BRIC-National Institute of Plant Genome Research

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BRIC-National Institute of Plant Genome Research

An Autonomous Institute of Biotechnology Research and Innovation Council
Deptartment of Biotechnology, Ministry of Science and Technology
Government of India

Sowing seeds for a better tomorrow

Dr. Subhra Chakraborty

PhD, FNA, FASc, FNASc, FNAAS

J. C. Bose National Fellow
Ph. D, Jawaharlal Nehru University

Profile

Research

Our research is focused in three main areas: Nutritional Genomics, Plant Immunity & Stress Genomics, and delayed fruit softening.

Nutritional Genomics

Our aim is to improve the nutritional quality of important food crops since the nutritional health of humans predominantly depends on pant food. As part of protein quality improvement program, we have cloned a seed albumin gene AmA1 from Amaranthus hypochondriacus and developed protein-rich transgenic potato. Currently, our laboratory is developing transgenic cereals using this novel gene for protein quality improvement. Alternatively, for removal of antinutrient element, we focus on oxalate toxicity as it is the major dietary factor involved in kidney related diseases. Towards this end, an oxalate degrading enzyme, oxalate decarboxylase is being used to develop low-oxalate transgenic plants. Also, we are developing enabling technologies for transforming oxalate-rich fruits and vegetables with oxalate decarboxylase.

Stress Genomics

A second area of our interest is Stress Genomics in plants with specific emphasis to fungal pathogenicity. Plants frequently encounter different biotic stresses that adversely affect growth, development and more importantly the overall productivity. Stress signals perceived by plant cells leads to changes in gene expression profiles that dictate how cells overcome these stresses. Oxalic acid is a potent elicitor in fungal pathogenicity in many crop plants. We have developed fungal resistant transgenic tomato plants that express oxalate decarboxylase. Our current interest is to unravel the role of oxalate decarboxylase in fungal tolerance. In addition, we are identifying resistant gene candidates and defense mechanism of plants in response to fungal wilt. Our laboratory is developing a genome wide transcriptome of legume against Fusarium wilt to study stress perception, differential gene expression and thereby changes in metabolic responses. Our aim is to understand the biological and pathophysiological role of differentially expressed gene/s that control fungal pathogens. The ultimate goal is to use few novel genes for developing transgenic crops with improved fungal tolerance.

A third area of our research is to investigate the regulation of fruit softening using tomato as a model system. We are interested in enhancing shelf-life of fruits and vegetables because delay in fruit softening is the key regulatory mechanism to control their spoilage. Experimental approaches include softening related gene mining and developing knock-out transgenic plants for the candidate genes.

The tools used in our laboratory are molecular biology, biochemistry, Microarray, RNA Seq., Proteomic technology, Computational biology and genetic transformation.

Career

Director, National Institute for Plant Genome Research (2020-2024)

Staff Scientist VII, National Institute for Plant Genome Research (2015-2020)

Staff Scientist VI, National Institute for Plant Genome Research (2011-2015)

Staff Scientist V, National Institute for Plant Genome Research (2007-2011)

Staff Scientist IV, National Institute for Plant Genome Research (2003-2007)

Staff Scientist III, National Institute for Plant Genome Research (2000-2003)

Staff Scientist II, National Institute for Plant Genome Research (1998-2000)

Research Scientist, Jawaharlal Nehru University (1997-1998)

Awards & Honors

Fellow, Indian National Science Academy (INSA), Delhi, India

Fellow, Indian Academy of Sciences, Bangalore, India

Fellow, National Academy of Sciences

Fellow, National Academy of Agricultural Sciences

J C Bose National Fellowship, SERB-DST (2020)

Professor (Mrs.) Archana Sharma Memorial Lecture Award, National Academy of Sciences, India (2020)

Sectional President, Biological Sciences, 89th NASI Annual Session (2019)

Platinum Jubilee Lecture Award, 103rd Indian Science Congress (2016)

TATA Innovation Award from The Department of Biotechnology, Govt of India (2014)

An Inspiring Women Engineer/Scientist Award (2014)

NASI-Reliance Industries Platinum Jubilee Award (2010)

Visiting Scientist, Yale University, USA (2008)

DBT Overseas Associateship, Govt. of India, India (2007)

Young Women Bioscientist of Promise, ISCA, India (2004)

National Young Women Bioscientist Award, DBT, India (2002)

Professor Hiralal Chakraborty Award, Indian Science Congress (2002)

Technology Development Award, DBT, Govt. of India (2000)

IRRI Core Research Fellowship, IRRI, Philippines (1995)

Young Scientist Award, IUBMB (1994)

Professor Hiralal Chakraborty Award, National Botanical Society (1990)

Elected Council Member, Human Proteome Organization (HUPO)

Member, Human proteome project-Scientific advisory board (HPP-SAB)

Co-Chair, Food & Nutrition Initiative, under Biology/Disease-driven HPP

Elected Council Member and Country Representative for India in Asia Oceania Agricultural Proteomics Organization (AOAPO)

President & Executive Council Member, Proteomics Society, India (PSI)

Executive Council Member, Society for Molecular Signaling, India

Life Member, Society for Biological Chemists, India

Life Member, Indian Society of Cell Biology

Life Member, Indian Society of Translational Research

Life Member, Indian Science Congress Association

Member, American Chemical Society, USA

Member, Society for Biological Chemists, India

Proteomic Society of India

Selected Publications

Narula K, Elagamey E, Abdellatef M, Sinha A, Ghosh S, Chakraborty N and┬аChakraborty S (2020)┬аChitosan-triggered immunity to Fusarium in chickpea is associated with changes in the plant extracellular matrix architecture, stomatal closure and remodelling of the plant metabolome and proteome.┬аPlant J.┬аdoi: 10.1111/tpj.14750

