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Hamdy SA, Prabha R, Singh DP, Farag MA. Cardamom seed bioactives: A review of agronomic factors, preparation, extraction and formulation methods based on emerging technologies to maximize spice aroma economic value and applications. Food Chem 2025; 462:141009. [PMID: 39213971 DOI: 10.1016/j.foodchem.2024.141009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 07/29/2024] [Accepted: 08/25/2024] [Indexed: 09/04/2024]
Abstract
Cardamom seed (Elettaria cardamomum (L.)) is a well-appreciated spice in food and pharmaceutical industries owing to its unique rich flavor dominated by oxygenated monoterpenoids, α-terpinyl acetate and 1,8-cineole, to which most of the quality of cardamom essential oil (CEO) is attributed. CEO output is greatly influenced by different agronomic factors, processing, and EO extraction methods. In that context, the goal of this study is to provide an overarching review regarding emerged technologies along with their optimization parameters to achieve optimal oil yield with the best flavor quality. Furthermore, the recent approaches employed in CEO stabilization were highlighted alongside their pharmaceutical and food applications. Moreover, the different aspects of superlative CEO production including agricultural aspects, climatic requirements, and processing methods were also explained.
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Kumar K, Durgesh K, Anjoy P, Srivastava H, Tribhuvan KU, Sevanthi AM, Singh A, Prabha R, Sharma S, Joshi R, Jain PK, Singh NK, Gaikwad K. Transcriptional Reprogramming and Allelic Variation in Pleiotropic QTL Regulates Days to Flowering and Growth Habit in Pigeonpea. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39704095 DOI: 10.1111/pce.15322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2024] [Revised: 10/16/2024] [Accepted: 11/26/2024] [Indexed: 12/21/2024]
Abstract
The present study investigated the linkage between days to flowering (DTF) and growth habit (GH) in pigeonpea using QTL mapping, QTL-seq, and GWAS approaches. The linkage map developed here is the largest to date, spanning 1825.56 cM with 7987 SNP markers. In total, eight and four QTLs were mapped for DTF and GH, respectively, harbouring 78 pigeonpea orthologs of Arabidopsis flowering time genes. Corroboratively, QTL-seq analysis identified a single linked QTL for both traits on chromosome 3, possessing 15 genes bearing genic variants. Together, these 91 genes were clustered primarily into autonomous, photoperiod, and epigenetic pathways. Further, we identified 39 associations for DTF and 111 associations for GH through GWAS in the QTL regions. Of these, nine associations were consistent and constituted nine haplotypes (five late, two early, one each for super-early and medium duration). The involvement of multiple genes explained the range of allelic effects and the presence of multiple LD blocks. Further, the linked QTL on chromosome 3 was fine-mapped to the 0.24-Mb region with an LOD score of 8.56, explaining 36.47% of the phenotypic variance. We identified a 10-bp deletion in the first exon of TFL1 gene of the ICPL 20338 variety, which may affect its interaction with the Apetala1 and Leafy genes, resulting in determinate GH and early flowering. Further, the genic marker developed for the deletion in the TFL1 gene could be utilized as a foreground marker in marker-assisted breeding programmes to develop early-flowering pigeonpea varieties.
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Lakhani KG, Hamid R, Gupta S, Prajapati P, Prabha R, Patel S, Suthar KP. Exploring the therapeutic mechanisms of millet in obesity through molecular docking, pharmacokinetics, and dynamic simulation. Front Nutr 2024; 11:1453819. [PMID: 39494311 PMCID: PMC11528469 DOI: 10.3389/fnut.2024.1453819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 09/26/2024] [Indexed: 11/05/2024] Open
Abstract
Obesity, a prevalent global health concern, is characterized by excessive fat accumulation, which confers significant nutritional and health risks, including a shortened lifespan and diminished wellbeing. Central to the regulation of energy balance and food intake is the fat mass and obesity-associated (FTO) protein, which modulates the interplay between caloric consumption and energy expenditure. Given its pivotal role in obesity regulation, the identification of effective inhibitors targeting the FTO protein is imperative for developing therapeutic interventions. Currently available anti-obesity drugs are often plagued by undesirable side effects. In contrast, natural plant-derived bioactive compounds are gaining prominence in the pharmaceutical industry due to their efficacy and lower incidence of adverse effects. Little Millet, a traditional cereal known for its rich nutritional profile and high satiety index, was investigated in this study using molecular docking and dynamics simulation approach for its potential as an anti-obesity agent. Our research demonstrates that four bioactive compounds from Little Millet exhibit superior binding energies ranging from 7.22 to 8.83 kcal/mol, compared to the standard anti-obesity drug, orlistat, which has a binding energy of 5.96 kcal/mol. These compounds fulfilled all drug-like criteria, including the Lipinski, Ghose, Veber, Egan, and Muegge rules, and exhibited favorable profiles in terms of distribution, metabolism, and prolonged half-life without toxicity. Conversely, orlistat was associated with hepatotoxicity, a reduced half-life, and multiple violations of drug-likeness parameters, undermining its efficacy. Molecular dynamics simulations and Gibbs free energy assessments revealed that the four identified compounds maintain stable interactions with key residues in the FTO protein's active site. We propose further validation through extensive In vitro, In vivo, and clinical studies to ascertain the therapeutic potential of these compounds in combating obesity.
