Dr. Vineet Gaur
Staff Scientist VPhone: 91-11-26741612/14/17 Ext. 252
Direct: 91-11-26735252
Fax: 91-11-26741658
Email: vgaur@nipgr.ac.in, vineetgaur1982@gmail.com
Collaborations
-
Dr. Wilhelm Boland, Dr.Axel Mithöfer (Max Planck Institute for
Chemical Ecology, Germany)
- Dr. Ralf Oelmüller (Institute of General Botany and Plant
- Physiology, FSU Jena, Germany)
- Dr. Edgar Pieter (University of Halle-Wittenberg, Germany)
- Dr. Arockiasamy Arulandu (ICGEB, Delhi)
- Dr. J.C Sekhar (Indian Institute of Maize Research, Delhi)
- Dr. Smrutisanchita Behra (IICT, Kolkata)
Resources
| Stress Combinations and their Interactions in Plants (SCIP) Database - http://223.31.159.3/plant_complete/index_orangesunset.php and https://db.nipgr.ac.in/plant_complete/index_orangesunset.php |
| VIGS database - https://vigs-database.btiscience.org/index.php |
| pssRNAit: Designing Effective and Specific Plant RNAi siRNAs with Genome-wide Off-target Gene Assessment - https://www.zhaolab.org/pssRNAit/ |
Profile
Research Area
Structural Biology, Protein biochemistry, and Biophysics.
Research Interest and recent work
The laboratory of Structural Biology at NIPGR is interested in understanding various DNA repair and recombination mechanisms in plants from structural and biochemical perspectives. Recently we have identified At-HIGLE, a GIY-YIG endonuclease to be a possible plant Slx1 with resolve Holliday Junction (four-way DNA molecules) resolving potential.
Awards and Fellowships
| SERB-Early Career Research Award from Department of Science and Technology, India (2016) |
| Innovative Young Biotechnologist Award (IYBA) 2015 from Department of Biotechnology, India (2016). |
| Young Scientist Award of Indian Society for Plant Physiology during 3rd International Plant Physiology Congress at New Delhi, India (2015). |
| CEPLAS Fellowship as a guest scientist at University of Cologne and Dusseldorf, Germany, (2015). |
| Ramalingaswamy Re-entry Fellowship from Department of Biotechnology, India, (2014). |
| INSPIRE faculty award for Plant and Agriculture from Department of Science and Technology, India (2014, Fellowship not availed). |
| F1000 Associate faculty member for Plant Genomes and Evolution for post-publication peer reviewing (2012 - 2017). |
| NSF Post-doctoral fellowship at University of California, Davis, USA (2011 – 2015). |
| The best PhD student publication 2010/11 in the category Plants or microbes, University of Cologne, Germany (2011). |
| North Rhine Westphalia international graduate fellowship for Ph.D.studies at University of Cologne, Germany (2006 – 2010). |
| IARI Gold Medal for outstanding academic performance in M.Sc (2007). |
| Junior Research Fellowship from Indian Council of Agricultural Research for M.Sc. studies (2004 – 2006). |
| BHU Gold Medal for standing 1st in B.Sc. (2005). |
| BHU merit scholarship for B.Sc.(Agriculture) at Banaras Hindu University, Varanasi (2000 – 2004). |
Books
| Gayacharan, Parida SK, Singh AK, Chattopadhyay D, Joshi DC, Katna G (2024) Rice Bean (Vigna umbellata (Thunb.) Ohwi & Ohashi) Potential Pulses: Genetic and Genomic Resources. CABI Publisher, pp. 100-115. DOI:10.1079/9781800624658.0006. |
| Basu U, Parida SK (2023) CLAVATA signaling pathway receptors modulate developmental traits and stress responses in crops. In: Upadhyay SK, Shumayla (eds), Plant Receptor-Like Kinases. Elsevier B.V., pp 371-392.https://doi.org/10.1016/B978-0-323-90594-7.00004-1. |
