Structural bioinformatics insights into ATP binding mechanism in zebrafish (Danio rerio) cyclin-dependent kinase-like 5 (zCDKL5) protein.

In mammalian systems, the conserved cyclin-dependent protein kinases (CDKs) control the process of cell division and curb the transcription mechanism in response to diverse signaling events that are essential for the catalytic activity. In zebrafish, zCDKL5 portrays differential expression profiling in several tissues and presumed to play a vital role in the neuronal development. In this present study, the sequence-structure relationship and mode of ATP binding in zCDKL5 was unveiled through theoretical modeling, molecular docking, and MD simulations. Like human CDKs, the modeled zCDKL5 was found to be bipartite in nature, where, ATP binds to the central cavity of the catalytic domain through a strong network of H-bonding, electrostatic, and hydrophobic interactions. MD simulation portrayed that conserved residues, viz, Ile10, Gly11, Glu12, Val18, Val64, Glu81, Cys143, and Asp144 were indispensable for tight anchoring of ATP and contribute to the stability of the zCDKL5-ATP complex. MM/PBSA binding free energy analysis displayed that van der Waal energy (ΔG vwd ) and Electrostatic energy (ΔG ele ) were the major contributors towards the overall binding free energy. Thus, the comparative structural bioinformatics approach has shed new insights into the dynamics and ATP binding mechanism of zCDKL5. The results from the study will help to undertake further research on the role of phosphorylated CDKL5 in the onset of neurodevelopmental disorders caused by mutations in higher eukaryotic systems.

Whole genome sequence analysis of shallot virus X from India reveals it to be a natural recombinant with positive selection pressure.

BACKGROUND: Shallots are infected by various viruses like Onion yellow dwarf virus (OYDV), Leek yellow stripe virus (LYSV), Shallot latent virus (SLV) and Shallot virus X (ShVX). In India, they have been found to be persistently infected by ShVX. ShVX also infects onion and garlic in combination with other carlaviruses and potyviruses. ShVX is a member of genus Allexivirus of family Alphaflexiviridae. ShVX has a monopartite genome, which is represented by positive sense single-stranded RNA. Globally, only six complete and 3 nearly complete genome sequences of ShV X are reported to date. This number is insufficient to measure a taxon's true molecular diversity. Moreover, the complete genome sequence of ShVX from Asia has not been reported as yet. Therefore, this study was undertaken to generate a complete genome sequence of ShVX from India. RESULTS: Shallot virus X (ShVX) is one of the significant threats to Allium crop production. In this study, we report the first complete genome sequence of the ShVX from India through Next-generation sequencing (NGS). The complete genome of the ShVX (Accession No. OK104171), from this study comprised 8911 nucleotides. In-silico analysis of the sequence revealed variability between this isolate and isolates from other countries. The dissimilarities are spread all over the genome specifically some non-coding intergenic regions. Statistical analysis of individual genes for site-specific selection indicates a positive selection in NABP region. The presence of a recombination event was detected in coat protein region. The sequence similarity percentage and phylogenetic analysis indicate ShVX Indian isolate is a distinctly different isolate. Recombination and site-specific selection may have a function in the evolution of this isolate. This is the first detailed study of the ShVX complete genome sequence from Southeast Asia. CONCLUSION: This study presents the first report of the entire genome sequence of an Indian isolate of ShVX along with an in-depth exploration of its evolutionary traits. The findings highlight the Indian variant as a naturally occurring recombinant, emphasizing the substantial role of recombination in the evolution of this viral species. This insight into the molecular diversity of strains within a specific geographical region holds immense significance for comprehending and forecasting potential epidemics. Consequently, the insights garnered from this research hold practical value for shaping ShVX management strategies and providing a foundation for forthcoming studies delving into its evolutionary trajectory.

Structural insights of Labeo catla (catla) myxovirus resistance protein,GTP binding recognition and constitutive expression induced with Poly I:C.