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Kumar D, Venkadesan S, Prabha R, Begam S, Dutta B, Mishra DC, Chaturvedi KK, Jha GK, Solanke AU, Sevanthi AM. RiceMetaSys: Drought-miR, a one-stop solution for drought responsive miRNAs-mRNA module in rice. Database (Oxford) 2024; 2024:baae076. [PMID: 39167719 PMCID: PMC11338179 DOI: 10.1093/database/baae076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/27/2024] [Accepted: 08/08/2024] [Indexed: 08/23/2024]
Abstract
MicroRNAs are key players involved in stress responses in plants and reports are available on the role of miRNAs in drought stress response in rice. This work reports the development of a database, RiceMetaSys: Drought-miR, based on the meta-analysis of publicly available sRNA datasets. From 28 drought stress-specific sRNA datasets, we identified 216 drought-responsive miRNAs (DRMs). The major features of the database include genotype-, tissue- and miRNA ID-specific search options and comparison of genotypes to identify common miRNAs. Co-localization of the DRMs with the known quantitative trait loci (QTLs), i.e., meta-QTL regions governing drought tolerance in rice pertaining to different drought adaptive traits, narrowed down this to 37 promising DRMs. To identify the high confidence target genes of DRMs under drought stress, degradome datasets and web resource on drought-responsive genes (RiceMetaSys: DRG) were used. Out of the 216 unique DRMs, only 193 had targets with high stringent parameters. Out of the 1081 target genes identified by Degradome datasets, 730 showed differential expression under drought stress in at least one accession. To retrieve complete information on the target genes, the database has been linked with RiceMetaSys: DRG. Further, we updated the RiceMetaSys: DRGv1 developed earlier with the addition of DRGs identified from RNA-seq datasets from five rice genotypes. We also identified 759 putative novel miRNAs and their target genes employing stringent criteria. Novel miRNA search has all the search options of known miRNAs and additionally, it gives information on their in silico validation features. Simple sequence repeat markers for both the miRNAs and their target genes have also been designed and made available in the database. Network analysis of the target genes identified 60 hub genes which primarily act through abscisic acid pathway and jasmonic acid pathway. Co-localization of the hub genes with the meta-QTL regions governing drought tolerance narrowed down this to 16 most promising DRGs. Database URL: http://14.139.229.201/RiceMetaSys_miRNA Updated database of RiceMetaSys URL: http://14.139.229.201/RiceMetaSysA/Drought/.
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Gouda MNR, D S, Gaikwad K, Prabha R, Kumar A, Subramanian S. Elucidation of ejaculatory bulb proteins in Bemisia tabaci Asia-1 and Asia II-1 and confirmation of their mating transfer via RNAi. Mol Biol Rep 2024; 51:861. [PMID: 39068620 DOI: 10.1007/s11033-024-09816-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND Bemisia tabaci, a significant agricultural pest in Asia, contains distinct genetic groups, Asia-1 and Asia II-1. Understanding its reproductive biology, particularly the role of ejaculatory bulb proteins (EBPs) in mating, is crucial. However, EBPs in B. tabaci were not well characterised until this study. METHODS AND RESULTS The EBPs have been characterised in the Asia-1 and Asia II-1 genetic groups of the whitefly B. tabaci, prevalent in Asia. The transcriptomic analysis yielded over 40,000,000 and 30,000,000 annotated transcripts, respectively, from Asia II-1 and Asia-1. Differential gene expression revealed the presence of 270 upregulated and 198 downregulated genes, with significant differences between these two genetic groups. Orphan genes (1992 numbers) were identified in both genetic groups. We report, for the first time, full-length sequences of EBP genes from B. tabaci. The 10 EBPs each deduced in B. tabaci Asia-1 and Asia II-1 are structurally akin to chemosensory proteins having four conserved cysteine residues. Additionally, we did domain analysis, protein structure prediction, mapping of these EBPs in the chromosomes of B. tabaci, and phylogenetic analysis to track their evolutionary lineage. We have specifically demonstrated the transfer of EBPs from males to females during mating using qPCR and further validated the transfer of EBPs through RNAi. Specifically, we targeted the highly expressed EBPs (EBP-3, 7, and 8 in BtAsia1; EBP-8, 9, and 10 in BtAsia II-1) through feeding bioassays of dsRNAs. Tracking by qPCR revealed that the females, when mated with dsRNA-treated males, did not show expression of the specific EBP, suggesting that the silencing of these genes in males hinders the transfer of EBP to females during mating. CONCLUSION Our findings provide novel insights into the genomic contours of EBPs in B. tabaci and underscore the potential of RNAi-based strategies for pest management by disrupting the reproductive processes.
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Deepthi RV, Arumadi M, Eriyat V, Mathew SK, Mathew BS, Agarwal I, Prabha R. Exposure to Mycophenolic Acid and Its Clinical Response in an Indian Pediatric Population with Nephrotic Syndrome. Indian J Nephrol 2024; 34:323-327. [PMID: 39156858 PMCID: PMC11326783 DOI: 10.25259/ijn_390_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/18/2023] [Indexed: 08/20/2024] Open
Abstract
Background Children with nephrotic syndrome experience many side effects and frequent relapses when treated with steroids and other drugs. Mycophenolic acid (MPA) is one of the effective and least toxic drug for the treatment of nephrotic syndrome. This drug needs to be monitored for maximal efficacy and minimal toxicity. The therapeutic reference range for this drug is not established for the aforementioned patient population of Indian origin. Materials and Methods In this observational study, children with nephrotic syndrome on mycophenolate mofetil were followed up for a minimum duration of three months. Following this, their clinical status (relapse/remission) was determined and the mycophenolate exposure was measured for over 12 hours. Results A total of 34 participants were included, with 17 (50%) in relapse. Median MPA Area under the curve over 12 hours (AUC0-12h) (36.5 µg·h/ml) in the remission group differed significantly compared to that in the relapse group (17.2 µg·h/ml). Conclusion Higher exposure to MPA AUC0-12h is associated with clinical remission of pediatric nephrotic syndrome.
