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Parthiban S, Vijeesh T, Gayathri T, Shanmugaraj B, Sharma A, Sathishkumar R. Artificial intelligence-driven systems engineering for next-generation plant-derived biopharmaceuticals. Front Plant Sci 2023; 14:1252166. [PMID: 38034587 PMCID: PMC10684705 DOI: 10.3389/fpls.2023.1252166] [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: 07/03/2023] [Accepted: 10/17/2023] [Indexed: 12/02/2023]
Abstract
Recombinant biopharmaceuticals including antigens, antibodies, hormones, cytokines, single-chain variable fragments, and peptides have been used as vaccines, diagnostics and therapeutics. Plant molecular pharming is a robust platform that uses plants as an expression system to produce simple and complex recombinant biopharmaceuticals on a large scale. Plant system has several advantages over other host systems such as humanized expression, glycosylation, scalability, reduced risk of human or animal pathogenic contaminants, rapid and cost-effective production. Despite many advantages, the expression of recombinant proteins in plant system is hindered by some factors such as non-human post-translational modifications, protein misfolding, conformation changes and instability. Artificial intelligence (AI) plays a vital role in various fields of biotechnology and in the aspect of plant molecular pharming, a significant increase in yield and stability can be achieved with the intervention of AI-based multi-approach to overcome the hindrance factors. Current limitations of plant-based recombinant biopharmaceutical production can be circumvented with the aid of synthetic biology tools and AI algorithms in plant-based glycan engineering for protein folding, stability, viability, catalytic activity and organelle targeting. The AI models, including but not limited to, neural network, support vector machines, linear regression, Gaussian process and regressor ensemble, work by predicting the training and experimental data sets to design and validate the protein structures thereby optimizing properties such as thermostability, catalytic activity, antibody affinity, and protein folding. This review focuses on, integrating systems engineering approaches and AI-based machine learning and deep learning algorithms in protein engineering and host engineering to augment protein production in plant systems to meet the ever-expanding therapeutics market.
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Affiliation(s)
- Subramanian Parthiban
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Thandarvalli Vijeesh
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Thashanamoorthi Gayathri
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Balamurugan Shanmugaraj
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Ashutosh Sharma
- Tecnologico de Monterrey, School of Engineering and Sciences, Centre of Bioengineering, Queretaro, Mexico
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
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Mahima K, Sunil Kumar KN, Rakhesh KV, Rajeswaran PS, Sharma A, Sathishkumar R. Advancements and future prospective of DNA barcodes in the herbal drug industry. Front Pharmacol 2022; 13:947512. [PMID: 36339543 PMCID: PMC9635000 DOI: 10.3389/fphar.2022.947512] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 05/18/2022] [Accepted: 10/10/2022] [Indexed: 08/04/2023] Open
Abstract
Ethnopharmacological relevance: The past couple of decades have witnessed the global resurgence of medicinal plants in the field of herbal-based health care. Increased consumption of medicinal plants and their derivative products is the major cause of the adulteration issues in herbal industries. As a result, the quality of herbal products is affected by spurious and unauthorized raw materials. Recent development in molecular plant identification using DNA barcodes has become a robust methodology to identify and authenticate the adulterants in herbal samples. Hence, rapid and accurate identification of medicinal plants is the key to success for the herbal industry. Aim of the study: This paper provides a comprehensive review of the application of DNA barcoding and advanced technologies that have emerged over the past 10 years related to medicinal plant identification and authentication and the future prospects of this technology. Materials and methods: Information on DNA barcodes was compiled from scientific databases (Google Scholar, Web of Science, SciFinder and PubMed). Additional information was obtained from books, Ph.D. thesis and MSc. Dissertations. Results: Working out an appropriate DNA barcode for plants is challenging; the single locus-based DNA barcodes (rbcL, ITS, ITS2, matK, rpoB, rpoC, trnH-psbA) to multi-locus DNA barcodes have become the successful species-level identification among herbal plants. Additionally, multi-loci have become efficient in the authentication of herbal products. Emerging advances in DNA barcoding and related technologies such as next-generation sequencing, high-resolution melting curve analysis, meta barcodes and mini barcodes have paved the way for successful herbal plant/samples identification. Conclusion: DNA barcoding needs to be employed together with other techniques to check and rationally and effectively quality control the herbal drugs. It is suggested that DNA barcoding techniques combined with metabolomics, transcriptomics, and proteomics could authenticate the herbal products. The invention of simple, cost-effective and improved DNA barcoding techniques to identify herbal drugs and their associated products of medicinal value in a fool-proof manner will be the future thrust of Pharmacopoeial monograph development for herbal drugs.
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Affiliation(s)
- Karthikeyan Mahima
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
- Department of Pharmacognosy, Siddha Central Research Institute, Chennai, Tamil Nadu, India
| | | | | | | | - Ashutosh Sharma
- Tecnologico de Monterrey, Centre of Bioengineering, Santiago de Queretaro, Queretaro, Mexico
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
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Adarshan S, Muthuramalingam P, Jeyasri R, Lakshmi MA, Sathishkumar R, Pandian SK, Shin H, Chen JT, Ramesh M. Vitex negundo L. derived specialized molecules unveil the multi-targeted therapeutic avenues against COPD: a systems pharmacology approach. FRONT BIOSCI-LANDMRK 2022; 27:87. [DOI: 10.31083/j.fbl2703087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 11/06/2022]
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Mahima K, Umapathy S, Sudhakar JV, Sathishkumar R. Systematic reinstatement of highly sacred Ficuskrishnae based on differences in morphology and DNA barcoding from Ficusbenghalensis (Moraceae). PhytoKeys 2021; 186:121-138. [PMID: 35002360 PMCID: PMC8677708 DOI: 10.3897/phytokeys.186.74086] [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] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/06/2021] [Indexed: 06/14/2023]
Abstract
Ficuskrishnae is considered as native to India and is well-known for the peculiarity in nature of its cup-shaped leaves where both the vernacular name (Krishna Fig) and specific epithet were derived. The taxonomic status of Ficuskrishnae is still unclear and currently treated as a subspecies or variety under Ficusbenghalensis. In the present study, morphological characters and molecular analysis were employed to address their species delimitation. The spacer markers ITS2 and trnH-psbA were used for constructing phylogenetic trees along with morphometric analysis. Ficuskrishnae distinctly differs from Ficusbenghalensis by having cup-forming leaves and the nature of the aerial roots, stipules, petioles, ostiolar bracts of the receptacle, DNA content, chromosome differences and nodal anatomy. The results showed that the highest divergence is observed in trnH-psbA (20.8 ± 12.2), followed by ITS2 (5.7 ± 3.2). The phylogenetic tree construction using Bayesian analysis showed a divergent boundary between the two species suggesting that F.krishnae could be an independent species, not a variety of F.benghalensis. The present study's findings support the view that these two floras can be treated as different species.
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Affiliation(s)
- Karthikeyan Mahima
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore–641 046, Tamil Nadu, IndiaBharathiar UniversityCoimbatoreIndia
| | - Senthilkumar Umapathy
- Department of Plant Biology and Plant Biotechnology, Madras Christian College, Chennai- 600 059, Tamil Nadu, IndiaMadras Christian CollegeChennaiIndia
| | - Jana Venkata Sudhakar
- Department of Botany, S.R.K Govt. Arts College, Pondicherry University–533 464, Tamil Nadu, India.Pondicherry UniversityPondicherryIndia
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore–641 046, Tamil Nadu, IndiaBharathiar UniversityCoimbatoreIndia
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Sreeram S, Sathishkumar R, Amritha PS. Targeting the ENV spike protein of HIV with naturally occurring compounds: an in-silico study for drug designing. ADV TRADIT MED (ADTM) 2021. [PMCID: PMC8506072 DOI: 10.1007/s13596-021-00617-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Bharadwaj R, Noceda C, Mohanapriya G, Kumar SR, Thiers KLL, Costa JH, Macedo ES, Kumari A, Gupta KJ, Srivastava S, Adholeya A, Oliveira M, Velada I, Sircar D, Sathishkumar R, Arnholdt-Schmitt B. Adaptive Reprogramming During Early Seed Germination Requires Temporarily Enhanced Fermentation-A Critical Role for Alternative Oxidase Regulation That Concerns Also Microbiota Effectiveness. Front Plant Sci 2021; 12:686274. [PMID: 34659277 PMCID: PMC8518632 DOI: 10.3389/fpls.2021.686274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/10/2021] [Indexed: 05/05/2023]
Abstract
Plants respond to environmental cues via adaptive cell reprogramming that can affect whole plant and ecosystem functionality. Microbiota constitutes part of the inner and outer environment of the plant. This Umwelt underlies steady dynamics, due to complex local and global biotic and abiotic changes. Hence, adaptive plant holobiont responses are crucial for continuous metabolic adjustment at the systems level. Plants require oxygen-dependent respiration for energy-dependent adaptive morphology, such as germination, root and shoot growth, and formation of adventitious, clonal, and reproductive organs, fruits, and seeds. Fermentative paths can help in acclimation and, to our view, the role of alternative oxidase (AOX) in coordinating complex metabolic and physiological adjustments is underestimated. Cellular levels of sucrose are an important sensor of environmental stress. We explored the role of exogenous sucrose and its interplay with AOX during early seed germination. We found that sucrose-dependent initiation of fermentation during the first 12 h after imbibition (HAI) was beneficial to germination. However, parallel upregulated AOX expression was essential to control negative effects by prolonged sucrose treatment. Early downregulated AOX activity until 12 HAI improved germination efficiency in the absence of sucrose but suppressed early germination in its presence. The results also suggest that seeds inoculated with arbuscular mycorrhizal fungi (AMF) can buffer sucrose stress during germination to restore normal respiration more efficiently. Following this approach, we propose a simple method to identify organic seeds and low-cost on-farm perspectives for early identifying disease tolerance, predicting plant holobiont behavior, and improving germination. Furthermore, the research strengthens the view that AOX can serve as a powerful functional marker source for seed hologenomes.
