Study of mercury resistance and Fourier transform infrared spectroscopy-based metabolic profiling of a potent Bacillus tropicus strain from forest soil.

Mercury (Hg) is a highly toxic heavy metal and Hg-resistant indigenous bacterial isolates may offer a green and cost-effective bioremediation strategy to counter Hg contamination. In this study, a potent Hg-resistant bacterium was isolated from the forest soil of a bird sanctuary. Identification using matrix-assisted laser desorption ionization-time of flight mass spectrometry depicted the isolate as a strain of Bacillus tropicus, validated by morphological, biochemical, and molecular studies. The isolate demonstrated biological Hg removal efficiency and capacity of 50.67% and 19.76 mg g-1 , respectively. The plasmid borne resistance determinant, merA, encoding mercuric reductase, was detected in the bacterium endowing it with effective Hg volatilization and resistance capability. A Fourier-transform infrared spectroscopic comparative metabolic profiling revealed the involvement of various functional groups like -COOH, -CH2 , -OH, PO4 - and so on, resulting in differential spectral patterns of the bacterium both in control and Hg-exposed situations. A temporal variance in metabolic signature was also observed during the early and mid-log phase of growth in the presence of Hg. The bacterium described in this study is the first indigenous Hg-resistant strain isolated from the Uttar Dinajpur region, which could be further explored and exploited as a potent bioresource for Hg remediation.

Trends and determinants in the utilization of maternal healthcare services in West Bengal, India: Findings from the 3rd and 4th round National Family and Health Survey.

BACKGROUND: Proper utilization of recommended healthcare services during the pregnancy is considered as critically important for better pregnancy outcomes, as well as a good health status of the mother. OBJECTIVE: The aim of the current study was to trace the trend in progress, and what are factors associated with the attendance at four Antenatal Care (ANC) visits, receive full ANC and institutional delivery in the study area. RESEARCH DESIGN/SETTING: The study has used a cross-sectional secondary data of the 3rd and 4th round National Family and Health Survey (NFHS) for India conducted in 2005-06 and 2015-2016 respectively. For West Bengal, a total of 6794 in 2005-06 and 17,668 in 2015-2016 ever-married women aged 15-49 who had experienced at least one live birth in the past five years preceding the survey were covered in this study. To analyze the data, the chi-square test was performed as it allows researcher to assess the association between outcome variables and independent variables. The univariate descriptive and multivariate statistical tools have been applied to analyse the data in this study. RESULTS: Our study indicated that the progress rate in attending at least four antenatal care visits, institutional delivery considerably good, but a noticeable gap exists across the different socio-economic groups. The coverage of full ANC services has remained very poor and unchanged over the decade. It was concluded that the wealth status of the households significant predictor of the attendance at least four ANC visits, full ANC and Institutional delivery in West Bengal. Other statistically significant socio-economic and demographic factors include level of women education, age of women, exposure to mass media, place of residence, and number of parities of birth. CONCLUSION: The present study suggests that the increasing strength in the coverage of all maternal healthcare services could be a significant focus during the program implementation in West Bengal. For strengthening and ascertaining the universal coverage of maternal healthcare services, there is an urgent need to reduce socioeconomic inequity in uses of the recommended maternal healthcare services. Moreover, our study found that the socio-economic and demographic factors play a significant role in utilization of maternal healthcare services. Thus the promotion of women education, empowerment and autonomy, and the frequent social marketing of government schemes and programs on maternal healthcare through the various types of mass media should be the unique future steps for achieving the universal coverage of maternal service in West Bengal.

Factors associated with delay in treatment-seeking behaviour for fever cases among caregivers of under-five children in India: Evidence from the National Family Health Survey-4, 2015-16.

BACKGROUND: Fever is one of the common clinical symptoms found among children suffering from various illnesses. India carries a substantial burden of febrile illness among under-five children which heighten the risk of malnutrition, mortality and morbidity. This study aims to determine the factors associated with delay in treatment-seeking for fever among under-five children in India. METHODS: A cross-sectional study was carried out using the large-scale nationally representative data from the National Family Health Survey (NFHS-4), conducted in 2015-2016. The data were collected by using four survey questionnaires i.e., Household Questionnaire, Woman's Questionnaire, Man's Questionnaire, and Biomarker Questionnaire. Delay in treatment-seeking was defined as taking a child for treatment after 24 hours of fever onset. Bivariate and multivariate logistic regression models were performed to assess the factors associated with delay in treatment-seeking behaviour for fever in under-five children. RESULTS: In India, 31.12% (n = 7229) of the caregivers sought treatment for children after 24 hours of the onset of fever. Findings show no significant differences in delay in treatment-seeking behaviour by age groups and sex of children. Multivariate analysis revealed that the odds of delay in treatment-seeking behaviour of fever were higher among children from the poorest wealth quintile (AOR: 2.06; 95% CI: 1.85, 2.31), belonging to the scheduled tribe (AOR: 1.35; 95% CI: 1.24, 1.48), children who resided in rural areas (AOR: 1.14; 95% CI: 1.07, 1.22), children from the northeast region (AOR: 1.29; 95% CI: 1.14, 1.46), and children of caregivers who perceived distance to health facilities as a 'big problem' (AOR: 1.16; 95% CI: 1.09, 1.23). CONCLUSION: The study shows a high prevalence of delay in seeking treatment for fever among caregivers of under-five children in India. Delay in seeking treatment is associated with socio-demographic and socio-economic factors. Therefore, there is a need for intensified health promotion programs to sensitize caregivers on the importance of early health-seeking behaviour.

