Spatio-temporal diversity of biological aerosols over Northeast India: a metagenomic approach

Northeast India is considered as one of the major biodiversity hotspots in the world, but the region is underexplored for their microbial biodiversity. Extensive characterization of biological aerosol (bioaerosol) samples collected from various locations of Northeast India was carried out for all four seasons in a year. These were characterized in terms of their constituents, such as pollens, fungal spores, animal debris, and non-biological components, and particulate matters, such as inhalable, thoracic, and alveolic, and finally, the bacterial diversity was determined by DNA-based metagenomic approach. The non-biological (non-viable) component of aerosols is found to vary from 30 to 89% in the pre-monsoon season, which coexists with pollens (4-20%), animal debris (1-24%), and fungal spores (1-17%). The highest number of culturable microbial populations in terms of CFU count was observed in the pre-monsoon samples (i.e., 125.24-632.45 CFU/m³), and the lowest CFU was observed in monsoon season (i.e., 20.83-319.0 CFU/m³). The metagenomic approach with the samples collected during pre-monsoon season showed a total of bacterial 184 OTUs (operational taxonomic units) with 28,028 abundance count comprising 7 major phylum, 6 classes, 10 orders, 15 families, 13 genus, and 8 species of bacteria. The species-level distribution clearly shows the presence of Gammaproteobacteria (52%) most abundantly, followed by Bacilli (21%), Alphaproteobacteria (14%), Betaproteobacteria (5%), Flavobacteria (5%), and Sphingobacteria (3%). It is the first report from the entire Northeast India to uncover spatio-temporal distribution of biological components and bacterial diversity in aerosol samples through a DNA-based metagenomic approach.

Accumulating Impact of Smoking and Co-morbidities on Severity and Mortality of COVID-19 Infection: A Systematic Review and Meta-analysis

Background

High prevalence, severity, and formidable morbidity have marked the recent emergence of the novel coronavirus disease (COVID-19) pandemic. The significant association with the pre-existing co-morbid conditions has increased the disease burden of this global health emergency, pushing the patients, healthcare workers and facilities to the verge of complete disruption.

Methods

Meta-analysis of pooled data was undertaken to assess the cumulative risk assessment of multiple co-morbid conditions associated with severe COVID-19. PubMed, Scopus, and Google Scholar were searched from January 1^st to June 27^th 2020 to generate a well-ordered, analytical, and critical review. The exercise began with keying in requisite keywords, followed by inclusion and exclusion criteria, data extraction, and quality evaluation. The final statistical meta-analysis of the risk factors of critical/severe and non-critical COVID-19 infection was carried out on Microsoft Excel (Ver. 2013), MedCalc (Ver.19.3), and RevMan software (Ver.5.3).

Results

We investigated 19 eligible studies, comprising 12037 COVID-19 disease patients, representing the People’s Republic of China (PRC), USA, and Europe. 18.2% (n = 2200) of total patients had critical/severe COVID-19 disease. The pooled analysis showed a significant association of COVID-19 disease severity risk with cardiovascular disease (RR: 3.11, p < 0.001), followed by diabetes (RR: 2.06, p < 0.001), hypertension (RR: 1.54, p < 0.001), and smoking (RR: 1.52, p < 006).

Conclusion

The review involved a sample size of 12037 COVID-19 patients across a wide geographical distribution. The reviewed reports have focussed on the association of individual risk assessment of co-morbid conditions with the heightened risk of COVID-19 disease. The present meta-analysis of cumulative risk assessment of co-morbidity from cardiovascular disease, diabetes, hypertension, and smoking signals a novel interpretation of inherent risk factors exacerbating COVID-19 disease severity. Consequently, there exists a definite window of opportunity for increasing survival of COVID-19 patients (with high risk and co-morbid conditions) by timely identification and implementation of appropriately suitable treatment modalities.

