Brian Dilkes WikiCV

Brian Dilkes Department of Biochemistry, Purdue University [1] West Lafayette, IN eMail: bdilkes tohellwithspammers purdue.edu Brian Dilkes OWW project page

EDUCATION

2003 Ph. D., University of Arizona, Department of Plant Sciences

1993 B. L. A., Oberlin College, Biology

RESEARCH EXPERIENCE

2015- Associate Professor, Department of Biochemistry, Purdue University

2009-2015 Assistant Professor, Department of Horticulture, Purdue University

2006-2008 Project Scientist University of California Davis, Prof. Luca Comai

2003-2005 USDA postdoctoral fellow, Biology Department, University of Washington, Prof. Luca Comai

1997-2003 Graduate research assistant, University of Arizona, Department of Plant Sciences, Prof. Brian Larkins

1992-1996 Undergraduate researcher, technician and graduate research assistant, University of Arizona, Department of Plant Sciences Prof. Ken Feldmann

AWARDS

Bill and Melinda Gates Foundation OPP1052924 “Developing a Functional Gene Discovery Platform for Sorghum Improvement” 2012-2015 Role: Co-PI

AFRI Competitive Grant No. 2012-67012-19817 “Maize endosperm development is affected by small RNA in interploidy crosses” 2012-2014 Role: Mentor

USDA Graduate Research Fellowship “Genetic and genomic investigation of water use efficiency in Zea mays” 2010-2015 supporting two students (R. Robinson 2010-2012, and E. Svedin 2012-2015) Role: Joint with M.V. Mickelbart

Ag Alumni Seed, Inc. “Maize genetic research” 2010 Role: PI

NIH R01 GM076103-01A1 “Dosage-dependent regulation in hybridization” 2006-2011 Role: Senior Personnel

NSF Plant Genome Research Project grant DBI-0077774/DBI-0501712 “Functional genomics of plant polyploids” 2005-2010 Role: Project Manager

USDA-CREES-NRI 2003-35300-13248 “Functional genomic analysis of plant responses to autopolyploidy” 2003-2005 Role: Project Director/PI

