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Niveditha D, Khan S, Khilari A, Nadkarni S, Bhalerao U, Kadam P, Yadav R, Kanekar JB, Shah N, Likhitkar B, Sawant R, Thakur S, Tupekar M, Nagar D, Rao AG, Jagtap R, Jogi S, Belekar M, Pathak M, Shah P, Ranade S, Phadke N, Das R, Joshi S, Karyakarte R, Ghose A, Kadoo N, Shashidhara LS, Monteiro JM, Shanmugam D, Raghunathan A, Karmodiya K. A tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India. J Infect Public Health 2023; 16:1290-1300. [PMID: 37331277 DOI: 10.1016/j.jiph.2023.06.004] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 06/20/2023] Open
Abstract
BACKGROUND Modern response to pandemics, critical for effective public health measures, is shaped by the availability and integration of diverse epidemiological outbreak data. Tracking variants of concern (VOC) is integral to understanding the evolution of SARS-CoV-2 in space and time, both at the local level and global context. This potentially generates actionable information when integrated with epidemiological outbreak data. METHODS A city-wide network of researchers, clinicians, and pathology diagnostic laboratories was formed for genome surveillance of COVID-19 in Pune, India. The genomic landscapes of 10,496 sequenced samples of SARS-CoV-2 driving peaks of infection in Pune between December-2020 to March-2022, were determined. As a modern response to the pandemic, a "band of five" outbreak data analytics approach was used. This integrated the genomic data (Band 1) of the virus through molecular phylogenetics with key outbreak data including sample collection dates and case numbers (Band 2), demographics like age and gender (Band 3-4), and geospatial mapping (Band 5). RESULTS The transmission dynamics of VOCs in 10,496 sequenced samples identified B.1.617.2 (Delta) and BA(x) (Omicron formerly known as B.1.1.529) variants as drivers of the second and third peaks of infection in Pune. Spike Protein mutational profiling during pre and post-Omicron VOCs indicated differential rank ordering of high-frequency mutations in specific domains that increased the charge and binding properties of the protein. Time-resolved phylogenetic analysis of Omicron sub-lineages identified a highly divergent BA.1 from Pune in addition to recombinant X lineages, XZ, XQ, and XM. CONCLUSIONS The band of five outbreak data analytics approach, which integrates five different types of data, highlights the importance of a strong surveillance system with high-quality meta-data for understanding the spatiotemporal evolution of the SARS-CoV-2 genome in Pune. These findings have important implications for pandemic preparedness and could be critical tools for understanding and responding to future outbreaks.
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Affiliation(s)
- Divya Niveditha
- Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Soumen Khan
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Ajinkya Khilari
- Biochemical Sciences Division, CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, India.; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, India
| | - Sanica Nadkarni
- Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Unnati Bhalerao
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Pradnya Kadam
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Ritu Yadav
- Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, India
| | - Jugal B Kanekar
- Biochemical Sciences Division, CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, India.; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, India
| | - Nikita Shah
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Bhagyashree Likhitkar
- Biochemical Sciences Division, CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, India.; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, India
| | - Rutuja Sawant
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Shikha Thakur
- Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, India
| | - Manisha Tupekar
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Dhriti Nagar
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Anjani G Rao
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Rutuja Jagtap
- Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Shraddha Jogi
- Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, India
| | - Madhuri Belekar
- Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, India
| | - Maitreyee Pathak
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Priyanki Shah
- The Pune Knowledge Cluster (PKC), Savitribai Phule Pune University, Ganeshkhind Road, 411007 Pune, India
| | | | - Nikhil Phadke
- GenePath Diagnostics India Private Limited, Pune 411004, India
| | - Rashmita Das
- Byramjee Jeejeebhoy Government Medical College (BJGMC), Jai Prakash Narayan Road, Pune 411001, India
| | - Suvarna Joshi
- Byramjee Jeejeebhoy Government Medical College (BJGMC), Jai Prakash Narayan Road, Pune 411001, India
| | - Rajesh Karyakarte
- Byramjee Jeejeebhoy Government Medical College (BJGMC), Jai Prakash Narayan Road, Pune 411001, India
| | - Aurnab Ghose
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Narendra Kadoo
- Biochemical Sciences Division, CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, India.; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, India
| | - L S Shashidhara
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India; The Pune Knowledge Cluster (PKC), Savitribai Phule Pune University, Ganeshkhind Road, 411007 Pune, India
| | - Joy Merwin Monteiro
- Department of Earth and Climate Science, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India; Department of Data Science, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Dhanasekaran Shanmugam
- Biochemical Sciences Division, CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, India.; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, India
| | - Anu Raghunathan
- Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad 201002, India.