Sinha A, Haider T, Narula K, Ghosh S, Chakraborty N and┬аChakraborty S (2020)┬аIntegrated seed proteome and phosphoproteome analyses reveal interplay of nutrient dynamics, carbon-nitrogen partitioning and oxidative signaling in chickpea.┬аProteomics┬а20: e1900267

Elagamey E, Narula K,┬аChakraborty N,┬аChakraborty S┬а(2020)┬аExtracellular Matrix Proteome: Isolation of ECM Proteins for Proteomics Studies.┬аMethods Mol Biol.┬а2057:155-172

Barua P, Lande NV, Kumar S,┬аChakraborty S,┬аChakraborty N┬а(2020)┬аQuantitative phosphoproteomic analysis of legume using TiO2-based enrichment coupled with isobaric labeling.┬аMethods Mol. Biol.2107: 395-406

Lande NV, Barua P, Gayen D, Kumar S, Varshney S, Sengupta S,┬аChakraborty S, Chakraborty N┬а(2020)┬аDehydration-induced alterations in chloroplast proteome and reprogramming of cellular metabolism in developing chickpea delineate interrelated adaptive responses.┬аPlant Physiol. Biochem.┬а146:337-348

Lande NV, Barua P, Gayen D, Kumar S,┬аChakraborty S,┬аChakraborty N┬а(2020)┬аProteomic dissection of the chloroplast: Moving beyond photosynthesis.┬аJ. Proteomics┬а212: 103542

Chakraborty S, Gowrishankar J, Joshi A, Kannan P, Kohli RK, Lakhotia SC, Misra G, Nautiyal CM, Ramasubramanian K, Sathyamurthy N and Singhvi AK┬а(2020)┬аSuggestions for a national framework for publication of and access to literature in science and technology in India.┬аCurrent Science┬а118: 1026-1034

Narula K, Choudhary P, Ghosh S, Elagamey E, Chakraborty N. and┬аChakraborty S┬а(2019)┬аComparative nuclear proteomics analysis provides insight into the mechanism of signalling and immune response to blast disease caused by┬аMagnaporthe oryzae┬аin rice.┬аProteomics┬а19: 1800188

Pareek A, Rathi D, Mishra D,┬аChakraborty S, Chakraborty N┬а(2019)┬аPhysiological plasticity to high temperature stress in chickpea: Adaptive responses and variable tolerance.┬аPlant Sci.┬а289: 110258

Rathi D, Pareek A, Zhang T, Pang Q, Chen S,┬аChakraborty S,┬аChakraborty, N.┬а(2019)┬аMetabolite signatures of grasspea suspension-cultured cells illustrate the complexity of dehydration response.┬аPlanta┬а250: 857-871

Rathi D, Gayali S, Pareek A,┬аChakraborty S┬аand Chakraborty N┬а(2019)┬аTranscriptome profiling illustrates expression signatures of dehydration tolerance in developing grasspea seedlings.┬аPlanta┬а250: 839-855

Gayen D, Barua P, Lande NV, Varshney S, Sengupta S,┬аChakraborty S┬аand Chakraborty N┬а(2019)┬аDehydration-responsive alterations in the chloroplast proteome and cell metabolomics profile of rice reveals key stress adaptation responses.┬аEnviron. Exp. Bot.┬а160: 12-24

Gayen D, Gayali S, Barua P, Lande NV, Varshney S, Sengupta S,┬аChakraborty S.┬аand Chakraborty N┬а(2019)┬аDehydration-induced proteomic landscape of mitochondria in chickpea reveals large-scale coordination of key biological processes.┬аJ. Proteomics┬а192: 267-279

Barua P, Lande NV, Subba P, Gayen D, Pinto S, Prasad TSK,┬аChakraborty S┬аand Chakraborty N┬а(2019)┬аDehydration-responsive nuclear proteome landscape of chickpea (Cicer arietinum┬аL.) reveals phosphorylation-mediated regulation of stress response.┬аPlant Cell Environ.┬а42: 230-244

Mishra D, Shekhar S,┬аChakraborty S┬аand Chakraborty N┬а(2018)┬аCarboxylase clamp tetratricopeptide repeat (TPR) domain containing Hsp90 cochaperones in Triticaace: an insight into structural and functional diversification.┬аEnviron. Exp. Bot.┬а155: 31-44

Aggarwal PR, Nag P, Choudhary P, Chakraborty N and┬аChakraborty S┬а(2018)┬аGenotype-independent┬аAgrobacterium rhizogenes-mediated root transformation of chickpea: a rapid and efficient method for reverse genetics studies.┬аPlant Methods14: 55

Rathi D, Pareek A, Gayali S,┬аChakraborty S,┬аChakraborty N┬а(2018)┬аVariety-specific nutrient acquisition and dehydration-induced proteomic landscape of grasspea (Lathyrus sativus L.).┬аJ. Proteomics┬а183:45-57

Ashraf, N, Basu S, Narula K, Ghosh S, Tayal R, Gangisetty N, Biswas S, Aggarwal P, Chakraborty N. and┬аChakraborty S (2018)┬аIntegrative network analysis of wilt transcriptome in chickpea reveal genotype dependent regulatory hubs in immunity and susceptibility.┬аSci. Rep.┬а8: 6528

