Ragu Ragupathy

• M.Sc. – University of Madras, India
• Ph.D. – University of Madras, India

My research is focuses on various themes at the crossroads of botany and genetics.  

Assemblage of Biodiversity Knowledge

I am interested in the diversity of plants: How many species are there? Why are some groups of plants so much more diverse than others? How do environmental and biological traits influence the species variation? Are there large-scale patterns in the history of life? By answering these questions, this concept is founded on the idea of an “assemblage” of biodiversity knowledge—a coming together of different ways of knowing and valorizing species variation by using DNA-based tools. My research demonstrates the potential of DNA-based methods as a reliable identification tool and for use in evaluating/authenticating and conserving genetic diversity of indigenous crops, medicinal herbs/products and associated traditional knowledge/modern natural health products system. Hence, the assemblage of biodiversity knowledge concept is used for seeking new medicines.  

Ethnobotany genomics

The ethnobotany genomics concept is founded on the ‘assemblage of biodiversity knowledge’. This includes a coming together of different ways of knowing and valorizing species variation in a novel approach seeking to add value to both traditional knowledge (TK) and scientific knowledge (SK). Ethnobotany genomics draws on an ancient body of knowledge concerning the variation in the biological diversity that surrounds different cultures; combined with modern genomic tools such as DNA probes it also explores the natural genetic variation found among plant species. This genomic variation is explored along a gradient of variation found within organisms on the landscape. The motivation for this new approach is a quest to understand the diversity of life that surrounds us and how we can utilize such diversity to serve society-at-large with nutrition, medicine and more. The impacts of ethnobotany genomics will extend well beyond biodiversity science where it may help to understand some of medicinal properties of medicinal plants. 

Natural Health Products authentication

Food security issues and global loss of biodiversity have resulted in considerable demands for natural, nutritional ingredients. This situation is intensified by the world-wide increase of 12-15% annually in the consumption of natural products; some products will not be sustainable within the next decade due to key ingredients, which are rare species. Consequently, the adulteration of natural health products (NHPs) is frequently in the news, which concerns consumers and brand owners who seek quality nutritional products. In fact, counterfeiting of products is on the rise and is a significant problem for many industry leaders faced with key uncertainties on how to properly identify botanical ingredients. This uncertainty is due to the fact that there is a knowledge gap between scientific innovations in molecular diagnostics and the industry uptake of novel biotechnology. The NHP Research Alliance invites international scientists to join in collaborative projects that build capacity for molecular diagnostics for NHPs to bridge this gap and develop a new industry standard for ingredient verification and validation. Species ingredient authenticity tests (validation) followed by system checks (verification) throughout the product processing chain ensure there is no adulteration, contamination or counterfeiting. Validation of botanicals includes a building a database with taxonomic herbarium vouchers of known provenance; genome scans to identify useful DNA markers for identification and validation of products; and two-factor validation using analytical chemistry (NMR) to establish chemical fingerprints together with DNA markers.  My research strategy is based on whole genome sequencing and metabolomics analysis of validated specimens with herbarium vouchers to establish reference libraries for the authentication of herbal products. It also focuses on the quantity of DNA obtained from products through different manufacturing and processing techniques. This is the largest known analysis of DNA quantity along a processing gradient from raw materials to the more complex and vigorous processing of botanical extracts. We observe a reduction in both the quantity and quality of DNA in more heavily processed and extracted products, which can impede the validation of heavily processed samples using DNA-based tools and probes. Hence, my research also focuses on developing techniques to improve our ability to generate high quality DNA and test results from challenging extracts. These techniques have been validated and fine-tuned by routine DNA testing of hundreds of extracts and other heavily processed products.

• Zitong Gao, Yang Liu, Xiaoyue Wang, Jingyuan Song, Shilin Chen, Subramanyam Ragupathy, Jianping Han & Steven G. Newmaster.  2017. Derivative Technology of DNA Barcoding (Nucleotide Signature and SNP Double Peak Methods) Detects Adulterants and Substitution in Chinese Patent Medicines. Nature Scientific Reports | 7: 5858 | DOI:10.1038/s41598-017-05892-y
• Shanmughanandhan, D., Ragupathy, S., Newmaster, S. G., Mohanasundaram, S., & Sathishkumar, R. (2016). Estimating Herbal Product Authentication and Adulteration in India Using a Vouchered, DNA-Based Biological Reference Material Library. Drug Safety, 1-17.
• Ragupathy, Subramanyam, Shanmughanandhan Dhivya, Kirit Patel, Abiran Sritharan, Kathirvelu Sambandan, Hom Gartaula, Ramalingam Sathishkumar and S.G. Newmaster. "DNA record of some traditional small millet landraces in India and Nepal." 3 Biotech 6, no. 2 (2016): 1-19.
• Liu, J., Yan, H.-F., Newmaster, S. G., Pei, N., Ragupathy, S., Ge, X.-J. (2014), The use of DNA barcoding as a tool for the conservation biogeography of subtropical forests in China. Diversity and Distributions. doi: 10.1111/ddi.12276.
• Nithaniyal S, Newmaster SG, Ragupathy S, Krishnamoorthy D, Vassou SL, et al. (2014) DNA Barcode Authentication of Wood Samples of Threatened and Commercial Timber Trees within the Tropical Dry Evergreen Forest of India. PLoS ONE 9(9): e107669. doi:10.1371/journal.pone.0107669.
• Steven G. Newmaster and Subramanyam Ragupathy. 2014. Ethnobotany Genomics: Discovery and Innovation in a New Era of Exploratory Research in Recent Advances in Plant-Based, Traditional, and Natural Medicines eds. S. Vemulpad and J. Jamie. Apple Academic Press Inc. pp. 277-298.
• Ragupathy, S., D.S. Seigler, J.E. Ebinger and B.R. Maslin. 2014. New combinations in Vachellia and Senegalia (Leguminosae: Mimosoideae) for south and west Asia. Phytotaxa 162(3): 174-180.
• Newmaster, S.G, Grguric, M., Dhivya, S., Sathishkumar, R. and S. Ragupathy. 2013.  DNA barcoding detects contamination and substitution in North American herbal products. BMC Medicine 2013, 11:222 (http://www.biomedcentral.com/1741-7015/11/222).
• WU, X.J., Liu, Y., Ragupathy, S., Motley, T. and C.L. Long.  2013. Pinellia hunanensis (Araceae), a new species supported by morphometric analysis and DNA barcoding.
Phytotaxa 130 (1): 1–13.
• Newmaster, S.G, Ragupathy, S., K. J. Berg, P. Shanmugarajan and C.B. Nirmala. 2013. The Role of Traditional Aboriginal Pedagogy in Contemporary University Education. Teaching and Learning Innovations Journal, Vol. 16. 1-10.