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India.
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Ben Ayed R, Moreau F, Ben Hlima H, Rebai A, Ercisli S, Kadoo N, Hanana M, Assouguem A, Ullah R, Ali EA. SNP discovery and structural insights into OeFAD2 unravelling high oleic/linoleic ratio in olive oil. Comput Struct Biotechnol J 2022; 20:1229-1243. [PMID: 35317231 PMCID: PMC8914465 DOI: 10.1016/j.csbj.2022.02.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 01/02/2023] Open
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Ranpariya B, Salunke G, Karmakar S, Babiya K, Sutar S, Kadoo N, Kumbhakar P, Ghosh S. Antimicrobial Synergy of Silver-Platinum Nanohybrids With Antibiotics. Front Microbiol 2021; 11:610968. [PMID: 33597929 PMCID: PMC7882503 DOI: 10.3389/fmicb.2020.610968] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/22/2020] [Indexed: 12/19/2022] Open
Abstract
Various bacterial pathogens are responsible for nosocomial infections resulting in critical pathophysiological conditions, mortality, and morbidity. Most of the bacterial infections are associated with biofilm formation, which is resistant to the available antimicrobial drugs. As a result, novel bactericidal agents need to be fabricated, which can effectively combat the biofilm-associated bacterial infections. Herein, for the first time we report the antimicrobial and antibiofilm properties of silver-platinum nanohybrids (AgPtNHs), silver nanoparticles (AgNPs), and platinum nanoparticles (PtNPs) against Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. The AgPtNHs were synthesized by a green route using Dioscorea bulbifera tuber extract at 100°C for 5 h. The AgPtNHs ranged in size from 20 to 80 nm, with an average of ∼59 nm. AgNPs, PtNPs, and AgPtNHs showed a zeta potential of -14.46, -1.09, and -11.39 mV, respectively. High antimicrobial activity was observed against P. aeruginosa and S. aureus and AgPtNHs exhibited potent antimicrobial synergy in combination with antibiotics such as streptomycin, rifampicin, chloramphenicol, novobiocin, and ampicillin up to variable degrees. Interestingly, AgPtNHs could inhibit bacterial biofilm formation significantly. Hence, co-administration of AgPtNHs and antibiotics may serve as a powerful strategy to treat bacterial infections.