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Kumar S, Behera SK, Gururaj K, Chaurasia A, Murmu S, Prabha R, Angadi UB, Pawaiya RS, Rai A. In silico mutation of aromatic with aliphatic amino acid residues in Clostridium perfringens epsilon toxin (ETX) reduces its binding efficiency to Caprine Myelin and lymphocyte (MAL) protein receptors. J Biomol Struct Dyn 2024; 42:2257-2269. [PMID: 37129165 DOI: 10.1080/07391102.2023.2204362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/11/2023] [Indexed: 05/03/2023]
Abstract
Enterotoxaemia (ET) is a severe disease that affects domestic ruminants, including sheep and goats, and is caused by Clostridium perfringens type B and D strains. The disease is characterized by the production of Epsilon toxin (ETX), which has a significant impact on the farming industry due to its high lethality. The binding of ETX to the host cell receptor is crucial, but still poorly understood. Therefore, the structural features of goat Myelin and lymphocytic (MAL) protein were investigated and defined in this study. We induced the mutations in aromatic amino acid residues of ETX and substituted them with aliphatic residues at domains I and II. Subsequently, protein-protein interactions (PPI) were performed between ETX (wild)-MAL and ETX (mutated)-MAL protein predicting the domain sites of ETX structure. Further, molecular dynamics (MD) simulation studies were performed for both complexes to investigate the dynamic behavior of the proteins. The binding efficiency between 'ETX (wild)-MAL protein' and 'ETX (mutated)-MAL protein complex' interactions were compared and showed that the former had stronger interactions and binding efficiency due to the higher stability of the complex. The MD analysis showed destabilization and higher fluctuations in the PPI of the mutated heterodimeric ETX-MAL complex which is otherwise essential for its functional conformation. Such kind of interactions with mutated functional domains of ligands provided much-needed clarity in understanding the pre-pore complex formation of epsilon toxin with the MAL protein receptor of goats. The findings from this study would provide an impetus for designing a novel vaccine for Enterotoxaemia in goats.Communicated by Ramaswamy H. Sarma.
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Mathew SK, Chapla A, Venkatesan P, Eriyat V, Aruldhas BW, Prabha R, Neely M, Rao SV, Kandasamy S, Mathew B. Genetic predisposition and high exposure to colistin in the early treatment period as independent risk factors for colistin-induced nephrotoxicity. Clin Transl Sci 2024; 17:e13764. [PMID: 38476095 PMCID: PMC10933594 DOI: 10.1111/cts.13764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/29/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Colistin is known to cause nephrotoxicity due to its extensive reabsorption and accumulation in renal tubules. In vitro studies have identified the functional role of colistin transporters such as OCTN2, PEPT2, megalin, and P-glycoprotein. However, the role of these transporter gene variants in colistin-induced nephrotoxicity has not been studied. Utilizing targeted next-generation sequencing, we screened for genetic polymorphisms covering the colistin transporters (SLC15A1, SLC15A2, SLC22A5, LRP2, and ABCB1) in 42 critically ill patients who received colistimethate sodium. The genetic variants rs2257212 ((NM_021082.4):c.1048C>G) and rs13397109 ((NM_004525.3):C.7626C > T) were identified as being associated with an increased incidence of acute kidney injury (AKI) on Day 7. Colistin area under the curve (AUC) was predicted using a previously published pharmacokinetic model of colistin. Using logistic regression analysis, the predicted 24-h AUC of colistin was identified as an important contributor for increased odds of AKI on Day 7. Among 42 patients, 4 (9.5%) were identified as having high predisposition to colistin-induced AKI based on the presence of predisposing genetic variants. Determination of the presence of the abovementioned genetic variants and early therapeutic drug monitoring may reduce or prevent colistin-induced nephrotoxicity and facilitate dose optimization of colistimethate sodium.
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Singh DP, Maurya S, Yerasu SR, Bisen MS, Farag MA, Prabha R, Shukla R, Chaturvedi KK, Farooqi MS, Srivastava S, Rai A, Sarma BK, Rai N, Behera TK. Metabolomics of early blight (Alternaria solani) susceptible tomato (Solanum lycopersicum) unfolds key biomarker metabolites and involved metabolic pathways. Sci Rep 2023; 13:21023. [PMID: 38030710 PMCID: PMC10687106 DOI: 10.1038/s41598-023-48269-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 11/24/2023] [Indexed: 12/01/2023] Open
Abstract
Tomato (Solanum lycopersicum) is among the most important commercial horticultural crops worldwide. The crop quality and production is largely hampered due to the fungal pathogen Alternaria solani causing necrotrophic foliage early blight disease. Crop plants usually respond to the biotic challenges with altered metabolic composition and physiological perturbations. We have deciphered altered metabolite composition, modulated metabolic pathways and identified metabolite biomarkers in A. solani-challenged susceptible tomato variety Kashi Aman using Liquid Chromatography-Mass Spectrometry (LC-MS) based metabolomics. Alteration in the metabolite feature composition of pathogen-challenged (m/z 9405) and non-challenged (m/z 9667) plant leaves including 8487 infection-exclusive and 8742 non-infection exclusive features was observed. Functional annotation revealed putatively annotated metabolites and pathway mapping indicated their enrichment in metabolic pathways, biosynthesis of secondary metabolites, ubiquinone and terpenoid-quinones, brassinosteroids, steroids, terpenoids, phenylpropanoids, carotenoids, oxy/sphingolipids and metabolism of biotin and porphyrin. PCA, multivariate PLS-DA and OPLS-DA analysis showed sample discrimination. Significantly up regulated 481 and down regulated 548 metabolite features were identified based on the fold change (threshold ≥ 2.0). OPLS-DA model based on variable importance in projection (VIP scores) and FC threshold (> 2.0) revealed 41 up regulated discriminant metabolite features annotated as sphingosine, fecosterol, melatonin, serotonin, glucose 6-phosphate, zeatin, dihydrozeatin and zeatin-β-D-glucoside. Similarly, 23 down regulated discriminant metabolites included histidinol, 4-aminobutyraldehyde, propanoate, tyramine and linalool. Melatonin and serotonin in the leaves were the two indoleamines being reported for the first time in tomato in response to the early blight pathogen. Receiver operating characteristic (ROC)-based biomarker analysis identified apigenin-7-glucoside, uridine, adenosyl-homocysteine, cGMP, tyrosine, pantothenic acid, riboflavin (as up regulated) and adenosine, homocyctine and azmaline (as down regulated) biomarkers. These results could aid in the development of metabolite-quantitative trait loci (mQTL). Furthermore, stress-induced biosynthetic pathways may be the potential targets for modifications through breeding programs or genetic engineering for improving crop performance in the fields.