Whole genome sequencing and comparative genomic analyses of Pseudomonas aeruginosa strain isolated from arable soil reveal novel insights into heavy metal resistance and codon biology.

Elevated concentration of non-essential persistent heavy metals and metalloids in the soil is detrimental to essential soil microbes and plants, resulting in diminished diversity and biomass. Thus, isolation, screening, and whole genomic analysis of potent strains of bacteria from arable lands with inherent capabilities of heavy metal resistance and plant growth promotion hold the key for bio remedial applications. This study is an attempt to do the same. In this study, a potent strain of Pseudomonas aeruginosa was isolated from paddy fields, followed by metabolic profiling using FTIR, metal uptake analysis employing ICP-MS, whole genome sequencing and comparative codon usage analysis. ICP-MS study provided insights into a high degree of Cd uptake during the exponential phase of growth under cumulative metal stress to Cd, Zn and Co, which was further corroborated by the detection of cadA gene along with czcCBA operon in the genome upon performing whole-genome sequencing. This potent strain of Pseudomonas aeruginosa also harboured genes, such as copA, chrA, znuA, mgtE, corA, and others conferring resistance against different heavy metals, such as Cd, Zn, Co, Cu, Cr, etc. A comparative codon usage bias analysis at the genomic and genic level, whereby several heavy metal resistant genes were considered in the backdrop of two housekeeping genes among 40 Pseudomonas spp. indicated the presence of a relatively strong codon usage bias in the studied strain. With this work, an effort was made to explore heavy metal-resistant bacteria (isolated from arable soil) and whole genome sequence analysis to get insight into metal resistance for future bio remedial applications.

Bacterial survival strategies and responses under heavy metal stress: a comprehensive overview.

Heavy metals bring long-term hazardous consequences and pose a serious threat to all life forms. Being non-biodegradable, they can remain in the food webs for a long period of time. Metal ions are essential for life and indispensable for almost all aspects of metabolism but can be toxic beyond threshold level to all living beings including microbes. Heavy metals are generally present in the environment, but many geogenic and anthropogenic activities has led to excess metal ion accumulation in the environment. To survive in harsh metal contaminated environments, bacteria have certain resistance mechanisms to metabolize and transform heavy metals into less hazardous forms. This also gives rise to different species of heavy metal resistant bacteria. Herein, we have tried to incorporate the different aspects of heavy metal toxicity in bacteria and provide an up-to-date and across-the-board review. The various aspects of heavy metal biology of bacteria encompassed in this review includes the biological notion of heavy metals, toxic effect of heavy metals on bacteria, the factors regulating bacterial heavy metal resistance, the diverse mechanisms governing bacterial heavy metal resistance, bacterial responses to heavy metal stress, and a brief overview of gene regulation under heavy metal stress.

Comparative Study of Heavy Metal Uptake and Analysis of Plant Growth Promotion Potential of Multiple Heavy Metal-Resistant Bacteria Isolated From Arable Land.

Heavy metal-induced pollution is a serious environmental concern. This study was aimed at exploring indigenous heavy metal-resistant and plant growth promoting bacteria from arable land that might be useful for developing green strategies to counter the challenges related to bioremediation and sustainable agriculture. A thorough screening and characterization of all the twenty heavy metal-resistant bacterial isolates obtained in this study was done. Of these, three potent isolates were further analyzed to unravel their heavy metal resistance and uptake potentiality. Minimum inhibitory concentration determination depicted considerable tolerance (≥ 500 µg/mL) of the three isolates to Ni, Zn, Fe, Cd, Cu, etc. Growth kinetics of the isolates in presence of various heavy metals indicated differences between normal and metal-induced growth. pH tolerance and pigmentation ability of the isolates were also analyzed. Inductively Coupled Plasma-Mass Spectrometry study revealed maximum Cd uptake by the isolates during exponential phase of growth. One of the isolates demonstrated plant growth promotion ability detected using different in vitro qualitative screening tests. Molecular identification using 16S rRNA depicted the isolates as strains of Pseudomonas aeruginosa. This was the first study of heavy metal-resistant and plant growth promoting bacteria from this region. Further exploration of such multi metal-resistant indigenous bacteria may pave the way for designing effective strategies for bioremediation and sustainable agriculture.