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Affiliation(s)
- Bansi Ranpariya
- Department of Microbiology, School of Science, RK University, Rajkot, India
| | - Gayatri Salunke
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Srikanta Karmakar
- Nanoscience Laboratory, Department of Physics, National Institute of Technology Durgapur, Durgapur, India
| | - Kaushik Babiya
- Department of Microbiology, School of Science, RK University, Rajkot, India
| | - Santosh Sutar
- Yashwantrao Chavan School of Rural Development, Shivaji University, Kolhapur, India
| | - Narendra Kadoo
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Pathik Kumbhakar
- Nanoscience Laboratory, Department of Physics, National Institute of Technology Durgapur, Durgapur, India
| | - Sougata Ghosh
- Department of Microbiology, School of Science, RK University, Rajkot, India
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Karade D, Vijayasarathi D, Kadoo N, Vyas R, Ingle PK, Karthikeyan M. Design of Novel Drug-like Molecules Using Informatics Rich Secondary Metabolites Analysis of Indian Medicinal and Aromatic Plants. Comb Chem High Throughput Screen 2020; 23:1113-1131. [PMID: 32504496 DOI: 10.2174/1386207323666200606211342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 02/29/2020] [Accepted: 03/26/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Several medicinal plants are being used in Indian medicine systems from ancient times. However, in most cases, the specific molecules or the active ingredients responsible for the medicinal or therapeutic properties are not yet known. OBJECTIVE This study aimed to report a computational protocol as well as a tool for generating novel potential drug candidates from the bioactive molecules of Indian medicinal and aromatic plants through the chemoinformatics approach. METHODS We built a database of the Indian medicinal and aromatic plants coupled with associated information (plant families, plant parts used for the medicinal purpose, structural information, therapeutic properties, etc.) We also developed a Java-based chemoinformatics open-source tool called DoMINE (Database of Medicinally Important Natural products from plantaE) for the generation of virtual library and screening of novel molecules from known medicinal plant molecules. We employed chemoinformatics approaches to in-silico screened metabolites from 104 Indian medicinal and aromatic plants and designed novel drug-like bioactive molecules. For this purpose, 1665 ring containing molecules were identified by text mining of literature related to the medicinal plant species, which were later used to extract 209 molecular scaffolds. Different scaffolds were further used to build a focused virtual library. Virtual screening was performed with cluster analysis to predict drug-like and lead-like molecules from these plant molecules in the context of drug discovery. The predicted drug-like and lead-like molecules were evaluated using chemoinformatics approaches and statistical parameters, and only the most significant molecules were proposed as the candidate molecules to develop new drugs. RESULTS AND CONCLUSION The supra network of molecules and scaffolds identifies the relationship between the plant molecules and drugs. Cluster analysis of virtual library molecules showed that novel molecules had more pharmacophoric properties than toxicophoric and chemophoric properties. We also developed the DoMINE toolkit for the advancement of natural product-based drug discovery through chemoinformatics approaches. This study will be useful in developing new drug molecules from the known medicinal plant molecules. Hence, this work will encourage experimental organic chemists to synthesize these molecules based on the predicted values. These synthesized molecules need to be subjected to biological screening to identify potential molecules for drug discovery research.
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Affiliation(s)
- Divya Karade
- Chemical Engineering and Process Development (CEPD) Division, CSIR-National Chemical Laboratory, Pune - 411008, India
| | - Durairaj Vijayasarathi
- Chemical Engineering and Process Development (CEPD) Division, CSIR-National Chemical Laboratory, Pune - 411008, India
| | - Narendra Kadoo
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Renu Vyas
- Bioengineering Sciences & Research, MIT ADT University, Pune-412201, India; 5Publication and Science Communication, CSIR-National Chemical Laboratory, Pune 411008, India
| | - P K Ingle
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Muthukumarasamy Karthikeyan
- Chemical Engineering and Process Development (CEPD) Division, CSIR-National Chemical Laboratory, Pune - 411008, India
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Mathur M, Nair A, Kadoo N. Plant-pathogen interactions: MicroRNA-mediated trans-kingdom gene regulation in fungi and their host plants. Genomics 2020; 112:3021-3035. [PMID: 32454170 DOI: 10.1016/j.ygeno.2020.05.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 04/07/2020] [Accepted: 05/20/2020] [Indexed: 12/25/2022]
Abstract
MicroRNAs (miRNAs) have been prevalently studied in plants, animals, and viruses. However, recent studies show evidences of miRNA-like RNAs (milRNAs) in fungi as well. It is known that after successful infection, pathogens hijack the host machinery and use it for their own growth and multiplication. Alternatively, resistant plants can overcome the pathogen attack by a variety of mechanisms. Based on this prior knowledge, we computationally predicted milRNAs from 13 fungi, and identified their targets in transcriptomes of the respective fungi as well as their host plants. The expressions of the milRNAs and targets were confirmed using qRT-PCR. We found that plant miRNAs targeted fungal virulence genes, while fungal milRNAs targeted plant resistance genes; corroborating miRNA-mediated trans-kingdom gene regulation and the roles of miRNAs in plant-pathogen interactions. Transgenic plants with miRNAs targeting fungal virulence genes, or anti-sense of fungal milRNAs, would be expected to be highly resistant to the fungal pathogens.
