Comparative mitochondrial genomics analysis of selected species of Schizothoracinae sub family to explore the differences at mitochondrial DNA level.

A comprehensive analysis of the whole mitochondrial genomes of the Schizothoracinae subfamily of the family Cyprinidae has been revealed for the first time. The species analyzed include Schizothorax niger, Schizothorax esocinus, Schizothorax labiatus and Schizothorax plagoistomus. The total mitochondrial DNA (mtDNA) length was determined to be 16585 bp, 16583 bp, 16582 bp and 16576 bp, respectively with 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 non-coding area genes. The combined mean base compositions of the four species were as follows: A: 29.91 % T: 25.47 % G: 17.65 % C 27.01 %. The range of the GC content is 45-44 %, respectively. All protein coding genes (PCGs) commenced with the typical ATG codon, except for the cytochrome c oxidase subunit 1 (COX1) gene with GTG. The analysis of vital amino acid biosynthesis genes (COX1, ATPase 6, ATPase 8) in four different species revealed no significant differences. All 13 PCGs had Ka/Ks ratios that were all lesser than one, demonstrating purifying selection on those molecules. These tRNA genes were predicted to fold into the typical cloverleaf secondary structures with normal base pairing and ranged in size from 66 to 75 nucleotides. Additionally, the phylogenetic tree analysis revealed that S. esocinus species that was most alike to S. labiatus. This study provides critical data for phylogenetic analysis of the Schizothoracinae subfamily, which will help to resolve taxonomic difficulties and identify evolutionary links. Detailed mtDNA data are an invaluable resource for studying genetic diversity, population structure, and gene flow. Understanding genetic makeup can help inform conservation plans, identify unique populations, and track genetic variation to ensure effective preservation.

Understanding and addressing microplastic pollution: Impacts, mitigation, and future perspectives.

Improper disposal of household and industrial waste into water bodies has transformed them into de facto dumping grounds. Plastic debris, weathered on beaches degrades into micro-particles and releases chemical additives that enter the water. Microplastic contamination is documented globally in both marine and freshwater environments, posing a significant threat to aquatic ecosystems. The small size of these particles makes them susceptible to ingestion by low trophic fauna, a trend expected to escalate. Ingestion leads to adverse effects like intestinal blockages, alterations in lipid metabolism, histopathological changes in the intestine, contributing to the extinction of vulnerable species and disrupting ecosystem balance. Notably, microplastics (MPs) can act as carriers for pathogens, potentially causing impaired reproductive activity, decreased immunity, and cancer in various organisms. Studies have identified seven principal sources of MPs, including synthetic textiles (35%) and tire abrasion (28%), highlighting the significant human contribution to this pollution. This review covers various aspects of microplastic pollution, including sources, extraction methods, and its profound impact on ecosystems. Additionally, it explores preventive measures, aiming to guide researchers in selecting techniques and inspiring further investigation into the far-reaching impacts of microplastic pollution, fostering effective solutions for this environmental challenge.

Behavioural changes, DNA damage and histological alterations in Labeo rohita fingerlings in response to organic-coated silver nanoparticles.

