Unveiling the Microbiome Landscape: A Metagenomic Study of Bacterial Diversity, Antibiotic Resistance, and Virulence Factors in the Sediments of the River Ganga, India.

The global rise in antibiotic resistance, fueled by indiscriminate antibiotic usage in medicine, aquaculture, agriculture, and the food industry, presents a significant public health challenge. Urban wastewater and sewage treatment plants have become key sources of antibiotic resistance proliferation. The present study focuses on the river Ganges in India, which is heavily impacted by human activities and serves as a potential hotspot for the spread of antibiotic resistance. We conducted a metagenomic analysis of sediment samples from six distinct locations along the river to assess the prevalence and diversity of antibiotic resistance genes (ARGs) within the microbial ecosystem. The metagenomic analysis revealed the predominance of Proteobacteria across regions of the river Ganges. The antimicrobial resistance (AMR) genes and virulence factors were determined by various databases. In addition to this, KEGG and COG analysis revealed important pathways related to AMR. The outcomes highlight noticeable regional differences in the prevalence of AMR genes. The findings suggest that enhancing health and sanitation infrastructure could play a crucial role in mitigating the global impact of AMR. This research contributes vital insights into the environmental aspects of antibiotic resistance, highlighting the importance of targeted public health interventions in the fight against AMR.

In†Vitro and in†Silico Studies of Lichen Compounds Atranorin and Salazinic Acid as Potential Antioxidant, Antibacterial and Anticancer Agents.

Lichens are symbiotic organisms made up of alga/cyanobacterium and fungus. We investigated antioxidant, antibacterial and anticancer properties of two lichen compounds, atranorin and salazinic acid, and five lichen species: Heterodermia boryi, Heterodermia diademata, Heterodermia hypocaesia, Parmotrema reticulatum, and Stereocaulon foliolosum. Free radical scavenging, Ferric reducing potential, Nitric oxide scavenging, and Trolox equivalent capacity were used to measure antioxidant activity. Strong radical scavenging action was demonstrated by atranorin and salazinic acid, with IC50 values of 39.31 µM and 12.14 µM, respectively. The Minimum Inhibitory Concentration (MIC) assay based on resazurin, was used to measure antibacterial activity. Parmotrema reticulatum demonstrated significant antibacterial activity against Raoultella planticola with MIC of 7.8 µg/mL. Cytotoxicity assay on breast cancer cell line was used to assess anticancer activity. To further understand the binding locations on the target proteins Er (Estrogen Receptor alpha), EGFR (Epidermal Growth Factor Receptor), mTOR (Mammalian Target of Rapamycin), and PgR (Progesterone Receptor), molecular docking experiments were conducted. Docking study showed that the binding energies of atranorin and salazinic acid with mTOR were -5.31 kcal/mol and -3.43 kcal/mol, respectively. The results suggest that atranorin has the potential to be a multitargeted molecule with natural antioxidant, antibacterial, and anticancer properties.

Regulatory role of miRNAs in Wnt signaling pathway linked with cardiovascular diseases.

MicroRNAs (miRNAs) are discovered in science about 23 years ago. These are short, a series of non-coding, single-stranded and evolutionary conserved RNA molecules found in eukaryotic cells. It involved post-transcriptional fine-tune protein expression and repressing the target of mRNA in different biological processes. These miRNAs binds with the 3'-UTR region of specific mRNAs to phosphorylate the mRNA degradation and inhibit the translation process in various tissues. Therefore, aberrant expression in miRNAs induces numerous cardiovascular diseases and developmental defects. Subsequently, the miRNAs and Wnt singling pathway are regulating a cellular process in cardiac development and regeneration, maintain the homeostasis and associated heart diseases. In Wnt signaling pathway majority of the signaling components are expressed and regulated by miRNAs, whereas the inhibition or dysfunction of the Wnt signaling pathway induces cardiovascular diseases. Moreover, inadequate studies about the important role of miRNAs in heart development and diseases through Wnt signaling pathway has been exist still now. For this reason in present review we summarize and update the involvement of miRNAs and the role of Wnt signaling in cardiovascular diseases. We have discussed the mechanism of miRNA functions which regulates the Wnt components in cellular signaling pathway. The fundamental understanding of Wnt signaling regulation and mechanisms of miRNAs is quite essential for study of heart development and related diseases. This approach definitely enlighten the future research to provide a new strategy for formulation of novel therapeutic approaches against cardiovascular diseases.

Understanding of environmental pollution and its anthropogenic impacts on biological resources during the COVID-19 period.