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Affiliation(s)
- Monika Mathur
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Aswathy Nair
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Narendra Kadoo
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Patil S, Shinde M, Prashant R, Kadoo N, Upadhyay A, Gupta V. Comparative Proteomics Unravels the Differences in Salt Stress Response of Own-Rooted and 110R-Grafted Thompson Seedless Grapevines. J Proteome Res 2019; 19:583-599. [PMID: 31808345 DOI: 10.1021/acs.jproteome.9b00420] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 01/20/2023]
Abstract
Thompson Seedless, a commonly grown table grape variety, is sensitive to salinity when grown on its own roots, and therefore, it is frequently grafted onto salinity-tolerant wild grapevine rootstocks. Rising soil salinity is a growing concern in irrigated agricultural systems. The accumulation of salts near the root zone severely hampers plant growth, leading to a decrease in the productive lifespan of grapevine and causing heavy yield losses to the farmer. In the present study, we investigated the differences in response to salinity between own-rooted Thompson Seedless (TSOR) and 110R-grafted Thompson Seedless (TS110R) grapevines, wherein 110R is reported to be a salt-tolerant rootstock. The grapevines were subjected to salt stress by treating them with a 150 mM NaCl solution. The stress-induced changes in protein abundance were investigated using a label-free shotgun proteomics approach at three time-points viz. 6 h, 48 h, and 7 days of salt treatment. A total of 2793 proteins were identified, of which 246 were differentially abundant at various time-points in TSOR and TS110R vines. The abundance of proteins involved in several biological processes such as photosynthesis, amino acid metabolism, translation, chlorophyll biosynthesis, and generation of precursor metabolites was significantly affected by salt stress in both the vines but at different stages of stress. The results revealed that TSOR vines responded fervently to salt stress, while TS110R vines adopted a preventive approach. The findings of this study add to the knowledge of salinity response in woody and grafted plants and hence open the scope for further studies on salt stress-specific differences induced by grafting.
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Affiliation(s)
- Sucheta Patil
- Biochemical Sciences Division , CSIR-National Chemical Laboratory , Pune 411008 , India.,Academy of Scientific and Innovative Research , Ghaziabad 201002 , India
| | - Manisha Shinde
- ICAR-National Research Centre for Grapes , Pune 412307 , India
| | - Ramya Prashant
- Biochemical Sciences Division , CSIR-National Chemical Laboratory , Pune 411008 , India
| | - Narendra Kadoo
- Biochemical Sciences Division , CSIR-National Chemical Laboratory , Pune 411008 , India.,Academy of Scientific and Innovative Research , Ghaziabad 201002 , India
| | | | - Vidya Gupta
- Biochemical Sciences Division , CSIR-National Chemical Laboratory , Pune 411008 , India.,Academy of Scientific and Innovative Research , Ghaziabad 201002 , India
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Sanghi S, Chirmade T, More S, Prabhune A, Gupta V, Kadoo N. Effect of Media Components and Growth Conditions for Improved Linoleic Acid Production by BeauveriaSpecies. J AM OIL CHEM SOC 2019. [DOI: 10.1002/aocs.12252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Smrati Sanghi