Parveen S, Pandey A, Jameel N,┬аChakraborty S┬аand Chakraborty N┬а(2017)┬аTranscriptional regulation of chickpea ferritin┬аCaFer1┬аinfluences its role in iron homeostasis and stress response.┬аJ. Plant Physiol.┬а222: 9-16

Verma JK, Wardhan V, Singh D,┬аChakraborty S┬аand Chakraborty N┬а(2018)┬аGenome-wide identification of the Alba gene family in plants and stress-responsive expression of the rice Alba genes.┬аGenes9: E183

Mishra P, Wardhan V, Pandey A,┬аChakraborty S, Garg G. and Chakraborty N.┬а(2017)┬аComparative analysis of sequence-structure function relationship of the SUN-domain protein CaSUN1.┬аJ. Phylogentics Evol. Biol.5: 189

Elagamey E, Narula K, Sinha A, Ghosh G, Abdellatef MAE, Chakraborty N and┬аChakraborty S (2017)┬аQuantitative extracellular matrix proteomics suggests cell wall reprogramming in host-specific immunity during vascular wilt caused by┬аFusarium oxysporum┬аin chickpea.┬аProteomics┬а17: 1600374

Elagamey E,┬аSinha A,┬аNarula K,┬аAbdellatef MAE,┬аChakraborty N┬аand┬аChakraborty S (2017)┬аMolecular dissection of extracellular matrix proteome reveals discrete mechanism regulating verticillium dahliae triggered vascular wilt disease in potato.┬аProteomics17: 1600373

Nag P, Aggarwal PR, Ghosh S, Narula K, Tayal R, Maheshwari N, Chakrabortyand N and┬аChakraborty S┬а(2017)┬аInterplay of neuronal and non-neuronal genes regulates intestinal DAF-16-mediated immune response during Fusarium infection of Caenorhabditis elegans.┬аCell Death Discov.┬а┬а3: e17073

Lande NV, Subba P, Barua P, Gayen D, Keshava PTS,┬аChakraborty S┬аand Chakraborty, N┬а(2017)┬аDissecting the chloroplast proteome of chickpea (Cicer arietinum L.) provides new insights into classical and non-classical functions.┬аJ. Proteomics165: 11-20

Barua P, Gayen D, Lande NV,┬аChakraborty S┬аand Chakraborty N.┬а(2017)┬аGlobal proteomic profiling and identification of stress-responsive proteins using two-dimensional gel electrophoresis.┬аMethods Mol. Biol.1631:┬а163-179

Pandey A,┬аChakraborty S┬аand Chakraborty N┬а(2017)┬аNuclear Proteome: Isolation of Intact Nuclei, Extraction of Nuclear Proteins, and 2-DE Analysis.Methods Mol. Biol.1696: 41-55

Mishra D, Shekhar S, Agrawal L,┬аChakraborty S┬аand Chakraborty N┬а(2017)┬аCultivar-specific high temperature stress responses in bread wheat (Triticum aestivum L.) associated with physicochemical traits and defense pathways.┬аFood Chem.┬а221:┬а 1077-1087

Parveen S, Gupta DB, Dass S, Kumar A, Pandey A,┬аChakraborty S┬аand Chakraborty N┬а(2016)┬аChickpea ferritin CaFer1 participates in oxidative stress response, and promotes growth and development.┬аSci. Rep.┬а6: 31218

Gayali S, Acharya S, Lande NV, Pandey A,┬аChakraborty S┬аand Chakraborty N┬а(2016)┬аCicerTransDB 1.0: a resource for expression and functional study of chickpea transcription factors.┬аBMC Plant Biol.┬а16: 169

Ghosh S, Narula K, Sinha A, Ghosh R, Jawa P, Chakraborty N and┬аChakraborty S┬а(2016)┬аProteometabolomic analysis of transgenic tomato overexpressing oxalate decarboxylase uncovers novel proteins potentially involved in defense mechanism against Sclerotinia.┬аJ. Proteomics┬а(doi 10.1016/j.jprot.2016.04.047)

Ghosh S, Narula K, Sinha A, Ghosh R, Jawa P, Chakraborty N. and┬аChakraborty S┬а(2016) Proteometabolomic study of compatible interaction in Tomato fruit challenged with┬аSclerotinia rolfsii┬аillustrates novel protein network during disease progression.┬аFront. Plant Sci (In Press)

Narula K, Ghosh S, Aggarwal PR, Sinha A, Chakraborty N,┬аChakraborty S.┬а(2016)┬аComparative proteomics of oxalate downregulated tomatoes points toward cross talk of signal components and metabolic consequences during post-harvest storage.┬аFront. Plant Sci.7: 1147

Biswas S, Aggarwal PR, Tayal R, Sarkar MP, Chakraborty N and┬аChakraborty S.┬а(2016)┬аRNA-seq analysis identifies key genes involved in chickpea (Cicer arietinum┬аL.) shoot development.┬аJ. Botan. Soc. Bengal70(1): 49-54

Ghosh S, Narula K, Mittal PK, Sarkar MP, Chakraborty N and┬аChakraborty S.┬а(2016)┬аProteomic profile reveals the diversity and complexity of leaf proteins in spinach (Beta vulgaris┬аvar. all green).┬аJ. Prot. Proteomics┬а7: 121-131