The global outbreak of the COVID-19 pandemic has given rise to a significant health emergency to adverse impact on environment, and human society. The COVID-19 post-pandemic not only affects human beings but also creates pollution crisis in environment. The post-pandemic situation has shown a drastic change in nature due to biomedical waste load and other components. The inadequate segregation of untreated healthcare wastes, chemical disinfectants, and single-use plastics leads to contamination of the water, air, and agricultural fields. These materials allow the growth of disease-causing agents and transmission. Particularly, the COVID-19 outbreak has posed a severe environmental and health concern in many developing countries for infectious waste. In 2030, plastic enhances a transboundary menace to natural ecological communities and public health. This review provides a complete overview of the COVID-19 pandemic on environmental pollution and its anthropogenic impacts to public health and natural ecosystem considering short- and long-term scenarios. The review thoroughly assesses the impacts on ecosystem in the terrestrial, marine, and atmospheric realms. The information from this evaluation can be utilized to assess the short-term and long-term solutions for minimizing any unfavorable effects. Especially, this topic focuses on the excessive use of plastics and their products, subsequently with the involvement of the scientific community, and policymakers will develop the proper management plan for the upcoming generation. This article also provides crucial research gap knowledge to boost national disaster preparedness in future perspectives.

Taxonomic profiling and functional gene annotation of microbial communities in sediment of river Ganga at Kanpur, India: insights from whole-genome metagenomics study.

The perennial river Ganga is recognized as one of India's largest rivers of India, but due to continuous anthropogenic activities, the river's ecosystem is under threat. Next-generation sequencing technology has transformed metagenomics in the exploration of microbiome and their imperative function in diverse aquatic ecosystems. In this study, we have uncovered the structure of community microbiome and their functions in sediments of river Ganga at Kanpur, India, at three polluted stretches through a high-resolution metagenomics approach using Illumina HiSeq 2500. Among the microbes, bacteria dominate more than 82% in the three polluted sediment samples of river Ganga. Pseudomonadota (alpha, beta, and gamma) is the major phylum of bacteria that dominates in three sediment samples. Genes involved in degradation of xenobiotic compounds involving nitrotoluene, benzoate, aminobenzoate, chlorocyclohexane, and chlorobenzene were significantly enriched in the microbiome of polluted stretches. Pathway analysis using KEGG database revealed a higher abundance of genes involved in energy metabolism such as oxidative phosphorylation, nitrogen, methane, sulfur, and carbon fixation pathways in the sediment metagenome data from the river Ganga. A higher abundance of pollutant degrading enzymes like 4-hydroxybenzoate 3-monooxygenase, catalase-peroxidase, and altronate hydrolase in the polluted microbiome indicates their role in degradation of plastics and dyes. Overall, our study has provided bacterial diversity and their dynamics in community structure and function from polluted river microbiome, which is expected to open up better avenues for exploration of novel functional genes/enzymes with potential application in health and bioremediation.

Nakazawaea odontotermitis f.a., sp. nov., a novel yeast isolated from the gut of Odontotermes horni in India.

Three strains, SMT1.3, SMT1.10, and SMT2.2, representing a novel asexual ascomycetous yeast species, were isolated from the gut of a termite Odontotermes horni in Maharashtra, India. Phylogenetic analyses of the LSU, ITS, and SSU sequences revealed that they belonged to the genus Nakazawaea, with N. siamensis as the closest relative. The new species differed from the type strain of N. siamensis (DMKU-RK467T) by 11 substitutions in the D1/D2 region of the large subunit (LSU) rRNA gene and by 8 substitutions and one gap in the small subunit (SSU) rRNA gene. Notable biochemical and physiological differences were also observed between N. siamensis and the new species. Hence, the species Nakazawaea odontotermitis f.a., sp. nov. is proposed. The type strain is SMT1.3 T (MTCC 13,105 = NFCCI 5011 = PYCC 9153). GenBank accession numbers of the LSU, ITS and SSU sequences of Nakazawaea odontotermitis f.a., sp. nov. are MZ234240, MZ234239, and OK384663. The MycoBank number is MB 841926.

Schottky junction devices by using bio-molecule DNA template-based one dimensional CdS-nanostructures.

Creating a well-defined nanostructure through de-oxyribo nucleic acid (DNA)-nanotechnology, and specifically the development of metal/inorganic semiconductor junctions on DNA-assembled nanostructures, is an emerging research area. Herein, we investigate the electrical properties of biomolecule DNA-template based one-dimensional nanowires (NWs)-CdS/Au and without-template based nanoparticles (NPs)-CdS/Au devices grown on the Indium Tin Oxide (ITO) glass substrates. More importantly, the NWs-CdS/Au device displays a dramatic augmentation of current flow and also a striking change in threshold voltage (~55 mV) in comparison to NPs (~190 mV) and reported bulk-CdS/Au (~680 mV) devices. Albeit the manifestation of non-linear/asymmetric current-voltage (I-V) characteristic establishes the CdS/Au junction as Schottky device, but captivatingly, the large ideality factor of about 24 found in NWs-CdS/Au device could be due to the DNA-assembled based organic process CdS-semiconductor. Capacitance-voltage (C-V) measurements of the NWs-CdS/Au divulge a remarkable hump-like feature at lower frequency owing to the frequency dispersion effect. In contrast, the effect appears to be enfeebled with increasing frequency. We conjecture that the density of surface/interface traps materialises at the interface of nanostructures-CdS/metal-Au results in the changes in underlying electrical properties. The observation of significant differences in the electrical properties of DNA-assembled NWs-based Schottky junctions could possibly be helpful for the fabrication of more sophisticated and higher multispecificity biosensors for medical applications.