Silver nanoparticles (AgNPs) have garnered significant global attention from researchers due to their unique physicochemical properties and wide-ranging applications in industry and medicine. However, their release into aquatic ecosystems has raised concerns regarding potential ecotoxicological consequences. The present study investigated the effects of polyvinyl pyrrolidone-coated silver nanoparticles on Labeo rohita fingerlings, focusing on behavioural reactions, genotoxic effects, histological changes and bioaccumulation. L. rohita fingerlings were exposed to polyvinyl pyrrolidone-coated silver nanoparticles with sizes ranging from 18 to 29 nm for 7 days at concentrations of 100, 200, 400 and 800 ug/l. The nanoparticle zeta potential was found to be extremely negative, measuring - 55.5 mV for 18 nm and - 31.4 mV for 29 nm. Behavioural abnormalities, including respiratory distress, reduced responsiveness and erratic swimming, were observed in exposed groups compared to controls, with severity increasing with higher nanoparticle concentrations. Genotoxicity assessment revealed significantly higher DNA damage in kidney cells compared to gill cells. Histological examination of gill tissues showed clogging in primary and secondary lamellae, along with distorted anatomy, necrosis and vacuolar atrophy in peripheral tubules of the kidneys. The kidneys exhibited greater nanoparticle accumulation than the gills with prolonged exposure. Moreover, 18 nm AgNPs induced more pronounced DNA damage and histological alterations in the kidney and gill tissues compared to 29 nm nanoparticles. This study elucidates the critical role of monitoring AgNPs in aquatic systems, providing essential data on their behaviour and environmental impacts. The findings highlight the need for improved detection techniques and effective management of AgNP contamination. Future research should focus on developing more sensitive analytical methods, understanding long-term ecological effects and exploring innovative remediation strategies.

In silico designing of multiepitope-based-peptide (MBP) vaccine against MAPK protein express for Alzheimer's disease in Zebrafish.

Understanding the role of the mitogen-activated protein kinases (MAPKs) signalling pathway is essential in advancing treatments for neurodegenerative disorders like Alzheimer's. In this study, we investigate in-silico techniques involving computer-based methods to extract the MAPK1 sequence. Our applied methods enable us to analyze the protein's structure, evaluate its properties, establish its evolutionary relationships, and assess its prevalence in populations. We also predict epitopes, assess their ability to trigger immune responses, and check for allergenicity using advanced computational tools to understand their immunological properties comprehensively. We apply virtual screening, docking, and structure modelling to identify promising drug candidates, analyze their interactions, and enhance drug design processes. We identified a total of 30 cell-targeting molecules against the MAPK1 protein, where we selected top 10 CTL epitopes (PAGGGPNPG, GGGPNPGSG, SAPAGGGPN, AVSAPAGGG, AGGGPNPGS, ATAAVSAPA, TAAVSAPAG, ENIIGINDI, INDIIRTPT, and NDIIRTPTI) for further evaluation to determine their potential efficacy, safety, and suitability for vaccine design based on strong binding potential. The potential to cover a large portion of the world's population with these vaccines is substantial-88.5 % for one type and 99.99 % for another. In exploring the molecular docking analyses, we examined a library of compounds from the ZINC database. Among them, we identified twelve compounds with the lowest binding energy. Critical residues in the MAPK1 protein, such as VAL48, LYS63, CYS175, ASP176, LYS160, ALA61, LEU165, TYR45, SER162, ARG33, PRO365, PHE363, ILE40, ASN163, and GLU42, are pivotal for interactions with these compounds. Our result suggests that these compounds could influence the protein's behaviour. Moreover, our docking analyses revealed that the predicted peptides have a strong affinity for the MAPK1 protein. These peptides form stable complexes, indicating their potential as potent inhibitors. This study contributes to the identification of new drug compounds and the screening of their desired properties. These compounds could potentially help reduce the excessive activity of MAPK1, which is linked to Alzheimer's disease.

Biogenic silver nanoparticles: Synthesis, applications and challenges in food sector with special emphasis on aquaculture.

Aquaculture, a rapidly expanding global food sector faces challenges like pathogenic infections, water quality management and sustainability. Silver nanoparticles (AgNPs) have emerged as promising tools in aquaculture due to their antimicrobial, antiviral and antifungal properties. AgNPs offer alternatives to traditional antimicrobial agents. Their small size and unique physicochemical properties enhance antimicrobial activity, effectively inhibiting pathogen growth and reducing disease incidence in aquatic organisms. Additionally, AgNPs can improve water quality by catalyzing the removal of pollutants, heavy metals and nutrients, reducing environmental impacts. Despite their potential benefits, several challenges and knowledge gaps exist in the utilization of AgNPs in aquaculture. Addressing challenges related to regulation, sustainability and environmental impact will be crucial for realizing their full potential in the industry. Therefore, the present review aims to provide insight into the role of AgNPs, its challenges in aquaculture and also highlights key areas for future research.