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Affiliation(s)
- Revuru Bharadwaj
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Carlos Noceda
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Cell and Molecular Biology of Plants (BIOCEMP)/Industrial Biotechnology and Bioproducts, Departamento de Ciencias de la Vida y de la Agricultura, Universidad de las Fuerzas Armadas-ESPE, Sangolquí, Ecuador
| | - Gunasekharan Mohanapriya
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Sarma Rajeev Kumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Karine Leitão Lima Thiers
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - José Hélio Costa
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Elisete Santos Macedo
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Aprajita Kumari
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- National Institute of Plant Genome Research, New Delhi, India
| | - Kapuganti Jagadis Gupta
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- National Institute of Plant Genome Research, New Delhi, India
| | - Shivani Srivastava
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Centre for Mycorrhizal Research, Sustainable Agriculture Division, The Energy and Resources Institute (TERI), TERI Gram, Gurugram, India
| | - Alok Adholeya
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Centre for Mycorrhizal Research, Sustainable Agriculture Division, The Energy and Resources Institute (TERI), TERI Gram, Gurugram, India
| | - Manuela Oliveira
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Department of Mathematics and CIMA - Center for Research on Mathematics and Its Applications, Universidade de Évora, Évora, Portugal
| | - Isabel Velada
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- MED—Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada, Universidade de Évora, Évora, Portugal
| | - Debabrata Sircar
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Birgit Arnholdt-Schmitt
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
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Bharadwaj R, Kumar SR, Sharma A, Sathishkumar R. Plant Metabolic Gene Clusters: Evolution, Organization, and Their Applications in Synthetic Biology. Front Plant Sci 2021; 12:697318. [PMID: 34490002 PMCID: PMC8418127 DOI: 10.3389/fpls.2021.697318] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/05/2021] [Indexed: 05/21/2023]
Abstract
Plants are a remarkable source of high-value specialized metabolites having significant physiological and ecological functions. Genes responsible for synthesizing specialized metabolites are often clustered together for a coordinated expression, which is commonly observed in bacteria and filamentous fungi. Similar to prokaryotic gene clustering, plants do have gene clusters encoding enzymes involved in the biosynthesis of specialized metabolites. More than 20 gene clusters involved in the biosynthesis of diverse metabolites have been identified across the plant kingdom. Recent studies demonstrate that gene clusters are evolved through gene duplications and neofunctionalization of primary metabolic pathway genes. Often, these clusters are tightly regulated at nucleosome level. The prevalence of gene clusters related to specialized metabolites offers an attractive possibility of an untapped source of highly useful biomolecules. Accordingly, the identification and functional characterization of novel biosynthetic pathways in plants need to be worked out. In this review, we summarize insights into the evolution of gene clusters and discuss the organization and importance of specific gene clusters in the biosynthesis of specialized metabolites. Regulatory mechanisms which operate in some of the important gene clusters have also been briefly described. Finally, we highlight the importance of gene clusters to develop future metabolic engineering or synthetic biology strategies for the heterologous production of novel metabolites.
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Affiliation(s)
- Revuru Bharadwaj
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Sarma R. Kumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Ashutosh Sharma
- Tecnologico de Monterrey, Centre of Bioengineering, Querétaro, Mexico
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
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Costa JH, Mohanapriya G, Bharadwaj R, Noceda C, Thiers KLL, Aziz S, Srivastava S, Oliveira M, Gupta KJ, Kumari A, Sircar D, Kumar SR, Achra A, Sathishkumar R, Adholeya A, Arnholdt-Schmitt B. ROS/RNS Balancing, Aerobic Fermentation Regulation and Cell Cycle Control - a Complex Early Trait ('CoV-MAC-TED') for Combating SARS-CoV-2-Induced Cell Reprogramming. Front Immunol 2021; 12:673692. [PMID: 34305903 PMCID: PMC8293103 DOI: 10.3389/fimmu.2021.673692] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 06/17/2021] [Indexed: 12/19/2022] Open
Abstract
In a perspective entitled 'From plant survival under severe stress to anti-viral human defense' we raised and justified the hypothesis that transcript level profiles of justified target genes established from in vitro somatic embryogenesis (SE) induction in plants as a reference compared to virus-induced profiles can identify differential virus signatures that link to harmful reprogramming. A standard profile of selected genes named 'ReprogVirus' was proposed for in vitro-scanning of early virus-induced reprogramming in critical primary infected cells/tissues as target trait. For data collection, the 'ReprogVirus platform' was initiated. This initiative aims to identify in a common effort across scientific boundaries critical virus footprints from diverse virus origins and variants as a basis for anti-viral strategy design. This approach is open for validation and extension. In the present study, we initiated validation by experimental transcriptome data available in public domain combined with advancing plant wet lab research. We compared plant-adapted transcriptomes according to 'RegroVirus' complemented by alternative oxidase (AOX) genes during de novo programming under SE-inducing conditions with in vitro corona virus-induced transcriptome profiles. This approach enabled identifying a major complex trait for early de novo programming during SARS-CoV-2 infection, called 'CoV-MAC-TED'. It consists of unbalanced ROS/RNS levels, which are connected to increased aerobic fermentation that links to alpha-tubulin-based cell restructuration and progression of cell cycle. We conclude that anti-viral/anti-SARS-CoV-2 strategies need to rigorously target 'CoV-MAC-TED' in primary infected nose and mouth cells through prophylactic and very early therapeutic strategies. We also discuss potential strategies in the view of the beneficial role of AOX for resilient behavior in plants. Furthermore, following the general observation that ROS/RNS equilibration/redox homeostasis is of utmost importance at the very beginning of viral infection, we highlight that 'de-stressing' disease and social handling should be seen as essential part of anti-viral/anti-SARS-CoV-2 strategies.
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Affiliation(s)
- José Hélio Costa
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Gunasekaran Mohanapriya
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Revuru Bharadwaj
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Carlos Noceda
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Cell and Molecular Biotechnology of Plants (BIOCEMP)/Industrial Biotechnology and Bioproducts, Departamento de Ciencias de la Vida y de la Agricultura, Universidad de las Fuerzas Armadas-ESPE, Sangolquí, Ecuador
| | - Karine Leitão Lima Thiers
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Shahid Aziz
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Shivani Srivastava
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Centre for Mycorrhizal Research, Sustainable Agriculture Division, The Energy and Resources, Institute (TERI), TERI Gram, Gurugram, India
| | - Manuela Oliveira
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Department of Mathematics and CIMA - Center for Research on Mathematics and Its Applications, Universidade de Évora, Évora, Portugal
| | - Kapuganti Jagadis Gupta
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Aprajita Kumari
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Debabrata Sircar
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Sarma Rajeev Kumar
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Arvind Achra
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Department of Microbiology, Atal Bihari Vajpayee Institute of Medical Sciences & Dr Ram Manohar Lohia Hospital, New Delhi, India
| | - Ramalingam Sathishkumar
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Alok Adholeya
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Centre for Mycorrhizal Research, Sustainable Agriculture Division, The Energy and Resources, Institute (TERI), TERI Gram, Gurugram, India
| | - Birgit Arnholdt-Schmitt
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
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Arnholdt-Schmitt B, Mohanapriya G, Bharadwaj R, Noceda C, Macedo ES, Sathishkumar R, Gupta KJ, Sircar D, Kumar SR, Srivastava S, Adholeya A, Thiers KL, Aziz S, Velada I, Oliveira M, Quaresma P, Achra A, Gupta N, Kumar A, Costa JH. From Plant Survival Under Severe Stress to Anti-Viral Human Defense - A Perspective That Calls for Common Efforts. Front Immunol 2021; 12:673723. [PMID: 34211468 PMCID: PMC8240590 DOI: 10.3389/fimmu.2021.673723] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/13/2021] [Indexed: 12/11/2022] Open
Abstract
Reprogramming of primary virus-infected cells is the critical step that turns viral attacks harmful to humans by initiating super-spreading at cell, organism and population levels. To develop early anti-viral therapies and proactive administration, it is important to understand the very first steps of this process. Plant somatic embryogenesis (SE) is the earliest and most studied model for de novo programming upon severe stress that, in contrast to virus attacks, promotes individual cell and organism survival. We argued that transcript level profiles of target genes established from in vitro SE induction as reference compared to virus-induced profiles can identify differential virus traits that link to harmful reprogramming. To validate this hypothesis, we selected a standard set of genes named 'ReprogVirus'. This approach was recently applied and published. It resulted in identifying 'CoV-MAC-TED', a complex trait that is promising to support combating SARS-CoV-2-induced cell reprogramming in primary infected nose and mouth cells. In this perspective, we aim to explain the rationale of our scientific approach. We are highlighting relevant background knowledge on SE, emphasize the role of alternative oxidase in plant reprogramming and resilience as a learning tool for designing human virus-defense strategies and, present the list of selected genes. As an outlook, we announce wider data collection in a 'ReprogVirus Platform' to support anti-viral strategy design through common efforts.