The Myxovirus resistance (Mx) proteins are critical effectors belonging to the super-family of guanidine triphosphatase, often stimulated by type I interferon (IFN) and mediates antiviral responses to restrict the replication of numerous viral genes in fishes. In teleosts, Mx proteins display diverse and complicated antiviral activity in different species. The present investigation seeks to characterize the Mx gene from Labeo catla upon induction by double-stranded (ds) RNA, polyinosinic-polycytidylic acid, (poly I: C). Molecular modeling and all-atoms molecular dynamics (MD) simulations were employed to understand the architecture of the GTPase domain and its plausible mode of GTP recognition in Mx protein. The full-length L. catla Mx (LcMx) gene sequence (1821 bp nucleotides) encodes an open reading frame of 606 amino acids. Domain search indicated conserved tripartite domain architecture of LcMx and forms a major cluster with the Mx from other teleosts. The positively charged Arginine and polar Glutamine residues from helix 3 and 4 of stalk region LcMx aid in homo-oligomerization. MD simulation portrayed the role of conserved critical residues aid in GTP recognition by the GTPase domain which perfectly corroborates with experimental findings and prior MD studies. After injection of poly I:C, the temporal mRNA profile showed that LcMx expression was significantly elevated in the spleen, brain, kidney, liver, muscle, heart, intestine, and gill tissues. Collectively, these results suggest that the elevated expression of the major innate immune defense gene Mx was able to inhibit the poly I: C mediated virulence in fish.Communicated by Ramaswamy H. Sarma.

Evaluation of biocontrol efficacy of rhizosphere dwelling bacteria for management of Fusarium wilt and Botrytis gray mold of chickpea.

BACKGROUND: Chickpea (Cicer arietinum L.) production is affected by many biotic factors, among them Fusarium wilt caused by Fusarium oxysporum f. sp. ciceri and Botrytis gray mold caused by Botrytis cinerea led to severe losses. As fungicide application is not advisable, biological management is the best alternative for plant protection. The rhizosphere-dwelling antagonistic bacteria are one of the important successful alternative strategy to manage these diseases of chickpea. Rhizosphere dwelling bacteria serve as biocontrol agents by different mechanisms like producing antibiotics, different enzymes, siderophores against pathogens and thereby reducing the growth of pathogens. RESULTS: The present study aimed to isolate rhizospheric bacteria from the soils of different chickpea fields to evaluate biocontrol efficacy of the isolated bacteria to manage Fusarium wilt and Botrytis gray mold in chickpea. A total of 67 bacteria were isolated from chickpea rhizosphere from Bundelkhand region of India. Study revealed the isolated bacteria could reduce the Fusarium oxysporum f. sp. ciceris and Botrytis cinerea infection in chickpea between 17.29 and 75.29%. After screening of all the bacteria for their biocontrol efficacy, 13 most promising bacterial isolates were considered for further study out of which, three bacterial isolates (15d, 9c and 14a) have shown the maximum in vitro antagonistic effects against Fusarium oxysporum f. sp. ciceri and Botrytis cinerea comparable to in vivo effects. However, Isolate (15d) showed highest 87.5% and 82.69% reduction in disease against Fusarium wilt and Botrytis gray mold respectively, under pot condition. Three most potential isolates were characterized at molecular level using 16S rRNA gene and found to be Priestia megaterium (9c and 14a) and Serratia marcescens (15d). CONCLUSION: This study identified two native biocontrol agents Priestia megaterium and Serratia marcescens from the rhizospheric soils of Bundelkhand region of India for control of Fusarium wilt, Botrytis gray mold. In future, efforts should be made to further validate the biocontrol agents in conjugation with nanomaterials for enhancing the synergistic effects in managing the fungal diseases in chickpea. This study will definitely enhance our understanding of these bioagents, and to increase their performance by developing effective formulations, application methods, and integrated strategies.

Assessment of Genetic Diversity and the Population Structure of Species from the Fusarium fujikuroi Species Complex Causing Fusarium Stalk Rot of Maize.

