Publications

All Publications:

1. Vivek Hari Sundar, Chenna Swetha, Debjani Basu, Kannan Pachamuthu, Steffi Raju, Tania Chakraborty, Rebecca A. Mosher and P. V. Shivaprasad (2023). Plant Polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains. Genome Research. 023. 33: 715-728 

2. Ashwin Nair, Harshith CY, Anushree N and P.V. Shivaprasad (March, 2023). Begomoviral βC1 orchestrates organellar genomic instability to augment viral infection by hijacking host RecA. The Plant Journal. 114: 934-950 

3. Ashwin Nair and P.V. Shivaprasad (2023). "Novel regulators in mitochondrial integrity" Journal of Biosciences. (In print)

4. Prasad Melvin, Priyanka Kataria, Sunayana Ningaraju, Kondalarao Bankapalli, Radhika Reddy, Chenna Swetha, Gautam Susarla, Radhika Venkatesan, Patrick D’Silva and P. V. Shivaprasad (July, 2022). Methylglyoxalase DJ-1D from Arabidopsis is a robust macromolecule deglycase. New Phytol.  236: 1061-1074

5. Tripathi Abhinandan, Singh Rajneesh, Verma Ashwani, Singh Akanksha, Mishra Parneeta, Dwivedi Varun, Narayan Shiv, Vivek Hari Sundar, Shirke Pramod, Shivaprasad P.V., Roy Sribash (March, 2023). "Indian Himalayan natural Arabidopsis thaliana accessions with abolished miR158 levels exhibit robust miR173-initiated trans-acting cascade silencing", is accepted for publication in The Plant Journal.

6. Deepa Jaganathan, Raja Rajakani, Dadakhalandar Doddamani, Divya Saravanan, Shalini Pulipati, Vivek Hari Sundar G, Gothandapani Sellamuthu, Shilpha Jayabalan, Kumkum Kumari, Pavithra Parthasarathy, Punitha S., Sivaprakash Ramalingam, Padubidri V. Shivaprasad & Gayatri Venkataraman (February, 2023). A conserved SNP variation in the pre-miR396c flanking region in Oryza sativa indica landraces correlates with mature miRNA abundance. Scientific Reports. 13, 2195

7. Pratibha Sanjenbam, P.V. Shivaprasad, and Deepa Agashe (July, 2022). Impact of phyllosphere Methylobacterium on host rice landraces. Microbiology Spectrum. 10:4

8. Varsha Tirumalai, Swetha Chenna, Anushree N., Vivek Hari Sundar, Sujith, T.N., P.V. Shivaprasad (June, 2022). Cultivar-specific miRNA targeting in grapes. Planta. 256:17

9. Vivek Hari Sundar, and P.V. Shivaprasad (June, 2022). Investigation of transposon DNA methylation and copy number in plants using Southern hybridization. Bio-Protoc. 12:e4432

10. Kannan Pachamuthu, Vivek Hari Sundar, Anushree N.,Rahul R Singh, Soumita Das, Harshith CY, Avik Pal, and Padubidri V Shivaprasad. (March, 2022). Nitrate-dependent regulation of miR444-OsMADS27 signaling cascade controls root development in rice. J. Exp. Bot. 73:3511-3530.

11. Swetha Chenna, Anushree N, Awadhesh Pandit, Varsha Tirumalai, and P. V. Shivaprasad (January, 2022). Degradome comparison between wild and cultivated rice identifies differential targeting by miRNAs. BMC Genomics 23:53

12. Vikram Jha, Anushree N., Debjani Basu, Kannan Pachamuthu, Swetha Chenna, Ashwin Nair, P.V. Shivaprasad. (August, 2021). Essential role of γ-clade RNA-dependent RNA polymerases in rice development and yield-related traits is linked to their atypical polymerase activities regulating specific genomic regions. New Phytol. 232:1674-1691

13. Lakshmanan V, T N Sujith, Bansal D, Padubidri V. Shivaprasad, Palakodeti D, Krishna S. (April, 2021). Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs). RNA. rna. 077701.120

14. Vinoth Kumar and P.V. Shivaprasad (October, 2020).  Plant-insect-virus tritrophic interaction: Insights into the functions of geminiviral virion-strand genes. Proceedings of Royal Soc. B. 287:20201846

15. Kannan Pachamuthu, Chenna Swetha, Debjani Basu, Soumita Das, Indira Singh, Vivek Hari Sunder, T.N. Sujith, and P.V. Shivaprasad (September, 2021). Rice-specific Argonaute 17 controls reproductive growth and yield-associated phenotypes. Plant Mol Biol.  105:99-114

16. Ashwin Nair, Kiran Chatterjee, Vikram Jha, Ranabir Das, P.V. Shivaprasad (August, 2020). Stability of Begomoviral pathogenicity determinant βC1 is modulated by mutually antagonistic SUMOylation and SIM interactions. BMC Biology. 18:110

17. Walavalkar K, Saravanan B, Singh AK, Jayani RS, Nair A, Farooq U, Islam Z, Soota D, Mann R, Shivaprasad PV, Freedman ML, Sabarinathan R, Haiman CA, Notani D. (July, 2020). A rare variant of African ancestry activates 8q24 lncRNA hub by modulating cancer associated enhancer. Nat Commun.  11:3598.