Therapeutic Potential of Curcumin as an Antimycobacterial Agent

Curcumin is the principal curcuminoid obtained from the plant Curcuma longa and has been extensively studied for its biological and chemical properties. Curcumin displays a vast range of pharmacological properties, including antimicrobial, anti-inflammatory, antioxidant, and antitumor activity. Specifically, curcumin has been linked to the improvement of the outcome of tuberculosis. There are many reviews on the pharmacological effects of curcumin; however, reviews of the antitubercular activity are comparatively scarcer. In this review, we attempt to discuss the different aspects of the research on the antitubercular activity of curcumin. These include antimycobacterial activity, modulation of the host immune response, and enhancement of BCG vaccine efficacy. Recent advances in the antimycobacterial activity of curcumin synthetic derivatives, the role of computer aided drug design in identifying curcumin targets, the hepatoprotective role of curcumin, and the dosage and toxicology of curcumin will be discussed. While growing evidence supports the use of curcumin and its derivatives for tuberculosis therapy, further preclinical and clinical investigations are of pivotal importance before recommending the use of curcumin formulations in public health.

Exploring rotavirus proteome to identify potential B- and T-cell epitope using computational immunoinformatics

Rotavirus is the most common cause of acute gastroenteritis in infants and children worldwide. The functional correlation of B- and T-cells to long-lasting immunity against rotavirus infection in the literature is limited. In this work, a series of computational immuno-informatics approaches were applied and identified 28 linear B-cells, 26 conformational B-cell, 44 T_C cell and 40 T_H cell binding epitopes for structural and non-structural proteins of rotavirus. Further selection of putative B and T cell epitopes in the multi-epitope vaccine construct was carried out based on immunogenicity, conservancy, allergenicity and the helical content of predicted epitopes. An in-silico vaccine constructs was developed using an N-terminal adjuvant (RGD motif) followed by T_C and T_H cell epitopes and B-cell epitope with an appropriate linker. Multi-threading models of multi-epitope vaccine construct with B- and T-cell epitopes were generated and molecular dynamics simulation was performed to determine the stability of designed vaccine. Codon optimized multi-epitope vaccine antigens was expressed and affinity purified using the E. coli expression system. Further the T cell epitope presentation assay using the recombinant multi-epitope constructs and the T cell epitope predicted and identified in this study have not been investigated. Multi-epitope vaccine construct encompassing predicted B- and T-cell epitopes may help to generate long-term immune responses against rotavirus. The computational findings reported in this study may provide information in developing epitope-based vaccine and diagnostic assay for rotavirus-led diarrhea in children's.

Essential role of the ESX-3 associated eccD3 locus in maintaining the cell wall integrity of Mycobacterium smegmatis

Mycobacterial pathogens have evolved a unique secretory apparatus called the Type VII secretion system (T7SS) which comprises of five gene clusters designated as ESX1, ESX2, ESX3, ESX4, and ESX5. Of these the ESX3 T7SS plays an important role in the regulatory uptake of iron from the environment, thereby enabling the bacteria to establish successful infection in the host. However, ESX3 secretion system is conserved among all the mycobacterial species including the fast-growing nonpathogenic species M. smegmatis. Although the function of ESX3 T7SS is known to be absolutely critical for establishing infection by M. tuberculosis, its conserved nature in all the pathogenic and nonpathogenic mycobacterial species intrigues to explore the additional functional roles in Mycobacterium species through which potent targets for drugs can be identified and developed. In the present study, we investigated the possible role of EccD3, a transmembrane protein of the ESX3 T7SS in M. smegmatis by deleting the entire eccD3 gene by efficient allelic exchange method. The preliminary investigations through the creation of knockout mutant of the eccD3 gene indicate that this secretory apparatus has an important role in maintaining the cell wall integrity which was evident from the abnormal colony morphology, lack of biofilm formation and difference in cell wall permeability.