Fusarium stalk rot (FSR), caused by the Fusarium species complex, is an economic threat to maize cultivation all over the world. We investigated the population structure and genetic diversity of Fusarium species obtained from five major maize-growing regions in India. The Tef-1α locus was used for phylogenetic analysis of geographically distinct isolates of Fusarium verticillioides, F. andiyazi, F. proliferatum, F. nygamai, and F. acutatum causing FSR. A phylogenetic tree showed monophyletic, polyphyletic, and paraphyletic groupings reflecting the complex evolutionary history and genetic diversity within the genus. Monophyletic groupings depicting strong bootstrap support were shown to have a single common ancestor and genetic coherence with limited genetic divergence among sequences. Polyphyletic groupings also presented significant genetic differentiation within the F. verticillioides sequences from diverse ecological niches. Nucleotide diversity of moderate level 0.02471 reflected genetic variations within populations that were attributed to factors such as mutation, genetic drift, or varying selection pressures. The Fst value of 0.98205 is particularly indicative of high genetic differentiation, implying that most of the genetic variance is due to differences between populations rather than within them. F. verticillioides, with 57 sequences, showed low genetic diversity with three segregating sites and a low haplotype diversity of 0.19486, suggesting the founder effect, where a reduced population expands from a limited genetic pool. The total data estimates across all populations for haplotype analysis showed 72 sequences, 44 segregating sites, and 9 haplotypes with a haplotype diversity of 0.48513. The evolutionary dynamics showed genetic differentiations among Fusarium species causing FSR. AMOVA indicated high within-population variations, depicting a substantial genetic diversity within individual populations. The results offer a comprehensive framework for discussing the implications of genetic diversity in pathogen management and the evolutionary dynamics of the Fusarium species causing FSR in maize in the Indian subcontinent.

Comparative metagenomic analysis from Sundarbans ecosystems advances our understanding of microbial communities and their functional roles.

The Sundarbans mangrove, located at the mouth of the Ganges and Brahmaputra Rivers, is the world's largest tidal mangrove forest. These mangroves are also one of the most striking sources of microbial diversity, essential in productivity, conservation, nutrient cycling, and rehabilitation. Hence, the main objective of this study was to use metagenome analysis and provide detailed insight into microbial communities and their functional roles in the Sundarbans mangrove ecosystem. A comparative analysis was also done with a non-mangrove region of the Sundarbans ecosystem to assess the capability of the environmental parameters to explain the variation in microbial community composition. The study found several dominant bacteria, viz., Alphaproteobacteria, Actinomycetota, Bacilli, Clostridia, Desulfobacterota, Gammaproteobacteria, and Nitrospira, from the mangrove region. The mangrove sampling site reports several salt-tolerant bacteria like Alkalibacillus haloalkaliphilus, Halomonas anticariensis, and Salinivibrio socompensis. We found some probiotic species, viz., Bacillus clausii, Lactobacillus curvatus, Vibrio mediterranei and Vibrio fluvialis, from the Sundarbans mangrove. Nitrifying bacteria in Sundarbans soils were Nitrococcus mobilis, Nitrosococcus oceani, Nitrosomonas halophila, Nitrospirade fluvii, and others. Methanogenic archaea, viz., Methanoculleus marisnigri, Methanobrevibacter gottschalkii, and Methanolacinia petrolearia, were highly abundant in the mangroves as compared to the non-mangrove soils. The identified methanotrophic bacterial species, viz., Methylobacter tundripaludum, Methylococcus capsulatus, Methylophaga thiooxydans, and Methylosarcina lacus are expected to play a significant role in the degradation of methane in mangrove soil. Among the bioremediation bacterial species identified, Pseudomonas alcaligenes, Pseudomonas mendocina, Paracoccus denitrificans, and Shewanella putrefaciens play a significant role in the remediation of environmental pollution. Overall, our study shows for the first time that the Sundarbans, the largest mangrove ecosystem in the world, has a wide range of methanogenic archaea, methanotrophs, pathogenic, salt-tolerant, probiotic, nitrifying, and bioremediation bacteria.

Metagenomic landscape of sediments of river Ganga reveals microbial diversity, potential plastic and xenobiotic degradation enzymes.