18. Varsha Tirumalai, Melvin Prasad, P.V. Shivaprasad (July, 2020). RNA blot analysis to quantify plant miRNAs. J. Vis Exp. 161

19. Anushree N, Ashwin Nair, Vivek Hari Sundar, Varsha Tirumalai, and P. V. Shivaprasad. (April, 2020). A conserved sequence signature is essential for robust plant miRNA biogenesis. Nucleic Acids Res. 48:3103-3118

20. Soumita Das, Chenna Swetha, K. Pachamuthu, Ashwin Nair, and P. V. Shivaprasad (March, 2020).  Oryza sativa Argonaute 18 is a regulator of male sterility and developmental phase transition. Plant Reprod. 33:59-73

21. Prathibha Sanjenbam, Radhika Budhidati, Radhika Venkatesan, P.V. Shivaprasad, Deepa Agashe (February, 2020). Phenotypic Diversity Of Methylobacterium Associated With Rice Landraces In Northeast India. PLOS One. 15(2):e0228550.

22. Varsha Tirumalai, Chenna Swetha, Ashwin Nair, and P. V. Shivaprasad (May, 2019). A cluster of miRNAs regulate MYB repressors to promote anthocyanin and flavonol accumulation in grapes.  J. Exp Bot. 70:4775-4792

23. Daniel  GR  Yim, S. Krishna, V.  Lakshmanan, J.L. V. Tirumalai, Koh, J. E. Park, J.  E.  Park, J.K. Cheong, J.L. Low, M.J. Lim, J.M. Nah, I. Tan, Huili Guo, S.K. Sze, A. Gulyani, P.V. Shivaprasad, S. Raghavan, D. Palakodeti, R. Dasgupta (July, 2019). Dynamic  expression  of  tRNA-derived  small  RNAs  define cellular  states. EMBO Rep. 20:e47789

24. Padubidri V. Shivaprasad (June, 2019). New clues into the mechanisms of rice domestication. J. Biosci. 44(2). 28

25. Chenna Swetha and P.V. Shivaprasad (April, 2019). Extraction and purification of laccases from rice. Bio-Protocol. 10.21769/ 3208

26. Chenna Swetha, Debjani Basu, Kannan Pachamuthu, Varsha Tirumalai, Ashwin Nair, Melvin Prasad, and P. V. Shivaprasad (November, 2018). Major domestication-related phenotypes in indica rice are associated with loss of miRNA-mediated cascade silencing of laccases. Plant Cell 30:2649–2662.

27. Soumita Das, Akshay Hegde, P.V. Shivaprasad (September, 2018). Molecular characterization of Synedrella yellow vein virus, a new Begomovirus from South India. Arch Virol. 163:2551-255

28. P.V. Shivaprasad (August, 2018). New insights into the mechanisms of crop domestication. Cambridge Scholars Publishers, UK

29. Prasad Melvin, K. Bankapalli, Patrick D’Silva, P. V. Shivaprasad (2017). Methylglyoxal detoxification by a DJ-1 family protein provides dual abiotic and biotic stress tolerance in transgenic plants. Plant Mol. Biol. 94:381-397.

30. Soumita Das, Rahul Singh, P.V. Shivaprasad (2017). Artificial induction and maintenance of epigenetic variations in plants. Plant Gene Silencing: Phenomena and Applications. CABI publishers, UK.

31. Shivaprasad, P.V.*, Hohn, T., Akbergenov R. (2015) Dicer-like activities in wheatgerm, PLOS one; 10(1):e0116736. (* corresponding author).

32. Soham Jagtap and P.V. Shivaprasad. (2014). Diversity, expression and mRNA targeting abilities of argonaute targeting miRNAs in plants. BMC Genomics. 15:1409.

Pre-NCBS Publications:

1. Padubidri Shivaprasad, Ho-Ming, Kanu Patel, Donna Bond, and David Baulcombe (2012). A micro RNA superfamily regulates disease resistance via effects on NBS-LRR mRNAs and secondary siRNAs. Plant Cell 24: 859-874.

2. Padubidri Shivaprasad, R. Dunn, B. Santos, A. Bassett, and D.C. Baulcombe (2012). Extraordinary transgressive phenotypes of hybrids are influenced by epigenetics and small silencing RNAs. EMBO J. 31:257-266.

3. S. Sunitha, P.V Shivaprasad, K. Sujata, K. Veluthambi (2012).  High frequency of T-DNA deletions in transgenic plants transformed with intron-containing hairpin RNA genes. Plant Mol Biol Rep. 30: 158-161.