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Affiliation(s)
- Birgit Arnholdt-Schmitt
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Gunasekaran Mohanapriya
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Revuru Bharadwaj
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Carlos Noceda
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Cell and Molecular Biotechnology of Plants (BIOCEMP)/Industrial Biotechnology and Bioproducts, Departamento de Ciencias de la Vida y de la Agricultura, Universidad de las Fuerzas Armadas-ESPE, Sangolquí, Ecuador
| | - Elisete Santos Macedo
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Ramalingam Sathishkumar
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Kapuganti Jagadis Gupta
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Debabrata Sircar
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Sarma Rajeev Kumar
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Shivani Srivastava
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Centre for Mycorrhizal Research, Sustainable Agriculture Division, The Energy and Resources Institute (TERI), TERI Gram, Gual Pahari, Gurugram, India
| | - Alok Adholeya
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Centre for Mycorrhizal Research, Sustainable Agriculture Division, The Energy and Resources Institute (TERI), TERI Gram, Gual Pahari, Gurugram, India
| | - KarineLeitão Lima Thiers
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Shahid Aziz
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Isabel Velada
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- MED—Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada, Universidade de Évora, Évora, Portugal
| | - Manuela Oliveira
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Department of Mathematics and CIMA - Center for Research on Mathematics and its Applications, Universidade de Évora, Évora, Portugal
| | - Paulo Quaresma
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- NOVA LINCS – Laboratory for Informatics and Computer Science, University of Évora, Évora, Portugal
| | - Arvind Achra
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Department of Microbiology, Atal Bihari Vajpayee Institute of Medical Sciences & Dr Ram Manohar Lohia Hospital, New Delhi, India
| | - Nidhi Gupta
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Ashwani Kumar
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Hargovind Khorana Chair, Jayoti Vidyapeeth Womens University, Jaipur, India
| | - José Hélio Costa
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
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10
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Dhivya S, Ashutosh S, Gowtham I, Baskar V, Harini AB, Mukunthakumar S, Sathishkumar R. Molecular identification and evolutionary relationships between the subspecies of Musa by DNA barcodes. BMC Genomics 2020; 21:659. [PMID: 32972362 PMCID: PMC7513480 DOI: 10.1186/s12864-020-07036-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 08/30/2020] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The banana (Musa sp., AAA) genome is constantly increasing due to high-frequency of somaclonal variations. Due to its large diversity, a conventional numerical and morphological based taxonomic identification of banana cultivars is laborious, difficult and often leads to subject of disagreements. RESULTS Hence, in the present study, we used universal DNA barcode ITS2 region to identify and to find the genetic relationship between the cultivars and varieties of banana. Herein, a total of 16 banana cultivars were PCR amplified using ITS2 primer pair. In addition, 321 sequences which were retrieved from GenBank, USA, were used in this study. The sequences were then aligned using Clustal W and genetic distances were computed using MEGA V5.1. The study showed significant divergence between the intra- and inter-specific genetic distances in ITS2 region. BLAST1 and Distance methods proved that ITS2 DNA barcode region successfully identified and distinguished the cultivar and varieties of banana. CONCLUSION Thus, from the results of the present study, it is clear that ITS2 is not only an efficient DNA barcode to identify the banana species but also a potential candidate for enumerating the phylogenetic relationships between the subspecies and cultivars. This is the first comprehensive study to categorically distinguish the economically important banana subspecies and varieties using DNA barcodes and to understand its evolutionary relationship.
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Affiliation(s)
- S Dhivya
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641046, India
| | - S Ashutosh
- Technologico de Monterrey, Centre of Bioengineering, Epigmenio Gonzalez #500, Fracc. San Pablo, Campus Queretaro, Santiago de Querétaro, Queretaro, Mexico
| | - I Gowtham
- Plant Biofarming Laboratory, DRDO-BU Centre for Life Sciences, Bharathiar University, Coimbatore, 641046, India
| | - V Baskar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641046, India
| | - A Baala Harini
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641046, India
| | - S Mukunthakumar
- Biotechnology and Bioinformatics Division, Jawaharlal Nehru Tropical Botanic Garden & Research Institute, Palode, Thiruvananthapuram, Kerala, 695 562, India
| | - R Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641046, India.
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11
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Abstract
The closely related species present in the subgenera of Urostigma are challenging to classify due to the existence of overlapping morphological characteristics, which makes identification habitually problematic. It is still unresolved whether the species of the Ficus virens complex, which includes F. virens, F. middletonii, F. caulocarpa, F. concinna, and F. superba, are the same or distinct species due to the complexities in classification. To clarify the circumscription between the species and re-evaluate the taxonomical status, morphological characteristics were extensively examined; further, a phylogenetic reconstruction based on two DNA markers (ITS2 and trnH-psbA) in combination with morphological traits was carried out. The phylogenetic tree constructed using the combined morphology and DNA markers revealed that the five species should be demarcated as independent species. This study supports the importance of using both molecular and morphological data for efficient discrimination of species having high similarities. Further investigation into the species present in the subgenera Urostigma may provide additional information regarding the ancestral traits and its evolutionary history.
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Affiliation(s)
- Karthikeyan Mahima
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
| | - Jana Venkata Sudhakar
- Department of Botany, S.R.K. Govt. Arts College, Affiliated to Pondicherry University, Yanam 533 464, UT of Puducherry, India
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
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12
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Lavanya G, Venkatapathy K, Magesh C, Perumal P, Sathishkumar R, Amudha P. The First Recyclable, Nanocrystalline CdS Thin Film Mediated Eco-benign Synthesis Of Hantzsch 1, 4 Dihyropyridines, 1, 8-Dioxodecahydroacridine and Polyhydroquinolines derivatives. Appl Organomet Chem 2019. [DOI: 10.1002/aoc.5026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- G. Lavanya
- P.G. & Research Department of Chemistry Arignar Anna Govt. Arts and Science College; Cheyyar Tamilnadu India 604 407
| | - K. Venkatapathy
- P.G. & Research Department of Chemistry Arignar Anna Govt. Arts and Science College; Cheyyar Tamilnadu India 604 407
| | - C.J. Magesh
- P.G. & Research Department of Chemistry Arignar Anna Govt. Arts and Science College; Cheyyar Tamilnadu India 604 407
| | - P.T. Perumal
- Department of Chemistry; B. S Abdur Rahman Crescent Institute of Science and Technology; Vandalur Chennai India 600 048
| | - R. Sathishkumar
- P.G. & Research Department of Physics Arignar Anna Govt. Arts and Science College; Cheyyar Tamilnadu India 604 407
| | - P. Amudha
- P.G. & Research Department of Chemistry Arignar Anna Govt. Arts and Science College; Cheyyar Tamilnadu India 604 407
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Anunanthini P, Manoj VM, Sarath Padmanabhan TS, Dhivya S, Narayan JA, Appunu C, Sathishkumar R. Corrigendum to: In silico characterisation and functional validation of chilling tolerant divergence 1 (COLD1) gene in monocots during abiotic stress. Funct Plant Biol 2019; 46:596. [PMID: 32172736 DOI: 10.1071/fp18189_co] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The G protein-coupled receptor is one of the major transmembrane proteins in plants. It consists of an α subunit, a β subunit and three γ subunits. Chilling tolerant divergence 1 (COLD1) includes a Golgi pH receptor (GPHR) domain, which maintains cell membrane organisation and dynamics, along with abscisic acid linked G protein-coupled receptor (ABA_GPCR) that regulates the signalling pathways during cold stress. In the present study, we performed characterisation of a homologous COLD1 from the economically important monocot species Oryza sativa L., Zea mays L., Sorghum bicolor (L.)Moench and Erianthus arundinaceus (L.) Beauv. IK 76-81, a wild relative of Saccharum. COLD1 was isolated from E. arundinaceus IK 76-81, analysed for its evolution, domain, membrane topology, followed by prediction of secondary, tertiary structures and functionally validated in all four different monocots. Gene expression studies of COLD1 revealed differential expression under heat, drought, salinity and cold stresses in selected monocots. This is the first study on regulation of native COLD1 during abiotic stress in monocots, which has opened up new leads for trait improvement strategies in this economically important crop species.
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14
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Ragupathy S, Faller AC, Shanmughanandhan D, Kesanakurti P, Shaanker RU, Ravikanth G, Sathishkumar R, Mathivanan N, Song J, Han J, Newmaster S. Exploring DNA quantity and quality from raw materials to botanical extracts. Heliyon 2019; 5:e01935. [PMID: 31245647 PMCID: PMC6582161 DOI: 10.1016/j.heliyon.2019.e01935] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 05/23/2019] [Accepted: 06/06/2019] [Indexed: 12/02/2022] Open
Abstract
OBJECTIVES The aim of this study was to explore the variability in DNA quality and quantity along a gradient of industrial processing of botanical ingredients from raw materials to extracts. METHODS A data matrix was assembled for 1242 botanical ingredient samples along a gradient of industrial processing commonly used in the Natural Health Product (NHP) industry. Multivariate statistics was used to explore dependant variables for quality and quantity. The success of attaining a positive DNA test result along a gradient of industrial processing was compared among four biotechnologies: DNA barcoding, NGS, Sanger sequencing and qPCR. RESULTS There was considerable variance in DNA quality and quantity among the samples, which could be interpreted along a gradient from raw materials with greater quantities (50-120 ng/μL) of DNA and longer DNA (400-500bp) sequences to extracts, which were characterized by lower quantities (0.1-10.0 ng/μL) and short fragments (50-150bp). CONCLUSIONS Targeted molecular diagnostic tests for species identity can be used in the NHP industry for raw and processed samples. Non-targeted tests or the use of NGS for any identity test needs considerable research and development and must be validated before it can be used in commercial operations as these methods are subject to considerable risk of false negative and positive results. Proper use of these tools can be used to ensure ingredient authenticity, and to avert adulteration, and contamination with plants that are a health concern. Lastly these tools can be used to prevent the exploitation of rare herbal species and the harvesting of native biodiversity for commercial purposes.
