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- Vasyl Tkach
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Office Tel: 701.777.4673
Starcher Hall Room 217
B.Sc. (Honors), 1996, Biological Sciences, University of Windsor
Ph.D., 2002, Biochemistry & Molecular Biology, University of British Columbia
- Post-doctoral Research Associate, Genome Canada , Michael Smith Laboratories, UBC, 2005 - 2007
- Post-doctoral Research Associate, Genome Canada , Dept. of Forest Sciences, UBC, 2002 - 2005
- Research Assistant, Dept. of Biological Sciences, U of W, 1993 -1996
- University of North Dakota New Faculty Scholar Award, 2008
- Arthur Neish Young Investigator, Phytochemistry Society of North America, 2006
- University Graduate Fellowship, UBC, 2000 - 2001
- Izaak Walton Killam Memorial Pre-doctoral Fellowship, 1998 - 2000
- Natural Sciences and Engineering Research Council of Canada Scholarship, 1996-2000
- Board of Governor's Medal in Biological Sciences, U of W, 1996
The genus Populus includes poplars, cottonwoods, and aspens, which are keystone species in temperate zone forest ecosystems in the Northern Hemisphere. Poplar is an ecologically dominant and environmentally important species for wildlife habitat (e.g., fire-following aspens), stream stabilization (e.g., riparian cottonwoods) and filtration of agricultural runoff. Poplars are also intensively cultivated in plantation forestry for the production of wood, pulp, and paper. Due to their rapid growth rates, several species in this genus have great economic potential for applications in carbon sequestration, phytoremediation, and as a feedstock for biofuel production. Poplar is a powerful model system for the study of growth, development, and adaptation in woody perennial plants, including the biology of secondary xylem formation, dormancy, adaptation to the environment, and biotic interactions. Poplar is well suited for laboratory studies due to its rapid growth in diverse environmental conditions, diploid inheritance, modest genome size (500 Mb), facile vegetative propagation and genetic transformation, propagation in cell culture, and relatively short reproduction cycle of 7-10 years. Recently, extensive genomic resources have been developed including dense genetic and physical maps, whole-genome microarrays, and a completed 7.5x genome sequence. With its ecological importance, suitability for experimental manipulation, and availability of genomic tools, poplar is a preferred model for studying the response to insect herbivory in long-lived woody perennials.
Forest insect pests pose a challenge to the sustainability of both natural and planted forests. The risk of forest insect pest epidemics, which cannot be addressed with short-term crop rotation or pesticide application, is increasing with the introduction of exotic pest species and with global climate change. The larvae of several insect herbivores [forest tent caterpillar (Malacosoma disstria), gypsy moth (Lymantria dispar), aspen blotch leafminer (Phyllonorycter tremuloidiella), large aspen tortrix (Choristoneura conflictana)] can cause extensive defoliation to poplar stands, particularly quaking aspen (Populus tremuloides). During outbreaks, trees covering millions of hectares are defoliated, with as many as 20,000 insects/tree. Defoliated trees have reduced photosynthetic capacity and produce less wood, thus reducing the productivity of poplar tree plantations. Although defoliation normally does not kill the tree, repeated attacks increase the incidence of fungal disease and infestation by other insects.
As sedentary organisms, trees cannot avoid or escape biotic (e.g., herbivorous insects and opportunistic pathogens) and abiotic (e.g., drought and temperature) stress in their local environment. Instead, trees have evolved an enormous diversity of anatomical structures and chemical defenses to protect themselves. Trees are a unique biological system in which to study plant-insect interactions as they are long-lived perennial organisms that must be able to mobilize multiple, overlapping defense mechanisms, facilitated by a highly plastic genome, in order to adapt to the changing environment during the lifespan of an individual tree (about 100 years for aspen). The enormous size of trees also allows for the study of spatial considerations in plant-insect interactions.