Gene expression profiling and physiological adaptations of pearl spot (Etroplus suratensis) under varying salinity conditions.

Eutroplus suratensis (Pearl spot) is naturally found in estuarine environments and has been noted to have a high salinity tolerance. By examining the impact of various salinity levels on the growth and survival of pearl spot, the present study aims to enhance aquaculture profitability by assessing their adaptability and physiological adjustments to changes in salinity and determining their potential to acclimate to a broad range of salinity regimes. Results revealed no mortality in the control group (0 ppt), and in 15, 25 and 35 ppt treatment groups. However, the remaining groups (45, 60, and 75 ppt) showed differing levels of mortality with 44 % mortality observed in the 45 ppt group and 100 % mortality in both the 60 and 75 ppt groups. The expression analysis showed that liver IGF-1 mRNA expression increased by 2.6-fold at 15 ppt, and HSP70 mRNA expression in the liver also showed a significant increase with rising salinity levels. In addition, OSTF1 expression exhibited an increase at 15 ppt, whereas SOD and CAT expression reached their highest levels at 25 ppt. At 15 ppt, the expression of NKA mRNA increased significantly by 2.8-fold. The study's overall findings suggested that utilizing a salinity level of 15 ppt for pearl spot production could be viable for profitable aquaculture.

Multifunctional analysis and antimicrobial activity of Adhatoda vasica: a traditional medicinal plant.

OBJECTIVES: Antibiotic resistance is rising, prompting innovative strategies for eradicating the epidemic. This study investigated the antibacterial properties of the leaves of a widely used medicinal plant, Adhatoda vasica. METHODS: The plant's polar (water, methanol) and non-polar (hexane) extracts were tested against several different bacterial strains using the disc diffusion technique. RESULTS: In a study, it was found that the water extract had the greatest inhibitory effect on Staphylococcus simulans and Staphylococcus aureus, with minimum inhibitory concentrations of 16.444 and 19.315 g/mL, respectively. Gram-negative strains were more susceptible to plant extracts than Gram-positive strains. The phytochemical analysis indicated the presence of secondary metabolites such as alkaloids, saponins, flavonoids, tannins, and steroids, where absorbance was recorded at 415 nm. The water extract had the highest amount of phenolics, with a total phenolic content of 53.92 0.47 mg and a total flavonoid content of 7.25 0.08 mg. Results suggest that the extract may have potential therapeutic applications for antimicrobial properties. CONCLUSIONS: The study concluded that the extract's phenolic group of secondary metabolites were responsible for its antibacterial activity. The study highlights A. vasica as a promising source for discovering new and effective antibacterial compounds.

Exploring the multifunctional roles of quantum dots for unlocking the future of biology and medicine.

With recent advancements in nanomedicines and their associated research with biological fields, their translation into clinically-applicable products is still below promises. Quantum dots (QDs) have received immense research attention and investment in the four decades since their discovery. We explored the extensive biomedical applications of QDs, viz. Bio-imaging, drug research, drug delivery, immune assays, biosensors, gene therapy, diagnostics, their toxic effects, and bio-compatibility. We unravelled the possibility of using emerging data-driven methodologies (bigdata, artificial intelligence, machine learning, high-throughput experimentation, computational automation) as excellent sources for time, space, and complexity optimization. We also discussed ongoing clinical trials, related challenges, and the technical aspects that should be considered to improve the clinical fate of QDs and promising future research directions.

Identification of RdRp inhibitors against SARS-CoV-2 through E-pharmacophore-based virtual screening, molecular docking and MD simulations approaches.