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Singh DP, Bisen MS, Prabha R, Maurya S, Yerasu SR, Shukla R, Tiwari JK, Chaturvedi KK, Farooqi MS, Srivastava S, Rai A, Sarma BK, Rai N, Singh PM, Behera TK, Farag MA. Untargeted Metabolomics of Alternaria solani-Challenged Wild Tomato Species Solanum cheesmaniae Revealed Key Metabolite Biomarkers and Insight into Altered Metabolic Pathways. Metabolites 2023; 13:585. [PMID: 37233626 PMCID: PMC10220610 DOI: 10.3390/metabo13050585] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 05/27/2023] Open
Abstract
Untargeted metabolomics of moderately resistant wild tomato species Solanum cheesmaniae revealed an altered metabolite profile in plant leaves in response to Alternaria solani pathogen. Leaf metabolites were significantly differentiated in non-stressed versus stressed plants. The samples were discriminated not only by the presence/absence of specific metabolites as distinguished markers of infection, but also on the basis of their relative abundance as important concluding factors. Annotation of metabolite features using the Arabidopsis thaliana (KEGG) database revealed 3371 compounds with KEGG identifiers belonging to biosynthetic pathways including secondary metabolites, cofactors, steroids, brassinosteroids, terpernoids, and fatty acids. Annotation using the Solanum lycopersicum database in PLANTCYC PMN revealed significantly upregulated (541) and downregulated (485) features distributed in metabolite classes that appeared to play a crucial role in defense, infection prevention, signaling, plant growth, and plant homeostasis to survive under stress conditions. The orthogonal partial least squares discriminant analysis (OPLS-DA), comprising a significant fold change (≥2.0) with VIP score (≥1.0), showed 34 upregulated biomarker metabolites including 5-phosphoribosylamine, kaur-16-en-18-oic acid, pantothenate, and O-acetyl-L-homoserine, along with 41 downregulated biomarkers. Downregulated metabolite biomarkers were mapped with pathways specifically known for plant defense, suggesting their prominent role in pathogen resistance. These results hold promise for identifying key biomarker metabolites that contribute to disease resistive metabolic traits/biosynthetic routes. This approach can assist in mQTL development for the stress breeding program in tomato against pathogen interactions.
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Mathew SK, Rao SV, Prabha R, Neely MN, Mathew BS, Aruldhas BW, Veeraraghavan B, Kandasamy S. Model-Informed Rationale for Early Therapeutic Drug Monitoring of Colistin in Critically Ill Patients. J Clin Pharmacol 2023; 63:57-65. [PMID: 35924629 DOI: 10.1002/jcph.2130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 07/25/2022] [Indexed: 12/15/2022]
Abstract
Adequate colistin exposure is important for microbiological clearance. This study was performed in critically ill patients >18 years old to develop a simplified nonparametric pharmacokinetic (PK) model of colistin for routine clinical use and to determine the role of dose optimization. The Non-Parametric Adaptive Grid algorithm within the Pmetrics software package for R was used to develop a PK model from 47 patients, and external validation of the final model was performed in 13 patients. A 1-compartment multiplicative gamma error model with 0-order input and first-order elimination of colistin was developed with creatinine clearance and serum albumin as covariates on elimination rate constant. An R2 for observed vs individual predicted colistin concentrations of 0.92 was obtained in the validation cohort. High interindividual variability in colistin steady-state area under the plasma concentration-time curve (AUC) from from 120 hours to 144 hours (coefficient of variation = 80.1%) and a high interoccasion variability (median coefficient of variation of AUC from time 0 to hours predicted every 8 hours for initial 96 hours after starting colistin = 23.8) was predicted in patients who received this antibiotic for a period of over 152 hours (n = 22). With the model-suggested dose regimen, only 20% of simulated profiles achieved AUC from time 0 to 24 hours in the range of 50 to 60 mg • h/L due to high variability in population PK. In this group of patients, steady-state colistin concentrations were predicted to be achieved >96 hours after initiation of colistimethate sodium. This study advocates the need for early and repeated therapeutic drug monitoring and dose optimization in critically ill patients to achieve adequate therapeutic concentration of colistin.
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Sivamani P, Eriyat V, Mathew SK, Singh A, Aaron R, Chacko RT, Joel A, Prabha R, Mathew BS. Identification of DPYD variants and estimation of uracil and dihydrouracil in a healthy Indian population. Per Med 2022; 20:39-53. [DOI: 10.2217/pme-2022-0042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Aim: This study aimed to identify DPYD variants and the related but previously unexplored phenotype (plasma uracil, dihydrouracil [DHU], and the DHU-to-uracil ratio) in a healthy adult Indian population. Methods: Healthy adult volunteers (n = 100) had their uracil and DHU levels measured and were genotyped for selected variants. Results: Among the nine variants studied, c.1906-14763G>A and c.85T>C were the most prevalent. Participants with any of the variants except for c.85T>C and c.1627A>G had a significantly lower DHU-to-uracil ratio and those with c.1905+1G>A variant had significantly increased uracil concentration compared with wild type. Conclusion: Participants with five variants were identified as having altered phenotypic measures, and 40% of the intermediate metabolizers had their phenotype in the terminal population percentiles.
