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Nagre K, Singh N, Ghoshal C, Tandon G, Iquebal MA, Nain T, Bana RS, Meena A. Probing the potential of bioactive compounds of millets as an inhibitor for lifestyle diseases: molecular docking and simulation-based approach. Front Nutr 2023; 10:1228172. [PMID: 37823087 PMCID: PMC10562582 DOI: 10.3389/fnut.2023.1228172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/07/2023] [Indexed: 10/13/2023] Open
Abstract
Millets are becoming more popular as a healthy substitute for people with lifestyle disorders. They offer dietary fiber, polyphenols, fatty acids, minerals, vitamins, protein, and antioxidants. The nutritional importance of millets leads to the present in-silico study of selective bioactive compounds docked against the targets of lifestyle diseases, viz., diabetes, hypertension, and atherosclerosis using molecular docking and molecular simulations approach. Pharmacokinetic analysis was also carried out to analyse ADME properties and toxicity analysis, drug-likeliness, and finally target prediction for new targets for uncharacterized compounds or secondary targets for recognized molecules by Swiss Target Prediction was also done. The docking results revealed that the bioactive compound flavan-4-ol, among all the 50 compounds studied, best docked to all the four targets of lifestyle diseases, viz., Human dipeptidyl peptidase IV (-5.94 kcal mol-1 binding energy), Sodium-glucose cotransporter-2 (-6.49 kcal mol-1) diabetes-related enzyme, the Human angiotensin-converting enzyme (-6.31 kcal mol-1) which plays a significant role in hypertension, and Proprotein convertase subtilisin kexin type 9 (-4.67 kcal mol-1) for atherosclerosis. Molecular dynamics simulation analysis substantiates that the flavan-4-ol forms a better stability complex with all the targets. ADMET profiles further strengthened the candidature of the flavan-4-ol bioactive compound to be considered for trial as an inhibitor of targets DPPIV, SGLT2, PCSK9, and hACE. We suggest that more research be conducted, taking Flavon-4-ol into account where it can be used as standard treatment for lifestyle diseases.
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Affiliation(s)
- Kajal Nagre
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, India
| | - Nirupma Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, India
| | - Chandrika Ghoshal
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, India
| | - Gitanjali Tandon
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi, India
| | - Tarsem Nain
- Department of Genetics, Maharshi Dayanand University, Rohtak, India
| | - Ram Swaroop Bana
- Division of Agronomy, Indian Agricultural Research Institute, Pusa Campus, New Delhi, India
| | - Anita Meena
- ICAR-Central Institute for Arid Horticulture, Beechwal, Bikaner, India
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Bhardwaj A, Tandon G, Pal Y, Sharma NK, Nayan V, Soni S, Iquebal MA, Jaiswal S, Legha RA, Talluri TR, Bhattacharya TK, Kumar D, Rai A, Tripathi BN. Genome-Wide Single-Nucleotide Polymorphism-Based Genomic Diversity and Runs of Homozygosity for Selection Signatures in Equine Breeds. Genes (Basel) 2023; 14:1623. [PMID: 37628674 PMCID: PMC10454598 DOI: 10.3390/genes14081623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
The horse, one of the most domesticated animals, has been used for several purposes, like transportation, hunting, in sport, or for agriculture-related works. Kathiawari, Marwari, Manipuri, Zanskari, Bhutia, Spiti, and Thoroughbred are the main breeds of horses, particularly due to their agroclimatic adaptation and role in any kind of strong physical activity, and these characteristics are majorly governed by genetic factors. The genetic diversity and phylogenetic relationship of these Indian equine breeds using microsatellite markers have been reported, but further studies exploring the SNP diversity and runs of homozygosity revealing the selection signature of breeds are still warranted. In our study, the identification of genes that play a vital role in muscle development is performed through SNP detection via the whole-genome sequencing approach. A total of 96 samples, categorized under seven breeds, and 620,721 SNPs were considered to ascertain the ROH patterns amongst all the seven breeds. Over 5444 ROH islands were mined, and the maximum number of ROHs was found to be present in Zanskari, while Thoroughbred was confined to the lowest number of ROHs. Gene enrichment of these ROH islands produced 6757 functional genes, with AGPAT1, CLEC4, and CFAP20 as important gene families. However, QTL annotation revealed that the maximum QTLs were associated with Wither's height trait ontology that falls under the growth trait in all seven breeds. An Equine SNP marker database (EqSNPDb) was developed to catalogue ROHs for all these equine breeds for the flexible and easy chromosome-wise retrieval of ROH along with the genotype details of all the SNPs. Such a study can reveal breed divergence in different climatic and ecological conditions.