A comparative genomics-based study of positive strand RNA viruses emphasizing on SARS-CoV-2 utilizing dinucleotide signature, codon usage and codon context analyses.

The novel corona virus disease or COVID-19 caused by a positive strand RNA virus (PRV) called SARS-CoV-2 is plaguing the entire planet as we conduct this study. In this study a multifaceted analysis was carried out employing dinucleotide signature, codon usage and codon context to compare and unravel the genomic as well as genic characteristics of the SARS-CoV-2 isolates and how they compare to other PRVs which represents some of the most pathogenic human viruses. The main emphasis of this study was to comprehend the codon biology of the SARS-CoV-2 in the backdrop of the other PRVs like Poliovirus, Japanese encephalitis virus, Hepatitis C virus, Norovirus, Rubella virus, Semliki Forest virus, Zika virus, Dengue virus, Human rhinoviruses and the Betacoronaviruses since codon usage pattern along with the nucleotide composition prevalent within the viral genome helps to understand the biology and evolution of viruses. Our results suggest discrete genomic dinucleotide signature within the PRVs. Some of the genes from the different SARS-CoV-2 isolates were also found to demonstrate heterogeneity in terms of their dinucleotide signature. The SARS-CoV-2 isolates also demonstrated a codon context trend characteristically dissimilar to the other PRVs. The findings of this study are expected to contribute to the developing global knowledge base in countering COVID-19.

Comparative in silico analysis of ftsZ gene from different bacteria reveals the preference for core set of codons in coding sequence structuring and secondary structural elements determination.

The deluge of sequence information in the recent times provide us with an excellent opportunity to compare organisms on a large genomic scale. In this study we have tried to decipher the variation in the gene organization and structuring of a vital bacterial gene called ftsZ which codes for an integral component of the bacterial cell division, the FtsZ protein. FtsZ is homologous to tubulin protein and has been found to be ubiquitous in eubacteria. FtsZ is showing increasing promise as a target for antibacterial drug discovery. Our study of ftsZ protein from 143 different bacterial species spanning a wider range of morphological and physiological type demonstrates that the ftsZ gene of about ninety three percent of the organisms show relatively biased codon usage profile and significant GC deviation from their genomic GC content. Comparative codon usage analysis of ftsZ and a core housekeeping gene rpoB demonstrated that codon usage pattern of ftsZ CDS is shaped by natural selection to a large extent and mimics that of a housekeeping gene. We have also detected a tendency among the different organisms to utilize a core set of codons in structuring the ftsZ coding sequence. We observed that the compositional frequency of the amino acid serine in the FtsZ protein appears to be a indicator of the bacterial lifestyle. Our meticulous analysis of the ftsZ gene linked with the corresponding FtsZ protein show that there is a bias towards the use of specific synonymous codons particularly in the helix and strand regions of the multi-domain FtsZ protein. Overall our findings suggest that in an indispensable and vital protein such as FtsZ, there is an inherent tendency to maintain form for optimized performance in spite of the extrinsic variability in coding features.

Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes.

Soil is a diversified and complex ecological niche, home to a myriad of microorganisms particularly bacteria. The physico-chemical complexities of soil results in a plethora of physiological variations to exist within the different types of soil dwelling bacteria, giving rise to a wide variation in genome structure and complexity. This serves as an attractive proposition to analyze and compare the genome of a large number soil bacteria to comprehend their genome complexity and evolution. In this study a combination of codon usage and molecular phylogenetics of the whole genome and key housekeeping genes like infB (translation initiation factor 2), trpB (tryptophan synthase, beta subunit), atpD (ATP synthase, beta subunit), and rpoB (RNA polymerase, beta subunit) of 92 soil bacterial species spread across the entire eubacterial domain and residing in different soil types was performed. The results indicated the direct relationship of genome size with codon bias and coding frequency in the studied bacteria. The codon usage profile demonstrated by the gene trpB was found to be relatively different from the rest of the housekeeping genes with a large number of bacteria having a greater percentage of genes with Nc values less than the Nc of trpB. The results from the overall codon usage bias profile also depicted that the codon usage bias in the key housekeeping genes of soil bacteria was majorly due to selectional pressure and not mutation. The analysis of hydrophobicity of the gene product encoded by the rpoB coding sequences demonstrated tight clustering across all the soil bacteria suggesting conservation of protein structure for maintenance of form and function. The phylogenetic affinities inferred using 16S rRNA gene and the housekeeping genes demonstrated conflicting signals with trpB gene being the noisiest one. The housekeeping gene atpD was found to depict the least amount of evolutionary change in the soil bacteria considered in this study except in two Clostridium species. The phylogenetic and codon usage analysis of the soil bacteria consistently demonstrated the relatedness of Azotobacter chroococcum with different species of the genus Pseudomonas.