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Kasinathan P, Prabha R, Sabeenian RS, Baskar K, Ramkumar A, Alemayehu S. Development of Deep Learning Technique of Features for the Analysis of Clinical Images Integrated with CANN. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2742274. [PMID: 36277892 PMCID: PMC9586784 DOI: 10.1155/2022/2742274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/30/2022] [Indexed: 11/23/2022]
Abstract
Computer tomography is an extensively used method for the detection of the disease in the subjects. Basically, computer-aided tomography depending on the artificial intelligence reveals its significance in smart health care monitoring system. Owing to its security and the private issue, analyzing the computed tomography dataset has become a tedious process. This study puts forward the convolutional autoencrypted deep learning neural network to assist unsupervised learning technique. By carrying out various experiments, our proposed method produces better results comparative to other traditional methods, which efficaciously solves the issues related to the artificial image description. Hence, the convolutional autoencoder is widely used in measuring the lumps in the bronchi. With the unsupervised machine learning, the extracted features are used for various applications.
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Singh DP, Bisen MS, Shukla R, Prabha R, Maurya S, Reddy YS, Singh PM, Rai N, Chaubey T, Chaturvedi KK, Srivastava S, Farooqi MS, Gupta VK, Sarma BK, Rai A, Behera TK. Metabolomics-Driven Mining of Metabolite Resources: Applications and Prospects for Improving Vegetable Crops. Int J Mol Sci 2022; 23:ijms232012062. [PMID: 36292920 PMCID: PMC9603451 DOI: 10.3390/ijms232012062] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/13/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
Vegetable crops possess a prominent nutri-metabolite pool that not only contributes to the crop performance in the fields, but also offers nutritional security for humans. In the pursuit of identifying, quantifying and functionally characterizing the cellular metabolome pool, biomolecule separation technologies, data acquisition platforms, chemical libraries, bioinformatics tools, databases and visualization techniques have come to play significant role. High-throughput metabolomics unravels structurally diverse nutrition-rich metabolites and their entangled interactions in vegetable plants. It has helped to link identified phytometabolites with unique phenotypic traits, nutri-functional characters, defense mechanisms and crop productivity. In this study, we explore mining diverse metabolites, localizing cellular metabolic pathways, classifying functional biomolecules and establishing linkages between metabolic fluxes and genomic regulations, using comprehensive metabolomics deciphers of the plant’s performance in the environment. We discuss exemplary reports covering the implications of metabolomics, addressing metabolic changes in vegetable plants during crop domestication, stage-dependent growth, fruit development, nutri-metabolic capabilities, climatic impacts, plant-microbe-pest interactions and anthropogenic activities. Efforts leading to identify biomarker metabolites, candidate proteins and the genes responsible for plant health, defense mechanisms and nutri-rich crop produce are documented. With the insights on metabolite-QTL (mQTL) driven genetic architecture, molecular breeding in vegetable crops can be revolutionized for developing better nutritional capabilities, improved tolerance against diseases/pests and enhanced climate resilience in plants.
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Wilfred PM, Mathew S, Chacko B, Prabha R, Mathew BS. Estimation of Free Phenytoin Concentration in Critically Ill Patients with Hypoalbuminemia: Direct-measurement vs Traditional Equations. Indian J Crit Care Med 2022; 26:682-687. [PMID: 35836626 PMCID: PMC9237157 DOI: 10.5005/jp-journals-10071-24235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Background In critically ill patients with low albumin, dose individualization of phenytoin is a challenge. The currently used Sheiner-Tozer equation does not accurately predict the free phenytoin concentration in serum and can result in incorrect dose modifications. The best measure to advocate in these patients is the direct-measurement of free phenytoin concentration. Aims and objectives Phenytoin exhibits complex pharmacokinetics, requiring careful therapeutic drug monitoring. This study aimed to compare the accuracy of the established Sheiner-Tozer calculation method against the direct-measurement of free phenytoin concentration in serum by high performance liquid chromatography in critically ill patients with low albumin. Materials and methods Blood specimens for direct-measurement of both total and free phenytoin concentration were obtained from 57 patients with hypoalbuminemia monitored in the intensive care unit. Results The median [inter-quartile range (IQR)] for Sheiner-Tozer equation calculated total phenytoin concentration and direct-measured total was 17.14 (10.63-24.53) and 9.82 (6.02-13.85) μg mL-1, respectively. Approximately 53 and 5% of patients were found to be subtherapeutic and supratherapeutic for direct-measured total phenytoin concentrations, respectively. In contrast, on applying the Sheiner-Tozer calculation, 23 and 40% had subtherapeutic and supratherapeutic concentrations, respectively, for total phenytoin concentration. The median (IQR) for direct-measured, routine and Sheiner-Tozer equation calculated free phenytoin concentration were 1.92 (1.06-2.76), 0.98 (0.60-1.39), and 1.71 (1.06-2.45) μg mL-1, respectively. Only 45.7% of patients were in agreement with respect to the therapeutic category when direct-measured free was compared against routine calculation free. Conclusion In patients with low albumin, free phenytoin concentration based on the Sheiner-Tozer corrected equation accurately classified patients based on their therapeutic category of free phenytoin in 73.7% of patients. Hence, for individualization of phenytoin dosage in critically ill patients with low albumin, we recommend direct-measurement of free phenytoin concentration. How to cite this article Wilfred PM, Mathew S, Chacko B, Prabha R, Mathew BS. Estimation of Free Phenytoin Concentration in Critically Ill Patients with Hypoalbuminemia: Direct-measurement vs Traditional Equations. Indian J Crit Care Med 2022;26(6):682-687.