- Biochemical Sciences DivisionCSIR‐National Chemical Laboratory Pune, 411008 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad, 201002 India
| | - Tejas Chirmade
- Biochemical Sciences DivisionCSIR‐National Chemical Laboratory Pune, 411008 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad, 201002 India
| | - Snehal More
- Biochemical Sciences DivisionCSIR‐National Chemical Laboratory Pune, 411008 India
| | - Asmita Prabhune
- Biochemical Sciences DivisionCSIR‐National Chemical Laboratory Pune, 411008 India
| | - Vidya Gupta
- Biochemical Sciences DivisionCSIR‐National Chemical Laboratory Pune, 411008 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad, 201002 India
| | - Narendra Kadoo
- Biochemical Sciences DivisionCSIR‐National Chemical Laboratory Pune, 411008 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad, 201002 India
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Kumar V, Shriram V, Bhagat R, Khare T, Kapse S, Kadoo N. Phytochemical profile, anti-oxidant, anti-inflammatory, and anti-proliferative activities of Pogostemon deccanensis essential oils. 3 Biotech 2019; 9:31. [PMID: 30622869 DOI: 10.1007/s13205-018-1560-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 12/29/2018] [Indexed: 01/12/2023] Open
Abstract
Essential oils (EOs) obtained from aerial parts of Pogostemon deccanensis were analyzed for GC-MS profiling, and evaluated for antioxidant, anti-inflammatory, and anti-proliferative activities. GC-MS analysis revealed a total of 47 constituents, establishing the EOs rich in sesquiterpene with > 20 sesquiterpenes constituting around 77% of the total EO yield. Major constituents included Curzerene (Benzofuran, 6-ethenyl-4,5,6,7-tetrahydro-3,6-dimethyl-5-isopropenyl-, trans-) (26.39%) and epi-Cadinol (22.68%), Ethanone, 1-(2,4,6-trihydroxyphenyl) (6.83%, Acetophenones), and Boldenone (3.47%, anabolic steroid). EOs found to be rich in phytochemicals attributed for antioxidant potentials of aromatic/medicinal plants, viz., flavonoids (2.71 µg quercetin equivalents g-1 EO), total phenols (3.94 µg gallic acid equivalents (GAE) g-1 EO), carotenoids (14.3 µg β-carotene equivalents g-1 EO), and ascorbic acid (2.21 µg ascorbic acid equivalents g-1 EO). P. deccanensis EOs exhibited striking antioxidant activities assessed by wide range of assays including ferric reducing antioxidant potential (FRAP, 255.3 GAE at 2 µg mL-1 EO), total antioxidant activity (TAA, 264.3 GAE at 2 µg ml-1) of EO, DPPH (65% inhibition at 2 µg mL-1), and OH (58% inhibition at 2 µg mL-1) scavenging. Interestingly, EOs showed considerably higher anti-lipid peroxidation activity than the standard antioxidant molecule ascorbic acid, with 50% protection by 1.29 µg mL-1 EO against 20.0 µg mL-1 standard. EOs showed strong anti-inflammatory activity with 50% inhibition at 1.95 µg mL-1 EO. The anti-proliferative activity of EOs was tested against mouse cancer cell line and the EOs proved a potent anti-proliferative agent with only 2.1% cell survival at 2 µg mL-1 EO, whereas the EOs were largely non-toxic-to-normal (non-cancerous) cells with approximately 80% cell survival at the 2 µg mL-1 EOs. This being the first attempt of phytochemical profiling and wide array of biological activities of P. deccanensis EOs holds significance as the striking activities were observed at very low concentrations, in some cases at lower than the commercial standards, and has, therefore, great potential for pharmaceutical or commercial exploration.