Anti-Proliferative Activities of Vasicinone on Lung Carcinoma Cells Mediated via Activation of Both Mitochondria-Dependent and Independent Pathways

Vasicinone, a quinazoline alkaloid from Adhatoda vasica Nees. is well known for its bronchodilator activity. However its antiproliferative activities is yet to be elucidated. Here-in we investigated the anti-proliferative effect of vasicinone and its underlying mechanism against A549 lung carcinoma cells. The A549 cells upon treatment with various doses of vasicinone (10, 30, 50, 70 µM) for 72 h showed significant decrease in cell viability. Vasicinone treatment also showed DNA fragmentation, LDH leakage, and disruption of mitochondrial potential, and lower wound healing ability in A549 cells. The Annexin V/PI staining showed disrupted plasma membrane integrity and permeability of PI in treated cells. Moreover vasicinone treatment also lead to down regulation of Bcl-2, Fas death receptor and up regulation of PARP, BAD and cytochrome c, suggesting the anti-proliferative nature of vasicinone which mediated apoptosis through both Fas death receptors as well as Bcl-2 regulated signaling. Furthermore, our preliminary studies with vasicinone treatment also showed to lower the ROS levels in A549 cells and have potential free radical scavenging (DPPH, Hydroxyl) activity and ferric reducing power in cell free systems. Thus combining all, vasicinone may be used to develop a new therapeutic agent against oxidative stress induced lung cancer.

Vermicompost and farmyard manure improves food quality, antioxidant and antibacterial potential of Cajanus cajan (L. Mill sp.) leaves

BACKGROUND

Pigeon pea (Cajanus cajan) leaves are a good source of nutrition and health benefitting phenolic compounds. However, its importance has not yet been effectively addressed. Recently, a 2-year field experiment was attempted in an alluvial soil to understand the role of various organic and inorganic fertilisers and their combinations not only on soil quality, but also on production of foremost phenolic compounds and imparting antioxidant and antibacterial properties in C. cajan under vermicompost treatments.

RESULTS

Notable enhancements in crude protein, soluble carbohydrate, ash content and total flavonoid content were recorded in Cajanus leaves under vermicompost treatments. We detected a significant rise in carlinoside content in C. cajan leaves, which is known to reduce bilirubin concentration in hepatitis affected human blood. Farmyard manure treatments resulted in a high crude fibre content coupled with a substantially high concentration of total phenols, and chlorophyll. In addition, incorporation of vermicompost with or without inorganic fertiliser in the soil had a significant impact on antioxidant and antibacterial properties of C. cajan leaves. Above and beyond, farmyard manure and vermicompost positively influenced the physico-chemical health of the soil.

CONCLUSION

The present nutrient management scheme based on organic input not only induced a higher yield of C. cajan endowed with improved antioxidant and antibacterial properties, but also enhanced the production of various phenolic compounds. © 2016 Society of Chemical Industry.

3D pharmacophore-based virtual screening, docking and density functional theory approach towards the discovery of novel human epidermal growth factor receptor-2 (HER2) inhibitors

Human epidermal growth factor receptor 2 (HER2) is one of the four members of the epidermal growth factor receptor (EGFR) family and is expressed to facilitate cellular proliferation across various tissue types. Therapies targeting HER2, which is a transmembrane glycoprotein with tyrosine kinase activity, offer promising prospects especially in breast and gastric/gastroesophageal cancer patients. Persistence of both primary and acquired resistance to various routine drugs/antibodies is a disappointing outcome in the treatment of many HER2 positive cancer patients and is a challenge that requires formulation of new and improved strategies to overcome the same. Identification of novel HER2 inhibitors with improved therapeutics index was performed with a highly correlating (r=0.975) ligand-based pharmacophore model (Hypo1) in this study. Hypo1 was generated from a training set of 22 compounds with HER2 inhibitory activity and this well-validated hypothesis was subsequently used as a 3D query to screen compounds in a total of four databases of which two were natural product databases. Further, these compounds were analyzed for compliance with Veber's drug-likeness rule and optimum ADMET parameters. The selected compounds were then subjected to molecular docking and Density Functional Theory (DFT) analysis to discern their molecular interactions at the active site of HER2. The findings thus presented would be an important starting point towards the development of novel HER2 inhibitors using well-validated computational techniques.