Insights into structure and dynamics of extracellular domain of Toll-like receptor 5 in Cirrhinus mrigala (mrigala): A molecular dynamics simulation approach.

The toll-like receptor 5 (TLR5) is the most conserved important pattern recognition receptors (PRRs) often stimulated by bacterial flagellins and plays a major role in the first-line defense against invading pathogenic bacteria and in immune homeostasis. Experimental crystallographic studies have shown that the extracellular domain (ECD) of TLR5 recognizes flagellin of bacteria and functions as a homodimer in model organism zebrafish. However, no structural information is available on TLR5 functionality in the major carp Cirrhinus mrigala (mrigala) and its interaction with bacterial flagellins. Therefore, the present study was undertaken to unravel the structural basis of TLR5-flagellin recognition in mrigala using structural homodimeric TLR5-flagellin complex of zebrafish as reference. Integrative structural modeling and molecular dynamics simulations were employed to explore the structural and mechanistic details of TLR5 recognition. Results from structural snapshots of MD simulation revealed that TLR5 consistently formed close interactions with the three helices of the D1 domain in flagellin on its lateral side mediated by several conserved amino acids. Results from the intermolecular contact analysis perfectly substantiate with the findings of per residue-free energy decomposition analysis. The differential recognition mediated by flagellin to TLR5 in mrigala involves charged residues at the interface of binding as compared to the zebrafish complex. Overall our results shows TLR5 of mrigala involved in innate immunity specifically recognized a conserved site on flagellin which advocates the scientific community to explore host-specific differences in receptor activation.

Elucidating the molecular interaction of Zebrafish (Danio rerio) peptidoglycan recognition protein 2 with diaminopimelic acid and lysine type peptidoglycans using in silico approaches.

Peptidoglycan recognition proteins (PGRPs) belong to the family of pattern recognition receptor, represent the major constituent of innate immunity. Although PGRPs are structurally conserved through evolution, their involvement in innate immunity is different in vertebrates and invertebrates. They are highly specific towards recognition of ligands and can hydrolyze bacterial peptidoglycans (PGNs). Zebrafish PGRPs (zPGRPs) have both peptidoglycans lytic amidase activity and broad-spectrum bactericidal activity, but far less is known about how these receptors recognize these microbial ligands. Such studies are hindered due to lack of structural and functional configuration of zPGRPs. Therefore, in this study, we predicted the three-dimensional structure of zPGRP2 through theoretical modeling, investigated the conformational and dynamic properties through molecular dynamics simulations. Molecular docking study revealed the microbial ligands, that is, muramyl pentapeptide-DAP , muramyl pentapeptide-LYS, muramyl tripeptide-DAP, muramyl tripeptide-Lys, muramyl tetrapeptide-DAP, muramyl tetrapeptide-LYS and tracheal cytotoxin interacts with the conserved amino acids of the ligand recognition site comprised of ß1, α2, α4, ß4 and loops connecting ß1 - α2, α2 - ß2, ß3 - ß4 and α4 - α5. Conserved His31, His32, Ala34, Ile35, Pro36, Lys38, Asp60, Trp61, Trp63, Ala89, His90, Asp106, His143 and Arg144 are predicted to essential for binding and provides stability to these zPGRP-PGN complexes. Our study provides basic molecular information for further research on the immune mechanisms of PGRP's in Zebrafish. The plasticity of the zPGRP's binding site revealed by these microbial ligands suggests an intrinsic capacity of the innate immune system to rapidly evolve specificities to meet new microbial challenges in the future.Communicated by Ramaswamy H. Sarma.

Radical scavenging, prolyl endopeptidase inhibitory, and antimicrobial potential of a cultured Himalayan lichen Cetrelia olivetorum.