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Affiliation(s)
- Subramanyam Ragupathy
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Adam C. Faller
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Dhivya Shanmughanandhan
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Prasad Kesanakurti
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - R. Uma Shaanker
- Department of Crop Physiology and School of Ecology and Conservation, University of Agricultural Sciences, GKVK, Bangalore, 560065, India
| | - Gudasalamani Ravikanth
- Conservation Genetics Lab, Ashoka Trust for Research in Ecology and the Environment (ATREE), Royal Enclave, Srirampura, Jakkur PO, Bengaluru, 560064, India
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, 641046, India
| | - Narayanasamy Mathivanan
- Centre for Advanced Studies in Botany, University of Madras Guindy Campus, Chennai, 600 025, Tamil Nadu, India
| | - Jingyuan Song
- Engineering Research Center of Traditional Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Jianping Han
- Engineering Research Center of Traditional Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Steven Newmaster
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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Anunanthini P, Manoj VM, Sarath Padmanabhan TS, Dhivya S, Narayan JA, Appunu C, Sathishkumar R. In silico characterisation and functional validation of chilling tolerant divergence 1 (COLD1) gene in monocots during abiotic stress. Funct Plant Biol 2019; 46:524-532. [PMID: 30940337 DOI: 10.1071/fp18189] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 01/24/2019] [Indexed: 06/09/2023]
Abstract
The G protein-coupled receptor is one of the major transmembrane proteins in plants. It consists of an α subunit, a β subunit and three γ subunits. Chilling tolerant divergence 1 (COLD1) includes a Golgi pH receptor (GPHR) domain, which maintains cell membrane organisation and dynamics, along with abscisic acid linked G protein-coupled receptor (ABA_GPCR) that regulates the signalling pathways during cold stress. In the present study, we performed characterisation of a homologous COLD1 from the economically important monocot species Oryza sativa L., Zea mays L., Sorghum bicolor (L.)Moench and Erianthus arundinaceus (L.) Beauv. IK 76-81, a wild relative of Saccharum. COLD1 was isolated from E. arundinaceus IK 76-81, analysed for its evolution, domain, membrane topology, followed by prediction of secondary, tertiary structures and functionally validated in all four different monocots. Gene expression studies of COLD1 revealed differential expression under heat, drought, salinity and cold stresses in selected monocots. This is the first study on regulation of native COLD1 during abiotic stress in monocots, which has opened up new leads for trait improvement strategies in this economically important crop species.
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Affiliation(s)
- P Anunanthini
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - V M Manoj
- Genetic Transformation Lab, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - T S Sarath Padmanabhan
- Genetic Transformation Lab, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - S Dhivya
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - J Ashwin Narayan
- Genetic Transformation Lab, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - C Appunu
- Genetic Transformation Lab, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, India; and Corresponding authors. Emails: ;
| | - R Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India; and Corresponding authors. Emails: ;
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Abstract
The unique medicinal and nutritional properties of honey are determined by its chemical composition. To evaluate the quality of honey, it is essential to study the surrounding vegetation where honeybees forage. In this study we used conventional melissopalynological and DNA barcoding techniques to determine the floral source of honey samples collected from different districts of the state of Mizoram, India. Pollen grains were isolated and genomic DNA was extracted from the honey samples. PCR amplification was carried out using universal barcode candidates ITS2 and rbcL to identify the plant species. Furthermore, TA cloning was carried out to screen the PCR amplicon libraries to identify the presence of multiple plant species. Results from both the melissopalynological and DNA barcoding analyses identified almost exactly the same 22 species, suggesting that both methods are suitable for analysis. However, DNA barcoding is easier and widely practiced. Hence, it can be concluded that DNA barcoding is a useful tool in determining the medicinal and commercial value of honey.
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Affiliation(s)
- Mohanasundaram Saravanan
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore - 641046, Tamil Nadu, India
| | - Gunasekaran Mohanapriya
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore - 641046, Tamil Nadu, India
| | - Ramachandra Laha
- Department of Botany, Mizoram University, Aizawl - 796004, Mizoram, India
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore - 641046, Tamil Nadu, India
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Manoj VM, Anunanthini P, Swathik PC, Dharshini S, Ashwin Narayan J, Manickavasagam M, Sathishkumar R, Suresha GS, Hemaprabha G, Ram B, Appunu C. Comparative analysis of glyoxalase pathway genes in Erianthus arundinaceus and commercial sugarcane hybrid under salinity and drought conditions. BMC Genomics 2019; 19:986. [PMID: 30999852 PMCID: PMC7402403 DOI: 10.1186/s12864-018-5349-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 05/23/2018] [Accepted: 12/03/2018] [Indexed: 11/26/2022] Open
Abstract
Background Glyoxalase pathway is a reactive carbonyl species (RCS) scavenging mechanism involved in the detoxification of methylglyoxal (MG), which is a reactive α-ketoaldehyde. In plants under abiotic stress, the cellular toxicity is reduced through glyoxalase pathway genes, i.e. Glyoxalase I (Gly I), Glyoxalase II (Gly II) and Glyoxalase III (Gly III). Salinity and water deficit stresses produce higher amounts of endogenous MG resulting in severe tissue damage. Thus, characterizing glyoxalase pathway genes that govern the MG metabolism should provide new insights on abiotic stress tolerance in Erianthus arundinaceus, a wild relative of sugarcane and commercial sugarcane hybrid (Co 86032). Results In this study, three glyoxalase genes (Glyoxalase I, II and III) from E. arundinaceus (a wild relative of sugarcane) and commercial sugarcane hybrid (Co 86032) were characterized. Comparative gene expression profiles (qRT-PCR) of Glyoxalase I, II and III under salinity and water deficit stress conditions revealed differential transcript expression with higher levels of Glyoxalase III in both the stress conditions. Significantly, E. arundinaceus had a higher expression level of glyoxalase genes compared to commercial sugarcane hybrid. On the other hand, gas exchange parameters like stomatal conductance and transpiration rate were declined to very low levels under both salt and drought induced stresses in commercial sugarcane hybrid when compared to E. arundinaceus. E. arundinaceus maintained better net photosynthetic rate compared to commercial sugarcane hybrid. The phylogenetic analysis of glyoxalase proteins showed its close evolutionary relationship with Sorghum bicolor and Zea mays. Glyoxalase I and II were predicted to possess 9 and 7 isoforms respectively whereas, Glyoxalase III couldn’t be identified as it comes under uncharacterized protein identified in recent past. Chromosomal mapping is also carried out for glyoxalase pathway genes and its isoforms. Docking studies revealed the binding affinities of glyoxalase proteins in both E. arundinaceus and commercial sugarcane hybrid with their substrate molecules. Conclusions This study emphasizes the role of Glyoxalase pathway genes in stress defensive mechanism which route to benefit in progressive plant adaptations and serves as potential candidates for development of salt and drought tolerant crops. Electronic supplementary material The online version of this article (10.1186/s12864-018-5349-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Peter Clarancia Swathik
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
| | - Selvarajan Dharshini
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
| | | | - Markandan Manickavasagam
- Department of Biotechnology, Bharathidasan University, Tiruchirapalli, Tamil Nadu, 620024, India
| | | | | | - Govind Hemaprabha
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
| | - Bakshi Ram
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
| | - Chinnaswamy Appunu
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India.
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Mohanapriya G, Bharadwaj R, Noceda C, Costa JH, Kumar SR, Sathishkumar R, Thiers KLL, Santos Macedo E, Silva S, Annicchiarico P, Groot SP, Kodde J, Kumari A, Gupta KJ, Arnholdt-Schmitt B. Alternative Oxidase (AOX) Senses Stress Levels to Coordinate Auxin-Induced Reprogramming From Seed Germination to Somatic Embryogenesis-A Role Relevant for Seed Vigor Prediction and Plant Robustness. Front Plant Sci 2019; 10:1134. [PMID: 31611888 PMCID: PMC6776121 DOI: 10.3389/fpls.2019.01134] [Citation(s) in RCA: 10] [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] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 08/16/2019] [Indexed: 05/21/2023]
Abstract
Somatic embryogenesis (SE) is the most striking and prominent example of plant plasticity upon severe stress. Inducing immature carrot seeds perform SE as substitute to germination by auxin treatment can be seen as switch between stress levels associated to morphophysiological plasticity. This experimental system is highly powerful to explore stress response factors that mediate the metabolic switch between cell and tissue identities. Developmental plasticity per se is an emerging trait for in vitro systems and crop improvement. It is supposed to underlie multi-stress tolerance. High plasticity can protect plants throughout life cycles against variable abiotic and biotic conditions. We provide proof of concepts for the existing hypothesis that alternative oxidase (AOX) can be relevant for developmental plasticity and be associated to yield stability. Our perspective on AOX as relevant coordinator of cell reprogramming is supported by real-time polymerase chain reaction (PCR) analyses and gross metabolism data from calorespirometry complemented by SHAM-inhibitor studies on primed, elevated partial pressure of oxygen (EPPO)-stressed, and endophyte-treated seeds. In silico studies on public experimental data from diverse species strengthen generality of our insights. Finally, we highlight ready-to-use concepts for plant selection and optimizing in vivo and in vitro propagation that do not require further details on molecular physiology and metabolism. This is demonstrated by applying our research & technology concepts to pea genotypes with differential yield performance in multilocation fields and chickpea types known for differential robustness in the field. By using these concepts and tools appropriately, also other marker candidates than AOX and complex genomics data can be efficiently validated for prebreeding and seed vigor prediction.