Elagamey E, Narula K, Sinha A, Aggarwal PR, Ghosh S, Chakraborty N,┬аChakraborty S┬з.┬а(2016)┬аExtracellular matrix proteome and phosphoproteome of potato reveals functionally distinct and diverse canonical and non-canonical proteoforms.┬аProteomes┬а4: 20

Shekhar S, Agrawal L, Mishra D, Buragohain AK, Unnikrishnan M, Chokkappan Mohan C,┬аChakraborty S┬з. and Chakraborty N.┬а(2016)┬аEctopic expression of amaranth seed storage albumin modulates photoassimilate transport and nutrient acquisition in sweetpotato.┬аSci. Rep.┬а(doi: 10.1038/srep25384)

Kumar V, Chattopadhyay A, Ghosh S, Irfan M, Chakraborty N,┬аChakraborty S┬аand Datta A┬а(2016)┬аImproving nutritional quality and fungal tolerance in soya bean and grass pea by expressing an oxalate decarboxylase.┬аPlant Biotechnol. J.┬а14:1394-405

Narula K, Aggarwal PR, Chakraborty N and┬аChakraborty S (2016)┬аPlant fungus interaction proteomics: An update. In G.H. Salekdeh (ed.) Agricultural Proteomics Volume 2 (pp. 227-250) Switzerland: Springer International Publishing

Narula K, Sinha A, Haider T, Chakraborty N and┬аChakraborty S (2016)┬аSeed proteomics: An overview. In G.H. Salekdeh (ed.) Agricultural Proteomics Volume 1 (pp. 31-52) Switzerland: Springer International Publishing

Wardhan V, Pandey A,┬аChakraborty S,┬аChakraborty N┬а(2016)┬аChickpea transcription factor CaTLP1 interacts with protein kinases, modulates ROS accumulation and promotes ABA-mediated stomatal closure.┬аSci. Rep.┬а6, 3812

Barua P, Subba P, Vikram Lande N, Mangalaparthi KK, Keshava Prasad TS,┬аChakraborty S┬аand Chakraborty N┬а(2016)┬аGel-based and gel-free search for plasma membrane proteins in chickpea (Cicer arietinum L.) augments the comprehensive data sets of membrane protein repertoire.┬аJ. Proteomics┬а[doi:10.1016/j.jprot.2016.04.015]

Shekhar S, Mishra D, Gayali S, Buragohain AK,┬аChakraborty S┬аand Chakraborty N┬а(2016)┬аComparison of proteomic and metabolomic profiles of two contrasting ecotypes of sweetpotato (Ipomoea batata┬аL).┬аJ. Proteomics┬а(doi: 10.1016/j.jprot.2016.03.028)

Irfan M, Ghosh S, Meli MS, Kumar A, Kumar V, Chakraborty N,┬аChakraborty S┬аand Datta A.┬а(2016)┬аFruit ripening regulation of alpha-Mannosidase expression by the MADS box transcription factor RIPENING INHIBITOR and ethylene.┬аFront. Plant Sci.┬а7: 10

Kumar V, Irfan M., Ghosh S, Chakraborty N,┬аChakraborty S┬аand Datta A┬а(2016)┬аFruit ripening mutants reveal cell metabolism and redox state during ripening.┬аProtoplasma┬а253: 581-594

Gupta DB, Rai Y, Gayali S,┬аChakraborty S┬аand Chakraborty N┬а(2016)┬аPlant organellar proteomics in response to dehydration: turning protein repertoire into insights.┬аFront. Plant Sci. 7: 460

Rathi D, Gayen D, Gayali S,┬аChakraborty S┬аand Chakraborty N┬а(2016)┬аLegume proteomics: Progress, prospects and challenges.┬аProteomics┬а16: 310-327

Rathi D,┬аChakraborty S┬аand Chakraborty N┬а(2015)┬аProteomics of an orphan legume, grasspea: current status and future strategy.┬аPlant Tissue Cult. & Biotech.┬а25: 117тАР141

Gupta S, Wardhan V, Kumar A, Rathi D, Pandey A,┬аChakraborty S┬аand Chakraborty N┬а(2015)┬аSecretome analysis of chickpea reveals dynamic extracellular remodeling and identifies a Bet v1-like protein, CaRRP1 that participates in stress response.┬аSci. Rep.┬а5: 18427

Narula K., Pandey A., Gayali S., Chakraborty N., and┬аChakraborty S┬а(2015) Birth of plant proteomics in India: a new horizon.┬аJ. Proteomics┬а(doi: 10.1016/j.jprot.2015.04.020)

Chakraborty S, Salekdeh G.H., Yang P., Woo S.H., Chin C.F., Gehring C., Haynes P.A., Mirzaei M. and Komatsu S. (2015) Proteomics of important food crops in the Asia Oceania region: current status and future perspectives.┬аJ. Proteome Res.┬а(doi: 10.1021/acs.jproteome.5b00211)

Shekhar S, Mishra D, Buragohain AK,┬аChakraborty S┬аand Chakraborty N. (2014) Comparative analysis of phytochemicals and nutrient availability in two contrasting cultivars of sweet potato (Ipomoea batatas┬аL.)┬аFood Chem. 173:┬а957-965

Irfan M, Ghosh S, Kumar V, Chakraborty N,┬аChakraborty S┬аand Datta A. (2014) Insights into transcriptional regulation of ╬▓-D-N acetylhexosaminidase,an N-glycan-processing enzyme involved in ripening-associated fruit softening.┬аJ. Exp. Bot. 65:┬а5835-5848

