Dinesh-Kumar Laboratory

PUBLICATIONS

From Yale

Patel, S. and Dinesh-Kumar, S.P. (2008) Arabidopsis BECLIN1 is required for autophagosome formation and to limit pathogen-associated cell death response. Autophagy 4:20-27.[Abstract]
Gong, W., He, K., Covington, M., Dinesh-Kumar, S.P., Snyder, M., Harmer, S.L., Zhu, Y.X., and Deng, X.W. (2008) The Development of Protein Microarrays and Their Application in DNA-Protein and Protein-Protein Interaction Analyses of Arabidopsis Transcription Factors.Molecular Plant1:27-41.
Dong, Y., Burch-Smith, T., Liu, Y., Mamillapalli, P., and Dinesh-Kumar, S.P. (2007) A ligation-independent cloning TRV vector for high-throughput virus induced gene silencing identifies roles for NbMADS4-1 and -2 in floral development. Plant Physiology 145:1161-1170. [Abstract]
Seay, M., and Dinesh-Kumar, S.P. (2007) Autophagy takes its TOLL on innate immunity. Cell Host & Microbe 2:69-70. [Abstract]
Popescu, S. C, Snyder, M., and Dinesh-Kumar, S.P. (2007) Arabidopsis protein microarrays for the high-throughput identification of protein-protein interactions. Plant Signaling & Behavior 2: Issue 5. [Abstract]
Bhattarai, K. K., Li, Q., Liu, Y., Dinesh-Kumar, S. P., and Kaloshian, I. (2007) The Mi-1-Mediated Pest Resistance Requires Hsp90 and Sgt1. Plant Physiology 144:312-323. [Abstract]
Burch-Smith, T.M., Schiff, M., Caplan, J., Tsao, J., Czymmek, K., and Dinesh-Kumar, S.P. (2007) A novel role for the TIR domain in association with pathogen-derived elicitors. PLoS Biology 5:e68:501-514. [Abstract]
Popescu, S. C, Popescu, G. V., Bachan, S., Zhang, Z., Seay, M., Gerstein, M., Snyder, M., and Dinesh-Kumar, S.P. (2007) Differential binding of calmodulin related proteins to their targets revealed using high-density Arabidopsis protein microarrays. Proceedings of the National Academy of Science 104:4730-4735. [Abstract]
*Burch-Smith, T.M., *Schiff, M., *Liu, Y., (*contributed equally) and Dinesh-Kumar, S.P. (2006) Efficient virus induced gene silencing in Arabidopsis thaliana. Plant Physiology. 142:21-27. [Abstract]
Patel, S., Caplan, J., and Dinesh-Kumar, S.P. (2006) Autophagy in control of programmed cell death. Current Opinion in Plant Biology 9:391-396. [Abstract]
*Seay, M., *Patel, S., (*contributed equally) and Dinesh-Kumar, S.P. (2006) Autophagy and plant innate immunity. Cellular Microbiology 8:899-906. [Abstract]
Seay, M., and Dinesh-Kumar, S.P. (2005) Life After Death: Are Autophagy Genes Involved in Cell Death and Survival During Plant Innate Immune Responses? Autophagy 1:185-186. [Abstract]
*Soosaar, J.L.M., *Burch-Smith, T.M., (*contributed equally) and Dinesh-Kumar, S.P. (2005) Mechanisms of plant resistance to viruses. Nature Reviews Microbiology 3:789-798. [Abstract]
Liu Y, Schiff M, Czymmek K, Talloczy Z, Levine B, Dinesh-Kumar SP. (2005) Autophagy regulates programmed cell death during the plant innate immune response. Cell 121:567-577. [Abstract]
Rubio V, Shen Y, Saijo Y, Liu Y, Gusmaroli G, Dinesh-Kumar SP, Deng XW. (2005) An alternative tandem affinity purification strategy applied to Arabidopsis protein complex isolation. Plant J. 41:767-778. [Abstract]
Marathe R, Guan Z, Anandalakshmi R, Zhao H, Dinesh-Kumar SP. (2004) Study of Arabidopsis thaliana resistome in response to cucumber mosaic virus infection using whole genome microarray. Plant Mol Biol. 55:501-520. [Abstract]
