SARS-CoV-2 nucleocapsid and Nsp3 binding: an in silico study

Archives of Microbiology - Severe acute respiratory syndrome virus 2 (SARS-CoV-2) belongs to the single-stranded positive-sense RNA family. The virus contains a large genome that encodes four...     

In silico studies of urease inhibitors to explore ligand-enzyme interactions

In continuation of our previous study on the urease inhibition by a number of chalcones, 2,3-dihydro-1,5-benzothiazepines and 2,3,4,5-tetrahydro-1,5-benzothiazepines, FlexX docking has been exploited to get a deeper insight into the mechanism of their inhibitory action. A comparison of the IC₅₀ values of the active compounds reveals that, of the three classes of compounds studied, 2,3-dihydro-1,5-benzothiazepines were the most potent urease inhibitors. An in silico examination of these compounds showed that the activity is related to the interaction of ligand with the nickel metallocentre, its interaction with two amino acid residues, Asp224 and Cys322, in addition to the orientation of rings A and B in the catalytic core of the enzyme. The most active compound 2,3-dihydro-1,5-benzothiazepine (4) anchor tightly through a network of interactions with Ni701 and Ni702. This includes a number of hydrogen bonds and hydrophobic contacts with the amino acid residues in its vicinity. For their reduced analogs, the difference in the activity of different diastereomers has been observed to be configuration-dependent. This may be ascribed mainly to the difference in the orientation of ring B of the two stereoisomers and the extent of their interaction with Asp224 and Cys322 present in the catalytic core of the enzyme.     

Isolation of Clostridium perfringens Type B in an Individual at First Clinical Presentation of Multiple Sclerosis Provides Clues for Environmental Triggers of the Disease

We have isolated Clostridium perfringens type B, an epsilon toxin-secreting bacillus, from a young woman at clinical presentation of Multiple Sclerosis (MS) with actively enhancing lesions on brain MRI. This finding represents the first time that C. perfringens type B has been detected in a human. Epsilon toxin’s tropism for the blood-brain barrier (BBB) and binding to oligodendrocytes/myelin makes it a provocative candidate for nascent lesion formation in MS. We examined a well-characterized population of MS patients and healthy controls for carriage of C. perfringens toxinotypes in the gastrointestinal tract. The human commensal Clostridium perfringens type A was present in approximately 50% of healthy human controls compared to only 23% in MS patients. We examined sera and CSF obtained from two tissue banks and found that immunoreactivity to ETX is 10 times more prevalent in people with MS than in healthy controls, indicating prior exposure to ETX in the MS population. C. perfringens epsilon toxin fits mechanistically with nascent MS lesion formation since these lesions are characterized by BBB permeability and oligodendrocyte cell death in the absence of an adaptive immune infiltrate.     

Urinary and Dietary Analysis of 18,470 Bangladeshis Reveal a Correlation of Rice Consumption with Arsenic Exposure and Toxicity

Background

We utilized data from the Health Effects of Arsenic Longitudinal Study (HEALS) in Araihazar, Bangladesh, to evaluate the association of steamed rice consumption with urinary total arsenic concentration and arsenical skin lesions in the overall study cohort (N=18,470) and in a subset with available urinary arsenic metabolite data (N=4,517).

Methods

General linear models with standardized beta coefficients were used to estimate associations between steamed rice consumption and urinary total arsenic concentration and urinary arsenic metabolites. Logistic regression models were used to estimate prevalence odds ratios (ORs) and their 95% confidence intervals (CIs) for the associations between rice intake and prevalent skin lesions at baseline. Discrete time hazard models were used to estimate discrete time (HRs) ratios and their 95% CIs for the associations between rice intake and incident skin lesions.

Results

Steamed rice consumption was positively associated with creatinine-adjusted urinary total arsenic (β=0.041, 95% CI: 0.032-0.051) and urinary total arsenic with statistical adjustment for creatinine in the model (β=0.043, 95% CI: 0.032-0.053). Additionally, we observed a significant trend in skin lesion prevalence (P-trend=0.007) and a moderate trend in skin lesion incidence (P-trend=0.07) associated with increased intake of steamed rice.

Conclusions

This study suggests that rice intake may be a source of arsenic exposure beyond drinking water.     

