Contact Information

• Riverbend Research Bldg. South
• 220 Riverbend Road
• Athens, Georgia
• Phone:706.542.1710
• FAX:706.542.8356
• 
  

Education

Ph.D.Purdue University, Department of Biochemistry (Dissertation: Regulation of aromatic amino acid biosynthesis in higher plants: The purification and characterization of DAHP synthases from carrots and spinach) 1986.

B.S. Stanford University, Department of Chemistry, 1980 B.S. Stanford University, Department of Biology, 1980

Area of Specialization

• Biochemistry and molecular biology of plant growth and development
• Wood formation and biodegradation
• Forest tree biotechnology
• Functional genomics in forestry and natural resources

Professional Experience

Professor, Forest Biotechnology, D.B. Warnell School of Forest Resources, University of Georgia, 2006- present

Associate Professor, Forest Biotechnology, D.B. Warnell School of Forestry and Natural Resources, University of Georgia, 2001- present

Adjunct Associate Professor, Department of Biochemistry and Molecular Biology, University of Georgia, 2001- present

Director, The Plant Center, University of Georgia, 2002-2005

Assistant Professor, Forest Biotechnology, D.B. Warnell School of Forestry and Natural Resources, University of Georgia, 1996 - 2001

Associate Research Scientist, Department of Biochemistry and Molecular Biology, University of Georgia, 1990 - 1996

Plant Physiologist (GS-11), Plant Hormone Laboratory, U.S. Department of Agriculture, Beltsville, MD

Courses Taught

• Current Topics in Forest Biotechnology (FORS 8040, 3 hrs, alternate years) This course covers applications of genetic, biochemical, and physiological principles to forest trees; forest products and organisms affecting forests, including in vitro propagation, genetic engineering, genomic mapping, bioprocessing, and biological control of tree pests and pathogens.
• Plant Biotechnology Research Journal Seminar (FORS 8070, 1 hr, every semester) This course involves critical review and discussion of current research reports in journals relating to plant biotechnology.
• Scientific Research in Forest Resources (FORS 8200, 3 hrs, spring semester) A graduate-level course emphasizing the scientific method, standards for good scientific conduct, research proposal writing and reviewing skills. Required for all M.S. students, and strongly recommended for all Ph.D. students.

Ongoing Research Projects

Pine Genomics. Through a large, collaborative effort involving several labs on the UGA campus and across the country, we have led an effort to catalog and made publicly available DNA sequence information for nearly 175,000 expressed sequence tags (ESTs) from loblolly pine. The data, which is available from GenBank, may also be obtained through a public access interface to our local database servers (Pine EST DB). The project has identified more than 30,000 unique genes expressed in pine, and we are using these genes to produce cDNA microarrays that can be used to analyze gene expression changes occurring in conifers during development and in response to environmental stress. This work has been funded by grants from the National Science Foundation, the U.S. Department of Agriculture, and the U.S. Forest Service.

A short video in which Dr. Dean discusses current needs and goals related to the Pine Genome Initiative.

Pine Genome Research - A Status Report

Arabidopsis Multicopper Oxidases (Laccases). The longest continuously running research program in my laboratory (13 years), this project, funded by the U.S. Department of Energy, seeks to identify the physiological function(s) in plants for all gene family members encoding a group of copper-dependent phenoloxidases commonly known as laccases. At different points in time, students working on the project have pursued various approaches -- chemical, biochemical, molecular genetic and classical genetic -- according to their interests to understand these enzymes. Most recently our work has focused on systematically knocking out each of the 17 laccase-like multicopper oxidase (LMCO) genes in Arabidopsis thaliana, and then characterizing the basis for the resulting phenotypes. Recent evidence strongly suggests involvement of one Arabidopsis LMCO gene in the early stages of endodermal development in young root roots, most probably with synthesis of lignin/suberin polymers in the Casparian strip.

Forest Health and Invasive Pests. The expansion of human populations into remote regions of the world coupled with high-speed transport around the globe has greatly increased the risk to both our native and commercial for introductions of insect and pathogen pests. We are using biochemical, molecular and genomic approaches to identify the mechanisms by which the recently introduced European woodwasp, Sirex noctilio, and its obligate fungal associate, Amylostereum areolatum, attack and kill a broad range of conifer species.

Phytoremediation. Plants have great potential as active agents in the clean up of environmental sites contaminated with organic wastes and heavy metals. We are using functional genomic techniques, such transcriptional profiling and DNA microarrays, to study the changes in gene expression that occur when plants encounter these compounds in their environment. Data from these studies should enable us to identify the key metabolic pathways that could be enhanced for the development of plants better suited for use in bioremediation processes. Students working on this project have been supported through the local US EPA laboratory and NNEMS graduate fellowships.

Longleaf Pine Ecosystem Restoration. A new project, we are working in collaboration with the U.S. Forest Service, The Longleaf Alliance, and other groups interested in restoring longleaf habitat to establish a Center for high-throughput development of genetic tools and molecular markers that can be used to analyze and monitor genetic diversity in populations of plants and animals endemic to this unique ecosystem.