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Affiliation(s)
- Gunasekaran Mohanapriya
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
| | - Revuru Bharadwaj
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
| | - Carlos Noceda
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
- Cell and Molecular Biology of Plants (BPOCEMP)/Industrial Biotechnology and Bioproducts, Department of Sciences of the Vidaydela Agriculture, University of the Armed Forces-ESPE, Milagro, Ecuador
- Faculty of Engineering, State University of Milagro (UNEMI), Milagro, Ecuador
| | - José Hélio Costa
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Sarma Rajeev Kumar
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
- *Correspondence: Birgit Arnholdt-Schmitt, ; Ramalingam Sathishkumar,
| | - Karine Leitão Lima Thiers
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Elisete Santos Macedo
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
| | - Sofia Silva
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
| | - Paolo Annicchiarico
- Council for Agricultural Research and Economics (CREA), Research Centre for Animal Production and Aquaculture, Lodi, Italy
| | - Steven P.C. Groot
- Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | - Jan Kodde
- Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | - Aprajita Kumari
- National Institute of Plant Genome Research, New Delhi, India
| | - Kapuganti Jagadis Gupta
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
- National Institute of Plant Genome Research, New Delhi, India
| | - Birgit Arnholdt-Schmitt
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
- CERNAS-Research Center for Natural Resources, Environment and Society, Department of Environment, Escola Superior Agrária de Coimbra, Coimbra, Portugal
- *Correspondence: Birgit Arnholdt-Schmitt, ; Ramalingam Sathishkumar,
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Venkatapathy K, Magesh CJ, Lavanya G, Perumal PT, Sathishkumar R. A nanocrystalline CdS thin film as a heterogeneous, recyclable catalyst for effective synthesis of dihydropyrimidinones and a new class of carbazolyl dihydropyrimidinones via an improved Biginelli protocol. NEW J CHEM 2019. [DOI: 10.1039/c9nj02139f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An improved Biginelli protocol for the efficient synthesis of a new class of carbazolyl dihydropyrimidinones mediated by CdS thin film nanoparticles deposited on the inner walls of a glass reactor as a recyclable, heterogeneous catalyst.
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Affiliation(s)
| | | | - G. Lavanya
- Department of Chemistry
- AAGA College
- Cheyyar
- India
| | - P. T. Perumal
- B. S. Abdur Rahman Crescent Insititute of Science & Technology
- Chennai
- India
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Sathishkumar R, Kumar SR, Hema J, Baskar V. Green Biotechnology: A Brief Update on Plastid Genome Engineering. Advances in Plant Transgenics: Methods and Applications 2019. [PMCID: PMC7120283 DOI: 10.1007/978-981-13-9624-3_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Plant genetic engineering has become an inevitable tool in the molecular breeding of crops. Significant progress has been made in the generation of novel plastid transformation vectors and optimized transformation protocols. There are several advantages of plastid genome engineering over conventional nuclear transformation. Some of the advantages include multigene engineering by expression of biosynthetic pathway genes as operons, extremely high-level expression of protein accumulation, lack of transgene silencing, etc. Transgene containment owing to maternal inheritance is another important advantage of plastid genome engineering. Chloroplast genome modification usually results in alteration of several thousand plastid genome copies in a cell. Several therapeutic proteins, edible vaccines, antimicrobial peptides, and industrially important enzymes have been successfully expressed in chloroplasts so far. Here, we critically recapitulate the latest developments in plastid genome engineering. Latest advancements in plastid genome sequencing are briefed. In addition, advancement of extending the toolbox for plastid engineering for selected applications in the area of molecular farming and production of industrially important enzyme is briefed.
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Affiliation(s)
- Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu India
| | | | - Jagadeesan Hema
- Department of Biotechnology, PSG College of Technology, Coimbatore, Tamil Nadu India
| | - Venkidasamy Baskar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu India
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21
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Sathish S, Preethy KS, Venkatesh R, Sathishkumar R. Rapid enhancement of α-tocopherol content in Nicotiana benthamiana by transient expression of Arabidopsis thaliana Tocopherol cyclase and Homogentisate phytyl transferase genes. 3 Biotech 2018; 8:485. [PMID: 30498659 DOI: 10.1007/s13205-018-1496-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 06/13/2018] [Accepted: 11/01/2018] [Indexed: 12/18/2022] Open
Abstract
Agrobacterium-mediated transient gene expression have become a method of choice over stable plant genetic transformation. Tocopherols are a family of vitamin E compounds, which are categorized along with tocotrienols occurring naturally in vegetable oils, nuts and leafy green vegetables. This is the first report involving AtTC and AtHPT transient expression in Nicotiana benthamiana and this system can be used efficiently for large scale production of vitamin E. Agroinfiltration studies were carried out in N.benthamiana for the expression of Arabidopsis thaliana (At) genes encoding homogentisate phytyltransferase (HPT) and tocopherol cyclase (TC) individually and in combination (HPT + TC). The transgene presence was analyzed by reverse transcription PCR, which showed the presence of both the vitamin E biosynthetic pathway genes. The gene expression analysis was carried out by (reverse transcription quantitative real-time polymerase chain reaction) RT-qPCR and α-tocopherol content was quantified using high performance liquid chromatography (HPLC). The relative gene expression analysis by RT-qPCR confirmed an increased expression pattern where TC + HPT combination recorded the highest of 231 fold, followed by TC gene with 186 fold, whereas the HPT gene recorded 178 fold. The α-tocopherol content in leaves expressing HPT, TC, and HPT + TC was increased by 4.2, 5.9 and 11.3 fold, respectively, as compared to the control. These results indicate that the transient expression of HPT and TC genes has enhanced the vitamin E levels and stable expression of both A. thaliana genes could be an efficient strategy to enhance vitamin E biosynthesis in agricultural crop breeding.
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Affiliation(s)
- Sundararajan Sathish
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641 046 India
| | - Kuppuraj Sree Preethy
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641 046 India
| | - Rajendran Venkatesh
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641 046 India
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641 046 India
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Dhivya S, Baskar V, Kumar SR, Sathishkumar R. An immunoinformatics approach to define T cell epitopes from polyketide and non-ribosomal peptide synthesis proteins ofMycobacterium tuberculosisas potential vaccine candidates. J Mol Recognit 2017; 31. [DOI: 10.1002/jmr.2685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/08/2017] [Accepted: 10/08/2017] [Indexed: 11/11/2022]
Affiliation(s)
- S. Dhivya
- Plant Genetic Engineering Laboratory, Department of Biotechnology; Bharathiar University; Coimbatore India
| | - V. Baskar
- Plant Genetic Engineering Laboratory, Department of Biotechnology; Bharathiar University; Coimbatore India
| | - S. R. Kumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology; Bharathiar University; Coimbatore India
| | - R. Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology; Bharathiar University; Coimbatore India
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Bala Murugan S, Sathishkumar R. Chikungunya infection: A potential re-emerging global threat. ASIAN PAC J TROP MED 2016; 9:933-937. [PMID: 27794385 DOI: 10.1016/j.apjtm.2016.07.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 05/17/2016] [Revised: 06/18/2016] [Accepted: 07/17/2016] [Indexed: 10/21/2022] Open
Abstract
Infectious diseases are indeed a lifelong threat to everyone irrespective of age, sex, lifestyle and socio-economic status. The infectious diseases have persisted among the prominent causes of death globally. Recently, re-emergence of Chikungunya viral infection harmed many in Asian and African countries. Chikungunya was considered as a major threat in developing and under-developed countries; the recent epidemiological outbreak of Chikungunya in La Reunion urges the global researchers to develop effective vaccine against this viral disease. In this review, Chikungunya, pathogenesis and epidemiology were briefly described.
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Affiliation(s)
- Shanmugaraj Bala Murugan
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India.
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India.
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24
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Abstract
"Molecular cloning" meaning creation of recombinant DNA molecules has impelled advancement throughout life sciences. DNA manipulation has become easy due to powerful tools showing exponential growth in applications and sophistication of recombinant DNA technology. Cloning genes has become simple what led to an explosion in the understanding of gene function by seamlessly stitching together multiple DNA fragments or by the use of swappable gene cassettes, maximizing swiftness and litheness. A novel archetype might materialize in the near future with synthetic biology techniques that will facilitate quicker assembly and iteration of DNA clones, accelerating the progress of gene therapy vectors, recombinant protein production processes and new vaccines by in vitro chemical synthesis of any in silico-specified DNA construct. The advent of innovative cloning techniques has opened the door to more refined applications such as identification and mapping of epigenetic modifications and high-throughput assembly of combinatorial libraries. In this review, we will examine the major breakthroughs in cloning techniques and their applications in various areas of biological research that have evolved mainly due to easy construction of novel expression systems.
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Affiliation(s)
- M Ashwini
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - S B Murugan
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India.,Department of Biotechnology, PSR College of Engineering, Sivakasi, Tamil Nadu, India
| | - S Balamurugan
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India.,Department of Genetic Engineering, SRM University, Chennai, Tamil Nadu, India
| | - R Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India.,
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Campos MD, Nogales A, Cardoso HG, Kumar SR, Nobre T, Sathishkumar R, Arnholdt-Schmitt B. Stress-Induced Accumulation of DcAOX1 and DcAOX2a Transcripts Coincides with Critical Time Point for Structural Biomass Prediction in Carrot Primary Cultures (Daucus carota L.). Front Genet 2016; 7:1. [PMID: 26858746 PMCID: PMC4731517 DOI: 10.3389/fgene.2016.00001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [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: 11/05/2015] [Accepted: 01/07/2016] [Indexed: 11/18/2022] Open
Abstract
Stress-adaptive cell plasticity in target tissues and cells for plant biomass growth is important for yield stability. In vitro systems with reproducible cell plasticity can help to identify relevant metabolic and molecular events during early cell reprogramming. In carrot, regulation of the central root meristem is a critical target for yield-determining secondary growth. Calorespirometry, a tool previously identified as promising for predictive growth phenotyping has been applied to measure the respiration rate in carrot meristem. In a carrot primary culture system (PCS), this tool allowed identifying an early peak related with structural biomass formation during lag phase of growth, around the 4th day of culture. In the present study, we report a dynamic and correlated expression of carrot AOX genes (DcAOX1 and DcAOX2a) during PCS lag phase and during exponential growth. Both genes showed an increase in transcript levels until 36 h after explant inoculation, and a subsequent down-regulation, before the initiation of exponential growth. In PCS growing at two different temperatures (21°C and 28°C), DcAOX1 was also found to be more expressed in the highest temperature. DcAOX genes' were further explored in a plant pot experiment in response to chilling, which confirmed the early AOX transcript increase prior to the induction of a specific anti-freezing gene. Our findings point to DcAOX1 and DcAOX2a as being reasonable candidates for functional marker development related to early cell reprogramming. While the genomic sequence of DcAOX2a was previously described, we characterize here the complete genomic sequence of DcAOX1.