The outbreak of novel Coronavirus, an enduring pandemic declared by WHO, has consequences to an alarming ongoing public health menace which has already claimed several million human lives. In addition to numerous vaccinations and medications for mild to moderate COVID-19 infection, lack of promising medication or therapeutic pharmaceuticals remains a serious concern to counter the ongoing coronavirus infections and to hinder its dreadful spread. Global health emergencies have called for urgency for potential drug discovery and time is the biggest constraint apart from the financial and human resources required for the high throughput drug screening. However, computational screening or in-silico approaches appeared to be an effective and faster approach to discover potential molecules without sacrificing the model animals. Accumulated shreds of evidence on computational studies against viral diseases have revealed significance of in-silico drug discovery approaches especially in the time of urgency. The central role of RdRp in SARS-CoV-2 replication makes it promising drug target to curtain on going infection and its spread. The present study aimed to employ E-pharmacophore-based virtual screening to reveal potent inhibitors of RdRp as potential leads to block the viral replication. An energy-optimised pharmacophore model was generated to screen the Enamine REAL DataBase (RDB). Then, ADME/T profiles were determined to validate the pharmacokinetics and pharmacodynamics properties of the hit compounds. Moreover, High Throughput Virtual Screening (HTVS) and molecular docking (SP & XP) were employed to screen the top hits from pharmacophore-based virtual screening and ADME/T screen. The binding free energies of the top hits were calculated by conducting MM-GBSA analysis followed by MD simulations to determine the stability of molecular interactions between top hits and RdRp protein. These virtual investigations revealed six compounds having binding free energies of -57.498, -45.776, -46.248, -35.67, -25.15 and -24.90 kcal/mol respectively as calculated by the MM-GBSA method. The MD simulation studies confirmed the stability of protein ligand complexes, hence, indicating as potent RdRp inhibitors and are promising candidate drugs to be further validated and translated into clinics in future.

Bioinformatics approaches and big data analytics opportunities in improving fisheries and aquaculture.

Aquaculture has witnessed an excellent growth rate during the last two decades and offers huge potential to provide nutritional as well as livelihood security. Genomic research has contributed significantly toward the development of beneficial technologies for aquaculture. The existing high throughput technologies like next-generation technologies generate oceanic data which requires extensive analysis using appropriate tools. Bioinformatics is a rapidly evolving science that involves integrating gene based information and computational technology to produce new knowledge for the benefit of aquaculture. Bioinformatics provides new opportunities as well as challenges for information and data processing in new generation aquaculture. Rapid technical advancements have opened up a world of possibilities for using current genomics to improve aquaculture performance. Understanding the genes that govern economically relevant characteristics, necessitates a significant amount of additional research. The various dimensions of data sources includes next-generation DNA sequencing, protein sequencing, RNA sequencing gene expression profiles, metabolic pathways, molecular markers, and so on. Appropriate bioinformatics tools are developed to mine the biologically relevant and commercially useful results. The purpose of this scoping review is to present various arms of diverse bioinformatics tools with special emphasis on practical translation to the aquaculture industry.

A comprehensive genomic study, mutation screening, phylogenetic and statistical analysis of SARS-CoV-2 and its variant omicron among different countries.