CONTEXT: Lichens are source of natural bioactive compounds which are traditionally used to cure a variety of ailments. OBJECTIVE: The objective of this study is to assess free radical scavenging, prolyl endopeptidase inhibitory (PEPI), and antimicrobial potential of a high altitude lichen species Cetrelia olivetorum (Nyl.) W. L. Culb. & C. F. Culb (Parmeliaceae). MATERIALS AND METHODS: Lichen C. olivetorum has been cultured in vitro, and optimized culture conditions were implemented in bioreactor to obtain high quantity of biomass for the study of radical scavenging, PEPI, and antimicrobial activities. Radical scavenging activity of methanol extract of Cetrelia olivetorum (MECO) was tested at 100 µg/mL, PEPI activity at 25 and 50 µg/mL, and antimicrobial activity at 5, 25, 50, and 100 µg/mL conc. All the biological activities of natural thallus extract and its derived culture extract were evaluated spectrophotometrically. RESULTS: Murashige and Skoog medium supplemented with 3% glucose and 100 ppb indole-3-butyric acid (IBA) supported biomass growth at flask level and yielded 5.095 g biomass in bioreactor. MECO of both the cultured and the natural lichen exhibited half inhibiting concentration (IC50) for radical scavenging activities in the range of 50-60 µg/mL, whereas the IC50 value of standard antioxidants was found to be in the range of 12-29 µg/mL. The IC50 value of lichen extract for PEPI activity was 144-288 µg/mL, whereas the IC50 value of standard prolyl endopeptidase inhibitor, Z-pro-prolinal, was 57.73 µg/mL. As far as the antimicrobial activity of MECO is concerned, minimum inhibitory concentration (MIC) value of lichen extracts against tested microorganisms was obtained in the range of 50-104 µg/mL and found to be more effective than commercially available standard erythromycin. DISCUSSION: Murashige and Skoog medium containing IBA was found to be suitable for maximum biomass production of C. olivetorum under bioreactor conditions. The cultured lichen biomass extract also showed antioxidant, PEPI, and antimicrobial potential. CONCLUSION: The present study indicates therapeutic potential of Himalayan lichen C. olivetorum against neurodegenerative diseases owing to its radical scavenging, PEPI, and antimicrobial activities. Further, the result encourages its commercial exploitation through mass culture for production of its bioactive components and their use in pharmaceutical and nutraceutical industries.

Antioxidative and cardiovascular-protective activities of metabolite usnic acid and psoromic acid produced by lichen species Usnea complanata under submerged fermentation.

CONTEXT: Lichens have been used for various purposes such as dyes, perfumes and remedies in folk medicine indicating the pharmaceutical potential of lichens. OBJECTIVE: Lichen growth in nature is very slow. To overcome this major drawback, we standardized the culture media to culture the lichen Usnea complanata (Müll.Arg.) Motyka (Parmeliaceae) for (1) in vitro synthesis of natural lichen substances, and (2) determination of antioxidative and cardiovascular-protective activity of usnic acid and psoromic acid. MATERIALS AND METHODS: Lichen U. complanata has been cultured in fermentor under submerged condition. Antioxidative and cardiovascular-protective activity of the extract and the purified lichen substances usnic and psoromic acid have been determined. RESULTS: Except methanol, all other extracts exhibited antioxidative action in terms of free radical scavenging activity (FRSA) with a half-inhibiting concentration (IC50) value of 22.86 to 25.0 µg/mL, nitric oxide radical scavenging activity (NORSA) 141.3 to 149.1 µg/mL and for lipid peroxidation inhibition (LPI) 125 to 157.9 µg/mL. Usnic acid or psoromic acid showed antioxidative action with IC50 values ranging from 0.174 to 0.271 mg/mL. Methanol and ethyl acetate extract showed hydroxy-3-methyl-glutaryl-CoA reductase (HMGR) inhibition of 65.18 to 74.81%. Only 43.47% inhibition of angiotensin converting enzyme (ACE) was shown by methanol extract. Usnic acid showed noncompetitive type of HMGR inhibition and uncompetitive type of ACE inhibition. Psoromic acid exhibited competitive type of HMGR inhibition and mixed type of ACE inhibition. DISCUSSION: U. complanata showed both cardiovascular-protective and antioxidant properties. The lichen species U. complanata may be a natural bioresource for possible pharmaceutical applications.

Tyrosinase-inhibitory activity in some species of the lichen family Graphidaceae.

Twenty-five species of the lichen family Graphidaceae have been investigated for tyrosinase-inhibitory activity. Tyrosinase-inhibiting material was extracted with solvents methanol, acetone, ethanol, dimethyl sulphoxide in water, and with water only. Methanol has been found to be suitable for extracting adequate amounts of tyrosinase-inhibiting component from the natural thallus. The lichen species such as Graphina glaucorufa, Graphina multistriata, Graphina salacinilabiata, Graphis assamensis, Graphis nakanishiana, and Phaeographopsis indica, have shown inhibition of tyrosinase over a range of 30-78%. Half-inhibiting concentration (IC(50), microg/ml) has been found to be much lower than the standard tyrosinase inhibitors and thus can compete with other commercially available tyrosinase inhibitors. The extracts of these species have been found to be stable at 4 degrees C.