A Lightweight Radio Propagation Model for Vehicular Communication in Road Tunnels

Radio propagation models (RPMs) are generally employed in Vehicular Ad Hoc Networks (VANETs) to predict path loss in multiple operating environments (e.g. modern road infrastructure such as flyovers, underpasses and road tunnels). For example, different RPMs have been developed to predict propagation behaviour in road tunnels. However, most existing RPMs for road tunnels are computationally complex and are based on field measurements in frequency band not suitable for VANET deployment. Furthermore, in tunnel applications, consequences of moving radio obstacles, such as large buses and delivery trucks, are generally not considered in existing RPMs. This paper proposes a computationally inexpensive RPM with minimal set of parameters to predict path loss in an acceptable range for road tunnels. The proposed RPM utilizes geometric properties of the tunnel, such as height and width along with the distance between sender and receiver, to predict the path loss. The proposed RPM also considers the additional attenuation caused by the moving radio obstacles in road tunnels, while requiring a negligible overhead in terms of computational complexity. To demonstrate the utility of our proposed RPM, we conduct a comparative summary and evaluate its performance. Specifically, an extensive data gathering campaign is carried out in order to evaluate the proposed RPM. The field measurements use the 5 GHz frequency band, which is suitable for vehicular communication. The results demonstrate that a close match exists between the predicted values and measured values of path loss. In particular, an average accuracy of 94% is found with R² = 0.86.     

Copper Oxide Nanomaterials Derived from Zanthoxylum armatum DC. and Berberis lycium Royle Plant Species: Characterization,Assessment of Free Radical Scavenging and Antibacterial Activity

Copper oxide nanomaterials were synthesized by a facile sustainable biological method using two plant species (Zanthoxylum armatum DC. and Berberis lycium Royle ). The formation of materials was confirmed by FT‐IR, ATR, UV‐visible, XRD, TEM, SEM, EDX, TGA and PL. The antibacterial activity was evaluated by agar well diffusion method to ascertain the efficacy of plant species extract and extract derived copper oxide nanomaterials against six Gram‐positive bacteria namely Staphylococcus aureus, Streptococcus mutans, Streptococcus pyogenes, Corynebacterium diphtheriae, Corynebacterium xerosis, Bacillus cereus and four Gram‐negative bacteria such as Klebsiella pneumonia, Escherichia coli, Pseudomonas aeruginosa and Proteus vulgaris against the standard drug, Ciprofloxacin for Gram‐positive and Gentamicin for Gram‐negative bacteria, respectively. In both cases, copper oxide nanomaterials were found to be sensitive in all the bacterial species. Sensitivity of copper oxide nanomaterials shows an be higher as compared to plant species extract against different bacteria. Scavenging activity of plant extracts along with nanomaterials have been accessed using previously reported protocols employing ascorbic acid as standard. Scavenging activity of copper oxide nanomaterials shows an increase with increase in concentration. The biological activity (bactericidal and scavenging efficiency) of plant derived copper oxide nanomaterials revealed that these materials can be used as potent antimicrobial agent and DPPH scavengers in industrial as well as pharmacological fields.     

Phytoremediation of landfill leachate waste contaminants through floating bed technique using water hyacinth and water lettuce

Abstract

In the present study, the effectiveness of water hyacinth and water lettuce was tested for the phytoremediation of landfill leachate for the period of 15?days. Fifteen plastic containers were used in experimental setup where aquatic plants were fitted as a floating bed with the help of thermo-pole sheet. It was observed that both plants significantly (p?<?0.05/p?<?0.01/p?<?0.001) reduce the physicochemical parameters pH, TDS, BOD, COD and heavy metals like Zn, Pb, Fe, Cu and Ni from landfill leachate. Maximum reduction in these parameters was obtained at 50% and 75% landfill leachate treatment and their removal rate gradually increased from day 3 to day 15 of the experiment. The maximum removal rate for heavy metals such as for Zn (80–90%), Fe (83–87%) and Pb (76–84%) was attained by Eichhornia crassipes and Pistia stratiotes. Value of bioconcentration and translocation factor was less than 1 which indicates the low transport of heavy metals from roots to the above-ground parts of the plants. Both these plants accumulate heavy metals inside their body without showing much reduction in growth and showing tolerance to all the present metals. Therefore, results obtained from the study suggest that these aquatic plants are suitable candidate for the removal of pollution load from landfill leachate.     