Kumar R, Kumar A, Subba P, Gayali S, Barua P,┬аChakraborty S┬аand┬аChakraborty N┬а(2014) Nuclear phosphoproteome of developing chickpea seedlings (Cicer arietinum┬аL.) and protein-kinase interaction network.┬аJ. Proteomics 105:┬а58-73

Verma JK, Gayali S, Dass S, Kumar A, Parveen S, Chakraborty S,┬аand Chakraborty N (2014) OsAlba1, a dehydration-responsive nuclear protein of rice (Oryza sativa┬аL.), participates in stress adaptation.┬аPhytochemistry 100:┬а16-25

Jaiswal DK, Mishra P, Subba P, Divya Rathi D,┬аChakraborty S,┬аand Chakraborty N (2014) Membrane-associated proteomics of chickpea identifies Sad1/UNC-84 protein (CaSUN1), a novel component of dehydration signaling.┬аSci. ┬аRep. 4:┬а4177 | DOI: 10.1038/srep04177

Agrawal L, Narula K, Basu S, Shekhar S, Ghosh S, Datta A, Chakraborty N and┬аChakraborty S┬а(2013)┬аComparative proteomics reveals a role for seed storage protein, AmA1 in cellular growth, development and nutrient accumulation.┬аJ. Proteome Res. 12:┬а4904тАУ4930

Chakraborty N, Ghosh R, Ghosh S, Narula K, Tayal R, Datta A,┬аChakraborty S┬а(2013) Reduction of oxalate levels in tomato fruit and consequent metabolic remodeling following overexpression of a fungal oxalate decarboxylase.┬аPlant Physiol. ┬а162:┬а364-378

Ghosh S, Singh UK, Meli VS, Kumar V, Kumar A, Irfan M, Chakraborty N,┬аChakraborty S,┬аand Datta A (2013) Induction of senescence and identification of differentially expressed genes in tomato in response to monoterpene.┬аPLOS one 8:┬аe76029

Narula K, Datta A, Chakraborty N, and┬аChakraborty S┬а(2013) Comparative analyses of nuclear proteome: extending its function.┬аFront. Plant Sci. 4:┬а100

Subba P,┬а Barua P, Kumar R, Datta A, Soni K,┬аChakraborty S, and Chakraborty N (2013) Phosphoproteomic Dynamics of Chickpea (Cicer arietinum┬аL.) Reveals Shared and Distinct Components of Dehydration Response.┬аJ. Proteome Res. 12:┬а5025-47

Jaiswal D, Ray D, Choudhary M, Subba P, Kumar A, Verma J, Kumar R, Datta A,┬аChakraborty S,┬аand Chakraborty N (2013) Comparative proteomics of dehydration response in the rice nucleus: new insights into the molecular basis of genotype specific adaptation.┬аProteomics. 13:┬а3478-97

Subba P, Kumar R, Gayali S, Shekhar S, Praveen S, Pandey A, Datta A,┬аChakraborty S, Chakraborty N (2013) Characterisation of the nuclear proteome of a dehydration-sensitive cultivar of chickpea and comparative proteomic analysis with a tolerant cultivar.┬аProteomics 13:┬а1973тАУ1992

Shekhar S, Agrawal L, Buragohain AK, Datta A,┬аChakraborty S┬аand Chakraborty N (2013) Genotype independent regeneration and┬аagrobacterium-mediated genetic transformation of sweet potato (Ipomoea batatas┬аL.).┬аPlant Tissue Cult. Biotech. 23:┬а87-100

Jaiswal DK, Ray D, Subba P, Mishra P, Gayali S, Datta A,┬аChakraborty S┬аand Chakraborty N (2012) Proteomic analysis reveals the diversity and complexity of membrane proteins in chickpea (Cicer arietinum┬аL.).┬аProteome Sci. 10:┬а59

Narula K., Elagamy E., Datta A., Chakraborty N., and ┬аChakraborty S┬а(2012) Comparative analyses of extracellular matrix proteome: An under-explored area in plant research. In A. Goyal (ed.) Crop Plants (pp. 145-166), Janeza Tradine, Croatia: InTech

Wardhan V, Jahan K, Gupta S, Chennareddy S, Datta A,┬аChakraborty S, and Chakraborty N (2012) Overexpression of CaTLP1, a putative transcription factor in chickpea (Cicer arietinum L.), promotes stress tolerance.┬аPlant Mol. Biol. 79:┬а479-493

Kamathan A, Kamthan M, Azam M, Chakraborty N,┬аChakraborty S,┬аDatta A (2012) Expression of a fungal sterol desaturase improves tomato drought tolerance, pathogen resistance and nutritional quality.┬аSci. Rep. 2:┬а951

Kamthan A, Kamthan M, Chakraborty N,┬аChakraborty S, Datta A (2012) A simple protocol for extraction, derivatization, and analysis of tomato leaf and fruit lipophilic metabolites using GC-MS.┬аNature Protocols. Protocol Exchange┬аdoi:10.1038 /protex. 2012.061

Kamthan M, Mukhopadhyay G, Chakraborty N,┬аChakraborty S┬аand Datta A (2012) Quantitative proteomics and metabolomics approaches to demonstrate N-acetyl-d-glucosamine inducible amino acid deprivation response as morphological switch in Candida albicans.┬аFungal Genet. Biol. 49:┬а369-378