REFEREED PUBLICATIONS

1. Strauch R, Svedin E, Dilkes BP, Chapple C, Li X 2015 Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana. Proceedings of the National Academy of Sciences U. S. A. 112:11726-11731
2. Chao D-Y, Baraniecka P, Danku J, Koprivova A, Lahner B, Luo H, Yakubova E, Dilkes B, Kopriva S, Salt DE 2014 Variation in sulfur and selenium accumulation is controlled by naturally occurring isoforms of the key sulfur assimilation enzyme APR2 across the Arabidopsis thaliana species range. Plant Physiology 166(3):1593-1608
3. Maharjan P, Dilkes BP, Shozo, F, Pencik A, Ljung K, Burow M, Halkier, B and Choe S. 2014 Arabidopsis gulliver1/superroot2-7 identifies a metabolic basis for auxin and brassinosteroid synergy. The Plant Journal 80:797-808
4. Buescher E, Moon JH, Hake S and Dilkes BP* 2014 Identification of novel genes regulating meristem maintenance and leaf angle in maize as epistatic Liguleless-narrow suppressors. G3, 114.014183
5. Li X, Huaping M, Svedin E, Atwell S, and Dilkes BP*, Chapple C* 2014 Exploiting Natural Variation of Secondary Metabolism Identifies a Gene Controlling the Glycosylation Diversity of Dihydroxybenzoic Acids in Arabidopsis thaliana. Genetics198:1267-1276
6. Henry IM, BP Dilkes and A Tyagi, B Christensen and L Comai 2014 The BOY NAMED SUE quantitative trait locus confers increased meiotic stability to an adapted natural allopolyploid of Arabidopsis. The Plant Cell 26:181-194
7. Cheon JN, Fujioka S, Dilkes BP*, Choe S* 2013 Brassinosteroids regulate plant growth through distinct signaling pathways in Selaginella and Arabidopsis. Plos One 8(12) e81938
8. Lin D, Dilkes B Luo H, Douglas A, Yakubova E, Lahner B and Salt DE 2013 Polyploids exhibit higher potassium uptake and salinity tolerance in Arabidopsis. Science 341 (6146), 658-659
9. Krothapalli K1, Buescher E1, Li X, Brown D, Chapple C, Dilkes BP* and Tuinstra M* 2013 Dhurrinase2 is required for cyanide release from Sorghum bicolor. In press at Genetics.
10. Burkart Waco D, Josefsson C, Dilkes BP and Comai L 2013 Early disruption of maternal-zygotic interaction and activation of defense responses in Arabidopsis interspecific incompatibility. Plant Physiology doi: http:/​/​dx.​doi.​org/​10.​1105/​tpc.​112.​108258.
11. Hollister JD, Arnold BJ, Svedin E, Xue KS, Dilkes BP, Bomblies K 2012 Genetic Adaptation Associated with Genome-Doubling in Autotetraploid Arabidopsis arenosa. PLoS Genet 8(12): e1003093. doi:10.1371/journal.pgen.1003093
12. Albertin CB et al., 2012 Cephalopod Genomics: A plan of strategies and organization. Standards in Genomic Sciences 7(1)
13. Dilkes BP* and I Baxter* 2012 Elemental profiles reflect plant adaptations to the environment. Science 336 (6089): 1661-1663
14. Burkart-Waco D, Josefsson C, Dilkes BP, Kozloff N, Torjek O, Meyer R, Altmann T and Comai L 2011 Hybrid incompatibility in Arabidopsis is determined by a multi-locus genetic network.Plant Physiology 158(2):801-12.
15. Correa R, Stanga J, Larget B, Roznowski A, Shu G, Dilkes B, Baum DA. 2011 An assessment of transgenomics as a tool for identifying genes involved in the evolutionary differentiation of closely related plant species. New Phytologist 193(2):494-503. doi: 10.1111/j.1469-8137.2011.03949.x.
16. Chang PL, Dilkes BP, McMahon M, Comai L and Nuzhdin SV. Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners. Genome Biology 2010, 11:R125
17. Henry IM, Dilkes BP, Miller ES, Burkart-Waco D, Comai L. 2010 Phenotypic Consequences of Aneuploidy in Arabidopsis thaliana. Genetics. 186(4):1231-1245
18. Pignatta D, Dilkes BP, Yoo, SY, Henry IM Madlung, A, Doerge, RW, Chen, JZ, Comai L. 2010 Differential sensitivity of the Arabidopsis thaliana transcriptome and enhancers to the effects of genome doubling. New Phytologist 186(1):194-206
19. Henry IM, Dilkes BP, Tyagi A, Lin H-S, and Comai L 2009 Dosage and parent-of-origin effects shaping aneuploid swarms in A. thaliana. Heredity doi: 10.1038/hdy.2009.81
20. Walia H, Josefsson C. Dilkes BP, Kirkbride R, Harada J and Comai L. 2009 Dosage-dependent deregulation of an AGAMOUS LIKE GENES cluster contributes to interspecific incompatibility. Current Biology 19(13):1128-32
21. Dilkes BP, Spielman M, Wiezbauer R, Burkart-Waco D, Watson B, Scott R, and Comai L 2008 The maternally-expressed WRKY transcription factor TTG2 controls lethality in interploidy crosses of Arabidopsis. PLoS Biol 6(12): e308 doi:10.1371/journal.pbio.0060308
22. Pignatta D, Dilkes BP, Wroblewski T, Michelmore RW, Comai L 2008 Transgene-induced gene silencing is not affected by a change in ploidy level. PLoS ONE 3(8): e3061. doi:10.1371/journal.pone.0003061
23. Henry IM, Dilkes BP, Comai L 2007 Genetic basis for dosage sensitivity in Arabidopsis thaliana. PLoS Genet 3(4): e70 doi:10.1371/journal.pgen.0030070
24. Henry IM, Dilkes BP, Comai L 2006 Molecular karyotyping and aneuploidy detection in A. thaliana using quantitative fluorescent PCR. Plant Journal, 48:307-319
25. Josefsson C, Dilkes B, Comai L 2006 Parent-dependent loss of gene silencing during interspecies hybridization. Current Biology 16:1322-1328
26. Coelho CM, Dante RA, Sabelli PA, Sun Y, Dilkes BP, Gordon-Kamm WJ Larkins BA 2005 Cyclin-dependent kinase inhibitors in maize endosperm and their potential role in endoreduplication. Plant Physiology 138: 2323-36
27. Henry IM, Dilkes BP, Young K, Watson B, Wu H, Comai L 2005 Aneuploidy and genetic variation in the Arabidopsis thaliana triploid bridge. Genetics 170: 1979-88
28. Dilkes BP, Comai L 2004 A differential dosage hypothesis for parental effects in seed development. Plant Cell 16:3174-80
29. Hunter BG, Beatty MK, Singletary GW, Hamaker BR, Dilkes BP, Larkins BA, and Jung R 2002 Maize opaque endosperm mutations create extensive changes in patterns of gene expression. Plant Cell 14: 14:2591-2612
30. Gordon-Kamm WJ, Dilkes BP, Lowe KS, Hoerster G, Sun X, Ross M, Church L, Bunde C, Farrell J, Hill P, Maddock S, Snyder J, Li X, Woo Y, Bidney D and Larkins BA 2002 Stimulation of the cell cycle and maize transformation by disruption of the plant retinoblastoma pathway. Proc. Natl. Acad. Sci. U S A 99: 11975-11980
31. Dilkes BP, Dante RD, Coelho C, Larkins BA. 2002 Genetic analyses of endoreduplication in Zea mays endosperm: evidence of sporophytic and zygotic maternal control. Genetics 160: 1163-117
32. Larkins BA, Dilkes BP, Dante RA, Coelho CM, Woo Y, Liu Y 2001 Investigating the hows and whys of DNA endoreduplication. J. Exp. Bot. 52: 183-92
33. Sun Y, Dilkes BP, Zhang C, Dante RA, Carneiro NP, Lowe KS, Jung R, Gordon-Kamm WJ, Larkins BA 1999 Characterization of maize (Zea mays L.) Wee1 and its activity in developing endosperm. Proc. Natl. Acad. Sci. U S A 96: 4180-5
34. Choe S, Dilkes BP, Gregory BD, Ross AS, Yuan H, Noguchi T, Fujioka S, Takatsuto S, Tanaka A, Yoshida S, Tax FE, Feldmann KA 1999 The Arabidopsis dwarf1 mutant is defective in the conversion of 24-methylenecholesterol to campesterol in brassinosteroid biosynthesis. Plant Physiol. 119: 897-907
35. Choe S, Dilkes BP, Fujioka S, Takatsuto S, Sakurai A, Feldmann KA 1998 The DWF4 gene of Arabidopsis encodes a cytochrome P450 that mediates multiple 22alpha-hydroxylation steps in brassinosteroid biosynthesis. Plant Cell 10: 231-43