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Iquebal MA, Jagannadham J, Jaiswal S, Prabha R, Rai A, Kumar D. Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review. Front Microbiol 2022; 13:708335. [PMID: 35655999 PMCID: PMC9152772 DOI: 10.3389/fmicb.2022.708335] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 03/17/2022] [Indexed: 12/12/2022] Open
Abstract
Agricultural productivity is highly influenced by its associated microbial community. With advancements in omics technology, metagenomics is known to play a vital role in microbial world studies by unlocking the uncultured microbial populations present in the environment. Metagenomics is a diagnostic tool to target unique signature loci of plant and animal pathogens as well as beneficial microorganisms from samples. Here, we reviewed various aspects of metagenomics from experimental methods to techniques used for sequencing, as well as diversified computational resources, including databases and software tools. Exhaustive focus and study are conducted on the application of metagenomics in agriculture, deciphering various areas, including pathogen and plant disease identification, disease resistance breeding, plant pest control, weed management, abiotic stress management, post-harvest management, discoveries in agriculture, source of novel molecules/compounds, biosurfactants and natural product, identification of biosynthetic molecules, use in genetically modified crops, and antibiotic-resistant genes. Metagenomics-wide association studies study in agriculture on crop productivity rates, intercropping analysis, and agronomic field is analyzed. This article is the first of its comprehensive study and prospects from an agriculture perspective, focusing on a wider range of applications of metagenomics and its association studies.
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Susan Mathew B, Mathew SK, Winston Aruldhas B, Prabha R, Gangadharan N, George David V, Varughese S, Tharayil John G. Analytical and clinical validation of Dried blood spot and Volumetric Absorptive Microsampling for measurement of tacrolimus and creatinine after renal transplantation. Clin Biochem 2022; 105-106:25-34. [PMID: 35490728 DOI: 10.1016/j.clinbiochem.2022.04.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 04/22/2022] [Accepted: 04/25/2022] [Indexed: 12/28/2022]
Abstract
BACKGROUND Serial monitoring of tacrolimus and serum creatinine after renal transplantation is of vital importance. In this study, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay for the estimation of tacrolimus and creatinine, obtained from dried blood spots (DBS) or by volumetric absorptive microsampling (VAMS) was validated and the two sampling strategies were compared with traditional venous sampling. METHODS The LC-MS/MS assay was validated using a shared extract for the estimation of tacrolimus and creatinine from DBS and VAMS independently. The relationship between the concentrations in DBS/VAMS specimens and in venous samples was assessed using Passing-Bablok (PB) analysis and the bias between the two methods was determined by the Bland Altman (BA) analysis. RESULTS The imprecision and bias of tacrolimus and creatinine estimated from DBS and VAMS samples was <12% and was independent of the hematocrit (Hct). Samples were stable for five days at ambient temperature. From the PB regression analysis, correction equations were generated for the prediction of tacrolimus and creatinine values from DBS and VAMS samples. In a separate cohort of patients for validation, the corrected DBS and VAMS concentrations had a mean (95% CI) bias for tacrolimus of -0.64 (-2.98 to 1.70)% and -0.92 (-3.69 to 1.85)% respectively and for creatinine of 1.00 (-2.73 to 4.72)% and -0.71 (-3.74 to 2.32)% respectively. Using DBS and VAMS respectively, for tacrolimus, 91.8 and 89.8% of patient values and for creatinine, 69.4 and 81.6% of patient values were within the limits of clinical acceptance (within 15% agreement against the venous samples). CONCLUSION We conclude that VAMS is the preferred single sampling option for estimating tacrolimus and creatinine in renal transplant patients.
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Prabha R, Mathew SK, Joseph AJ, Mathew BS. Exposure of Azathioprine Metabolites and Clinical Outcome in Indian Patients with Crohn’s Disease. J Pharmacol Pharmacother 2022. [DOI: 10.1177/0976500x221085804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Aim: The aim of this study was to determine the concentration of 6-thioguanine nucleotide (6-TGN) and 6-methylmercaptopurine (6-MMP), the interpatient variability, and the relationship with disease activity in patients with Chron’s disease on long-term stable doses of azathioprine (AZA). Methods: This is a prospective, tertiary care single-center hospital study in adult Chron’s disease patients treated with AZA. The quantification of phenotypic thiopurine methyltransferase enzyme activity in red blood cells and the estimation of the concentration of 6-TGN and 6-MMP in whole blood was performed using the HPLC-UV detector method. A clinical response was categorized as remission (Harvey-Bradshaw Index [HBI] < 5) or improvement (drop from baseline of at least three points of HBI) based on HBI. Exposure to metabolite concentrations and the clinical response to AZA treatment was observed. Results: Study analysis included 30 patients who were initiated on AZA, and they were followed up with an estimation of metabolite concentrations to determine their clinical outcome. At six months, 93% of ( n = 28) patients continued to be on AZA and had clinical improvement. All the patients achieved remission of Chron’s disease. Only two patients developed adverse effects such as joint pain and thrombocytopenia. Conclusion: AZA is a safe and effective therapy in managing Chron’s disease when administered after determining thiopurine methyltransferase phenotype and with dose optimization performed using therapeutic drug monitoring of 6-TGN and 6-MMP.