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Affiliation(s)
- Anuradha Bhardwaj
- ICAR-National Research Centre on Equines, Sirsa Road, Hisar 125001, India; (Y.P.)
| | - Gitanjali Tandon
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India; (G.T.); (N.K.S.); (D.K.)
| | - Yash Pal
- ICAR-National Research Centre on Equines, Sirsa Road, Hisar 125001, India; (Y.P.)
| | - Nitesh Kumar Sharma
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India; (G.T.); (N.K.S.); (D.K.)
| | - Varij Nayan
- ICAR-Central Institute for Research on Buffaloes, Hisar 125001, India;
| | - Sonali Soni
- ICAR-National Research Centre on Equines, Sirsa Road, Hisar 125001, India; (Y.P.)
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India; (G.T.); (N.K.S.); (D.K.)
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India; (G.T.); (N.K.S.); (D.K.)
| | - Ram Avatar Legha
- ICAR-National Research Centre on Equines, Sirsa Road, Hisar 125001, India; (Y.P.)
| | | | | | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India; (G.T.); (N.K.S.); (D.K.)
| | - Anil Rai
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India; (G.T.); (N.K.S.); (D.K.)
| | - B. N. Tripathi
- ICAR-National Research Centre on Equines, Sirsa Road, Hisar 125001, India; (Y.P.)
- Indian Council of Agricultural Research, Krishi Bhawan, New Delhi 110001, India
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Srivastav M, Radadiya N, Ramachandra S, Jayaswal PK, Singh N, Singh S, Mahato AK, Tandon G, Gupta A, Devi R, Subrayagowda SH, Kumar G, Prakash P, Singh S, Sharma N, Nagaraja A, Kar A, Rudra SG, Sethi S, Jaiswal S, Iquebal MA, Singh R, Singh SK, Singh NK. High resolution mapping of QTLs for fruit color and firmness in Amrapali/Sensation mango hybrids. Front Plant Sci 2023; 14:1135285. [PMID: 37351213 PMCID: PMC10282835 DOI: 10.3389/fpls.2023.1135285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 05/08/2023] [Indexed: 06/24/2023]
Abstract
Introduction Mango (Mangifera indica L.), acclaimed as the 'king of fruits' in the tropical world, has historical, religious, and economic values. It is grown commercially in more than 100 countries, and fresh mango world trade accounts for ~3,200 million US dollars for the year 2020. Mango is widely cultivated in sub-tropical and tropical regions of the world, with India, China, and Thailand being the top three producers. Mango fruit is adored for its taste, color, flavor, and aroma. Fruit color and firmness are important fruit quality traits for consumer acceptance, but their genetics is poorly understood. Methods For mapping of fruit color and firmness, mango varieties Amrapali and Sensation, having contrasting fruit quality traits, were crossed for the development of a mapping population. Ninety-two bi-parental progenies obtained from this cross were used for the construction of a high-density linkage map and identification of QTLs. Genotyping was carried out using an 80K SNP chip array. Results and discussion Initially, we constructed two high-density linkage maps based on the segregation of female and male parents. A female map with 3,213 SNPs and male map with 1,781 SNPs were distributed on 20 linkages groups covering map lengths of 2,844.39 and 2,684.22cM, respectively. Finally, the integrated map was constructed comprised of 4,361 SNP markers distributed on 20 linkage groups, which consisted of the chromosome haploid number in Mangifera indica (n =20). The integrated genetic map covered the entire genome of Mangifera indica cv. Dashehari, with a total genetic distance of 2,982.75 cM and an average distance between markers of 0.68 cM. The length of LGs varied from 85.78 to 218.28 cM, with a mean size of 149.14 cM. Phenotyping for fruit color and firmness traits was done for two consecutive seasons. We identified important consistent QTLs for 12 out of 20 traits, with integrated genetic linkages having significant LOD scores in at least one season. Important consistent QTLs for fruit peel color are located at Chr 3 and 18, and firmness on Chr 11 and 20. The QTLs mapped in this study would be useful in the marker-assisted breeding of mango for improved efficiency.