Assessment of grain quality in terms of functional group response to elevated [CO2], water,and nitrogen using a meta‐analysis: Grain protein,zinc, and iron under future climate

The increasing [CO₂] in the atmosphere increases crop productivity. However, grain quality of cereals and pulses are substantially decreased and consequently compromise human health. Meta‐analysis techniques were employed to investigate the effect of elevated [CO₂] (e[CO₂]) on protein, zinc (Zn), and iron (Fe) concentrations of major food crops (542 experimental observations from 135 studies) including wheat, rice, soybean, field peas, and corn considering different levels of water and nitrogen (N). Each crop, except soybean, had decreased protein, Zn, and Fe concentrations when grown at e[CO₂] concentration (≥550 μmol/mol) compared to ambient [CO₂] (a[CO₂]) concentration (≤380 μmol/mol). Grain protein, Zn, and Fe concentrations were reduced under e[CO₂]; however, the responses of protein, Zn, and Fe concentrations to e[CO₂] were modified by water stress and N. There was an increase in Fe concentration in soybean under medium N and wet conditions but nonsignificant. The reductions in protein concentrations for wheat and rice were ~5%–10%, and the reductions in Zn and Fe concentrations were ~3%–12%. For soybean, there was a small and nonsignificant increase of 0.37% in its protein concentration under medium N and dry water, while Zn and Fe concentrations were reduced by ~2%–5%. The protein concentration of field peas decreased by 1.7%, and the reductions in Zn and Fe concentrations were ~4%–10%. The reductions in protein, Zn, and Fe concentrations of corn were ~5%–10%. Bias in the dataset was assessed using a regression test and rank correlation. The analysis indicated that there are medium levels of bias within published meta‐analysis studies of crops responses to free‐air [CO₂] enrichment (FACE). However, the integration of the influence of reporting bias did not affect the significance or the direction of the [CO₂] effects.     

An approach to identify cold-induced low-abundant proteins in rice leaf

A proteomic approach has been adopted to investigate the low-abundant proteins in rice leaf in response to cold stress. Rice seedlings were exposed to different temperatures, such as 5 or 10 degrees C, and samples were collected after different time course. To eliminate the high-abundant proteins in leaf tissues such as ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), proteins were fractionated by polyethylene glycol (PEG). The elimination of Rubisco from the protein samples was confirmed by Western blot analysis. The PEG fractionated protein samples were separated by 2-DE and visualized by silver or CBB staining. A total 12 up-regulated protein spots were identified using the analysis of MALDI-TOF mass spectrometry or ESI MS/MS. We identified some novel proteins such as cysteine proteinase, thioredoxin peroxidase, a RING zinc finger protein-like, drought-inducible late embryogenesis abundant, and a fibrillin-like protein that had not yet been reported in the earlier reports on cold proteomic analysis. The identification of some novel low-abundant proteins in response to cold stress may provide a new homeostasis to develop enhanced cold tolerance transgenic plants. Thus, we propose that a PEG fractionation system can be used as an influential protein extraction method from the leaf samples, which can lead to knowledge of the expression pattern of low-abundant proteins in response to various biotic or abiotic stresses.     

Ultrasound promoted green synthesis,anticancer evaluation,and molecular docking studies of hydrazines: a pilot trial

We reported herein an efficient, environmentally friendly synthesis of hydrazine carboxamides (6a–l) in a water-glycerol (6:4) solvent system using ultrasonic irradiation. Ultrasonicated reactions were found to be much faster and more productive than conventional synthesis. The prepared compounds (6a–l) were tested against nine panels of 60 cancer cell lines according to the National Cancer Institute (NCI US) protocol. N-(4-Chlorophenyl)-2-(2-oxoindolin-3-ylidene)hydrazine-1-carboxamide (6b) was discovered to be promising anticancer agents with higher sensitivity against CCRF-CEM, HOP-92, UO-31, RMPI-8226, HL-60(TB), and MDA-MB-468 with percent growth inhibitions (%GIs) of 143.44, 33.46, 33.21, 33.09, 29.81, and 29.55 respectively. Compounds (6a–l) tested showed greater anticancer activity than Imatinib, except for compound 6k. Compounds 6b and 6c were found to be lethal on the CCRF-CEM leukaemia cell line, with %GIs of 143.44 and 108.91, respectively. Furthermore, molecular docking analysis was performed to investigate ligand binding affinity at the active site of epidermal growth factor (EGFR).