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Kumar S, Kirubakaran N, Punnen A, Prabha R, Agarwal I. Therapeutic drug monitoring of mycophenolate mofetil for the treatment of pediatric lupus nephritis: A cross-sectional study. INDIAN JOURNAL OF RHEUMATOLOGY 2022. [DOI: 10.4103/injr.injr_130_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Lokesh S, Prabha R, Pramodhini S, Easow J. A case series on pulmonary and tissue aspergillosis. Biomedicine (Taipei) 2021. [DOI: 10.51248/.v41i2.807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Aspergilli species cause opportunistic fungal infection in immunocompromised individuals. Invasive aspergillosis is a highly fatal opportunistic infection that accounts for amajor risk to immunocompromised patients. Among these species, A.fumigatus is the main opportunistic pathogen followed by A.niger and A.flavus. In immunocompetent individuals, the effective innate immunity eliminates theinhaled conidia and Allergic bronchopulmonary aspergillosis and aspergilloma are the only infections noted in them. Thus,A.fumigatus was considered for years to beainfirm pathogen. With increase in the number of immunosuppressed patients, however, there has been a marked increase in fatal invasive aspergillosis, which is now the widespread mold infection. In this case series, we have described four cases of aspergillosis. Male preponderance is seen, commonly seen in 4th to 5th decade, 3 out of 4 cases are immunocompromised having diabetes, chronic kidney disease, past history of tuberculosis and only one case was not associated with any comorbid illness. In case 4, the recurrence of polypoidalsinosis itself could be a risk factor causing erosion of nasal mucosa and chronic secretion.The morphological features of intraluminal lesions were of prognostic value. Most of the Aspergillosis patients had a good prognosis with early diagnosis and effective antifungal therapy.It can bedeadly if not diagnosed and treated properly.Very rarely aspergillosis may occur in immunocompetent individuals, which urged us to point outthese cases. With studies suggesting surging incidence and mortality rates, early diagnosis and treatment are paramount to upgrade patient survival.
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Jacob J, Mathew SK, Chacko RT, Aruldhas BW, Singh A, Prabha R, Mathew BS. Systemic exposure to 5-fluorouracil and its metabolite, 5,6-dihydrofluorouracil, and development of a limited sampling strategy for therapeutic drug management of 5-fluorouracil in patients with gastrointestinal malignancy. Br J Clin Pharmacol 2020; 87:937-945. [PMID: 32592630 DOI: 10.1111/bcp.14444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/27/2020] [Accepted: 06/05/2020] [Indexed: 11/28/2022] Open
Abstract
AIMS 5-Fluorouracil (5-FU) is widely used in combination chemotherapy, and literature suggests pharmacokinetic-guided dosing to improve clinical efficacy and reduce toxicity. This study aimed to determine the pharmacokinetic exposure of both 5-FU and its metabolite, 5,6-dihydrofluorouracil (DHFU), in patients with gastrointestinal malignancy and to establish a simplified strategy to assist in therapeutic drug management for dose optimization. METHODS This was a prospective, observational study, performed in 27 patients diagnosed with gastrointestinal malignancy who were prescribed 5-FU. Multiple samples were collected per patient over the slow bolus (15-20 min) and continuous infusion period (over 44 h) in doses 1 and 3, and the concentrations of 5-FU and DHFU were measured. RESULTS A higher proportion of patients had exposures within the therapeutic range in dose 3 (50%) as compared to dose 1 (37.5%) with 5-FU. There was an association between delayed time to maximum concentration of DHFU and a high maximum concentration of 5-FU. A limited sampling strategy was developed with 4 samples, 2 during the bolus period and 2 during the continuous period (at 18 h and the end of infusion), which accurately predicted the total area under the curve of 5-FU. CONCLUSION Using body surface area-based dosing with 5-FU, 50-60% of patients were outside of the therapeutic range. In the absence of genotype testing, measurement of the metabolite DHFU could be a phenotypical measure of dihydropyrimidine dehydrogenase enzyme activity. A limited sampling strategy was developed in patients who were prescribed a combination regimen of slow bolus, followed by a 44-hour continuous infusion of 5-FU to assist in the therapeutic drug management of patients.
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Singh DP, Singh V, Shukla R, Sahu P, Prabha R, Gupta A, Sarma BK, Gupta VK. Stage-dependent concomitant microbial fortification improves soil nutrient status, plant growth, antioxidative defense system and gene expression in rice. Microbiol Res 2020; 239:126538. [PMID: 32717536 DOI: 10.1016/j.micres.2020.126538] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022]
Abstract
Stage-dependent concomitant fortification of rice (Oryza sativa L.) varieties PB1612 and CO51 with microbial inoculants Trichoderma asperellum and Pseudomonas fluorescens as seed coating, seedling root inoculation and soil application enhanced growth, activated antioxidant enzymes and modulated defence-related genes in plants. Microbial inoculants improved shoot height, tiller numbers, fresh weight and dry biomass. Co-inoculation was more impactful in enhancing plant growth and development as compared to single inoculation. Single and co-inoculation improved organic carbon (OC) and N, P and K content in the soil substantially. Mean values between control and co-inoculation varied significantly for OC in PB1612 (p0.001) and CO51 (p0.019) and phosphorus content in PB1612 (p0.044) and CO51 (p0.021). Microbial inoculation enhanced soil nutrients and increased their bioavailability for the plants. Total polyphenolics, flavonoids and protein content increased in the leaves following microbial inoculation. Enhanced non-enzymatic antioxidant parameters (ABTS, DPPH, Fe-ion reducing power and Fe-ion chelation) was found in microbe inoculated rice reflecting high free radical scavenging activity in polyphenolics-rich leaf extracts. Increased enzyme activity of superoxide dismutase (SOD), glutathione reductase (GR), phenylalanine ammonia-lyase (PAL), peroxidase (PO), glutathione peroxidase (GPX), ascorbate peroxidase (APX) and catalase (CAT) showed improved ROS scavenging in rice plants having co-inoculation. Over-expression of PAL, cCuZn-SOD and CAT genes in microbial inoculated rice plants was recorded. The study concludes that plant stage-wise concomitant fortification by microbial inoculants could play multi-pronged manifestations at physiological, biochemical and molecular level in rice to positively influence growth, development and defense attributes in plants.