*Liu Y, *Nakayama N, (*contributed equally), Schiff M, Litt A, Irish VF, Dinesh-Kumar SP. (2004) Virus induced gene silencing of a DEFICIENS ortholog in Nicotiana benthamiana. Plant Mol Biol. 54:701-711. [Abstract]
*Burch-Smith TM, *Anderson JC, (*contributed equally), Martin GB, Dinesh-Kumar SP. (2004) Applications and advantages of virus-induced gene silencing for gene function studies in plants. Plant J. 39:734-746. [Abstract]
Gong W, Shen YP, Ma LG, Pan Y, Du YL, Wang DH, Yang JY, Hu LD, Liu XF, Dong CX, Ma L, Chen YH, Yang XY, Gao Y, Zhu D, Tan X, Mu JY, Zhang DB, Liu YL, Dinesh-Kumar SP, Li Y, Wang XP, Gu HY, Qu LJ, Bai SN, Lu YT, Li JY, Zhao JD, Zuo J, Huang H, Deng XW, Zhu YX. (2004) Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes. Plant Physiol. 135:773-782. Abstract
Liu Y, Schiff M, Dinesh-Kumar SP. (2004) Involvement of MEK1 MAPKK, NTF6 MAPK, WRKY/MYB transcription factors, COI1 and CTR1 in N-mediated resistance to tobacco mosaic virus. Plant J. 38:800-809. Abstract
*Liu Y, *Burch-Smith T, (*contributed equally), Schiff M, Feng S, Dinesh-Kumar SP. (2004) Molecular Chaperone Hsp90 Associates with Resistance Protein N and Its Signaling Proteins SGT1 and Rar1 to Modulate an Innate Immune Response in Plants. J Biol Chem. 279:2101-8. Epub 2003 Oct 28. Abstract
Ekengren SK, Liu Y, Schiff M, Dinesh-Kumar SP, Martin GB. (2003) Two MAPK cascades, NPR1, and TGA transcription factors play a role in Pto-mediated disease resistance in tomato. Plant J. 36:905-917. Abstract
Dinesh-Kumar SP, Anandalakshmi R, Marathe R, Schiff M, Liu Y. (2003), Virus-induced gene silencing. Methods Mol Biol. 236:287-294. Abstract
Bilgin DD, Liu Y, Schiff M, Dinesh-Kumar SP. (2003) P58IPK, a plant ortholog of double-stranded RNA-dependent protein kinase PKR inhibitor, functions in viral pathogenesis. Dev Cell. 4:651-661. Abstract
Feng S, Ma L, Wang X, Xie D, Dinesh-Kumar SP, Wei N, Deng XW. (2003) The COP9 signalosome interacts physically with SCF COI1 and modulates jasmonate responses. Plant Cell. 15:1083-1094.
Marathe R, Dinesh-Kumar SP. (2003) Plant defense: one post, multiple guards?! Mol Cell. 11:284-286. Abstract
Marathe R, Dinesh-Kumar SP. (2003) Plant defense: one post, multiple guards?! Mol Cell. 11:284-286. [Abstract]
Takahashi H, Miller J, Nozaki Y, Takeda M, Shah J, Hase S, Ikegami M, Ehara Y, Dinesh-Kumar SP. (2002) RCY1, an Arabidopsis thaliana RPP8/HRT family resistance gene, conferring resistance to cucumber mosaic virus requires salicylic acid, ethylene and a novel signal transduction mechanism. Plant J. 32:655-667. Abstract
Marathe, R., Anandalakshmi, R., Liu, Y., and Dinesh-Kumar, S.P. (2002) The tobacco mosaic virus resistance gene, N. Molecular Plant Pathology 3:167-172.
Liu Y, Schiff M, Dinesh-Kumar SP. (2002) Virus-induced gene silencing in tomato. Plant J. 31:777-686. Abstract
Liu Y, Schiff M, Serino G, Deng XW, Dinesh-Kumar SP. (2002) Role of SCF ubiquitin-ligase and the COP9 signalosome in the N gene-mediated resistance response to Tobacco mosaic virus. Plant Cell. 14:1483-1496. Abstract
Liu Y, Schiff M, Marathe R, Dinesh-Kumar SP. (2002) Tobacco Rar1, EDS1 and NPR1/NIM1 like genes are required for N-mediated resistance to tobacco mosaic virus. Plant J. 30:415-429. Abstract
Dinesh-Kumar SP, Tham WH, Baker BJ. (2002) Structure-function analysis of the tobacco mosaic virus resistance gene N. Proc Natl Acad Sci 97:14789-14794. Abstract