Synthesis of curcumin-loaded chitosan phosphate nanoparticle and study of its cytotoxicity and antimicrobial activity

Curcumin has acquired an important position in the treatment of various diseases. But its use, as a chemotherapeutic agent, is limited due to its low water solubility, poor bioavailability, and its sensitive nature at the physiological pH. To overcome this, curcumin was loaded into chitosan phosphate nanoparticles (CPNs). The loading efficiency was found to be 84%. DLS studies revealed the average particle size of CPNs and curcumin-loaded CPNs as 53 and 91 nm, respectively, and TEM results supplemented these values. A sustained release pattern was noticed and the amount of curcumin released in acidic pH was higher than at physiological pH. The curcumin nanoformulation exhibited proficient activity against both Gram-positive and Gram-negative bacteria as well as fungus. Cytocompatibility of the nanoformulations against peripheral blood mononuclear cells (PBMCs) and murine monocyte-macrophage cell line was confirmed by incubating with PBMCs and murine monocyte-macrophage cell line.

Discrepancy among the synonymous codons with respect to their selection as optimal codon in bacteria

The different triplets encoding the same amino acid, termed as synonymous codons, are not equally abundant in a genome. Factors such as G + C% and tRNA are known to influence their abundance in a genome. However, the order of the nucleotide in each codon per se might also be another factor impacting on its abundance values. Of the synonymous codons for specific amino acids, some are preferentially used in the high expression genes that are referred to as the 'optimal codons' (OCs). In this study, we compared OCs of the 18 amino acids in 221 species of bacteria. It is observed that there is amino acid specific influence for the selection of OCs. There is also influence of phylogeny in the choice of OCs for some amino acids such as Glu, Gln, Lys and Leu. The phenomenon of codon bias is also supported by the comparative studies of the abundance values of the synonymous codons with same G + C. It is likely that the order of the nucleotides in the triplet codon is also perhaps involved in the phenomenon of codon usage bias in organisms.

Ectopic expression of amaranth seed storage albumin modulates photoassimilate transport and nutrient acquisition in sweetpotato

Storage proteins in plants, because of high nutrient value, have been a subject of intensive investigation. These proteins are synthesized de novo in the cytoplasm and transported to the storage organelles where they serve as reservoir of energy and supplement of nitrogen during rapid growth and development. Sweetpotato is the seventh most important food crop worldwide, and has a significant contribution to the source of nutrition, albeit with low protein content. To determine the behaviour of seed storage proteins in non-native system, a seed albumin, AmA1, was overexpressed in sweetpotato with an additional aim of improving nutritional quality of tuber proteins. Introduction of AmA1 imparted an increase in protein and amino acid contents as well as the phytophenols. The proteometabolomics analysis revealed a rebalancing of the proteome, with no significant effects on the global metabolome profile of the transgenic tubers. Additionally, the slower degradation of starch and cellulose in transgenic tubers, led to increased post-harvest durability. Present study provides a new insight into the role of a seed storage protein in the modulation of photoassimilate movement and nutrient acquisition.

Cigarette smoke compounds induce cellular redox imbalance, activate NF-κB, and increase TNF-α/CRP secretion: a possible pathway in the pathogenesis of COPD

Cigarette smoke has always been considered as a risk factor for chronic obstructive pulmonary diseases (COPD). In this study, we have examined the effect of ten individual cigarette smoke compounds (nicotine, benzo[a]pyrene, naphthalene, formaldehyde, ammonia, acrylic acid, toluene, benzene, m-xylene, and hexamine) on glutathione S transferase (GST) activity, an important Phase II metabolic enzyme and their possible role in inflammatory pathophysiology leading to COPD. Lower Glutathione (GSH) levels and GST activity and higher CRP, TNF-α, and IL-6 levels were observed in COPD patients compared to age and gender-matched controls. Using human recombinant GST and plasma as well as erythrocytes collected from normal subjects this study demonstrates that out of the ten compounds, nicotine (5 mg mL^-1), benzo[a]pyrene (10 ng mL^-1), naphthalene (250 μg mL^-1), and formaldehyde (5 pg mL^-1) caused a significant decrease in recombinant, plasma, and erythrocyte GST activity. Further cell culture studies show that exposure to nicotine, benzo[a]pyrene, naphthalene, and formaldehyde caused a significant decrease in GSH levels and GST activity and its protein expression and an increase in intracellular ROS production in THP-1 monocytes. Interestingly, treatment with benzo[a]pyrene and naphthalene significantly up regulated the phosphorylation of the p65 subunit of NF-κB and increased the secretion of TNF-α and CRP compared to control. This study suggests the potential role of benzo[a]pyrene and naphthalene in the activation of the inflammatory signaling pathway leading to cigarette smoke-induced COPD.