Gupta S, Wardhan V, Verma S, Gayali S, Rajamani U, Datta A,┬аChakraborty S┬аand Chakraborty N (2011) Characterization of the secretome of chickpea suspension culture reveals pathway abundance and the expected and unexpected secreted proteins.┬аJ. Proteome Res.10:┬а5006-5015

Bhushan D, Jaiswal DK, Ray D, Basu D, Datta A,┬аChakraborty S┬аand Chakraborty N (2011) Dehydration-responsive reversible and irreversible changes in the extracellular matrix: comparative proteomics of chickpea genotypes with contrasting tolerance.┬аJ. Proteome Res. 10:┬а2027-2046

Ghosh S, Meli VS, Kumar A, Thakur A, Chakraborty N,┬аChakraborty S┬аand Datta A (2011) The N-glycan processing enzymes a-mannosidase and b-D-N-acetylhexosaminidase are involved in ripening-associated softening in the non-climacteric fruits of capsicum.┬аJ. Exp. Bot. 62:┬а571-582

Chattopadhyay A, Subba P, Pandey A, Bhushan D, Kumar R, Datta A,┬аChakraborty S┬аand Chakraborty N (2011) Analysis of the grasspea proteome and identification of stress-responsive proteins upon exposure to high salinity, low temperature and abscisic acid treatment.┬аPhytochemistry 72:┬а1293-1307

Chakraborty S, Chakraborty N, Agrawal L, Ghosh S, Narula K, Shekhar S, Naik PS, Pande PC, Chakraborti SK and Datta A (2010) Next-generation protein-rich potato expressing the seed protein gene AmA1 is a result of proteome rebalancing in transgenic tuber.┬аProc. Natl. Acad. Sci. USA 107:┬а17533-17538

Meli VS, Ghosh S, Prabha TN, Chakraborty N,┬аChakraborty S┬аand Datta A (2010) Enhancement of fruit shelf life by suppressing N-glycan processing enzymes.┬аProc. Natl. Acad. Sci. USA 107:┬а2413-2418

Pandey A, Rajamani U, Verma J, Subba P, Chakraborty N, Datta A,┬аChakraborty S┬аand Chakraborty N (2010) Identification of Extracellular Matrix Proteins of Rice (Oryza sativa┬аL) Involved in Dehydration-Responsive Network: A Proteomic Approach.┬аJ. Proteome Res. 9:┬а3443-3464

Choudhary MK, Basu D, Datta A, Chakraborty N and┬аChakraborty S┬а(2009) Dehydration-responsive nuclear proteome of rice (Oryza sativa┬аL.) illustrates protein network, novel regulators of cellular adaptation and evolutionary perspect.┬аMol. Cell. Proteomics 8:┬а1579-1598

Ashraf N, Ghai D, Barman P, Basu S, Gangisetty N, Mondal MK, Chakraborty N, Datta A and┬аChakraborty S┬а(2009) Comparative analyses of genotype dependent expressed sequence tags and stress-responsive transcriptome of chickpea wilt illustrates predicted and unexpected genes and novel regulators of plant immunity.┬аBMC Genomics 10:┬а415

Pandey A,┬аChakraborty S┬аand Datta A, Chakraborty N (2008) Proteomics approach to identify dehydration responsive nuclear proteins from chickpea (Cicer arietinum┬аL.).┬аMol. Cell. Proteomics 7:┬а88-107

Agrawal L,┬аChakraborty S,┬аJaiswal DK, Gupta S, Datta A and Chakraborty N (2008) Comparative proteomics of tuber induction, development and maturation reveal the complexity of tuberization process in potato (Solanum tuberosum┬аL)┬аJ. Proteome Res. 7:┬а3803-3817

Bhushan D, Pandey A, Choudhary MK, Datta A,┬аChakraborty S┬аand Chakraborty N (2007) Comparative proteomics analysis of differentially expressed proteins in chickpea extracellular matrix during dehydration stress.┬аMol. Cell. Proteomics 6:┬а1868-1884

Pandey A., Choudhary MK, Bhushan D, Chattopadhyay A,┬аChakraborty S,┬аDatta A and Chakraborty N (2006) The nuclear proteome of chickpea (Cicer arietinum┬аL.) reveals predicted and unexpected proteins.┬аJ. Proteome Res. 5:┬а3301-3311

Bhushan D, Pandey A, Chattopadhyay A, Choudhary MK,┬аChakraborty S,┬аDatta A and Chakraborty N (2006) Extracellular matrix proteome of chickpea (Cicer arietinum) illustrates pathway abundance, novel protein functions and evolutionary perspect.┬аJ. Proteome Res. 5:┬а1711-1720

Chakraborty N,┬аDatta A and┬аChakraborty S┬а(2003) Nutritional genomics: quest for GM crops for better nutrition.┬аEverymanтАЩs Science. 38:┬а41-43

Chakraborty S,┬аChakraborty N, Jain D, Salunke DM, and Datta A (2002)┬аActive site geometry of oxalate decarboxylase from┬аFlammulina velutipes: Role of histidine coordinated manganese in substrate recognition.┬аProtein Sci. 11:┬а2138-2147

Sarmah B, Chakraborty N,┬аChakraborty S,┬аand Datta A (2002) Plant pre-Mrna splicing in fission yeast,┬аSchizosaccharomyces pombe.┬аBiochem. Biophy. Res. Commn. 293:┬а1209-1216