Book Chapters

Burch-Smith, T., and Dinesh-Kumar, S.P. (2007) Driving Innate Immunity: ‘R’ we there yet? Biology of Plant-Microbe Interactions Vol. 6 (in press).
Padmanabhan, M.S. and Dinesh-Kumar, S.P. (2007) Virus induced gene silencing. Encyclopedia of Virology. (in press).
*Miller, J., *Burch-Smith, T., (*contributed equally) and Dinesh-Kumar, S.P. (2006) Viral Resistance in Plants: Natural and Engineered. Handbook of Plant Virology Ed. Jawaid A. Khan and Jeanne Dijkstra, The Haworth Press, Inc. NY. Pages 221-234.
Caplan, J., and Dinesh-Kumar, S.P. (2006) Recognition and signal transduction associated with R gene-mediated resistance. Natural Resistance Mechanisms of Plants to Viruses Ed. G. Loebenstein and J. P. Carr. Kluwer Academic Publishers, Netherlands . pages 73-98.
Seay, M., Dinesh-Kumar, S.P., and Levine, B. (2005) Digesting oneself and digesting microbes: autophagy as a host response to viral infection. Modulation of host gene expression and of innate immunity by viruses Ed. P. Palese. Springer, Life Sciences, Biomedical. 245-279.
Dinesh-Kumar, S.P., Marathe, R., and Anandalakshim, R. (2004) Virus induced gene silencing. “ Encyclopedia of Plant and Crop Science ” Ed. Robert M. Goodman, Marcel Dekker, Inc. NY. DOI/101081EEPCS120010638; pp 1276-1279
*Burch-Smith, T., *Miller, J., (*contributed equally) and Dinesh-Kumar, S.P. (2003) PTGS Approaches to Large-Scale Functional Genomics in Plants. RNAi: A guide to gene silencing Ed. Gregory Hannon, Cold Spring Harbor Laboratory press, NY, pp 243-263.
Whitham , S.A. , and Dinesh-Kumar, S.P. (2002) Signaling in plant-virus interactions. Plant Signal Transduction: Frontiers in Molecular Biology Ed. Dierk Scheel and Claus Wasternack, Oxford University Press. 38:226-249. *Book reviewed in (2002) Cell 111: 455-456.