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Affiliation(s)
- M. Doroteia Campos
- EU Marie Curie Chair, ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, IIFA-Instituto de Formação e Investigação Avançada, Universidade de ÉvoraÉvora, Portugal
| | - Amaia Nogales
- EU Marie Curie Chair, ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, IIFA-Instituto de Formação e Investigação Avançada, Universidade de ÉvoraÉvora, Portugal
| | - Hélia G. Cardoso
- EU Marie Curie Chair, ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, IIFA-Instituto de Formação e Investigação Avançada, Universidade de ÉvoraÉvora, Portugal
| | - Sarma R. Kumar
- EU Marie Curie Chair, ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, IIFA-Instituto de Formação e Investigação Avançada, Universidade de ÉvoraÉvora, Portugal
- Molecular Plant Biology and Biotechnology Division, Council of Scientific and Industrial Research–Central Institute of Medicinal and Aromatic Plants Research CentreBangalore, India
| | - Tânia Nobre
- EU Marie Curie Chair, ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, IIFA-Instituto de Formação e Investigação Avançada, Universidade de ÉvoraÉvora, Portugal
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar UniversityCoimbatore, India
| | - Birgit Arnholdt-Schmitt
- EU Marie Curie Chair, ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, IIFA-Instituto de Formação e Investigação Avançada, Universidade de ÉvoraÉvora, Portugal
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Rajeevkumar S, Anunanthini P, Sathishkumar R. Epigenetic silencing in transgenic plants. Front Plant Sci 2015; 6:693. [PMID: 26442010 PMCID: PMC4564723 DOI: 10.3389/fpls.2015.00693] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 08/21/2015] [Indexed: 05/18/2023]
Abstract
Epigenetic silencing is a natural phenomenon in which the expression of genes is regulated through modifications of DNA, RNA, or histone proteins. It is a mechanism for defending host genomes against the effects of transposable elements and viral infection, and acts as a modulator of expression of duplicated gene family members and as a silencer of transgenes. A major breakthrough in understanding the mechanism of epigenetic silencing was the discovery of silencing in transgenic tobacco plants due to the interaction between two homologous promoters. The molecular mechanism of epigenetic mechanism is highly complicated and it is not completely understood yet. Two different molecular routes have been proposed for this, that is, transcriptional gene silencing, which is associated with heavy methylation of promoter regions and blocks the transcription of transgenes, and post-transcriptional gene silencing (PTGS), the basic mechanism is degradation of the cytosolic mRNA of transgenes or endogenous genes. Undesired transgene silencing is of major concern in the transgenic technologies used in crop improvement. A complete understanding of this phenomenon will be very useful for transgenic applications, where silencing of specific genes is required. The current status of epigenetic silencing in transgenic technology is discussed and summarized in this mini-review.
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Affiliation(s)
- Sarma Rajeevkumar
- Molecular Plant Biology and Biotechnology Division, Central Institute of Medicinal and Aromatic Plants Research Centre, BangaloreIndia
| | - Pushpanathan Anunanthini
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, CoimbatoreIndia
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, CoimbatoreIndia
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Murali KS, Sivasubramanian S, Vincent S, Murugan SB, Giridaran B, Dinesh S, Gunasekaran P, Krishnasamy K, Sathishkumar R. Anti-chikungunya activity of luteolin and apigenin rich fraction from Cynodon dactylon. ASIAN PAC J TROP MED 2015; 8:352-8. [PMID: 26003593 DOI: 10.1016/s1995-7645(14)60343-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE To obtain luteolin and apigenin rich fraction from the ethanolic extract of Cynodon dactylon (L.) (C. dactylon) Pers and evaluate the fraction's cytotoxicity and anti-Chikungunya potential using Vero cells. METHODS The ethanolic extract of C. dactylon was subjected to silica gel column chromatography to obtain anti-chikungunya virus (CHIKV) fraction. Reverse phase-HPLC and GC-MS studies were carried out to identify the major phytochemicals in the fraction using phytochemical standards. Cytotoxicity and the potential of the fraction against CHIKV were evaluated in vitro using Vero cells. Reduction in viral replication was assessed by reverse transcriptase-polymerase chain reaction (RT-PCR) after treating the viral infected Vero cells with the fraction. RESULTS Reverse Phase-HPLC and GC-MS studies confirmed the presence of flavonoids, luteolin and apigenin as major phytochemicals in the anti-CHIKV ethanolic fraction of C. dactylon. The fraction was found to exhibit potent viral inhibitory activity (about 98%) at the concentration of 50 µg/mL as observed by reduction in cytopathic effect, and the cytotoxic concentration of the fraction was found to be 250 µg/mL. RT-PCR analyses indicated that the reduction in viral mRNA synthesis in fraction treated infected cells was much higher than the viral infected control cells. CONCLUSIONS Luteolin and apigenin rich ethanolic fraction from C. dactylon can be utilized as a potential therapeutic agent against CHIKV infection as the fraction does not show cytotoxicity while inhibiting the virus.
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Affiliation(s)
- Krishnan Saravana Murali
- Plant Genetic Engineering Lab, Department of Biotechnology, Bharathiar University, Coimbatore, Tamilnadu, India; Department of Virology, King Institute of Preventive Medicine and Research, Chennai-600032, Tamilnadu, India
| | - Srinivasan Sivasubramanian
- Centre for Environmental Research and Development and Loyola Institute of Frontier Energy, Loyola College, Chennai-600034, Tamilnadu, India
| | - Savariar Vincent
- Centre for Environmental Research and Development and Loyola Institute of Frontier Energy, Loyola College, Chennai-600034, Tamilnadu, India
| | - Shanmugaraj Bala Murugan
- Plant Genetic Engineering Lab, Department of Biotechnology, Bharathiar University, Coimbatore, Tamilnadu, India
| | - Bupesh Giridaran
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai-600032, Tamilnadu, India
| | - Sundaram Dinesh
- Vellore Institute of Technology, Vellore-632001, Tamilnadu, India
| | - Palani Gunasekaran
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai-600032, Tamilnadu, India
| | - Kaveri Krishnasamy
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai-600032, Tamilnadu, India
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Lab, Department of Biotechnology, Bharathiar University, Coimbatore, Tamilnadu, India.
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Abstract
Phenanthrimidazole based iridium(iii) complexes show good performance in terms of brightness and power and current efficiencies.
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30
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Abstract
The first examples of organic alloys of two room temperature liquids, obtained and characterizedvia in situcryo-crystallography, are presented. Thiophenol and selenophenol, which exhibit isostructurality and similar modes of S⋯S and Se⋯Se homo-chalcogen interactions along with weak and rare S–H⋯S and Se–H⋯Se hydrogen bonds, are shown to form solid solutions exhibiting Veggard's law-like trends.
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Affiliation(s)
- Sajesh P. Thomas
- Solid state and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore
- India
- School of Chemistry and Biochemistry
| | - R. Sathishkumar
- Solid state and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore
- India
| | - T. N. Guru Row
- Solid state and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore
- India
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31
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Xie WH, Zhu CC, Zhang NS, Li DW, Yang WD, Liu JS, Sathishkumar R, Li HY. Construction of novel chloroplast expression vector and development of an efficient transformation system for the diatom Phaeodactylum tricornutum. Mar Biotechnol (NY) 2014; 16:538-46. [PMID: 24763817 PMCID: PMC4169106 DOI: 10.1007/s10126-014-9570-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 03/05/2014] [Indexed: 05/03/2023]
Abstract
Plastids are ideal subcellular hosts for the expression of transgenes and have been successfully used for the production of different biopolymers, therapeutic proteins and industrial enzymes. Phaeodactylum tricornutum is a widely used aquatic feed species. In this study, we focused on developing a high-efficiency plastid expression system for P. tricornutum. In the plastid transformation vector, the site selected for integration was the transcriptionally active intergenic region present between the trnI and trnA genes, located in the IR (inverted repeat) regions of the plastid genome. Initially, a CAT reporter gene (encoding chloramphenicol acetyltransferase) was integrated at this site in the plastid genome. The expression of CAT in the transformed microalgae conferred resistance to the antibiotic chloramphenicol, which enabled growth in the selection media. Overall, the plastid transformation efficiency was found to be approximately one transplastomic colony per 1,000 microalgae cells. Subsequently, a heterologous gene expression cassette for high-level expression of the target gene was created and cloned between the homologous recombination elements. A TA cloning strategy based on the designed XcmI-XcmI sites could conveniently clone the heterologous gene. An eGFP (green fluorescent protein) reporter gene was used to test the expression level in the plastid system. The relatively high-level expression of eGFP without codon optimisation in stably transformed microalgae was determined to account for 0.12 % of the total soluble protein. Thus, this study presents the first and convenient plastid gene expression system for diatoms and represents an interesting tool to study diatom plastids.