The Ganga is the largest river in India, serves as a lifeline for agriculture, drinking water, and religious rites. However, it became highly polluted due to the influx of industrial wastes and untreated sewages, leading to the decline of aquatic biodiversity. This study investigated the microbial diversity and plastic-xenobiotic degrading enzymes of six sediment metagenomes of river Ganga at Prayagraj (RDG, TSG, SDG) and Devprayag (KRG, BNG, BRG). The water quality parameters, higher values of BOD (1.8-3.7 ppm), COD (23-29.2 ppm) and organic carbon (0.18-0.51%) were recorded at Prayagraj. Comparative analysis of microbial community structure between Prayagraj and Devprayag revealed significant differences between Bacteroidetes and Firmicutes, which emerging as the predominant bacterial phyla across six sediment samples. Notably, their prevalence was highest in the BRG samples. Furthermore, 25 OTUs at genus level were consistent across all six samples. Alpha diversity exhibited minimal variation among samples, while beta diversity indicated an inverse relationship between species richness and diversity. Co-occurrence network analysis established that genera from the same and different groups of phyla show positive co-relations with each other. Thirteen plastic degrading enzymes, including Laccase, Alkane-1 monooxygenase and Alkane monooxygenase, were identified from six sediment metagenomes of river Ganga, which can degrade non-biodegradable plastic viz. Polyethylene, Polystyrene and Low-density Polyethelene. Further, 18 xenobiotic degradation enzymes were identified for the degradation of Bisphenol, Xylene, Toluene, Polycyclic aromatic hydrocarbon, Styrene, Atrazene and Dioxin etc. This is the first report on the identification of non-biodegradable plastic degrading enzymes from sediment metagenomes of river Ganga, India. The findings of this study would help in pollution abatement and sustainable management of riverine ecosystem.

A review on structure-function mechanism and signaling pathway of serine/threonine protein PIM kinases as a therapeutic target.

The proviral integration for the Moloney murine leukemia virus (PIM) kinases, belonging to serine/threonine kinase family, have been found to be overexpressed in various types of cancers, such as prostate, breast, colon, endometrial, gastric, and pancreatic cancer. The three isoforms PIM kinases i.e., PIM1, PIM2, and PIM3 share a high degree of sequence and structural similarity and phosphorylate substrates controlling tumorigenic phenotypes like proliferation and cell survival. Targeting short-lived PIM kinases presents an intriguing strategy as in vivo knock-down studies result in non-lethal phenotypes, indicating that clinical inhibition of PIM might have fewer adverse effects. The ATP binding site (hinge region) possesses distinctive attributes, which led to the development of novel small molecule scaffolds that target either one or all three PIM isoforms. Machine learning and structure-based approaches have been at the forefront of developing novel and effective chemical therapeutics against PIM in preclinical and clinical settings, and none have yet received approval for cancer treatment. The stability of PIM isoforms is maintained by PIM kinase activity, which leads to resistance against PIM inhibitors and chemotherapy; thus, to overcome such effects, PIM proteolysis targeting chimeras (PROTACs) are now being developed that specifically degrade PIM proteins. In this review, we recapitulate an overview of the oncogenic functions of PIM kinases, their structure, function, and crucial signaling network in different types of cancer, and the potential of pharmacological small-molecule inhibitors. Further, our comprehensive review also provides valuable insights for developing novel antitumor drugs that specifically target PIM kinases in the future. In conclusion, we provide insights into the benefits of degrading PIM kinases as opposed to blocking their catalytic activity to address the oncogenic potential of PIM kinases.

An Improved Machine Learning-Based Approach to Assess the Microbial Diversity in Major North Indian River Ecosystems.