RELEVANT TECHNICAL PUBLICATIONS

1. Gordon-Kamm WJ, Lowe KS, Gregory CA, Hoerster GJ, Larkins BA, Dilkes B, Burnett R 2004 Methods of using viral replicase polynucleotides and polypeptides. U.S. Patent 6,770,800
2. Sun Y, Dilkes B, Larkins BA, Lowe KS, Gordon-Kamm WJ, Dante RA 2004 Cell cycle nucleic acids, polypeptides and uses thereof. U.S. Patent 6,777,590
3. Gordon-Kamm WJ, Lowe KS Bailey MA, Gregory CA, Hoerster GJ, Larkins BA, Dilkes B, Burnett R, Woo, Y 2002 Methods of using viral replicase polynucleotides and polypeptides. U.S. Patent 6,452,070
4. Gordon-Kamm WJ, Lowe KS Bailey MA, Gregory CA, Hoerster GJ, Larkins BA, Dilkes B, Burnett R, Woo, Y 2001 Methods of using viral replicase polynucleotides and polypeptides. U.S. Patent 6,284,947
5. Dilkes, BP and Larkins BA 1999 "Transgenic plants: where is this technology leading us" in Biowork II (A. Borem, M.P. Giudice and N.S. Sakiyama, eds.), Federal University of Vicosa, Vicosa, Brasil, 213-240
6. Dilkes BP, , Feldmann KA 1998 Cloning genes from T-DNA tagged mutants. Methods Mol. Biol. 82: 339-51
7. Schulz B, Bennett MJ, Dilkes BP, and Feldmann KA 1995 “T-DNA tagging in Arabidopsis thaliana: cloning by gene disruption” in Plant Molecular Biology Manual (Gelvin, S, ed.) Kluwer Academic Publishers, The Netherlands pp. K3:1-17

CURRENT TEACHING ASSIGNMENTS

Undergraduate level

Biochemistry 290 - This is an introduction to experimental design and research methods.

Graduate level

Agronomy 530 - This is an advanced genetics course available to students interested in deepening their understanding of modern genetics and forging links between genomics, population genetics, classical genetics, and development. This is a primary literature-driven course. There is no barrel of monkeys more fun than this course.