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Affiliation(s)
- Manish Srivastav
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Nidhi Radadiya
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Sridhar Ramachandra
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Pawan Kumar Jayaswal
- Genomics Laboratory, Indian Council of Agricultural Research (ICAR)- National Institute for Plant Biotechnology, New Delhi, India
| | - Nisha Singh
- Genomics Laboratory, Indian Council of Agricultural Research (ICAR)- National Institute for Plant Biotechnology, New Delhi, India
| | - Sangeeta Singh
- Genomics Laboratory, Indian Council of Agricultural Research (ICAR)- National Institute for Plant Biotechnology, New Delhi, India
| | - Ajay Kumar Mahato
- Genomics Laboratory, Indian Council of Agricultural Research (ICAR)- National Institute for Plant Biotechnology, New Delhi, India
| | - Gitanjali Tandon
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ankit Gupta
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Rajni Devi
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Sreekanth Halli Subrayagowda
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Gulshan Kumar
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Pragya Prakash
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Shivani Singh
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Nimisha Sharma
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - A. Nagaraja
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Abhijit Kar
- Division of Food Science and Postharvest Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Shalini Gaur Rudra
- Division of Food Science and Postharvest Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Shruti Sethi
- Division of Food Science and Postharvest Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sanjay Kumar Singh
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Nagendra Kumar Singh
- Genomics Laboratory, Indian Council of Agricultural Research (ICAR)- National Institute for Plant Biotechnology, New Delhi, India
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Mishra P, Tandon G, Kumar M, Paital B, Swain SS, Kumar S, Samanta L. Promoter sequence interaction and structure based multi-targeted (redox regulatory genes) molecular docking analysis of vitamin E and curcumin in T4 induced oxidative stress model using H9C2 cardiac cell line. J Biomol Struct Dyn 2022; 40:12316-12335. [PMID: 34463220 DOI: 10.1080/07391102.2021.1970624] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A positive association between oxidative stress and hyper-thyroid conditions is well established. Vitamin E (VIT-E) and curcumin (CRM) are considered as potent antioxidant small molecules. Nuclear factor erythroid 2-related factor 2(NRF-2) is known to bind with antioxidant response element and subsequently activate expression of antioxidant enzymes. However, the activation of NRF-2 depends on removal of its regulator Kelch-like ECH-associated protein 1(NRF-2). In the current study, an attempt is made to demonstrate whether effects of VIT-E and CRM are due to direct interaction with the target proteins (i.e. NRF-2, NRF-2, SOD, catalase and LDH) or by possible interaction with the flanking region of their promoters by in silico analysis. Further, these results were corroborated by pretreatment of H9C2 cells (1 x 106 cells per mL of media) with VIT-E (50 μM) and/or CRM (20 μM) for 24 h followed by induction of oxidative stress via T4 (100 nm) administration and assaying the active oxygen metabolism. Discriminant function analyses (DFA) indicated that T4 has a definite role in increasing oxidative stress as evidenced by induction of ROS generation, increase in mitochondrial membrane potential and elevated lipid peroxidation (LPx). Pretreatment with the two antioxidants have ameliorative effects more so when given in combination. The decline in biological activities of the principal antioxidant enzymes SOD and CAT with respect to T4 treatment and its restoration in antioxidant pretreated group further validated our in silico data. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pallavi Mishra
- Redox Biology & Proteomics Laboratory, Center of Excellence in Environment and Public Health, Department of Zoology, Ravenshaw University, Cuttack, Odisha, India
| | - Gitanjali Tandon
- School of Biosciences, IMS University Courses Campus, Ghaziabad, Uttar Pradesh, India
| | - Manoj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, Delhi, India
| | - Biswaranjan Paital
- Redox Regulation Laboratory, Department of Zoology, College of Basic Science and Humanities, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Shasanka Sekhar Swain
- Division of Microbiology and NCDs, ICMR-Regional Medical Research Centre Bhubaneswar, Bhubaneswar, Odisha, India
| | - Sunil Kumar
- Computer Building, Centre for Agricultural Bioinformatics (CABIN), ICAR-Indian Agricultural Statistics Research Institute (IASRI), New Delhi, Delhi, India
| | - Luna Samanta
- Redox Biology & Proteomics Laboratory, Center of Excellence in Environment and Public Health, Department of Zoology, Ravenshaw University, Cuttack, Odisha, India