Chakraborty S,┬аSarmah B, Chakraborty N and Datta A (2002) Premature termination of RNA polymerase II mediated transcription of a seed protein gene in┬аSchizosaccharomyces pombe.┬аNuclei Acids. Res. 30:┬а2940-2949

Azam M, Kesarwani M,┬аChakraborty S, Natarajan K and Datta A (2002) Cloning and characterization of 5тАЩ-flanking region of oxalate decarboxylase gene from┬аFlammulina velutipes.┬аBiochem J.367:┬а66-75

Chakarborty S,┬аChakarborty N and Datta A (2000) Increased nutritive value of transgenic potato by expressing a nonallergenic seed albumin gene from┬аAmaranthus hypochondriacus.┬аProc. Natl. Acad. Sci. USA 97:┬а 3724-3729

Book Chapter

Mishra D, Shekhar S, Singh D,┬аChakraborty S┬аand Chakraborty N (2018) Heat shock proteins and abiotic stress tolerance in plants. In Regulation of heat shock protein responses. Eds. A. Asea and P. Kaur, Springer, Cham, Switzerland, pp. 41-69

Pandey A,┬аChakraborty S┬аand Chakraborty N (2018). Nuclear proteome: isolation of intact nuclei, extraction of nuclear proteins, and 2-de analysis. In Plant Membrane Proteomics. Eds. H. Mock A. Matros and K. Witzel, Humana Press, New York, NY, pp. 41-55

Narula K, Aggarwal PR, Chakraborty N and┬аChakraborty S┬а(2016a)┬аPlant fungus interaction proteomics: An update. In G.H. Salekdeh (ed.) Agricultural Proteomics Volume 2 (pp. 227-250) Switzerland: Springer International Publishing

Narula K, Sinha A, Haider T, Chakraborty N and┬аChakraborty S┬а(2016b)┬аSeed proteomics: An overview. In G.H. Salekdeh (ed.) Agricultural Proteomics Volume 1 (pp. 31-52) Switzerland: Springer International Publishing

Narula K, Elagamy E, Datta A, Chakraborty N and┬аChakraborty S┬а(2012) Comparative analyses of extracellular matrix proteome: An under-explored area in plant research. In┬аA. Goyal┬а(ed.)Crop Plants (pp. 145-166), Janeza Tradine, Croatia: InTech

Chakraborty S,┬аPandey A, Datta A and Chakraborty N (2008) Nucleus.┬аInG.K. Agrawal and R. Rakwa(eds.)Plant Proteomics: Technology, Strategies, and Applications (pp. 327-338)John Wiley & Sons, Inc

Chakraborty N,┬аChakraborty S┬аand Datta A (2005) Nutritional genomics: Commitment to society. In P. Tandon, M. Sharma and R. Swarup (eds.) Biodiversity: Status and Prospects (pp.35-42), New Delhi: Narosa Publishing House Pvt. Ltd

Chakraborty N,┬аChakraborty S┬аand Datta A (2005) Designer GM potato with increased nutritive value. In JS Singh and VP Sharma (eds.) Glimpses of the work on environment and development in India (pp.269-272), New Delhi: Angkor Publishers (P) Ltd

Chakraborty N,┬аChakraborty S,┬аKesarwani M, Mohammad A and Datta A (1998) Increased nutritive and qualitative value of transgenic plants expressing genes specifying amaranth seed albumin and┬аCollybia┬аoxalate decarboxylase. In K.T. Shao (eds.) Frontiers in Biology: The Challenges of Biodiversity Biotechnology. (pp 125-131), Taipei: Academia Sinica

Mehta A, Natarajan K, Raina A,┬аBiswas S,┬аChakraborty N and Datta A (1997) Molecular analysis of genes encoding┬аAmaranthus┬аseed specific protein and┬аCollybia┬аoxalate decarboxylase to develop transgenic plants. Plant Molecular Biology and Biotechnology. In K.K. Tiwari and G.S. Singhal (eds.), (pp 321-326) New Delhi: Narosa Publishing House

Patent

US Patent

Chakraborty S, Chakraborty N, Datta A, Asraf N, Basu S, Nag P and Singh M┬а┬а(2015)┬аPolynucleotides derived from chickpea and uses thereof (US Patent No. 9,163,255)

Datta, A.,┬аChakraborty S, Chakraborty N, Meli, V, Ghosh, S. (2015). Polynucleotide Sequence of fruit Softening Associated B-D-N-Acetylhexosaminidase and its uses for enhancing fruit shelf life (US Patent No. 8,987,556)

Datta, A.,┬аChakraborty S, Chakraborty N, Meli, V, Ghosh, S. (2015). Polynucleotide sequence of fruit softening associated ╬▒-mannosidase and its uses for enhancing fruit shelf life (US Patent No. 8,962,918)

Chakraborty N,┬аChakraborty S, Datta A, Wardhan V and Jahan K. Polynucleotide encoding CaTLP1 protein and uses thereof. (US No.14/399,706). Published by USPTO on 07/05/2015 (US20150128305 A1)

Chakraborty N,┬аChakraborty S, Jaiswal DK, Mishra P, Subba P and Rathi D. Method of producing stress tolerant plants overexpressing CaSUN1. (US No. 14/588,737). Published by USPTO on 02/07/2015 (US20150184190 A1)