4. R. Mosher, M. Lewsey and P.V. Shivaprasad (2010). RNA silencing in plants: Flash report Silence 1:13.

5. P V. Shivaprasad, R. Rajeswaran, T. Blevins, J. Schoelz, F. Meins, Jr, T. Hohn and M. M. Pooggin (2008). The CaMV transactivator/viroplasmin interferes with RDR6-dependent trans-acting and secondary siRNA pathways in Arabidopsis. Nucleic Acids Research 36: 5896-5909.

6. R. Rajeswaran, P.V. Shivaprasad and K. Veluthambi (2007). RNA silencing in plants: Scope for applications in plants. In: Food Legumes for Nutritional Security and Sustainable Agriculture, M. C. Kharkwal (ed.), Indian Society of Genetics and Plant Breeding. Delhi, India.

7. Vogler, H., Akbergenov, R., Shivaprasad, P.V., Dang, V., Fasler, M., Kwon, M.O., Zhanybekova, S., Hohn, T., and Heinlein, M. (2007). Modification of small RNAs associated with suppression of RNA silencing by tobamovirus replicase protein. Journal of Virology 81:10379-10388.

8. Rajeswaran, R., Sunitha, S., Shivaprasad, P.V., Pooggin, M.M., Hohn, T., and Veluthambi, K. (2007) Mungbean yellow mosaic virus (MYMV) AC2 transactivates the AV1 promoter and causes toxicity in transgenic tobacco plants. Molecular Plant-Microbe Interact. 20:1545-1554.

9. Blevins, T., Rajeswaran, R., Shivaprasad, P.V., Beknazariants, D., Si-Ammour, A., Park, H.S., Vazquez, F., Robertson, D., Meins, F. Jr., Hohn, T., Pooggin, M.M. (2007).  Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing. Nucleic Acids Res. 34:6233-6246. 

10. P.V. Shivaprasad, M. Thomas, V. Balamani, D. Biswas, R. Vanitharani, A.S. Karthikeyan, and K. Veluthambi (2006). Factors contributing to deletion in geminivirus partial dimers in binary vectors used for agroinfection. Journal of Virological Methods 137:72-81.

11. P.V. Shivaprasad, P. Thillaichidambaram, V. Balaji and K. Veluthambi (2006). Expression of full-length and truncated Rep genes from Mungbean yellow mosaic virus-Vigna inhibits viral replication in transgenic tobacco. Virus Genes 33:363-372. 

12. P.V. Shivaprasad, R. Akbergenov, D. Trinks, R. Rajeswaran, K. Veluthambi, Thomas Hohn and Mikhail Pooggin (2005).  Promoters, transcripts and regulatory proteins of Mungbean yellow mosaic geminivirus. Journal of Virology 79:8149-8163.

13. D. Trinks, R. Rajeswaran, P.V. Shivaprasad, R. Akbergenov, E. J. Oakeley, K. Veluthambi, Thomas Hohn and Mikhail M. Pooggin. (2005). Suppression of RNA silencing by a geminivirus nuclear protein, AC2, correlates with transcriptional activation of host genes.  Journal of Virology 79:2517-2527.

14. A.S. Karthikeyan, R. Vanitharani, V. Balaji, V. Anuradha, T. Chidambaram, P.V. Shivaprasad, C. Parameswari, V. Balamani, M. Saminathan and K. Veluthambi (2004). Analysis of an isolate of Mungbean yellow mosaic virus (MYMV) with a highly variable DNA B component.  Archives of Virology 149:1643-1652.

15. M. M. Pooggin, P.V. Shivaprasad, K. Veluthambi, and T. Hohn. (2003). RNAi targeting DNA virus in plants. Nature Biotechnology 21:131-132.

Publications in Forestry:

B. K. Vasanthraj, Shivaprasad, P. V. and K. R. Chandrashekar (2004). Studies on the structure of Jalsur Reserve Forest, India. Journal of Tropical Forest Science 17:13-32.

Ramakrishna Marati, P.V. Shivaprasad, K. R. Chandrashekar (2003). Studies on the vegetation of Islands of Karwar, Uttara Kannada district of Karnataka. J. Econ. Taxon. Bot. 26(1):49-54

Shivaprasad, P. V., B. K. Vasanthraj and K. R. Chandrashekar (2002). Studies on the structure of Pilarkhan Reserve Forest, India. Journal of Tropical Forest Science 14(1):71-81.

Shivaprasad, P. V., B. K. Vasanthraj and K. R. Chandrashekar (2001). Dipterocarps of the Western Ghats of Karnataka. Indian Journal of Forestry. (In) Higher Plants of Indian Sub-Continent Series, B. P. Singh (Ed.) Dehra Dun, India. Vol 9: 201-206.

Dr PV Shivaprasad's Google Scholar Page