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Affiliation(s)
- Wei-Hong Xie
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institute, Jinan University, 510632 Guangzhou, China
| | - Cong-Cong Zhu
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institute, Jinan University, 510632 Guangzhou, China
| | - Nai-Sheng Zhang
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institute, Jinan University, 510632 Guangzhou, China
| | - Da-Wei Li
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institute, Jinan University, 510632 Guangzhou, China
| | - Wei-Dong Yang
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institute, Jinan University, 510632 Guangzhou, China
| | - Jie-Sheng Liu
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institute, Jinan University, 510632 Guangzhou, China
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu 641046 India
| | - Hong-Ye Li
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institute, Jinan University, 510632 Guangzhou, China
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Sathiyadash K, Muthukumar T, Murugan SB, Sathishkumar R, Pandey RR. In vitro symbiotic seed germination of South Indian endemic orchid Coelogyne nervosa. MYCOSCIENCE 2014. [DOI: 10.1016/j.myc.2013.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Jayabharathi J, Sathishkumar R, Thanikachalam V. Organic light-emitting materials based on iridium(III) complexes bearing phenanthroimidazole ligands. J PHYS ORG CHEM 2014. [DOI: 10.1002/poc.3292] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Karunakaran C, Jayabharathi J, Sathishkumar R, Jayamoorthy K, Vimal K. Contrasting emission behaviour of phenanthroimidazole with ZnO nanoparticles. Spectrochim Acta A Mol Biomol Spectrosc 2013; 115:488-492. [PMID: 23871976 DOI: 10.1016/j.saa.2013.06.073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 05/10/2013] [Accepted: 06/20/2013] [Indexed: 06/02/2023]
Abstract
A new fluorophore 2-(4-fluorophenyl)-1-phenyl-1H-phenanthro [9,10-d]imidazole has been synthesized and characterized by spectroscopic techniques. Nanoparticulate ZnO enhances the fluorescence of the synthesised fluorophore. The absorption, fluorescence, lifetime, cyclic voltammetry and infrared studies reveal that fluorophore is attached to the surface of ZnO semiconductor. Photo-induced electron transfer (PET) explains the enhancement of fluorescence by nanoparticulate ZnO and the apparent binding constant has been obtained. Adsorption of the fluorophore on ZnO nanoparticle lowers the HOMO and LUMO energy levels of the fluorophore. The strong adsorption of the phenanthrimidazole derivative on the surface of ZnO nanocrystals is likely due to the chemical affinity of the nitrogen atom of the organic molecule to the zinc ion on the surface of nanocrystal.
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Affiliation(s)
- C Karunakaran
- Department of Chemistry, Annamalai University, Annamalainagar 608 002, Tamil Nadu, India
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Jayabharathi J, Thanikachalam V, Sathishkumar R. Excited Charge Transfer States in Donor–Acceptor Fluorescent Phenanthroimidazole Derivatives. J Fluoresc 2013; 24:431-44. [DOI: 10.1007/s10895-013-1309-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 09/27/2013] [Indexed: 10/26/2022]
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Mohandas T, Sathishkumar R, Jayabharathi J, Pasupathi A, Sakthivel P. 1-(4-Meth-oxy-phen-yl)-2-[4-(tri-fluoro-meth-yl)phen-yl]-1H-phenanthro[9,10-d]imidazole. Acta Crystallogr Sect E Struct Rep Online 2013; 69:o1293-o1294. [PMID: 24109372 PMCID: PMC3793785 DOI: 10.1107/s1600536813019351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 07/13/2013] [Indexed: 06/02/2023]
Abstract
In the title compound, C29H19F3N2O, a phenanthroline-fused imidazole tetra-cyclic system, the fused benzene rings deviate slightly from the central ring and make dihedral angles with this ring of 3.47 (8) and 3.05 (8)°. The tri-fluoro-methyl-phenyl ring is roughly coplanar with the phenanthroline-fused imidazole tetra-cyclic system [dihedral angle = 11.02 (6)°], while the meth-oxy-phenyl ring is almost perpendicular [dihedral angle = 87.65 (6)°]. There are intra-molecular C-H ⋯π inter-actions involving the meth-oxy-phenyl ring and the central phenanthroline ring, as well as an inter-molecular C-H⋯π inter-action involving the phenanthroline ring. In addition, there is an inter-molecular π-π inter-action involving the central phenanthroline ring and the tri-fluoro-methyl-phenyl ring [centroid-centroid distance = 3.685 (2) Å], as well as C-H⋯N inter-actions linking the mol-ecules into dimers.
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Affiliation(s)
- T. Mohandas
- Shri Angalamman College of Engineering and Technology, Siruganoor, Tiruchirappalli 621 105, India
| | - R. Sathishkumar
- Department of Chemistry, Annamalai University, Annamalainagar, Chidambaram, India
| | - J. Jayabharathi
- Department of Chemistry, Annamalai University, Annamalainagar, Chidambaram, India
| | - A. Pasupathi
- Department of Chemistry, Urumudhanalakshmi College, Tiruchirappalli 620 019, India
| | - P. Sakthivel
- Department of Physics, Urumudhanalakshmi College, Tiruchirappalli 620 019, India
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Karunakaran C, Jayabharathi J, Sathishkumar R, Jayamoorthy K. Interaction of fluorescent sensor with superparamagnetic iron oxide nanoparticles. Spectrochim Acta A Mol Biomol Spectrosc 2013; 110:151-156. [PMID: 23562745 DOI: 10.1016/j.saa.2013.03.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 01/02/2013] [Accepted: 03/04/2013] [Indexed: 06/02/2023]
Abstract
To sense superparamagnetic iron oxides (Fe2O3 and Fe3O4) nanocrystals a sensitive bioactive phenanthroimidazole based fluorescent molecule, 2-(4-fluorophenyl)-1-phenyl-1H-phenanthro [9,10-d] imidazole has been designed and synthesized. Electronic spectral studies show that phenanthroimidazole is bound to the surface of iron oxide semiconductors. Fluorescent enhancement has been explained on the basis of photo-induced electron transfer (PET) mechanism and apparent binding constants have been deduced. Binding of phenanthroimidazole with iron oxide nanoparticles lowers the HOMO and LUMO energy levels of phenanthroimidazole molecule. Chemical affinity between the nitrogen atom of the phenanthroimidazole and Fe(2+) and Fe(3+) ions on the surface of the nano-oxide may result in strong binding of the phenanthroimidazole derivative with the nanoparticles. The electron injection from the photoexcited phenanthroimidazole to the iron oxides conduction band explains the enhanced fluorescence.
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Jayabharathi J, Jayamoorthy K, Thanikachalam V, Sathishkumar R. Fluorescence quenching of bovine serum albumin by NNMB. Spectrochim Acta A Mol Biomol Spectrosc 2013; 108:146-150. [PMID: 23466325 DOI: 10.1016/j.saa.2013.01.092] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Revised: 01/26/2013] [Accepted: 01/28/2013] [Indexed: 06/01/2023]
Abstract
A new type of fluorophore 2-(naphthalen-1-yl)-1-((naphthalen-1-yl)methyl)-1H-benzimidazole (NNMB) has been prepared and characterized by (1)H NMR, (13)C NMR, mass and IR spectral analysis. Absorption, fluorescence and synchronous fluorescence spectral studies have been made for the mutual interaction of NNMB with bovine serum albumin (BSA). Absorption spectroscopy proved the formation of a ground state BSA…NNMB complex. Fluorescence spectrum of BSA in the presence of NNMB clearly shows that NNMB acts as a quencher. Based on the theory of Forester's non-radiation energy transfer (FRET) binding distance has been deduced. The Stern-Volmer quenching constant (KSV), binding site number (n), apparent binding constant (KA) and corresponding thermodynamic parameters (ΔG, ΔH and ΔS) were determined.
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Affiliation(s)
- J Jayabharathi
- Department of Chemistry, Annamalai University, Annamalainagar, Tamilnadu 608 002, India.
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Mohandas T, Sathishkumar R, Jayabharathi J, Pasupathy A, Sakthivel P. 1-(4-Methyl-phen-yl)-2-[4-(trifluoro-methyl)phen-yl]-1H-phenanthro[9,10-d]imida-zole. Acta Crystallogr Sect E Struct Rep Online 2013; 69:o710. [PMID: 23723863 PMCID: PMC3648243 DOI: 10.1107/s1600536813009471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 04/07/2013] [Indexed: 11/10/2022]
Abstract
In the title compound, C29H19F3N2, the tetra-cyclic ring system is essentially planar [maximum deviation from the best plane = 0.076 (1) Å] and makes dihedral angles of 78.10 (5) and 33.71 (4)° with the methyl-phenyl and fluoro-phenyl rings, respectively. An intra-molecular C-H⋯π inter-action occurs. In the crystal, pairs of C-H⋯π inter-actions link inversion-related mol-ecules.
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Affiliation(s)
- T Mohandas
- Department of Physics, Shri Angalamman College of Engineering and Technology, Siruganoor, Tiruchirappalli 621 105, India
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Mohandas T, Sathishkumar R, Sakthivel P, Jayabharathi J. 2-(4-Fluoro-phen-yl)-1-(4-meth-oxy-phen-yl)-1H-phenanthro[9,10-d]imidazole. Acta Crystallogr Sect E Struct Rep Online 2013; 69:o368. [PMID: 23476557 PMCID: PMC3588432 DOI: 10.1107/s1600536813003504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Accepted: 02/04/2013] [Indexed: 06/01/2023]
Abstract
In the title compound, C28H19FN2O, the phenanthrene fused with an imidazole ring, constituting an essentially planar tetra-cyclic system [maximum deviation = 0.032 (2) Å], makes dihedral angles of 60.83 (4) and 80.55 (4)° with the fluoro-benzene and meth-oxy-benzene rings, respectively. The dihedral angle between the the meth-oxy-benzene and fluoro-benzene rings is 69.45 (6)°. In the crystal, C-H⋯O hydrogen bonds connect the mol-ecules into infinite strands along the b axis. The crystal structure is further consolidated by C-H⋯π inter-actions.
