Bioprospecting of novel peroxidase from Streptomyces coelicolor strain SPR7 for carcinogenic azo dyes decolorization.

Peroxidase (POX) is a heme-containing oxidoreductase, its voluminous immuno-diagnostic and bioremediatory intuitions have incited optimization and large scale-generation from novel microbial repertoires. Azo dyes are the most detrimental classes of synthetic dyes and they are the common ecotoxic industrial pollutants in wastewater. In addition, azo dyes are refractory to degradation owing to their chemical nature, comprising of azoic linkages, amino moieties with recalcitrant traits. Moreover, they are major carcinogenic and mutagenic on humans and animals, whereby emphasizing the need for decolorization. In the present study, a novel POX from Streptomyces coelicolor strain SPR7 was investigated for the deterioration of ecotoxic dyestuffs. The initial medium component screening for POX production was achieved using, One Factor at a Time and Placket-Burman methodologies with starch, casein and temperature as essential parameters. In auxiliary, Response Surface Methodology (RSM) was recruited and followed by model validation using Back propagation algorithm (BPA). RSM-BPA composite approach prophesied that combination of starch, casein, and temperature at optimal values 2.5%, 0.035% and 35 °C respectively, has resulted in 7 folds enhancement of POX outturn (2.52 U/mL) compared to the unoptimized media (0.36 U/mL). The concentrated enzyme decolorized 75.4% and 90% of the two azo dyes with lignin (10 mM), respectively. Hence, this investigation confirms the potentiality of mangrove actinomycete derived POX for elimination of noxious azo dyes to overcome their carcinogenic, mutagenic and teratogenic effects on humans and aquatic organisms.

Unravelling the emerging carcinogenic contaminants from industrial waste water for prospective remediation by electrocoagulation - A review.

The need of the hour relies on finding new but sustainable ways to curb rising pollution levels. The accelerated levels of urbanization and increase in population deplete the finite resources essential for human sustenance. In this aspect, water is one of the non-renewable sources that is running out very fast and is polluted drastically day by day. One way of tackling the problem is to reduce the pollution levels by decreasing the usage of chemicals in the process, and the other is to find ways to reuse or reduce the contaminants in the effluent by treatment methods. Most of the available water recycling or treatment methods are not sustainable. Some of them even use toxic chemicals in the processing steps. Treatment of organic wastes from industries is a challenging task as they are hard to remove. Electrocoagulation is one of the emerging water treatment technologies that is highly sustainable and has a comparatively cheaper operating cost. Being a broad-spectrum treatment process, it is suitable for treating the most common water pollutants ranging from oils, bacteria, heavy metals, and others. The process is also straightforward, where electrical current is used to coagulate the contaminates. The presence of carcinogens in these waste water increases the need for its treatment towards further use. The present investigation is made as an extensive analysis of the emerging carcinogens and their various sources from process industries, especially in the form of organic waste and their removal by electrocoagulation and its coupled techniques. The paper also aims to ascertain why the electrocoagulation technique may be a better alternative compared with other methods for the removal of carcinogens in organic wastewater, an analysis which has not been explored before.

Advances in bioremediation of emerging contaminants from industrial wastewater by oxidoreductase enzymes.

The bioremediation of emerging recalcitrant pollutants in wastewater via enzyme biotechnology has been evolving as cost-effective with an input of low-energy technological approach. However, the enzyme based bioremediation technology is still not fully developed at a commercial level. The oxidoreductases being the domineering biocatalysts are promising candidates for wastewater treatments. Henceforth, comprehending their global market and biotransformation efficacy is mandatory for establishing these techno-economic bio-enzymes in commercial scale. The biocatalytic strategy can be established as a combinatorial approach with existing treatment technology to achieve towering bioremediation and effective removal of emerging pollutants from wastewater. This review provides a novel insight on the toxicological xenobiotics released from industries such as paper and pulps, soap and detergents, pharmaceuticals, textiles, pesticides, explosives and aptitude of peroxidases, nitroreductase and cellobiose dehydrogenase in their bio-based treatment. Moreover, the review comprehensively covers environmental relevance of wastewater pollution and the critical challenges based on remediation achieved through biocatalysts for future prospectives.

Cultivating Lifestyle Transformations in Obstructive Sleep Apnea.

Today, our well-being and awareness have become markedly determined by our way of living through our everyday activities. Needless to say, daily practices specifically have a significant impact on the quality of sleep. Obstructive sleep apnea (OSA) is an exhausting sleep disorder regulating an individual's routine life. Although several therapeutic modalities are available for curing OSA, behavioral therapies are also utilized for a positive outcome. Besides, several studies are performed to prove the efficacy of lifestyle strategies to resolute OSA in adults. Reducing weight, quitting alcohol and smoking, eating a nutritional diet, and exercising are the modifications to benefit people. This review aims to expand our knowledge of the association between alterations to comportment and better treatment outcomes for sleep apnea.

Development of EST-SSR markers for genetic diversity analysis in coconut (Cocos nucifera L.).

