future risk of enhanced metal pollution in near future in this mangrove ecosystem.