Synthesis and characterization of SiO2/polyaniline/Ag core–shell particles and studies of their electrical and hemolytic properties: multifunctional core–shell particles

Three layers of conducting core–shell nanocomposite particles composed of SiO₂/polyaniline (PAni)/Ag were prepared in the presence of silicon dioxide (SiO₂) in an aqueous solution containing sodium dodecyl benzenesulfonate (SDBS) as a surfactant.

Comparative analysis of phytochemicals and nutrient availability in two contrasting cultivars of sweet potato (Ipomoea batatas L.)

Sweet potato ranks as the world's seventh most important food crop, and has major contribution to energy and phytochemical source of nutrition. To unravel the molecular basis for differential nutrient availability, and to exploit the natural genetic variation(s) of sweet potato, a series of physiochemical and proteomics experiment was conducted using two contrasting cultivars, an orange-fleshed sweet potato (OFSP) and a white-fleshed sweet potato (WFSP). Phytochemical screening revealed high percentage of carbohydrate, reducing sugar and phenolics in WFSP, whereas OFSP showed increased levels of total protein, flavonoids, anthocyanins, and carotenoids. The rate of starch and cellulose degradation was found to be less in OFSP during storage, indicating tight regulation of gene(s) responsible for starch-degradation. Comparative proteomics displayed a cultivar-dependent expression of proteins along with evolutionarily conserved proteins. These results suggest that cultivar-specific expression of proteins and/or their interacting partners might play a crucial role for nutrient acquisition in sweet potato.

Constraint on di-nucleotides by codon usage bias in bacterial genomes

It has been reported earlier that the relative di-nucleotide frequency (RDF) in different parts of a genome is similar while the frequency is variable among different genomes. So RDF is termed as genome signature in bacteria. It is not known if the constancy in RDF is governed by genome wide mutational bias or by selection. Here we did comparative analysis of RDF between the inter-genic and the coding sequences in seventeen bacterial genomes, whose gene expression data was available. The constraint on di-nucleotides was found to be higher in the coding sequences than that in the inter-genic regions and the constraint at the 2nd codon position was more than that in the 3rd position within a genome. Further analysis revealed that the constraint on di-nucleotides at the 2nd codon position is greater in the high expression genes (HEG) than that in the whole genomes as well as in the low expression genes (LEG). We analyzed RDF at the 2nd and the 3rd codon positions in simulated coding sequences that were computationally generated by keeping the codon usage bias (CUB) according to genome G+C composition and the sequence of amino acids unaltered. In the simulated coding sequences, the constraint observed was significantly low and no significant difference was observed between the HEG and the LEG in terms of di-nucleotide constraint. This indicated that the greater constraint on di-nucleotides in the HEG was due to the stronger selection on CUB in these genes in comparison to the LEG within a genome. Further, we did comparative analyses of the RDF in the HEG rpoB and rpoC of 199 bacteria, which revealed a common pattern of constraints on di-nucleotides at the 2nd codon position across these bacteria. To validate the role of CUB on di-nucleotide constraint, we analyzed RDF at the 2nd and the 3rd codon positions in simulated rpoB/rpoC sequences. The analysis revealed that selection on CUB is an important attribute for the constraint on di-nucleotides at these positions in bacterial genomes. We believe that this study has come with major findings of the role of CUB on di-nucleotide constraint in bacterial genomes.