Genetic improvement in coconut relies on exploiting the vast existing diversity among coconut accessions. Robust molecular markers are a pre-requisite for efficient characterization of genetic diversity. Microsatellites or simple sequence repeats (SSRs), mined from expressed sequence tags (ESTs), constitute an important resource for analysis of genetic diversity as they are abundant, polymorphic and represent function regions of the genome. We have identified a total of 318,528 putative EST-SSRs from 130,942 unigenes utilizing a leaf transcriptome dataset of coconut. Among the EST-SSRs, dinucleotide repeats were abundant (219,912; 69.04%) followed by trinucleotide (70,722; 22.2%) and tetra-nucleotide repeats (6281; 1.9%). Among the dinucleotide repeat motifs, the dominant repeat was AG/CT (35.87%), followed by AT/AT (18.59%), while the dominant trinucleotide repeat was AAG/CTT (4.59%). One hundred and twenty EST-SSR primer pairs were designed and utilized to amplify six DNA samples of coconut accessions. Fifty primers (41.7%) produced reproducible polymorphic fragments of expected sizes, from which a total of 10 primers were selected for the diversity assessment in 186 palms of 50 coconut accessions, comprising of 25 each of tall and dwarf accessions. A total of 137 alleles were detected with an average of 13.7 alleles per SSR locus. The number of alleles observed at each locus in the data set ranged from 7 to 22. All the loci showed 100% polymorphism with respect to the samples screened. The average observed heterozygosity was 0.46. The PIC values ranged from 0.79 (CnKGDEST129 and CnKGDEST100) to 0.91 (CnKGDEST117 and CnKGDEST122) with a mean value of 0.85, indicating the capacity of the EST-SSR markers to detect high levels of polymorphism. The cluster analysis revealed that accessions were generally clustered based on their relative similarity and irrespective of their geographic origins. The present study demonstrates the usefulness of transcriptome sequencing as a rapid and cost-effective methodology for the development of molecular markers. The EST-SSR markers generated through this study constitute useful and reliable tools for assessment of genetic diversity and marker-assisted selection in coconut.

Characterization of perineural invasion in different histological grades and variants of oral squamous cell carcinoma.

BACKGROUND: Oral squamous cell carcinoma (OSCC) accounts for 3% of all malignant neoplasms and is the fifth most frequent cancer in the world. They usually spread by hematogenous or lymphatic spread, and perineural invasion (PNI) is considered an alternate method of tumor spread where it is described as the tumor affinity toward a neural tissue. AIM AND OBJECTIVES: The present study aims to evaluate the biological behavior of OSCC with respect to PNI and to evaluate the importance of PNI with respect to different histopathological grades and variants, tumor stage and lymph node status of OSCC. PNI was also assessed with respect to its frequency, patterns, types and number in various grades of OSCC. MATERIALS AND METHODS: This retrospective, double-blind study was conducted on 148 histopathologically proven cases of different histopathological grades and variants of OSCC. The tissue sections were examined for PNI and its patterns and were further compared with habit history, site of the lesion, tumor staging, grading and lymph node status. RESULTS: A Chi-square test was performed. A percentage positivity of 45.27% (67 cases) among 148 cases was found. PNI positivity of 63.6% and 50% was observed in T4 and T3 tumor stages, respectively, with high significance. Seventy percent of cases belonging to poorly differentiated squamous cell carcinoma showed positivity for PNI, which was statistically significant. PNI positivity with respect to lymph node status is nonsignificant. CONCLUSION: The present study showed that there is a direct proportionality between PNI and different grades and stages of OSCC. Given this context, a histopathologist ought to examine for PNI and make it mandatory to report the same to the clinician for better treatment and follow-up of the patient.

Estimating Strengths of Individual Hydrogen Bonds in RNA Base Pairs: Toward a Consensus between Different Computational Approaches.

Noncoding RNA molecules are composed of a large variety of noncanonical base pairs that shape up their functionally competent folded structures. Each base pair is composed of at least two interbase hydrogen bonds (H-bonds). It is expected that the characteristic geometry and stability of different noncanonical base pairs are determined collectively by the properties of these interbase H-bonds. We have studied the ground-state electronic properties [using density functional theory (DFT) and DFT-D3-based methods] of all the 118 normal base pairs and 36 modified base pairs, belonging to 12 different geometric families (cis and trans of WW, WH, HH, WS, HS, and SS) that occur in a nonredundant set of high-resolution RNA crystal structures. Having addressed some of the limitations of the earlier approaches, we provide here a comprehensive compilation of the average energies of different types of interbase H-bonds (E HB). We have also characterized each interbase H-bond using 13 different parameters that describe its geometry, charge distribution at its bond critical point (BCP), and n → σ*-type charge transfer from filled π orbitals of the H-bond acceptor to the empty antibonding orbital of the H-bond donor. On the basis of the extent of their linear correlation with the H-bonding energy, we have shortlisted five parameters to model linear equations for predicting E HB values. They are (i) electron density at the BCP: ρ, (ii) its Laplacian: ∇2ρ, (iii) stabilization energy due to n → σ*-type charge transfer: E(2), (iv) donor-hydrogen distance, and (v) hydrogen-acceptor distance. We have performed single variable and multivariable linear regression analysis over the normal base pairs and have modeled sets of linear relationships between these five parameters and E HB. Performance testing of our model over the set of modified base pairs shows promising results, at least for the moderately strong H-bonds.