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Affiliation(s)
- T. Mohandas
- Department of Physics, Shri Angalamman College of Engineering and Technology, Siruganoor, Tiruchirappalli 621 105, India
| | - R. Sathishkumar
- Department of Chemistry, Annamalai University, Annamalainagar 608 002, India
| | - P. Sakthivel
- Department of Physics, Urumu Dhanalakshmi College, Tiruchirappalli 620 019, India
| | - J. Jayabharathi
- Department of Chemistry, Annamalai University, Annamalainagar 608 002, India
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Sathishkumar R, Mohandas T, Sakthivel P, Jayabharathi J. 1-(3,5-Dimethyl-phen-yl)-2-(4-fluoro-phen-yl)-1H-phenanthro[9,10-d]imidazole. Acta Crystallogr Sect E Struct Rep Online 2013; 69:o367. [PMID: 23476556 PMCID: PMC3588452 DOI: 10.1107/s1600536813003486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 02/04/2013] [Indexed: 11/15/2022]
Abstract
In the title compound, C29H21FN2, the phenanthro tricyclic ring system is essentially planar with a maximum deviation of 0.030 (2) Å and makes dihedral angles between of 77.96 (6) and 37.18 (7)° with the dimethylphenyl and fluorophenyl rings, respectively. The crystal packing features weak C—H⋯π interactions involving the dimethylphenyl and other phenyl rings.
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Affiliation(s)
- R Sathishkumar
- Department of Chemistry, Annamalai University, Annamalainagar 608 002, India
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Newmaster SG, Ragupathy S, Dhivya S, Jijo CJ, Sathishkumar R, Patel K. Genomic valorization of the fine scale classification of small millet landraces in southern India. Genome 2013; 56:123-7. [PMID: 23517322 DOI: 10.1139/gen-2012-0183] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [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
Our research seeks to investigate genomic diversity of landraces of millet, addressing a key uncertainty that will provide a framework for (i) a DNA barcode method that could be used for fast, sensitive, and accurate identification of millet landraces, and (ii) millet landrace conservation including biocultural diversity. We found considerable intraspecific variation among 15 landraces representing six species of small millets using nuclear regions (ITS, ITS1, and ITS2); there was no variation in plastid regions (rbcL, matK, and trnH-psbA). An efficacious ITS2 DNA barcode was used to make 100% accurate landrace assignments for 150 blind samples representing 15 landraces. Our research revealed that genomic variation is aligned with a fine-scale classification of landraces using traditional knowledge (TK) of local farmers. The landrace classification was highly correlated with traits (morphological, agricultural, and cultural utility) associated with considerable factors such as yield, drought tolerance, growing season, medicinal properties, and nutrition. This could provide a DNA-based model for conservation of genetic diversity and the associated bicultural diversity (TK) of millet landraces, which has sustained marginal farming communities in harsh environments for many generations.
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Affiliation(s)
- Steven G Newmaster
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada.
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Jayabharathi J, Thanikachalam V, Sathishkumar R, Jayamoorthy K. Physico-chemical studies of fused phenanthrimidazole derivative as sensitive NLO material. Spectrochim Acta A Mol Biomol Spectrosc 2013; 101:249-253. [PMID: 23103466 DOI: 10.1016/j.saa.2012.09.089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 09/22/2012] [Accepted: 09/26/2012] [Indexed: 06/01/2023]
Abstract
Heterocyclic phenanthrimidazole derivative, 2-(4-fluorophenyl)-1-p-tolyl-1H-imidazo[4,5-f] [1,10] phenanthroline (FPTIP) has been synthesized and characterised by NMR, mass and CHN analysis. The FPTIP was evaluated concerning their solvatochromic properties and molecular optical nonlinearities. Their electric dipole moment (μ), polarizability (α) and hyperpolarizability (β) have been calculated theoretically and the results indicate that the extension of the π-framework of the ligands has an effect on the NLO properties. The energies of the HOMO and LUMO levels and the molecular electrostatic potential (MEP) energy surface studies have exploited the existence of intramolecular charge transfer (ICT) within the molecule.
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Affiliation(s)
- Jayaraman Jayabharathi
- Department of Chemistry, Annamalai University, Annamalainagar, 608 002 Tamil Nadu, India.
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Paul N, Sathishkumar R, Anuba C, Muthusubramanian S. Reactions of diphenacylaniline and diphenacyl sulfide under Gewald conditions: generation of enamines and thioamides. RSC Adv 2013. [DOI: 10.1039/c3ra21556c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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Jayabharathi J, Thanikachalam V, Sathishkumar R, Jayamoorthy K. Fluorescence investigation of the interaction of 2-(4-fluorophenyl)-1-phenyl-1H-phenanthro [9,10-d] imidazole with bovine serum albumin. Journal of Photochemistry and Photobiology B: Biology 2012; 117:222-7. [DOI: 10.1016/j.jphotobiol.2012.10.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 10/09/2012] [Accepted: 10/15/2012] [Indexed: 11/16/2022]
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Sathishkumar R, Kollimalla SK, Mishra MK. Dynamic energy management of micro grids using battery super capacitor combined storage. 2012 Annual IEEE India Conference (INDICON) 2012. [DOI: 10.1109/indcon.2012.6420777] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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Jayabharathi J, Thanikachalam V, Jayamoorthy K, Sathishkumar R. Selective quenching of benzimidazole derivatives by Cu²+ metal ion. Spectrochim Acta A Mol Biomol Spectrosc 2012; 97:384-387. [PMID: 22813989 DOI: 10.1016/j.saa.2012.06.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 06/05/2012] [Accepted: 06/06/2012] [Indexed: 06/01/2023]
Abstract
It is a very big challenge to develop a Cu(2+) selective fluorescent sensor with the ability to exclude the interference of some metal ions such as Fe(3+), Mg(2+), Ag(+), K(+) and Na(+). Herein, we report a fluorescence quenching of some benzimidazole derivatives (1-6) with Cu(2+) metal ion. These benzimidazole derivatives have been shown to bind copper ions resulting in quenching of its fluorescence. The response to Cu(2+) is rapid, selective and reversible upon addition of a copper chelator. These benzimidazole derivatives were characterized by (1)H, (13)C NMR mass and elemental analysis. XRD analysis was carried out for 1-(4-methylbenzyl)-2-p-tolyl-1H-benzo[d]imidazole.
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Affiliation(s)
- J Jayabharathi
- Department of Chemistry, Annamalai University, Annamalainagar 608 002, Tamil Nadu, India.
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Jayabharathi J, Thanikachalam V, Sathishkumar R. Characterization, physiochemical and computational studies of the newly synthesized novel imidazole derivative. Spectrochim Acta A Mol Biomol Spectrosc 2012; 97:582-588. [PMID: 22842353 DOI: 10.1016/j.saa.2012.06.050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 06/06/2012] [Accepted: 06/25/2012] [Indexed: 06/01/2023]
Abstract
The photophysical properties of imidazole derivative were studied in several solvents. The observed fluorescence quantum yield is attributed to a loss of planarity in the excited state provided by the non co-planarity of the aryl rings attached to C(2) and N(1) atoms of the imidazole ring. The solvent effect on the absorption and fluorescence bands was analyzed by a multi-component linear regression in which several solvent parameters were analyzed simultaneously. DFT calculations were carried out in order to find out the NBO analysis, HOMO-LUMO energies, MEP studies and hyperpolarisability behaviour. This chromophore possess more appropriate ratio of off-diagonal versus diagonal β tensorial component (r=β(xyy)/β(xxx)=0.12) which reflects the in plane non-linearity anisotropy. Since they have largest μβ(0) value, the reported imidazole can be used as potential NLO material. Within this context, reasonable conclusions concerning the steric hindrance in the chromospheres, push-pull character, hyperpolarisability of the imidazole and their application as NLO materials will be drawn.
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Rosepriya S, Thiruvalluvar A, Sathishkumar R, Jayabharathi J, Öztürk Yildirim S, Butcher R. 2-(4-Fluorophenyl)-1-(4-methylphenyl)-1 H-phenanthro[9,10- d]imidazole. Acta Crystallogr Sect E Struct Rep Online 2012; 68:o2880. [PMID: 23125678 PMCID: PMC3470234 DOI: 10.1107/s1600536812037592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 08/31/2012] [Indexed: 11/13/2022]
Abstract
The phenanthrene tricyclic ring system in the title molecule, C28H19FN2, is slightly skewed with a dihedral angle of 7.50 (6)° between the outer benzene rings. The p-tolyl and fluorobenzene rings are twisted from the attached imidazole ring by 70.40 (7) and 28.33 (7)°, respectively. In the crystal, C—H⋯F hydrogen bonds link the molecules into zigzag chains in [001], and weak C—H⋯π interactions further consolidate the crystal packing.
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Devarajegowda HC, Jeyaseelan S, Sathishkumar R, D’souza AS, D’souza A. 4-[(E)-(4-Fluoro-benzyl-idene)amino]-3-methyl-1H-1,2,4-triazole-5(4H)-thione. Acta Crystallogr Sect E Struct Rep Online 2012; 68:o1607. [PMID: 22719413 PMCID: PMC3379215 DOI: 10.1107/s1600536812019174] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 04/28/2012] [Indexed: 11/20/2022]
Abstract
In the asymmetric unit of the title compound, C(10)H(9)FN(4)S, there are two independent mol-ecules in which the dihedral angles between the 1,2,4-triazole and benzene rings are 36.85 (10) and 7.81 (10)°. In the crystal, N-H⋯S inter-actions link pairs of independent mol-ecules into dimers. There are also π-π inter-actions between the triazole and benzene rings of inversion-related pairs of the more planar mol-ecule [centroid-centroid distance = 3.6430 (13) Å].
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Affiliation(s)
- H. C. Devarajegowda
- Department of Physics, Yuvaraja’s College (Constituent College), University of Mysore, Mysore 570 005, Karnataka, India
| | - S. Jeyaseelan
- Department of Physics, Yuvaraja’s College (Constituent College), University of Mysore, Mysore 570 005, Karnataka, India
| | - R. Sathishkumar
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Agnes Sylvia D’souza
- Department of Chemistry, St. Philomena’s College, Mysore 570 015, Karnataka, India
| | - Alphonsus D’souza
- Department of Chemistry, St. Philomena’s College, Mysore 570 015, Karnataka, India
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