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Singh DP, Singh V, Gupta VK, Shukla R, Prabha R, Sarma BK, Patel JS. Microbial inoculation in rice regulates antioxidative reactions and defense related genes to mitigate drought stress. Sci Rep 2020; 10:4818. [PMID: 32179779 PMCID: PMC7076003 DOI: 10.1038/s41598-020-61140-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 01/31/2020] [Indexed: 12/24/2022] Open
Abstract
Microbial inoculation in drought challenged rice triggered multipronged steps at enzymatic, non-enzymatic and gene expression level. These multifarious modulations in plants were related to stress tolerance mechanisms. Drought suppressed growth of rice plants but inoculation with Trichoderma, Pseudomonas and their combination minimized the impact of watering regime. Induced PAL gene expression and enzyme activity due to microbial inoculation led to increased accumulation of polyphenolics in plants. Enhanced antioxidant concentration of polyphenolics from microbe inoculated and drought challenged plants showed substantially high values of DPPH, ABTS, Fe-ion reducing power and Fe-ion chelation activity, which established the role of polyphenolic extract as free radical scavengers. Activation of superoxide dismutase that catalyzes superoxide (O2-) and leads to the accumulation of H2O2 was linked with the hypersensitive cell death response in leaves. Microbial inoculation in plants enhanced activity of peroxidase, ascorbate peroxidase, glutathione peroxidase and glutathione reductase enzymes. This has further contributed in reducing ROS burden in plants. Genes of key metabolic pathways including phenylpropanoid (PAL), superoxide dismutation (SODs), H2O2 peroxidation (APX, PO) and oxidative defense response (CAT) were over-expressed due to microbial inoculation. Enhanced expression of OSPiP linked to less-water permeability, drought-adaptation gene DHN and dehydration related stress inducible DREB gene in rice inoculated with microbial inoculants after drought challenge was also reported. The impact of Pseudomonas on gene expression was consistently remained the most prominent. These findings suggested that microbial inoculation directly caused over-expression of genes linked with defense processes in plants challenged with drought stress. Enhanced enzymatic and non-enzymatic antioxidant reactions that helped in minimizing antioxidative load, were the repercussions of enhanced gene expression in microbe inoculated plants. These mechanisms contributed strongly towards stress mitigation. The study demonstrated that microbial inoculants were successful in improving intrinsic biochemical and molecular capabilities of rice plants under stress. Results encouraged us to advocate that the practice of growing plants with microbial inoculants may find strategic place in raising crops under abiotic stressed environments.
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Prabha R, Singh DP, Gupta S, Gupta VK, El-Enshasy HA, Verma MK. Rhizosphere Metagenomics of Paspalum scrobiculatum L. (Kodo Millet) Reveals Rhizobiome Multifunctionalities. Microorganisms 2019; 7:microorganisms7120608. [PMID: 31771141 PMCID: PMC6956225 DOI: 10.3390/microorganisms7120608] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 10/15/2019] [Indexed: 12/23/2022] Open
Abstract
Multifunctionalities linked with the microbial communities associated with the millet crop rhizosphere has remained unexplored. In this study, we are analyzing microbial communities inhabiting rhizosphere of kodo millet and their associated functions and its impact over plant growth and survival. Metagenomics of Paspalum scrobiculatum L.(kodo millet) rhizopshere revealed taxonomic communities with functional capabilities linked to support growth and development of the plants under nutrient-deprived, semi-arid and dry biotic conditions. Among 65 taxonomically diverse phyla identified in the rhizobiome, Actinobacteria were the most abundant followed by the Proteobacteria. Functions identified for different genes/proteins led to revelations that multifunctional rhizobiome performs several metabolic functions including carbon fixation, nitrogen, phosphorus, sulfur, iron and aromatic compound metabolism, stress response, secondary metabolite synthesis and virulence, disease, and defense. Abundance of genes linked with N, P, S, Fe and aromatic compound metabolism and phytohormone synthesis—along with other prominent functions—clearly justifies growth, development, and survival of the plants under nutrient deprived dry environment conditions. The dominance of actinobacteria, the known antibiotic producing communities shows that the kodo rhizobiome possesses metabolic capabilities to defend themselves against biotic stresses. The study opens avenues to revisit multi-functionalities of the crop rhizosphere for establishing link between taxonomic abundance and targeted functions that help plant growth and development in stressed and nutrient deprived soil conditions. It further helps in understanding the role of rhizosphere microbiome in adaptation and survival of plants in harsh abiotic conditions.
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Pawar S, Chaudhari A, Prabha R, Shukla R, Singh DP. Microbial Pyrrolnitrin: Natural Metabolite with Immense Practical Utility. Biomolecules 2019; 9:E443. [PMID: 31484394 PMCID: PMC6769897 DOI: 10.3390/biom9090443] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/12/2019] [Accepted: 07/12/2019] [Indexed: 12/26/2022] Open
Abstract
Pyrrolnitrin (PRN) is a microbial pyrrole halometabolite of immense antimicrobial significance for agricultural, pharmaceutical and industrial implications. The compound and its derivatives have been isolated from rhizospheric fluorescent or non-fluorescent pseudomonads, Serratia and Burkholderia. They are known to confer biological control against a wide range of phytopathogenic fungi, and thus offer strong plant protection prospects against soil and seed-borne phytopathogenic diseases. Although chemical synthesis of PRN has been obtained using different steps, microbial production is still the most useful option for producing this metabolite. In many of the plant-associated isolates of Serratia and Burkholderia, production of PRN is dependent on the quorum-sensing regulation that usually involves N-acylhomoserine lactone (AHL) autoinducer signals. When applied on the organisms as antimicrobial agent, the molecule impedes synthesis of key biomolecules (DNA, RNA and protein), uncouples with oxidative phosphorylation, inhibits mitotic division and hampers several biological mechanisms. With its potential broad-spectrum activities, low phototoxicity, non-toxic nature and specificity for impacts on non-target organisms, the metabolite has emerged as a lead molecule of industrial importance, which has led to developing cost-effective methods for the biosynthesis of PRN using microbial fermentation. Quantum of work narrating focused research efforts in the emergence of this potential microbial metabolite is summarized here to present a consolidated, sequential and updated insight into the chemistry, biology and applicability of this natural molecule.
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