Pairing interactions between nucleobases and ligands in aptamer:ligand complexes of riboswitches: crystal structure analysis, classification, optimal structures, and accurate interaction energies.

In the present work, 67 crystal structures of the aptamer domains of RNA riboswitches are chosen for analysis of the structure and strength of hydrogen bonding (pairing) interactions between nucleobases constituting the aptamer binding pockets and the bound ligands. A total of 80 unique base:ligand hydrogen-bonded pairs containing at least two hydrogen bonds were identified through visual inspection. Classification of these contacts in terms of the interacting edge of the aptamer nucleobase revealed that interactions involving the Watson-Crick edge are the most common, followed by the sugar edge of purines and the Hoogsteen edge of uracil. Alternatively, classification in terms of the chemical constitution of the ligand yields five unique classes of base:ligand pairs: base:base, base:amino acid, base:sugar, base:phosphate, and base:other. Further, quantum mechanical (QM) geometry optimizations revealed that 67 out of 80 pairs exhibit stable geometries and optimal deviations from their macromolecular crystal occurrences. This indicates that these contacts are well-defined RNA aptamer:ligand interaction motifs. QM calculated interaction energies of base:ligand pairs reveal a rich hydrogen bonding landscape, ranging from weak interactions (base:other, -3 kcal/mol) to strong (base:phosphate, -48 kcal/mol) contacts. The analysis was further extended to study the biological importance of base:ligand interactions in the binding pocket of the tetrahydrofolate riboswitch and thiamine pyrophosphate riboswitch. Overall, our study helps in understanding the structural and energetic features of base:ligand pairs in riboswitches, which could aid in developing meaningful hypotheses in the context of RNA:ligand recognition. This can, in turn, contribute toward current efforts to develop antimicrobials that target RNAs.

Structural landscape of base pairs containing post-transcriptional modifications in RNA.

Base pairs involving post-transcriptionally modified nucleobases are believed to play important roles in a wide variety of functional RNAs. Here we present our attempts toward understanding the structural and functional role of naturally occurring modified base pairs using a combination of X-ray crystal structure database analysis, sequence analysis, and advanced quantum chemical methods. Our bioinformatics analysis reveals that despite their presence in all major secondary structural elements, modified base pairs are most prevalent in tRNA crystal structures and most commonly involve guanine or uridine modifications. Further, analysis of tRNA sequences reveals additional examples of modified base pairs at structurally conserved tRNA regions and highlights the conservation patterns of these base pairs in three domains of life. Comparison of structures and binding energies of modified base pairs with their unmodified counterparts, using quantum chemical methods, allowed us to classify the base modifications in terms of the nature of their electronic structure effects on base-pairing. Analysis of specific structural contexts of modified base pairs in RNA crystal structures revealed several interesting scenarios, including those at the tRNA:rRNA interface, antibiotic-binding sites on the ribosome, and the three-way junctions within tRNA. These scenarios, when analyzed in the context of available experimental data, allowed us to correlate the occurrence and strength of modified base pairs with their specific functional roles. Overall, our study highlights the structural importance of modified base pairs in RNA and points toward the need for greater appreciation of the role of modified bases and their interactions, in the context of many biological processes involving RNA.

Comparative evaluation of subgingivally delivered chlorhexidine varnish and chlorhexidine gel in reducing microbial count after mechanical periodontal therapy.

CONTEXT: Antimicrobial efficacy of subgingival chlorhexidine (CHX) application using two different vehicles of delivery. AIMS: The aim was to evaluate the efficacy of CHX varnish and gel as an adjunct to scaling and root planing (SRP) in reducing microbial count within moderate to deep periodontal pockets. SETTINGS AND DESIGN: Experimental parallel mouth study. SUBJECTS AND METHODS: A total of 30 subjects between the age groups 25 and 55 years having moderate to severe periodontitis, with pocket depth ≥ 5 mm were selected for the study. The selected patients were randomized into three groups of 10 each. Subjects in Group 1 received SRP followed by subgingival application of CHX varnish, subjects in Group 2 received SRP followed by subgingival application of CHX gel, subjects in Group 3 received SRP alone. Subgingival plaque samples were collected to estimate mean motile and nonmotile microbial counts using dark field microscopy at baseline, 1 week, 1 month, and 3 months. RESULTS: After 3 months, there was statistically significant reduction in nonmotile microbial count in all the three groups. Motile microbial count was significantly reduced in all the three groups till 1 month from baseline. Only subjects in Group 1 who received subgingival CHXvarnish after SRP showed a significant reduction in motile microbial count till 3 months from baseline. CONCLUSIONS: Subgingival application of highly concentrated CHX varnish following SRP is beneficial in reducing microbial count in moderate to deep periodontal pockets.