BACKGROUND: With the rapid development of the genomic sequence data for the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants Delta (B.1.617.2) and Omicron (B.1.1.529), it is vital to successfully identify mutations within the genome. OBJECTIVE: The main objective of the study is to investigate the full-length genome mutation analysis of 157 SARS-CoV-2 and its variant Delta and Omicron isolates. This study also provides possible effects at the structural level to understand the role of mutations and new insights into the evolution of COVID-19 and evaluates the differential level analysis in viral genome sequence among different nations. We have also tried to offer a mutation snapshot for these differences that could help in vaccine formulation. This study utilizes a unique and efficient method of targeting the stable genes for the drug discovery approach. METHODS: Complete genome sequence information of SARS-CoV-2, Delta, and Omicron from online resources were used to predict structure domain identification, data mining, and screening; employing different bioinformatics tools. BioEdit software was used to perform their genomic alignments across countries and a phylogenetic tree as per the confidence of 500 bootstrapping values was constructed. Heterozygosity ratios were determined in-silico. A minimum spanning network (MSN) of selected populations was determined by Bruvo's distance role-based framework. RESULTS: Out of all 157 different strains of SARS-CoV-2 and its variants, and their complete genome sequences from different countries, Corona nucleoca and DUF5515 were observed to be the most conserved domains. All genomes obtained changes in comparison to the Wuhan-Hu-1 strain, mainly in the TRS region (CUAAAC or ACGAAC). We discovered 596 mutations in all genes, with the highest number (321) found in ORF1ab (QHD43415.1), or TRS site mutations found only in ORF7a (1) and ORF10 (2). The Omicron variant has 30 mutations in the Spike protein and has a higher alpha-helix shape (23.46%) than the Delta version (22.03%). T478 was also discovered to be a prevalent polymorphism in Delta and Omicron variations, as well as genomic gaps ranging from 45 to 65aa. All 157 sequences contained variations and conformed to Nei's Genetic distance. We discovered heterozygosity (Hs) 0.01, mean anticipated Hs 0.32, the genetic diversity index (GDI) 0.01943989, and GD within population 0.01266951. The Hedrick value was 0.52324978, the GD coefficient was 0.52324978, the average Hs was 0.01371452, and the GD coefficient was 0.52324978. Among other countries, Brazil has the highest standard error (SE) rate (1.398), whereas Japan has the highest ratio of Nei's gene diversity (0.01). CONCLUSIONS: The study's findings will assist in comprehending the shape and kind of complete genome, their streaming genomic sequences, and mutations in various additions of SARS-CoV-2, as well as its different variant strains like Omicron. These results will provide a scientific basis to design the vaccines and understand the genomic study of these viruses.

Effect of the combination of biological, chemical control and agronomic technique in integrated management pea root rot and its productivity.

Root rot of pea caused by Fusarium spp. is one of the important diseases of pea (Pisum sativum L.). The causal fungus of the disease isolated from naturally infected pea plants was identified as Fusarium solani f. sp. pisi (Jones). Evaluation of four bio agents and nine fungicides was done in vitro against Fusarium solani. Trichoderma harzianum was the most effective bio agent in inhibiting the mycelial growth of F. solani by (82.62%). Carbendazim 50 WP was the most effective fungicide in inhibiting the mycelial growth of F. solani by (91.06%). Carbendazim at the rate of 0.1% and T. harzianum at concentration of 109 cfu when used as seed treatment under field conditions were evaluated along with three planting techniques v.i.z, raised beds, ridges and flat beds. It was found that Carbendazim at the rate of 0.1% when given as seed treatment in raised beds exhibited the lowest disease incidence (10.97%), intensity (2.89%) and the maximum pod yield (89.63 q ha-1) as compared to control.

Structural, genomic information and computational analysis of emerging coronavirus (SARS-CoV-2).

Background: The emerging viral pandemic worldwide is associated with a novel coronavirus, SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). This virus is said to emerge from its epidemic center in Wuhan, China, in 2019. Coronaviruses (CoVs) are single-stranded, giant, enveloped RNA viruses that come under the family of coronaviridae and order Nidovirales which are the crucial pathogens for humans and other vertebrates. Main body: Coronaviruses are divided into several subfamilies and genera based on the genomic structure and phylogenetic relationship. The name corona is raised due to the presence of spike protein on the envelope of the virus. The structural and genomic study revealed that the total genome size of SARS-CoV-2 is from 29.8 kb to 29.9 kb. The spike protein (S) is a glycoprotein that attaches to the receptor of host cells for entry into the host cell, followed by the attachment of virus RNA to the host ribosome for translation. The phylogenetic analysis of SARS-CoV-2 revealed the similarity (75-88%) with bat SARS-like coronavirus. Conclusion: The sign and symptoms of novel severe acute respiratory syndrome coronavirus 2 are also discussed in this paper. The worldwide outbreak and prevention from severe acute respiratory syndrome coronavirus 2 are overviewed in the present article. The latest variant of coronavirus and the status of vaccines are also overviewed in the present article.