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Affiliation(s)
- Vinay Kumar
- 1Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Ganeshkhind, Pune, 411016 India
- 2Department of Environmental Science, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007 India
| | - Varsha Shriram
- 3Department of Botany, Prof. Ramkrishna More Arts, Commerce and Science College (Savitribai Phule Pune University), Akurdi, Pune, 411044 India
| | - Rani Bhagat
- 4Department of Botany, Baburaoji Gholap College (Savitribai Phule Pune University), Sangvi, Pune, 411027 India
| | - Tushar Khare
- 1Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Ganeshkhind, Pune, 411016 India
| | - Shivanjali Kapse
- 1Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Ganeshkhind, Pune, 411016 India
| | - Narendra Kadoo
- 5Biochemical Sciences Division, CSIR National Chemical Laboratory, Pune, 411008 India
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Dube G, Kadoo N, Prashant R. Exploring the biological roles of Dothideomycetes ABC proteins: Leads from their phylogenetic relationships with functionally-characterized Ascomycetes homologs. PLoS One 2018; 13:e0197447. [PMID: 30071023 PMCID: PMC6071951 DOI: 10.1371/journal.pone.0197447] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 05/02/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The ATP-binding cassette (ABC) superfamily is one of the largest, ubiquitous and diverse protein families in nature. Categorized into nine subfamilies, its members are important to most organisms including fungi, where they play varied roles in fundamental cellular processes, plant pathogenesis or fungicide tolerance. However, these proteins are not yet well-understood in the class Dothideomycetes, which includes several phytopathogens that infect a wide range of food crops including wheat, barley and maize and cause major economic losses. RESULTS We analyzed the genomes of 14 Dothideomycetes fungi (Test set) and seven well-known Ascomycetes fungi (Model set- that possessed gene expression/ functional analysis data about the ABC genes) and predicted 578 and 338 ABC proteins from each set respectively. These proteins were classified into subfamilies A to I, which revealed the distribution of the subfamily members across the Dothideomycetes and Ascomycetes genomes. Phylogenetic analysis of Dothideomycetes ABC proteins indicated evolutionary relationships among the subfamilies within this class. Further, phylogenetic relationships among the ABC proteins from the Model and the Test fungi within each subfamily were analyzed, which aided in classifying these proteins into subgroups. We compiled and curated functional and gene expression information from the previous literature for 118 ABC genes and mapped them on the phylogenetic trees, which suggested possible roles in pathogenesis and/or fungicide tolerance for the newly identified Dothideomycetes ABC proteins. CONCLUSIONS The present analysis is one of the firsts to extensively analyze ABC proteins from Dothideomycetes fungi. Their phylogenetic analysis and annotating the clades with functional information indicated a subset of Dothideomycetes ABC genes that could be considered for experimental validation for their roles in plant pathogenesis and/or fungicide tolerance.
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Affiliation(s)
- Gaurav Dube
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India
| | - Narendra Kadoo
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Ramya Prashant
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India
- MIT School of Bioengineering Sciences & Research, MIT-Art, Design and Technology University, Pune, India
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Tellis M, Mathur M, Gurjar G, Kadoo N, Gupta V. Cover Image, Volume 85, Issue 11. Proteins 2017. [DOI: 10.1002/prot.25391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Meenakshi Tellis
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory; Pune India
| | - Monika Mathur
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory; Pune India
| | - Gayatri Gurjar
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory; Pune India
- Department of Biotechnology; Fergusson College; Pune India
| | - Narendra Kadoo
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory; Pune India
| | - Vidya Gupta
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory; Pune India
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Tellis M, Mathur M, Gurjar G, Kadoo N, Gupta V. Identification and functionality prediction of pathogenesis-related protein 1 from legume family. Proteins 2017; 85:2066-2080. [PMID: 28762578 DOI: 10.1002/prot.25361] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/19/2017] [Accepted: 07/27/2017] [Indexed: 11/11/2022]
Abstract
The production and accumulation of pathogenesis-related (PR) proteins in plants is one of the important responses to biotic and abiotic stress. Large number of identified PR proteins has been categorized into 17 functional families based on their structure, phylogenetics, and biological activities. However, they are not widely studied in legume crops. Using 29 PR1 proteins from Arabidopsis thaliana, as query, here we have predicted 92 candidate PR1 proteins through the PSI-BLAST and HMMER programs. These candidate proteins were comprehensively analyzed with, multiple sequence alignment, domain architecture studies, signal peptide, and motif extraction followed by phylogenetic analysis. Further, response of two candidate PR1 proteins from chickpea against Fusarium oxysporum f.sp.ciceri attack was validated using qRT-PCR followed by their 3D structure prediction. To decipher mode of action for PR1s, docking of pathogen extracellular matrix components along with fungal elicitors was performed with two chickpea PR1 proteins. Based on these findings, we propose carbohydrate to be the unique pathogen-recognition feature for PR1 proteins and β-glucanase activity via β-glucan binding or modification.