Before Yale

Paul, CP., Barry, JK., Dinesh-Kumar, SP., Brault, V., and Miller, WA. (2001) A sequence required for -1 ribosomal frameshifting located four kilobases downstream of the frameshift site. Journal of Molecular Biology, 310:987-999. Abstract
Dinesh-Kumar, SP. and Baker, B. (2000). Alternatively spliced N resistance gene transcripts: Their possible role in tobacco mosaic virus resistance. Proceedings of the National Academy of Science. 97:1908-1913. Abstract
Erickson, FL, Dinesh-Kumar, SP, Holzberg, S, Ustach, CV, Dutton, M, Handley, V, Corr, C, and Baker, B. (1999). Interactions between tobacco mosaic virus and the tobacco N gene. Philosophical Transactions Royal Society of London, Biological Sciences, 354:653-658. Abstract
Koev, G, Mohan, BR, Dinesh-Kumar, SP, Torbert, KA, Somers, DA, and Miller, WA. (1999). Extreme reduction of disease in oats transformed with the 5' half of the barley yellow dwarf virus-PAV genome. Phytopathology, 88:1013-1019.
Baker, B, Zambryski, P, Staskawicz, B, and Dinesh-Kumar, SP. (1997). Signaling in plant-microbe interactions. Science 276:726-733. Abstract
Brown, CM, Dinesh-Kumar, SP, and Miller, WA. (1996). Local and distant sequences are required for efficient readthrough of the barley yellow dwarf virus PAV coat protein gene stop codon. Journal of Virology, 70:5884-5892. Abstract
Chay, CA, Gunasinge, UB, Dinesh-Kumar, SP, Miller, WA, Gray, SM. (1996). Aphid transmission and systemic plant infection determinants of barley yellow dwarf luteovirus-PAV are contained in the coat protein readthrough domain and 17-kDa protein respectively. Virology 219:57-65. Abstract
Dinesh-Kumar, S.P, Whitham, S, Choi, D, Hehl R, Corr, C, and Baker, B. (1995). Transposon tagging of tobacco mosaic virus resistance gene N:its possible role in the TMV-N-mediated signal transduction pathway. Proceedings of the National Academy of Science. 92:4175-80. Abstract
Thatiparthi, VR, Dinesh-Kumar, SP, Peterson, PA. (1995). Permanent fixation of a transposable element insert in the A2 gene of maize (Zea mays L.) Journal of Heredity, 86:167-71. Abstract
Mohan, BR, Dinesh-Kumar, SP, Miller, WA. (1995). Genes and cis-acting sequences involved in replication of barley yellow dwarf virus-PAV RNA. Virology 212:186-95. Abstract
Miller, WA, Dinesh-Kumar, SP, and Paul, CP. (1995). Luteovirus gene expression. CRC Reviews in Plant Science 4:179-211.
Silver, SL, Rasochova, L, Dinesh-Kumar, SP, and Miller, WA. (1995). Self cleavage and replication of barley yellow dwarf virus satellite RNA. In "Biotechnology and Plant Protection: Viral Pathogenesis and Disease Resistance. Proceedings of the Fifth International Symposium, 19-21 October 1992. (Bills, D.D. and Kung, S.-D. eds) World Scientific Publishing., Singapore pp. 231-241.
Whitham, S, Dinesh-Kumar, SP, Choi, D, Hehl, R, Corr, C, and Baker, B. (1994). The product of the tobacco mosaic virus resistance gene N: Similarity to Toll and the interleukin-1 receptor. Cell 78: 1101-1115. Abstract
Baker, B, Dinesh-Kumar, SP, Choi, D, Hehl, R, Corr, C, Whitham, S. (1994). Isolation of the tobacco mosaic virus resistance gene N. Advances in Molecular Genetics of Plant-Microbe Interactions, Vol. 3. (M. J. Daniels, J. A. Downie and A. E. Osbourn eds.,) pp 297-302.
Silver, SL, Rasochova, L, Dinesh-Kumar, SP, and Miller, WA. (1994). Replication of barley yellow dwarf virus satellite RNA transcripts in Oat protoplasts. Virology 198:331-335. Abstract
Dinesh-Kumar, SP, and Miller, WA. (1993). Control of start codon choice on a plant viral RNA encoding overlapping genes. Plant Cell 5: 679-692. Abstract
Di, R, Dinesh-Kumar, SP, and Miller, WA. (1993). Translational frameshifting by barley yellow dwarf virus RNA (PAV serotype) in Escherichia coli and in eukaryotic cell-free extracts. Molecular Plant Microbe Interactions 6:444-452. Abstract
Dinesh-Kumar, SP, Brault, V, and Miller, WA. (1992). Precise mapping and in vitro translation of a trifunctional subgenomic RNA of barley yellow dwarf virus. Virology 187: 711-722. Abstract
Dinesh-Kumar, SP, Sashidhar, VR, Ravikumar, RL, Seetharam, A, and Gowda, BTS. (1992). Identification of true genetic dwarfing sources in foxtail millet (Setaria italica). Euphytica 60:207-212.
Ravikumar, RL., Dinesh-Kumar, SP., and Seetharam, A. (1991). Association of seed color with seed protein, phenol, tannin and blast susceptibility in finger millet (Eleusine coracana). SABRAO J. 23:91-94.
Dinesh-Kumar, SP., Sashidhar, VR., Prasad, TG., Udaya Kumar, M., and Seetharam, A. (1987). Solute accumulation, solute potential, germinability and seedling vigor of seeds of finger millet (Eleusine coracana) raised under rain-fed conditions and under irrigation. Plant, Cell & Environment 10:661-665.