The rapidly evolving high-throughput sequencing (HTS) technologies generate voluminous genomic and metagenomic sequences, which can help classify the microbial communities with high accuracy in many ecosystems. Conventionally, the rule-based binning techniques are used to classify the contigs or scaffolds based on either sequence composition or sequence similarity. However, the accurate classification of the microbial communities remains a major challenge due to massive data volumes at hand as well as a requirement of efficient binning methods and classification algorithms. Therefore, we attempted here to implement iterative K-Means clustering for the initial binning of metagenomics sequences and applied various machine learning algorithms (MLAs) to classify the newly identified unknown microbes. The cluster annotation was achieved through the BLAST program of NCBI, which resulted in the grouping of assembled scaffolds into five classes, i.e., bacteria, archaea, eukaryota, viruses and others. The annotated cluster sequences were used to train machine learning algorithms (MLAs) to develop prediction models to classify unknown metagenomic sequences. In this study, we used metagenomic datasets of samples collected from the Ganga (Kanpur and Farakka) and the Yamuna (Delhi) rivers in India for clustering and training the MLA models. Further, the performance of MLAs was evaluated by 10-fold cross validation. The results revealed that the developed model based on the Random Forest had a superior performance compared to the other considered learning algorithms. The proposed method can be used for annotating the metagenomic scaffolds/contigs being complementary to existing methods of metagenomic data analysis. An offline predictor source code with the best prediction model is available at (https://github.com/Nalinikanta7/metagenomics).

Bacteriophages diversity in India's major river Ganga: a repository to regulate pathogenic bacteria in the aquatic environment.

Bacteriophages are key viruses that can kill thousands of harmful microbes generally present at polluted sites. Such bacteriophages are abundantly present in the river Ganga, where millions of people in India and abroad drink its water and take baths every day for spiritual reasons. Besides bacteriophages, several pathogenic and zoonotic microbes are present in the river Ganga. It is interesting to study the diversity and abundance of bacteria and their respective phages present in polluted or non-polluted sites. Thus, the metagenomics study was carried out at the most polluted sites of river Ganga near Kanpur and non-polluted sites at Farakka, which harbors several harmful bacteria and their phages. The results revealed a significantly higher percentage of Microviridae phage family, ssDNA viruses, and Mimiviridae virus family near Kanpur than Farakka. In addition, compared to Kanpur, Farakka has a more significant percentage of Myoviridae, an unidentified phage family, and Retroviridae viral families. Despite heavy drainage of untreated and contaminated effluents from the leather industry, pesticide industry, paper mills, metropolitan cities, and other sources, the vast number of said phages kills several harmful pathogenic microbes in polluted sites to maintain the Ganga water's healing power or natural sterility. In a polluted aquatic environment, the varieties of bacteriophages were identified in the Ganga and their interaction with the microbial host. The taxonomic diversity of several bacteriophages found in pathogenic host systems was investigated to get exceptional knowledge of these small viruses in the aquatic environment.

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.

Plastisphere community assemblage of aquatic environment: plastic-microbe interaction, role in degradation and characterization technologies.

It is undeniable that plastics are ubiquitous and a threat to global ecosystems. Plastic waste is transformed into microplastics (MPs) through physical and chemical disruption processes within the aquatic environment. MPs are detected in almost every environment due to their worldwide transportability through ocean currents or wind, which allows them to reach even the most remote regions of our planet. MPs colonized by biofilm-forming microbial communities are known as the ''plastisphere". The revelation that this unique substrate can aid microbial dispersal has piqued interest in the ground of microbial ecology. MPs have synergetic effects on the development, transportation, persistence, and ecology of microorganisms. This review summarizes the studies of plastisphere in recent years and the microbial community assemblage (viz. autotrophs, heterotrophs, predators, and pathogens). We also discussed plastic-microbe interactions and the potential sources of plastic degrading microorganisms. Finally, it also focuses on current technologies used to characterize those microbial inhabitants and recommendations for further research.

Molecular characterization and structural dynamics of Aquaporin1 from walking catfish in lipid bilayers.