Molecular modeling, docking and dynamic simulations of growth hormone receptor (GHR) of Labeo rohita.

Growth hormones (GH) have diverse functions like growth promotion, metabolism, appetite, reproduction and social behavior in vertebrates, which is mediated through the growth hormone receptor (GHR). This work was aimed to analyze structural features, homology modeling and molecular docking of Labeo rohita GHR protein. A physicochemical characteristic, like molecular weight was 67.2 kDa and hydropathicity was 0.336. Protein modeling and structure confirmation of L. rohita GHR protein showed 92.7% residues are in the favored region. Selection of ligands and molecular docking shown Melengestrol and Riboflavin ligand showed uppermost binding energy values -7.8 and -7.3 kcal/mol. Molecular interactions describe conventional hydrogen bonding of Melengestrol was observed with VAL94, GLU97, GLU95, TRP57, PHE33, THR34, PRO35, ASP36, PRO37, ARG49, GLY292, LYS291, ILE290, ALA287, LYS289 residues. Riboflavin hydrogen bonds interaction was at PRO37, ASP36, PRO35, THR34, ARG49, SER144, VAL443, GLN442, PRO284, ASP294, ILE285, PRO286, SER408, ALA287, GLY292, LYS291, ILE290, PRO288, LYS287. Molecular dynamics simulation outcomes revealed that complex 2 (Riboflavin and GHR protein) is better than complex1 (Melengestrol and GHR protein). Overall, the results of the present work lead identification of novel molecules that may be agonistic of growth hormone receptor protein and can be used to surge growth in fish. Communicated by Ramaswamy H. Sarma.

Genome wide identification, phylogeny, and synteny analysis of sox gene family in common carp (Cyprinus carpio).

Common carp (Cyprinus carpio) is a commercial fish species valuable for nutritious components and plays a vital role in human healthy nutrition. The SOX (SRY-related genes systematically characterized by a high-mobility group HMG-box) encoded important gene regulatory proteins, a family of transcription factors found in a broad range of animal taxa and extensively known for its contribution in multiple developmental processes including contribution in sex determination across phyla. In our current study, we initially accomplished a genome-wide analysis to report the SOX gene family in common carp fish based on available genomic sequences of zebrafish retrieved from gene repository databases, we focused on the global identification of the Sox gene family in Common carp among wide range of vertebrates and teleosts based on bioinformatics tools and techniques and explore the evolutionary relationships. In our results, a total of 27 SOX (high-mobility group HMG-box) domain genes were identified in the C. carp genome. The full length sequences of SOX genes ranging from 3496 (SOX6) to 924bp (SOX17b) which coded with putative proteins series from 307 to 509 amino acids and all gene having exon number expect SOX9 and SOX13. All the SOX proteins contained at least one conserved DNA-binding HMG-box domain and two (SOX7 and SOX18) were found C terminal. The Gene ontology revealed SOX proteins maximum involvement is in metabolic process 49.796 %, average in biological regulation 45.188 %, biosynthetic process (19.992 %), regulation of cellular process 39.68, 45.508 % organic substance metabolic process, multicellular organismal process 23.23 %,developmental process 21.74 %, system development 16.59 %, gene expression 16.05 % and 14.337 % of RNA metabolic process. Chromosomal location and syntanic analysis show all SOX gene are located on different chromosomes and apparently does not fallow the unique pattern. The maximum linkage of chromosome is (2) on Unplaced Scaffold region. Finally, our results provide important genomic suggestion for upcoming studies of biochemical, physiological, and phylogenetic understanding on SOX genes among teleost.

Identification, functional characterization and expression profiling of cytochrome p450 1A (CYP1A) gene in Labeo rohita against emamectin benzoate.