| Jha UC, Nayyar H, Parida SK, Siddique KHM (2022) Horse gram, an underutilized climate-resilientlegume: Breeding and genomic approach for improving future genetic gain. Developing Climate Resilient Grain and Forage Legumes. 167-178. |
| Daware A, Parida SK, Tyagi AK (2020) Integrated genomic strategies for cereal genetic enhancement: combining QTL and association mapping. Cereal Genomics 2072:15-25. |
| Tripathi S, Singh RK, Parida SK, Chaturvedi SK, Gaur PM, Kumar S, Dikshit HK, Mishra GP, Singh A (2022) Biofortification of Chickpea. Biofortification of Staple Crops, Springer Singapore, pp 335-344 doi.org/10.1007/978-981-16-3280-8_13. |
| Mohanty JK, Parida SK (2022) Small RNA-omics: Decoding the regulatory networks associated with horticultural traits. Omics in Horticultural Crops doi.org/10.1016/B978-0-323-89905-5.00001-X. |
| Jha UC, Bohra A, Nayyar H, Rani A, Devi P, Saabale PR, Parida SK (2019) Breeding and Genomics Approaches for Improving Productivity Gains in Chickpea Under Changing Climate. In: Kole C. (eds) Genomic Designing of Climate-Smart Pulse Crops. Springer, Cham, pp-135-164. |
| Jha UC, Barh D, Parida SK, Jha R, Singh NP (2016) Whole-genome resequencing: current status and future prospects in genomics-assisted crop improvement. Applied Molecular Biotechnology: The Next Generation of Genetic Engineering, CRC Press, Taylor & Francis Group, Inc, 209-234. |
| Das S, Parida SK (2015) Synergistic plant genomics and molecular breeding approaches for ensuring food security. In Genomics, Proteomics and Metabolomics in Nutraceuticals and Functional Foods, Second Edition (eds Bagchi D, Swaroop A, Bagchi M), John Wiley & Sons, Ltd, Chichester, UK. DOI: 10.1002/9781118930458.ch14. |
| Parida SK, Mohapatra T (2010) Whole genome sequencing. In: Kole C, Abbott AG (Eds) Principles and Practices of Plant Genomics, Vol 3, Advanced Genomics, Science Publishers, Inc, New Hampshire and Edenbridge Ltd, British Isles, pp 120-174. |
Review Articles
| Mohanty JK, Parida SK (2024) Stripping off the rice panicle: induced genetic variation awakens the sheathed spikelet for a better yield. Journal of Experimental Botany 75:5459-5462. |
| Jha UC, Nayyar H, Roychowdhury R, Prasad PVV, Parida SK, Siddique KHM (2024) Non-coding RNAs (ncRNAs) in plant: Master regulators for adapting to extreme temperature conditions. Plant Physiology Biochemistry 205:108164 |
| Basu U, Parida SK (2021) Restructuring plant types for developing tailor-made crops. Plant Biotechnology Journal 21:1106-1122. |
| Basu U and Parida SK (2023) The developmental dynamics in cool season legumes with focus on chickpea. Plant Molecular Biology 111:473-491. |
| Giri J, Parida SK, Raghuvanshi S and Tyagi AK (2021) Emerging molecular strategies for improving rice drought tolerance. Current Genomics 22:16-25. |
| Pandey S, Singh A, Parida SK, Prasad M (2022) Combining speed breeding approaches with conventional and genomics-assisted breeding for crop improvement. Plant Breeding 141:301-313. |
| Daware A, Parida SK, Tyagi AK (2020) Integrated genomic strategies for cereal genetic enhancement: combining QTL and association mapping. Cereal Genomics 2072:15-25. |
| Jha UC, Bohra A, Pandey S, Parida SK (2020) Breeding, genetics, and genomics approaches for improving Fusarium wilt resistance in major grain legumes. Frontiers in Genetics 11:1001. |