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Tandon G, Yadav S, Kaur S. Pathway modeling and simulation analysis. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00007-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Agnihotry S, Agrawal P, Ajjarapu SM, Avashthi H, Awasthi A, Bani Baker Q, Bhandawat A, Bishnoi R, Chandra M, Chatterjee T, Chaudhary KK, Choubey J, Choudhari J, Gautam B, Goswami K, Harbola A, Hussain I, Jaiswar A, Jasrotia RS, Junior MC, Kaur S, Kesharwani RK, Kumar I, Kumar P, Kumar S, Manchanda M, Maurya R, Mishra A, Mishra B, Mishra P, Mishra S, Mittal S, Narad P, Naresh G, Negi A, Negi D, Ojha KK, Pant S, Pathak RK, Ramteke PW, Redhu N, Roy J, Sahariah B, Sanan-Mishra N, Saxena R, Sengupta A, Sharma G, Sharma H, Sharma PK, Sharma V, Sharma V, Shivam, Shrinet J, Shukla A, Shukla R, Shukla S, Singh A, Singh A, Singh DB, Singh I, Singh P, Singh PK, Singh R, Singh S, Singh S, Singh SP, Singh TR, Singh VK, Singla D, Sote WO, Tandon G, Thakur Z, Tiwari A, Tiwari A, Tyagi R, Verma M, Verma S, Yadav AK, Yadav IS, Yadav MK, Yadav N, Yadav NS, Yadav S. List of contributors. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00031-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Kumar S, Dehury B, Tandon G, Jaiswal S, Iquebal MA, Ahmad K, Nagrale DT, Singh UB, Jha Y, Singh MK, Singh A, Rai A, Paital B, Kumar D. An insight into molecular interaction of PGIP with PG for banana cultivar. Front Biosci (Landmark Ed) 2020; 25:335-362. [PMID: 31585892 DOI: 10.2741/4809] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
PolyGalacturonase Inhibiting Proteins (PGIPs) are leucine rich repeat pathogenesis-related (PR) cell wall proteins, which interact and inhibit the PolyGalacturonase (PG), an enzyme secreted by the pathogen to degrade pectin. Interaction of PGIP with PG limits the vulnerability of PG by the activation of host defense response against pathogenic attack. Erwinia is gram-negative soft rot bacteria responsible for rhizome rot disease in banana and many other crop plants. The interaction of PG with PGIP is one of the crucial steps for plant-pathogen interaction. To study the molecular mechanism of PR proteins, we employed molecular modelling, protein-protein docking and molecular dynamics simulations of banana PGIP (bPGIP) with Erwinia carotovora PG (ecPG). Further, insilico site-directed mutagenesis was performed in Phaseolus vulgaris PGIP (pvPGIP2) to elucidate the interaction with ecPG. Docking and simulation studies divulge that binding of bPGIP and PvPGIP2 with active site residues of EcPG induces structural changes and thereby inhibit the enzyme. This study provides a unique insight into PG-PGIP interaction, which may help in the development of bacterial soft-rot resistant banana cultivars.
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Affiliation(s)
- Sunil Kumar
- ICAR-NBAIM, Kushmaur, Maunath Bhanjan (UP)-275103, India,
| | | | - Gitanjali Tandon
- ICAR-IASRI, CABIN, Library Avenue, PUSA, New Delhi-110012, India, School of Biosciences, IMS, Ghaziabad-201012
| | - Sarika Jaiswal
- ICAR-IASRI, CABIN, Library Avenue, PUSA, New Delhi-110012, India
| | - Mir Asif Iquebal
- ICAR-IASRI, CABIN, Library Avenue, PUSA, New Delhi-110012, India
| | - Khurshid Ahmad
- ICAR-NBAIM, Kushmaur, Maunath Bhanjan (UP)-275103, India
| | | | - Udai B Singh
- ICAR-NBAIM, Kushmaur, Maunath Bhanjan (UP)-275103, India
| | - Yachana Jha
- N. V Patel College of Pure and Applied Sciences, V. V Nagar, Anand, Gujarat-388120, India
| | | | - Arjun Singh
- ICAR-NBAIM, Kushmaur, Maunath Bhanjan (UP)-275103, India
| | - Anil Rai
- ICAR-IASRI, CABIN, Library Avenue, PUSA, New Delhi-110012, India
| | - B Paital
- Redox Regulation Laboratory, Department of Zoology, Odisha University of Agriculture and Technology, College of Basic Science and Humanities, Bhubaneswar-751003, Odisha, India
| | - Dinesh Kumar
- ICAR-IASRI, CABIN, Library Avenue, PUSA, New Delhi-110012, India
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Tandon G, Singh S, Kaur S, Sarika, Iquebal MA, Rai A, Kumar D. Computational deciphering of biotic stress associated genes in tomato ( Solanum lycopersicum). Genom Data 2017; 14:82-90. [PMID: 29062693 PMCID: PMC5643083 DOI: 10.1016/j.gdata.2017.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 09/20/2017] [Accepted: 09/23/2017] [Indexed: 01/17/2023]
Abstract
Tomato (Solanum lycopersicum) is one of the major vegetable plant and a model system for fruit development. Its global importance is due to its lycopene pigment which has anti-oxidative and anti-cancerous properties. Though > 1.5 M biotic stress associated ESTs of tomato are available but cumulative analysis to predict genes is warranted. Availability of whole genome de novo assembly can advantageously be used to map them over different chromosome. Further, available 0.14 M catalogued markers can be used to introgress specific desirable genes in varietal improvement program. We report here 57 novel genes associated with biotic stress of tomato along with 50 genes having physical location over different chromosomes. We also report 52 cis-regulating elements and 69 putative miRNAs which are involved in regulation of these biotic stresses associated genes. These putative candidate genes associated with biotic stress can be used in molecular breeding in the endeavor of tomato productivity along with its sustainable germplasm management. ESts related to biotic stress were collected and assembled into contigs. Total 57 novel genes were computationally mined from the assembled contigs. Among the predicted novel gene, 50 genes were mapped on tomato genome. 52 cis-regulating elements and 69 putative miRNAs were predicted for the novel genes.