The cytochrome p450 1A (CYP1A) plays vital role in detoxification of xenobiotic compounds in living organisms. In the present study, full-length CYP1A gene was sequenced from liver of Labeo rohita and mRNA expression analysis were carried out at 0, 2, 4, 8, 12, 24, 48, 72, 96 and 120 h (h) time points after emamectin benzoate treatment. The full-length cDNA sequence of CYP1A was 1741 bp which consist of open reading frame (ORF) of 1618 bp, 5'-untranslated region (UTR) 48 bp and 75 bp 3'-UTR respectively. ORF encodes 526 amino acids with a molecular mass a 59.05 kDa and an isoelectric point of 8.74. The subcellular localization confirmed presence of the CYP1A protein was higher in plasma membrane (45.8%), followed by the mitochondrial region (13.9%) and nuclear region (9.2%). The CYP1A protein interaction was found to intermingle more with other CYP family proteins. Analysis of tissue distribution revealed that CYP1A gene was predominantly expressed in the liver compared to other tissues kidney, gills, muscle and intestine. Furthermore, present study reveals that CYP1A mRNA level in emamectin benzoate treated group @ 20 mgkg-1 body was significantly (p < 0.05) higher compared with the control. The CYP1A mRNA expression levels were found upregulating with time and highest expression levels at 24 h. Histological examination found that emamectin benzoate treated liver revealed vacuolisation, hepatocyte infiltrations, cytoplasmic degeneration of hepatocytes compared to control. Overall, present results lay a strong basis for CYP1A is important biomarker for drug detoxification in aquatic animals.

Molecular and computational analysis of Ghrelin, growth hormone Secretagogues receptor and mRNA expression of Growth-related genes after exogenous administered ghrelin peptide in Labeo rohita.

Ghrelin is a peptide hormone secreted primarily by the stomach and is involved in controlling growth by governing different functions in vertebrates including feed intake and metabolism in vertebrates. This work was aimed to identify sequences of ghrelin gene and growth hormone secretagogue receptor (GHSR) in Labeo rohita. The full-length cDNA sequence of ghrelin is 453 bp including 5'-untranslated region (UTR) of 65 bp, 3'-UTR of 76 bp with a poly-A frame. An open reading frame (ORF) is 312 bp, which encodes a peptide of 103 amino acid residues. A secondary structure of GHSR protein consists of alpha helix 66.0%, 16% disordered and 43% transmembrane helix. Molecular docking and interaction between synthetic ghrelin peptides and GHSR in the contact map revealed 19 amino acid residues closer than 4.5 Šdistance. The mRNA expression level of ghrelin, leptin, GHSR, growth hormone releasing hormone (GHRH) and insulin growth factor-I (IGF-1) revealed significant changes (p < 0.05), in the different treatments. The outcome of the present work contributes to understanding the role of ghrelin and its mechanism of action in regulating the expression of growth-related genes and feed intake in fish.

Structural analysis, molecular docking and molecular dynamics simulations of G-protein-coupled receptor (kisspeptin) in fish.