Research projects in my lab focus on understanding interactions between forest trees and insect pests and consist of laboratory, greenhouse and field work. A broad range of techniques are employed in the lab including microarray transcript profiling, quantitative real-time PCR, biochemical assays for protein characterization, RNA interference to modulate gene expression, and bioassays for insect performance. Students will have an opportunity to conduct research that spans multiple disciplines including plant genomics, molecular biology, biochemistry, forest tree biology and ecology.
Peer-Reviewed Scientific Publications
37. *Philippe RN, *Ralph SG, Külheim C, Jancsik SI and Bohlmann J (2009) Poplar defense against insects: genome analysis, full-length cDNA cloning, and transcriptome and protein analysis of the poplar Kunitz-type protease inhibitor family. New Phytologist 184:865-884.
36. Ralph SG (2009) Studying Populus defenses against insect herbivores in the post-genomic era. Critical Reviews in Plant Sciences 28:335-345; invited paper.
35. Lippert DN, Ralph SG, Phillips M, White R, Smith D, Hardie D, Gershenzon J, Ritland K, Borchers CH and Bohlmann J (2009) Quantitative iTRAQ proteome and comparative transcriptome analysis of elicitor-induced Norway spruce (Picea abies) cells reveals elements of calcium signaling in the early conifer defense response. Proteomics 9:350-367.
34. Ralph SG, Chun HJE, Kolosova N, Cooper D, Oddy C, Ritland CE, Kirkpatrick R, Moore R, Barber S, Holt RA, Jones SJM, Marra MA, Douglas CJ, Ritland K and Bohlmann J (2008) A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis). BMC Genomics 9:484 (17 pages).
33. de Azevedo Souza C, Barbazuk B, Ralph SG, Bohlmann J, Hamberger B and Douglas CJ (2008) Genome-wide analysis of a land plant-specific acyl:coenzymeA synthetase (ACS) gene family in Arabidopsis, poplar, rice and Physcomitrella. New Phytologist 179: 987-1003.
32. *Ralph SG, *Chun HJE, Cooper D, Kirkpatrick R, Kolosova N, Gunter L, Tuskan GA, Douglas CJ, Holt RA, Jones SJM, Marra MA and Bohlmann J (2008) Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding. BMC Genomics 9:57 (18 pages).
31. Holliday JA, Ralph SG, White R, Bohlmann J and Aitken SN (2008) Global monitoring of autumn gene expression within and among phenotypically divergent populations of Sitka spruce (Picea sitchensis). New Phytologist 178: 103-122.
30. Phillips MA, Walter MH, Ralph SG, Dabrowska P, Luck K, Urós EM, Boland W, Strack D, Rodriquez-Concepción M, Bohlmann J and Gershenzon J (2007) Functional identification and differential expression of 1-deoxy-D-xylulose 5-phosphate synthase in induced terpenoid resin formation of Norway spruce (Picea abies). Plant Molecular Biology 65: 243-257.
29. Ralph SG, Jancsik S and Bohlmann J (2007) Dirigent proteins in conifer defense II: Extended gene discovery, phylogeny, and constitutive and stress-responsive gene expression analysis in spruce (Picea spp.). Phytochemistry 68: 1974-1990; invited paper.
28. *Miranda M, *Ralph SG, Mellway R, White R, Heath MC, Bohlmann J and Constabel CP (2007) The transcriptional response of hybrid poplar (Populus trichocarpa x P. deltoides) to infection by Melampsora medusae leaf rust involves induction of flavonoid pathway genes leading to the accumulation of proanthocyanidins. Molecular Plant-Microbe Interactions 20: 816-831.
27. *Ralph SG, *Hudgins JW, Jancsik S, Franceschi VR and Bohlmann J (2007) Aminocyclopropane carboxylic acid synthase is a regulated step in ethylene-dependent induced conifer defense: Full-length cDNA cloning of a multigene family, differential constitutive, and wound- and insect-induced expression, and cellular and subcellular localization in spruce and Douglas fir. Plant Physiology 143: 410-424.