Aquaporin's (AQPs) are the major superfamily of small integral membrane proteins that facilitates transportation of water, urea, ammonia, glycerol and ions across biological cell membranes. Despite of recent advancements made in understanding the biology of Aquaporin's, only few isoforms of aquaporin 1 (AQP1) some of the teleost fish species have been characterized at molecular scale. In this study, we made an attempt to elucidate the molecular mechanism of water transportation in AQP1 from walking catfish (Clarias batrachus), a model species capable of breathing in air and inhabits in challenging environments. Using state-of-the-art computational modelling and all-atoms molecular dynamics simulation, we explored the structural dynamics of full-length aquaporin 1 from walking catfish (CbAQP1) in lipid mimetic bilayers. Unlike AQP1 of human and bovine, structural ensembles of CbAQP1 from MD revealed discrete positioning of pore lining residues at the intracellular end. Snapshots from MD simulation displayed differential dynamics of aromatic/arginine (ar/R) filter and extracellular loop C bridging transmembrane (TM) helix H3 and H4. Distinct conformation of large extracellular loops, loop bridging TM2 domain and HB helix along with positioning of selectivity filter lining residues controls the permeability of water across the bilayer. Moreover, the identified unique and conserved lipid binding sites with 100% lipid occupancy signifies lipid mediated structural dynamics of CbAQP1. All-together, this is the first ever report on structural-dynamics of aquaporin 1 in walking catfish which will be useful to understand the molecular basis of transportation of water and other small molecules under varying degree of hyperosmotic environment.

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.

Structural insights into the RNA interaction with Yam bean Mosaic virus (coat protein) from Pachyrhizus erosus using bioinformatics approach.

Plants are constantly threatened by a virus infection, i.e., Potyviruses, the second largest genus of plant viruses which results in several million-dollar losses in various essential crops globally. Yam bean (Pachyrhizus erosus) is considered to be one of the essential tuberous legume crops holding a great potential source of starch. Yam Bean Mosaic Virus (YBMV) of Potyvirus group belonging to the family potyviridae affects Yam bean and several angiosperms both in the tropical and sub-tropical regions causing large economical losses in crops. In this study, we attempted to understand the sequence-structure relationship and mode of RNA binding mechanism in YBMV CP using in silico integrative modeling and all-atoms molecular dynamics (MD) simulations. The assembly of coat protein (CP) subunits from YBMV and the plausible mode of RNA binding were compared with the experimental structure of CP from Watermelon mosaic virus potyvirus (5ODV). The transmembrane helix region is present in the YBMV CP sequence ranging from 76 to 91 amino acids. Like the close structural-homolog, 24 CPs monomeric sub-units formed YBMV a conserved fold. Our computational study showed that ARG124, ARG155, and TYR151 orient towards the inner side of the virion, while, THR122, GLN125, SER92, ASP94 reside towards the outer side of the virion. Despite sharing very low sequence similarity with CPs from other plant viruses, the strongly conserved residues Ser, Arg, and Asp within the RNA binding pocket of YBMV CP indicate the presence of a highly conserved RNA binding site in CPs from different families. Using several bioinformatics tools and comprehensive analysis from MD simulation, our study has provided novel insights into the RNA binding mechanism in YBMV CP. Thus, we anticipate that our findings from this study will be useful for the development of new therapeutic agents against the pathogen, paving the way for researchers to better control this destructive plant virus.

Community structure and function of microbiomes in polluted stretches of river Yamuna in New Delhi, India, using shotgun metagenomics.