| Daware A, Parida SK, Tyagi AK (2019) Integrated Genomic Strategies for Cereal Genetic Enhancement: Combining QTL and Association Mapping. Methods Molecular Biology 2072:15-25. |
| Jha UC, Bohra A, Jha R, Parida SK (2019) Salinity stress response and 'omics' approaches for improving salinity stress tolerance in major grain legumes. Plant Cell Reports 38:255-277. |
| Jha UC, Sharma, KD, Nayyar H, Parida SK, Siddique KHM (2022) Breeding and Genomics Interventions for Developing Ascochyta Blight Resistant Grain Legumes. International Journal of Molecular Science 23:2217. |
| Agarwal P, Parida SK, Raghuvanshi S, Kapoor S, Khurana P, Khurana JP, Tyagi AK (2016) Rice improvement through genome-based functional analysis and molecular breeding in India. Rice 9:1. |
| Agarwal P, Parida SK, Mahto A, Das S, Mathew IE, Malik N, Tyagi AK (2014) Expanding frontiers in plant transcriptomics in aid of functional genomics and molecular breeding. Biotechnology Journal 9:1480-1492. |
| Kujur A, Saxena MS, Bajaj D, Laxmi, Parida SK (2013) Integrated genomics and molecular breeding approaches for dissecting the complex quantitative traits in crop plants. Journal of Biosciences 38:971-987. |
| Das A, Parida SK (2013) Advances in biotechnological applications in three important food legumes. Plant Biotechnology Reports 8:83-99. |
PDB AND PROTEIN SEQUENCE ENTRIES
| 3LP9: Crystal structure of LS-24, seed albumin from Lathyrus sativus. |
| 3EHK: Crystal structure of Pru du amandin, an allergenic protein from Prunus dulcis. |
| 3OYO: Crystal structure of hemopexin fold protein CP4 from Vigna unguiculata. |
| 4QW8, 4QW9, 4QWA, 4QWB, 4QWC, 4QWD, 4QWE: Ternary Crystal Structures of a Y-family DNA polymerase Dpo4 from Sulfolobus solfataricus in complex with DNA and dCTP or its L-analogs. |
| 4HOG, 4HOI, 4HOH: Structural evaluation of a mimicry recognizing paratope: plasticity in antigen-antibody interactions manifests in molecular mimicry. |
| 4XLG, 4XM5:Structural and mechanistic analysis of the Slx1-Slx4 endonuclease from Candida glabrata. |
| 6SEH, 6SEI: Recognition and processing of branched DNA substrate by Slx1-Slx4 nuclease from Thermothielavioides terrestris. |
| 7WME: Crystal Structure of the catalytic domain of At-HIGLE from Arabidopsis thaliana. |
| P86190: Protein sequence of LS-24 from Lathyrus sativus. |
Selected Publications
| Verma P, Kumari P, Negi S, Yadav G, Gaur V*. Holliday junction resolution by At-HIGLE: an SLX1 lineage endonuclease from Arabidopsis thaliana with a novel in-built regulatory mechanism. (2022) Nucleic Acids Research. 50: 4630–4646 (* Corresponding author). |
| Raul B, Bhattacharjee O, Ghosh A, Upadhyay P, Tembhare K, Singh A, Shaheen T, Ghosh AK, Torres-Jerez I, Krom N, Clevenger J, Udvardi M, Scheffler BE, Akins PO, Sharma RD, Bandyopadhyay K, Gaur V, Kumar S, Sinharoy S. Microscopic and transcriptomic analyses of Dalbergoid legume peanut reveal a divergent evolution leading to Nod Factor dependent epidermal crack-entry and terminal bacteroid differentiation. (2022) Mol Plant Microbe Interact.35: 131-145. |
| Verma P, Tandon R, Yadav G, Gaur V*. Structural aspects of DNA repair and recombination in crop improvement. (2020) Frontiers in Genetics. 11: 1-30. (* Corresponding author). |