26. DiGuistini S, Ralph SG, Lim YW, Holt R, Jones S, Bohlmann J and Breuil C (2007) Generation and annotation of lodgepole pine and oleoresin-induced expressed sequences from the blue-stain fungus Ophiostoma clavigerum, a mountain pine beetle-associated pathogen. FEMS Microbiology Letters 267: 151-158.
25. Friedmann M, Ralph SG, Aeschliman D, Zhuang J, Ritland K, Ellis BE, Bohlmann J and Douglas CJ (2007) Microarray gene expression profiling of developmental transitions in Sitka spruce (Picea sitchensis) apical shoots. Journal of Experimental Botany 58: 593-614.
24. Lippert D, Chowrira S, Ralph SG, Zhuang J, Aeschliman D, Ritland C, Ritland K and Bohlmann J (2007) Conifer defense against insects: Proteome analysis of Sitka spruce (Picea sitchensis) bark induced by mechanical wounding or feeding by white pine weevils (Pissodes strobi). Proteomics 7: 248-270.
23. Bérubé Y, Zhuang J, Rungis D, Ralph S, Bohlmann J and Ritland K (2007) Characterization of EST-SSRs in loblolly pine and spruce. Tree Genetics and Genomes 3: 251-259.
22. *Hudgins JW, *Ralph SG, Franceschi VR and Bohlmann J (2006) Ethylene in induced conifer defense: cDNA cloning, protein expression, and cellular and subcellular localization of 1-aminocyclopropane-1-carboxylate oxidase in resin duct and phloem parenchyma cells. Planta 224: 865-877.
21. Ralph SG, Yueh H, Friedmann M, Aeschliman D, Zeznik JA, Nelson CC, Butterfield YSN, Kirkpatrick R, Liu J, Jones SJM, Marra MA, Douglas CJ, Ritland K and Bohlmann J (2006) Conifer defense against insects: Microarray gene expression profiling of Sitka spruce (Picea sitchensis) induced by mechanical wounding or feeding by spruce budworms (Choristoneura occidentalis) or white pine weevils (Pissodes strobi) reveals large-scale changes of the host transcriptome. Plant, Cell and Environment 29: 1545-1570.
20. Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Déjardin A, dePamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjärvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leplé J-C, Locascio P, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouzé P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai C-J, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y and Rokhsar D (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604.
19. Ritland K, Ralph S, Lippert D, Rungis D and Bohlmann J (2006) New directions in conifer genomics. In Williams C (ed): Landscapes, Genomics and Transgenic Conifer Forests. New York : Kluwer-Springer Press, pp 75-84.
18. Ralph S, Oddy C, Cooper D, Yueh H, Jancsik S, Kolosova N, Philippe RN, Aeschliman D, White R, Huber D, Ritland CE, Benoit F, Rigby T, Nantel A, Butterfield YSN, Kirkpatrick R, Chun E, Liu J, Palmquist D, Wynhoven B, Stott J, Yang G, Barber S, Holt RA, Siddiqui A, Jones SJM, Marra MA, Ellis BE, Douglas CJ, Ritland K and Bohlmann J (2006) Genomics of hybrid poplar (Populus trichocarpa x deltoides) interacting with forest tent caterpillars (Malacosoma disstria): Normalized and full-length cDNA libraries, expressed sequence tags (ESTs), and a cDNA microarray for the study of insect-induced defenses in poplar. Molecular Ecology 15: 1275-1297; invited paper.
17. *Ralph S, *Park JY, Bohlmann J and Mansfield SD (2006) Dirigent proteins in conifer defense: gene discovery, phylogeny and differential wound- and insect-induced expression of a family of DIR and DIR-like genes in spruce (Picea spp.). Plant Molecular Biology 60: 21-40.
16. Lippert D, Zhuang J, Ralph S, Ellis DE, Gilbert M, Olafson R, Ritland K, Ellis B, Douglas CJ and Bohlmann J (2005) Proteome analysis of early somatic embryogenesis in Picea glauca. Proteomics 5: 461-473.