The large population residing in the northern region of India surrounding Delhi mostly depends on water of River Yamuna, a tributary of mighty Ganga for agriculture, drinking and various religious activities. However, continuous anthropogenic activities mostly due to pollution mediated by rapid urbanization and industrialization have profoundly affected river microflora and their function thus its health. In this study, potential of whole-genome metagenomics was exploited to unravel the novel consortia of microbiome and their functional potential in the polluted sediments of the river at Delhi. Analysis of high-quality metagenome data from Illumina NextSeq500 revealed substantial differences in composition of microbiota at different sites dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Chloroflexi phyla. The presence of highly dominant anaerobic bacteria like Dechloromonas aromatica (benzene reducing and denitrifying), Rhodopseudomonas palustris (organic matter reducing), Syntrophus aciditrophicus (fatty acid reducing) and Syntrophobacter fumaroxidans (sulphate reducing) in the polluted river Yamuna signifies the impact of unchecked pollution in declining health of the river ecosystem. A decline in abundance of phages was also noticed along the downstream river Yamuna. Mining of mycobiome reads uncovered plethora of fungal communities (i.e. Nakaseomyces, Aspergillus, Schizosaccharomyces and Lodderomyces) in the polluted stretches due to the availability of higher organic carbon and total nitrogen (%) could be decoded as promising bioindicators of river trophic status. Pathway analysis through KEGG revealed higher abundance of genes involved in energy metabolism (nitrogen and sulphur), methane metabolism, degradation of xenobiotics (Nitrotoluene, Benzoate and Atrazine), two-component system (atoB, cusA and silA) and membrane transport (ABC transporters). Catalase-peroxidase and 4-hydroxybenzoate 3-monooxygenase were the most enriched pollution degrading enzymes in the polluted study sites of river Yamuna. Overall, our results provide crucial insights into microbial dynamics and their function in response to high pollution and could be insightful to the ongoing remediation strategies to clean river Yamuna.

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.

Cloning, characterization and ontogenetic expression profile of RAG-2 and IgM in angelfish (Pterophyllum scalare).

Early larval developmental stages of fish are highly susceptible to opportunistic pathogens until the complete maturation of the lymphoid organs. Knowledge of the expression pattern of important markers of adaptive immune system during the ontogenetic development is essential before vaccinating the fish. In the present study, Pterophyllum scalare (angelfish) was taken to explore the relative expression profile of developmental markers of adaptive immunity, recombination activating gene-2 (RAG-2) and immunoglobulin M (IgM). The fishes were bred and early developmental stages (0-45 days post-hatched) were used to assess the expression profile. The genes, RAG-2 and IgM were cloned and sequenced with the base pair lengths of 1958 bp and 225 bp respectively. The mRNA expression of RAG-2 appeared at insignificant level at the first day of hatching, but the expression was significantly increased from 24 dph (days post-hatching) onwards and reached its peak at 27 dph. The results proved that the maturation of lymphoid organs was completed at 27 dph as the respective protein is involved in the V(D)J recombination, important for the maturation of lymphoid organs. A similar trend was also observed in the mRNA transcript levels of IgM gene and a significantly high expression was detected from 27 dph onwards. The present study suggested that the suitable time for vaccination in P. scalare could be taken at 27 dph, as the maturation and development of lymphoid organs is completed thus helps in stimulating the adaptive response of immunity against any pathogen.

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.

Metagenomic study focusing on antibiotic resistance genes from the sediments of River Yamuna.

Antibiotic resistance is one of the major health concerns of the present century. The direct discharge of urban sewage, hospital effluents, and pharmaceutical wastes increases the concentration of antibiotics in riverine ecosystems. This provides selection pressure for the development of novel antibiotic-resistant strains. In this study, metagenomics approach was employed a for constructing a comprehensive profile of the Antibiotic Resistance Genes (ARGs) identified in the sediments of the Yamuna River. A total of 139 ARGs were identified from 39 microbial species. Abundance analysis revealed that, aminoglycoside, beta-lactam, macrolide, and tetracycline resistance genes were highly abundant in the sediment samples obtained from the Yamuna River. The evolutionary relationships among the ARGs were studied by phylogenetic analyses, which revealed that, the identified resistome comprised eight clusters. Network analysis was performed for investigating the broad-spectrum profiles of the ARGs and their enrichment in different biological functions and pathways. Protein-protein interaction (PPI) analyses revealed that, 76, 36, 18, and 5 Gene Ontology (GO)-terms were significantly enriched in Biological process, Molecular Function, Cellular Component, and KEGG Pathways analysis, respectively. The present study elucidates the ecology of microbial antibiotic resistance in the riverine ecosystem of the Yamuna River and provides novel insights into the environmental hotspots that are amenable to the emergence of ARGs in the contaminated riverine hydrosphere.