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Affiliation(s)
- G Tandon
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 1100 12, India.,Departments of Computational Biology & Bioinformatics, Jacob School of Biotechnology & Bio-Engineering, SHUATS, Allahabad 211007, India
| | - S Singh
- Departments of Computational Biology & Bioinformatics, Jacob School of Biotechnology & Bio-Engineering, SHUATS, Allahabad 211007, India
| | - S Kaur
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 1100 12, India.,Departments of Computational Biology & Bioinformatics, Jacob School of Biotechnology & Bio-Engineering, SHUATS, Allahabad 211007, India
| | - Sarika
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 1100 12, India
| | - M A Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 1100 12, India
| | - A Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 1100 12, India
| | - D Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 1100 12, India
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Mishra AK, Tandon G, Sharma R, Chandrasekharan H, Pandey PS. In silico structural and functional analysis of protein encoded by wheat early salt-stress response gene (WESR3). Indian J Biochem Biophys 2015; 52:95-100. [PMID: 26040116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Salt stress is one of the major abiotic stresses limiting grain yield in wheat (Triticum aestivum L.). Wheat early salt-stress response gene (WESR3) is one of the major salt stress genes, which is affected in the first phase of salt stress. In this study, sequence and structural analysis of protein coded by WESR3 gene was carried out using various bioinformatics tools. Sequence analysis of WESR3 protein revealed the presence of highly conserved regions of Mlo gene family. Three-dimensional modeling was carried out to elucidate its structure and its active site. The sequence analysis revealed that WESR3 protein might be involved in fungal pathogen attack pathway. Thus, in addition to its involvement in abiotic stresses, it also seemed to play an important part in biotic stress pathways. Out of the three modeled protein structures obtained from I-TASSER, HHPred and QUARK, the I-TASSER protein model was the best model based on high confidence score and lesser number of bad contacts. The Ramchandran plot analysis also showed that all amino acid residues of I-TASSER model lie in the allowed region and thus indicating towards the overall good quality of the predicted model. Seventeen active sites were predicted in the protein bearing resemblance to the Mlo family conserved regions. In conclusion, a detailed analysis of WESR3 protein suggested an important role of WESR3 in biotic and abiotic stress. These results aid to the experimental data and help to build up a complete view of WESR3 proteins and their role in plant stress response.
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Tandon G, Jaiswal S, Iquebal M, Kumar S, Kaur S, Rai A, Kumar D. Evidence of salicylic acid pathway with EDS1 and PAD4 proteins by molecular dynamics simulation for grape improvement. J Biomol Struct Dyn 2015; 33:2180-91. [DOI: 10.1080/07391102.2014.996187] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Gitanjali Tandon
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute , Library Avenue, Pusa, New Delhi 110012, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute , Library Avenue, Pusa, New Delhi 110012, India
| | - M.A. Iquebal
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute , Library Avenue, Pusa, New Delhi 110012, India
| | - Sunil Kumar
- Bioinformatics Centre, National Bureau of Agriculturally Important Microorganisms , Kusmaur, Mau Nath Bhanjan, Uttar Pradesh 275101 , India
- Institute of Life Sciences , Nalco Square, Bhubaneswar 751023, India
| | - Sukhdeep Kaur
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute , Library Avenue, Pusa, New Delhi 110012, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute , Library Avenue, Pusa, New Delhi 110012, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute , Library Avenue, Pusa, New Delhi 110012, India
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Mital VN, Gupta MC, Arora SN, Tandon G. Coarctation of aorta, dextrocardia with situs inversus totalis and Kartagener's syndrome. Indian Heart J 1965; 17:376-80. [PMID: 5294436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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