| Gaur V, Ziajko W, Nirwal S, Szlachcic A, Gapińska M, Nowotny M. Recognition and processing of branched DNA substrates by Slx1-Slx4 nuclease. (2019) Nucleic Acids Research. 47: 11681-11690. |
| Jaciuk M*, Swuec P*, Gaur V*, Kasprzak JM, Renault L, Dobrychłop M, Nirwal S, Bujnicki JM, Costa A, Nowotny M. A combined structural and biochemical approach reveals translocation and stalling of UvrB on the DNA lesion as a mechanism of damage verification in bacterial nucleotide excision repair. (2019) DNA Repair. 85: 102746. (* Equal contribution). |
| Nowotny M*, Gaur V*. Structure and mechanism of nucleases regulated by SLX4. (2016) Curr Opin Struct Biol. 36: 97–105. (* Corresponding authors). |
| Gaur V, Wyatt HD, Komorowska W, Szczepanowski RH, de Sanctis D, Gorecka KM, West SC, Nowotny M. Structural and Mechanistic Analysis of the Slx1-Slx4 Endonuclease. (2015) Cell Reports. 10: 1467–1476. |
| Gaur V, Vyas R, Fowler JD, Efthimiopoulos G, Feng JY, Suo Z. Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase. (2014) Nucleic Acids Research. 42: 9984–9995. |
| Espinoza-Herrera SJ, Gaur V, Suo Z, Carey PR. Following DNA chain extension and protein conformational changes in crystals of a Y-family DNA polymerase via Raman crystallography. (2013) Biochemistry 52: 4881-4890. |
| Tapryal S*, Gaur V*, Kaur KJ, Salunke DM. Structural evaluation of a mimicry-recognizing paratope: plasticity in antigen-antibody interactions manifests in molecular mimicry. (2013) J Immunol. 191:456-63. (* Equal contribution). |
| Gaur V, Chanana V, Jain A, Salunke DM. The structure of a haemopexin-fold protein from cow pea (Vigna unguiculata) suggests functional diversity of haemopexins in plants. (2011) Acta Cryst. F67: 193-200. |
| Gaur V, Qureshi IA, Singh A, Chanana V, Salunke DM. Crystal structure and functional insights of hemopexin fold protein from grass pea. (2010) Plant Physiology 152: 1842-1850. |
| Gupta P, Gaur V and Salunke DM. Purification, identification and preliminary crystallographic studies of a 2S albumin seed protein from Lens culinaris. (2008) Acta Cryst. F64: 733–736. |
| Gaur V, Sethi DK and Salunke DM. Purification, identification and preliminary crystallographic studies of Pru du amandin, an allergenic protein from Prunus dulcis. (2008) Acta Cryst. F64: 32–35 |
Group Members
| Present | ||
| Dr. Praveen Kumar | (RA-1) | |
| Ms. Kavya J | (PA-1) | |
| Past | ||
| Ms. Shreya Negi | (PA-1) | |
| Ms. Reetika Tandon | (PA-1) | |
Professional & Academic Background
| Staff Scientist V (January 2022 – present) : National Institute of Plant Genome Research, New Delhi. |
| Staff Scientist IV (August 2018 – December 2021) : National Institute of Plant Genome Research, New Delhi. |
| Staff Scientist III (April 2015 – August 2018) : National Institute of Plant Genome Research, New Delhi. |
| Invited Guest Scientist (2015) : Cluster of Excellence on Plant Sciences, University of Cologne and Dusseldorf, Germany. |
| Post-Doctoral Fellow (2011 – 2015): Department of Plant Biology, University of California, Davis, USA. |
| Ph.D. (2006 – 2010): International Graduate School in Genetics and Functional Genomics, University of Cologne, Germany. |
| M.Sc. (2004 – 2006): National Research Center on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi. |
| B.Sc. (2000 – 2004): Institute of Agricultural Sciences, Banaras Hindu University, Varanasi. |