Genotype Independent Regeneration and Agrobacterium?mediated Genetic Transformation of Sweet Potato (Ipomoea batatas L.)

Development of an efficient genotype independent regeneration and genetic transformation system in sweet potato continues to be of great interest. Agrobacterium?mediated genetic transformation protocol was established in two different cultivars of sweet potato using Agrobacterium strain EHA105 harbouring binary plasmid pBI121 containing GUS and nptII genes. The internodal stem segments from 30?day?old micropropogated plants were used as explant with different combinations of media and hormones. MS and LS media with various concentrations of growth regulators proved to be non?responsive and the infecundity was severe with the addition of cytokinins. Nonetheless, MS with 2,4?D and TDZ gave a good percentage of callusing but with low differentiation. In different concentrations of NAA, significant amount of callusing was observed but percentage of rooting remained low in both the genotypes. Gamborg’s B5 supplemented with NAA proved to be the most suitable media and hormone combination, which yielded shoot formation after 8 ? 10 weeks with a regenera? tion efficiency of 40 ? 70%. Stable integration of transgene was confirmed by PCR analysis. Furthermore, qRT?PCR analysis was performed to assess the transcript accumulation in addition to the GUS enzymatic assay in the transgenic lines.Plant Tissue Cult. & Biotech. 23(1): 87?100, 2013 (June)DOI: http://dx.doi.org/10.3329/ptcb.v23i1.15565D.O.I. 10.3329/ptcb.v23i1.15565

A study in entire chromosomes of violations of the intra-strand parity of complementary nucleotides (Chargaff's second parity rule)

Chargaff's rule of intra-strand parity (ISP) between complementary mono/oligonucleotides in chromosomes is well established in the scientific literature. Although a large numbers of papers have been published citing works and discussions on ISP in the genomic era, scientists are yet to find all the factors responsible for such a universal phenomenon in the chromosomes. In the present work, we have tried to address the issue from a new perspective, which is a parallel feature to ISP. The compositional abundance values of mono/oligonucleotides were determined in all non-overlapping sub-chromosomal regions of specific size. Also the frequency distributions of the mono/oligonucleotides among the regions were compared using the Kolmogorov–Smirnov test. Interestingly, the frequency distributions between the complementary mono/oligonucleotides revealed statistical similarity, which we named as intra-strand frequency distribution parity (ISFDP). ISFDP was observed as a general feature in chromosomes of bacteria, archaea and eukaryotes. Violation of ISFDP was also observed in several chromosomes. Chromosomes of different strains belonging a species in bacteria/archaea (Haemophilus influenza, Xylella fastidiosa etc.) and chromosomes of a eukaryote are found to be different among each other with respect to ISFDP violation. ISFDP correlates weakly with ISP in chromosomes suggesting that the latter one is not entirely responsible for the former. Asymmetry of replication topography and composition of forward-encoded sequences between the strands in chromosomes are found to be insufficient to explain the ISFDP feature in all chromosomes. This suggests that multiple factors in chromosomes are responsible for establishing ISFDP.

The infectivity of dimeric potato yellow mosaic geminivirus clones in different hosts

Head-to-tail dimeric clones of both DNA A and DNA B of potato yellow mosaic geminivirus (PYMV) were constructed. These constructs were infectious when inoculated onto Nicotiana benthamiana plants either as DNA or by agroinoculation and were also infectious for tomato plants by agroinoculation. The dimers were not infectious for potato plants following inoculation by either method. Symptom induction required both DNA A and DNA B but agroinoculation with DNA A alone resulted in virus spread in 30% of the inoculated N. benthamiana plants. Leaf disc explants of N. benthamiana, tomato and potato could all be infected by agroinoculation indicating that the method of delivery of the DNA to intact potato plants was unsuitable for successful inoculation rather than an inherent inability of the virus to replicate/spread in potato per se. Neither whole plants nor leaf discs of sugar beet supported the replication of PYMV DNA.