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Affiliation(s)
- Meenakshi Tellis
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Monika Mathur
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Gayatri Gurjar
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India.,Department of Biotechnology, Fergusson College, Pune, India
| | - Narendra Kadoo
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Vidya Gupta
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
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Ahmad Siddiqui E, Ahmad A, Julius A, Syed A, Khan S, Kharat M, Pai K, Kadoo N, Gupta V. Biosynthesis of Anti-Proliferative Gold Nanoparticles Using Endophytic Fusarium oxysporum Strain Isolated from Neem (A. indica) Leaves. Curr Top Med Chem 2016; 16:2036-42. [DOI: 10.2174/1568026616666160215160644] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/28/2015] [Accepted: 09/01/2015] [Indexed: 11/22/2022]
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Dalal S, Mhashal A, Kadoo N, Gaikwad SM. Functional stability and structural transitions of Kallikrein: spectroscopic and molecular dynamics studies. J Biomol Struct Dyn 2016; 35:330-342. [DOI: 10.1080/07391102.2016.1138884] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Sayli Dalal
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Anil Mhashal
- Division of Physical Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Narendra Kadoo
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Sushama M. Gaikwad
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
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Prashant R, Mani E, Rai R, Gupta R, Tiwari R, Dholakia B, Oak M, Röder M, Kadoo N, Gupta V. Genotype × environment interactions and QTL clusters underlying dough rheology traits in Triticum aestivum L. J Cereal Sci 2015. [DOI: 10.1016/j.jcs.2015.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Prashant R, Kadoo N, Desale C, Kore P, Dhaliwal HS, Chhuneja P, Gupta V. Kernel morphometric traits in hexaploid wheat (Triticum aestivum L.) are modulated by intricate QTL × QTL and genotype × environment interactions. J Cereal Sci 2012. [DOI: 10.1016/j.jcs.2012.05.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Ramya P, Chaubal A, Kulkarni K, Gupta L, Kadoo N, Dhaliwal HS, Chhuneja P, Lagu M, Gupta V. QTL mapping of 1000-kernel weight, kernel length, and kernel width in bread wheat (Triticum aestivum L.). J Appl Genet 2011; 51:421-9. [PMID: 21063060 DOI: 10.1007/bf03208872] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Kernel size and morphology influence the market value and milling yield of bread wheat (Triticum aestivum L.). The objective of this study was to identify quantitative trait loci (QTLs) controlling kernel traits in hexaploid wheat. We recorded 1000-kernel weight, kernel length, and kernel width for 185 recombinant inbred lines from the cross Rye Selection 111 × Chinese Spring grown in 2 agro-climatic regions in India for many years. Composite interval mapping (CIM) was employed for QTL detection using a linkage map with 169 simple sequence repeat (SSR) markers. For 1000-kernel weight, 10 QTLs were identified on wheat chromosomes 1A, 1D, 2B, 2D, 4B, 5B, and 6B, whereas 6 QTLs for kernel length were detected on 1A, 2B, 2D, 5A, 5B and 5D. Chromosomes 1D, 2B, 2D, 4B, 5B and 5D had 9 QTLs for kernel width. Chromosomal regions with QTLs detected consistently for multiple year-location combinations were identified for each trait. Pleiotropic QTLs were found on chromosomes 2B, 2D, 4B, and 5B. The identified genomic regions controlling wheat kernel size and shape can be targeted during further studies for their genetic dissection.
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Affiliation(s)
- P Ramya
- Plant Molecular Biology Group, Division of Biochemical Sciences, National Chemical Laboratory, Maharashtra, India
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