15. Miller B, Madilao LL, Ralph S and Bohlmann J (2005) Insect-induced conifer defense. White pine weevil and methyl jasmonate induce traumatic resinosis, de novo formed volatile emissions, and accumulation of terpenoid synthase and putative octadecanoid pathway transcripts in Sitka spruce. Plant Physiology 137: 369-382.
14. Park JY, Ralph S, Bohlmann J and Mansfield SD (2005) The multigene dirigent family of Sitka Spruce (Picea sitchensis): differential gene expression in response to wounding. Proceedings of the 13th International Symposium on Wood and Pulping Chemistry (ISWPC), Auckland, New Zealand. Vol. 2: 181-188.
13. Huber DP, Ralph S and Bohlmann J (2004) Genomic hardwiring and phenotypic plasticity of terpenoid-based defenses in conifers. Journal of Chemical Ecology 30: 2399-2418.
12. Rungis D, Bérubé Y, Zhuang J, Ralph S, Ritland CE, Ellis BE, Douglas C, Bohlmann J and Ritland K (2004) Robust simple sequence repeat markers for spruce (Picea spp.) from expressed sequence tags . Theoretical & Applied Genetics 109: 1283-1294.
11. Kolosova N, Miller B, Ralph S, Ellis BE, Douglas C, Ritland K and Bohlmann J (2004) Isolation of high-quality RNA from gymnosperm and angiosperm trees. Biotechniques 36: 821-824.
10. Sheps JA, Ralph S, Zhao Z, Baillie DL and Ling V (2004) The ABC transporter gene family of Caenorhabditis elegans has implications for the evolutionary dynamics of multidrug resistance in eukaryotes. Genome Biology 5: R15.1-R15.17.
9. Ralph SG (2002) mRNA expression profiling of the ATP-Binding Cassette transporter family. Ph.D. dissertation, Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada, pp 1-223.
8. Guan Y, Ralph S and Hogge DE (2002) Polyclonal normal hematopoietic progenitors in patients with acute myeloid leukemia. Experimental Hematology 30: 721-728.
7. Ralph S and Petras M (1998) Caged amphibian tadpoles and in situ genotoxicity monitoring of aquatic environments with the alkaline single cell gel electrophoresis (comet) assay. Mutation Research 413: 235-250.
6. Ralph S and Petras M (1998) Comparison of sensitivity to methyl methanesulphonate among tadpole developmental stages using the alkaline single-cell gel electrophoresis (comet) assay. Environmental & Molecular Mutagenesis 31: 374-382.
5. Clements C, Ralph S and Petras M (1997) Genotoxicity of select herbicides in Rana catesbeiana tadpoles using the alkaline single cell gel DNA electrophoresis (comet) assay. Environmental & Molecular Mutagenesis 29: 277-288.
4. Ralph S and Petras M (1997) Genotoxicity monitoring of small bodies of water using two species of tadpoles and the alkaline single cell gel (comet) assay. Environmental & Molecular Mutagenesis 29: 418-430.
3. Ralph S, Petras M, Pandrangi R and Vrzoc M (1996) Alkaline single cell gel (comet) assay and genotoxicity monitoring using two species of tadpoles. Environmental & Molecular Mutagenesis 28: 112-120.
2. Petras M, Vrzoc M, Pandrangi R, Ralph S and Perry K (1995) Biological monitoring of environmental genotoxicity in southwestern Ontario. In Butterworth FM, Corkum LD, Guzman-Rincon J (eds.): Biomonitors and Biomarkers as Indicators of Environmental Change. New York : Plenum Press, pp 115-137.
1. Pandrangi R, Petras M, Ralph S and Vrzoc M (1995) Alkaline single cell gel (comet) assay and genotoxicity monitoring using bullheads and carp. Environmental & Molecular Mutagenesis 26: 345-356.
*contributed equally as first authors