Chakraborty N,┬аChakraborty S, Verma JK, Gayali S, Dass S and Kumar A.┬а(2015)┬аMethod of producing stress tolerant plants overexpressing OsAlba1. (US No.┬а20,150,247,161). Published by USPTO on 03/09/2015 (US20150247161 A1)

Chakraborty N,┬аChakraborty S,┬аDatta A and Bhushan D.┬а(2012)┬аExtracellular matrix localized ferritin-1 for iron uptake, storage, and stress tolerance (US patent No. 8,163,977)

Datta A, Raina A and┬аBiswas S.┬а(1998)┬аMethod of making seed specific DNA (US Patent No. 5,846,736)

Datta A, Raina A and┬аBiswas S.┬а(1997)┬аSeed storage protein with nutritionally balanced amino acid composition (US Patent No. 5670635)

PCT Patents

Chakraborty S, Chakraborty N, Datta A, Asraf N, Basu S, Nag P and Singh M (2017) Polynucleotides derived from chickpea and uses thereof for improving immunity to fungal pathogens (CP No. 2,772,654)

Chakraborty, N.,┬аChakraborty, S., Wardhan, V., Rathi, D., Gupta. S. (2017). Method of generating stress tolerant plant over-expressing CaRRP1, reagents and uses thereof (WO2017098530 A1)

Chakraborty S, Chakraborty N, Datta A, Ashraf N, Basu S, Nag P and Singh M (2016) Polynucleotides derived from chickpea and uses thereof (EP No. 2470663)

Chakraborty S, Chakraborty N, Datta A, Asraf N, Basu S, Nag P and Singh M (2015) Polynucleotides derived from chickpea and uses thereof (APA No. 2010288112)

Datta A,┬аChakraborty S, Chakraborty N and┬а Meli V (2014) Polynucleotide Sequence of fruit Softening Associated B-D-N-Acetylhexosaminidase and its uses for enhancing fruit shelf life (EP-2315830)

Datta A,┬аChakraborty S,┬аChakraborty N, Ghosh S and Meli SV (2015) Polynucleotide sequence of fruit softening associated┬а╬▒-mannosidase and its uses for enhancing fruit shelf life (EP 2315835)

Chakraborty N,┬аChakraborty S, Datta A, Wardhan V and Jahan K (2014) Polynucleotide encoding CaTLP1 and uses thereof (WO2013168181 A1)

Chakraborty N,┬аChakraborty S, Datta A and Bhushan D (2013) Extracellular matrix localized ferritin-1 for iron uptake, storage, and stress tolerance (WO 2007141808 A2)

Chakraborty S, Chakraborty N, Datta A, Asraf N, Basu S, Nag P and Singh M (2011) Polynucleotides derived from chickpea and uses thereof (WO2011024207A3)

Indian Patents

Chakraborty N,┬аChakraborty S, Wardhan V, Rathi D, Gupta S┬а(2015)┬аMethod of generating stress tolerant plant over-expressing CaRRP1, reagents and uses thereof [IPA No.3983/DEL/2015

Chakraborty N,┬аChakraborty S,┬аVerma JK, Dass S, Gayali S, Kumar A, Praveen S (2014) A method of producing stress tolerant plants over-expressing OsAlba1 [IPA No. 3759/DEL/2013]

Datta A, Chakraborty N,┬аChakraborty S, Kamthan M and Kamthan A (2014). Polynucleotide Associated with Ergosterol Biosynthesis and uses thereof [IPA-925/DEL/2014]

Chakraborty N,┬аChakraborty S,┬аJaiswal DK, Mishra P, Subba P and Rathi D (2014) A method of producing stress tolerant plants (IPA No. 8/DEL/2014)

Chakraborty N,┬аChakraborty S,┬аVerma JK, Gayali S, Dass S and Kumar A (2013) A method of producing stress tolerance rice plants (IPA No. 3759/DEL/2013)

Chakraborty N,┬аChakraborty S,┬аDatta A, Wardhan V and Jahan K┬а(2012)┬аPolynucleotide encoding CaTLP1 and uses thereof (IPA No.1406/DEL/2012)

Datta A,┬аChakraborty S,┬аChakraborty N, Kamthan M and Kamthan A┬а(2012)┬аPolynucleotide sequence of an ergosterol biosynthesis enzyme тИЖ7-sterol-C-5-desaturase and uses thereof (IPA No. 3671/DEL/2012)

Datta A,┬аChakraborty S,┬аChakraborty N, Ghosh S and Meli SV┬а(2010)┬аPolynucleotide sequence of fruit softening associated┬а╬▒-mannosidase and its uses for enhancing fruit shelf life (IPA No.1647/DEL/2008). Published by Indian Patent Office on 16.04.2010

Datta A,┬аChakraborty S,┬аChakraborty N, Ghosh S and Meli SV┬а(2010)┬аPolynucleotide sequence of fruit softening associated┬а╬▓-D-N-acetyhexosaminidase and its uses for enhancing fruit shelf life (IPA No.1648/DEL/2008). Published by Indian Patent Office on 23.04.2010

Chakraborty S, Datta A, Chakraborty N, Asraf N and Basu S┬а(2009)┬аFunctional genomics and stress responsive polynucloetides from chickpea (IPA No.1565/DEL/2009)

Chakraborty N,┬аChakraborty S, Datta A and Bhushan D┬а┬а(2006)┬аExtracellular matrix localized ferritin-1 for iron uptake, storage, and stress tolerance (IPA No.1371/DEL/2006)

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