Kisspeptins are neuropeptide that has emerged as an essential gatekeeper for reproduction and onset of puberty in higher vertebrates including fish. In present study, structural analysis, molecular docking and molecular dynamics simulations of kisspeptin receptor (kiss2r) were carried out, which is a G-protein-coupled receptor. An open reading frame of kiss2r is 1101 bp encoding a putative protein of 366 amino acids. Secondary structure protein consists of alpha helix 69.70%, beta-turn 2%, disordered 18% and 43% transmembrane helix. Sub-cellular localization and gene ontology revealed kiss2r protein is maximum localized in the plasma membrane (99.1%) with score of 4.958 and gene ontology analysis showed molecular function of 89.8%, biological process 30.6% and cellular component 41.2%. Homology modeling and structure validation of kiss2r confirm 97.5% residues are in the favored region and 2.5% residues are in the allowed region. Virtual screening of ligands and molecular docking revealed 2-(4-(2-Carboxyethyl) phenethylamino) 5'-N-ethylcarboxamidoadenosine and N-ethyl-5'-carboxamido adenosine ligand exhibited highest binding energy values 9.437 and 7.476 kcal/mol. Molecular interactions depict conventional hydrogen bonding with GLU197 THR198 GLN288 HIS297 LYS303 and TYR313 residues. Molecular dynamic simulation results revealed that complex 2 (N-ethyl-5'-carboxamido adenosine and kiss2r protein) is better than complex 1 (2-(4-(2-Carboxyethyl) phenethylamino)-5'-N-ethylcarboxamidoadenosine and kiss2r protein) and its connotation in drug designing. The outcome of this work sheds light on the protein modeling, molecular docking and virtual screening of agonist ligands against kiss2 and thus may significantly contribute in designing and optimizing therapeutic strategies to cure various reproductive dysfunctions in fish. Abbreviations3-Dthree-dimensionala.aAmino acidBLASTBasic local alignment search toolAMBERAssisted Model Building with Energy RefinementCDScoding sequenceCIDCompound identification numberDOPEDiscrete optimized protein energyGnRHGonadotropin-releasing hormoneGPR54G protein-coupled receptor 54GROMACSGroningen Machine for Chemicals SimulationsGUIGraphical user interfaceHPGHypothalamic-pituitary-gonadalKiss1rkisspeptin1 receptorkiss2rkisspeptin2 receptorMEGAMolecular Evolutionary Genetics Analysis.MDMolecular dynamicsNCBINational Center for Biotechnology InformationORFOpen reading framePDBProtein Data BankRMSDRoot-mean-square deviationSBDDStructure-based drug designingTMDsTransmembrane domainsYASARAYet Another Scientific Artificial Reality ApplicationCommunicated by Ramaswamy H. Sarma.

Genome-Wide identification of doublesex and Mab-3-Related transcription factor (DMRT) genes in nile tilapia (oreochromis niloticus).

Doublesex and Mab-3-related transcription factor (DMRT) gene family is extensively known for its contribution in sex determination and differentiation across phyla. Here we report the identification of five DM (doublesex and mab-3) domain genes in the Nile tilapia which includes DMRT1, DMRTa2, DMRT2a, DMRT2b and DMRT3a. The full-length sequence of DMRT genes ranges from 3526 (DMRTA2) to 1471bp (DMRT1) which encode putative proteins series from 469 to 372 amino acids. All the DMRT proteins contained at least one conserved DNA-binding DM domain. Sub-cellular localization and gene ontology revealed DMRT1 protein is maximum localized in nuclear region and gene ontology analysis showed the molecular function of 48.2%, biological process 43.6% and cellular component 25%. Chromosomal location and synteny analysis displayed that DMRT genes mostly cluster linkage group 12. Altogether, our findings provide vital genomic information for future studies of biochemical, physiological, and phylogenetic studies on DMRT genes in teleost.

Comprehensive review on wastewater discharged from the coal-related industries - characteristics and treatment strategies.

Wastewaters discharged from various coal-related activities deteriorate fresh water quality and inflict possibilities of groundwater contamination. Their characteristics mostly depend on the parent coal properties, though some of the pollutants are cyanide, thiocyanate, ammonia, phenol, heavy metals and suspended solids. This paper has reviewed the treatment techniques along with the characteristics of all such kinds of wastewater and also identified the challenges and future perspectives. Primarily, demineralization of coal can attenuate and control release of pollutants in wastewaters if implemented successfully. Mine water from non-lignite mines can be purified using simple techniques, for its reutilization. Acidic mine water and leachates can be treated using passive bioreactors with microbial activity, different organic substrates and limestone drains. Additionally bio-electrochemical systems, membranes, macrocapsules, zeolite filters, ores, physical barriers, and aquatic plants can also be used at various stages. Coal washery wastewater can be treated using natural coagulants obtained from plant extracts along with conventional coagulants. Nitrification and denitrification bacteria fixed in reactors along with activated carbon and zero-valent iron can treat coke oven wastewater. Some other sophisticated techniques are vacuum distillation, super critical oxidation, nanofiltration and reverse osmosis. Practical use of these methods, wisely in an integrated way, can reduce freshwater consumption.