Recent Grant Awards

U.S. Department of Agriculture (USDA), "Conifer Translational Genomics Network CAP," $50,000 (subcontract) from UC Davis, PI D.B. Neale, Project total $6 million)

U.S. Department of Energy - Joint Genome Institute (DOE-JGI), Community Sequencing Proposal, "An Expanded EST Resource for Pines and Other Conifers,"

Georgia Traditional Industries Program in Pulp & Paper (TIP3), "Sirex noctilio: Genetic Approaches to Managing a Newly Introduced Insect Pest of North American Pines and Conifers," $102,886

USDA Forest Service, Agenda 2020 Program, "Assessing the Impact of Intensive Forest Management Practices on Wood Formation and Quality at the Level of Gene Expression," October 2005 - September 2008, $369,380

National Science Foundation (NSF), “Knowledge discovery in genomic databases: A PASI on Data Mining Applications for Genomics and Bioinformatics,” Sept 2003 - Aug 2004, $91,380

U.S. Department of Energy (DOE), “Localization and Function of Two Multicopper Oxidases in Arabidopsis thaliana,” Nov 2003 - Oct 2006, $330,000

National Science Foundation, “Transcriptome Responses to Environmental Conditions in Loblolly Pine Roots,” Sept 2002 - Aug 2006, $1,650,000

U.S. Department of Agriculture (IFAFS), “Allele Discovery for Genes Controlling Economic Traits in Loblolly Pine,” Oct 2001 - Sept 2005, $242,448

Selected Meeting Abstracts

Dean, J.F.D. (1997) Forest biology in the age of biotechnology. 5th International Congress of Plant Molecular Biology, September 21-27 1997, Singapore, Abstr. 319

Dean, J.F.D., Cordonnier-Pratt, M-M., Covert, S.F., Merkle, S.M., Pratt, L.H., Gingle, A.R., Lorenz, W.W., Nairn, C.J., and Will, R. (2003) Transcriptome responses to environmental conditions in loblolly pine roots. XIth Plant and Animal Genomes Conference, January 11-15, San Diego, CA, Abstr. P-561

Dean, J.F.D., Lorenz, W.W., Pratt, L.H., Cordonnier-Pratt, M-M. (2003) The response of loblolly pine root ESTs to water stress. Biennial Meeting of the IUFRO Unit on Molecular Biology of Forest Trees, June 7-12, Umeå, Sweden, Abstr. S4.2

Dean, J.F.D., Lorenz, W.W., Pratt, L.H., Cordonnier-Pratt, M-M. (2003) The response of loblolly pine root ESTs to water stress. Proc. 7th International Congress of Plant Molecular Biology, 23-28 June 2003, Barcelona. Abstr. S05-109

Ekman, D.R., Lorenz, W.W., Przybyla, A.E., Wolfe, N.L., McCutcheon, S.C. and Dean, J.F.D. (2004) Transcriptional profiling of Arabidopsis thaliana root responses to munitions, Proc. 4th Annual Meeting of the American Ecological Engineering Society, 9-12 June 2004, Fayetteville, AR. Abstr. 7A

Wang, C-T., and Dean, J.F.D. (2005) Functional analysis of a laccase-like multicopper oxidase (LMCO) in Arabidopsis thaliana. 16th International Conference on Arabidopsis Research, June 15-19, Madison, WI

Dean, J.F.D. (2005) Using functional genomics to dissect drought responses in pine. Biennial Meeting of the IUFRO Unit on Molecular Biology of Forest Trees, November 7-11, Pretoria, South Africa

Yuan, S., Barnes, J.R., Dean, J.F.D. (2006) Ethylene biosynthetic gene responses and compression wood formation in loblolly pine. Plant Physiol. P03003

Nairn, C.J., Wood-Jones, A., Lorenz, W., Dean, J.F.D. (2006) Analysis of candidate genes for wood formation in loblolly pine by quantitative real-time RT PCR. Plant Physiol. P03014

Bordeaux, J.M, Dean, J.F.D. (2007) Screens for Amylostereum areolatum resistance in loblolly pine (Pinus taeda L.) USDA Interagency Research Forum on Invasive Species, January 9-12, 2007, Annapolis, MD

Nairn, C.J., Lennon, D., Wood-Jones, A., Dean, J.F.D. (2007). Carbohydrate-related genes and cell wall biosynthesis in vascular tissues of loblolly pine. North American Forest Biology Workshop, May 20-23, Bloomington, IN

Dean, J.F.D. (2007) Opportunities For Sirex Research In The Genomics Era. International Sirex Symposium, Pretoria, South Africa, 10-11 May 2007

Dean, J.F.D. (2007) When you can't run or hide. Understanding tree responses to abiotic challenge. Biennial Meeting of the IUFRO Unit on Molecular Biology of Forest Trees, June 3-8, Ponta Delgada, Azores

Bordeaux, J.M, Dean, J.F.D. (2007) Phenoloxidase Production by Amylostereum areolatum and its Possible Role in the Sirex noctilio/Pinus taeda (L.) Pathosystem, USDA Interagency Research Forum on Invasive Species, January 8-11, 2008, Annapolis, MD

Dean, J.F.D., Howe, G.T., Jermstad, K., Neale, D.B., Rogers D.L. (2008) The JGI Community Sequencing Project for Conifer ESTs. XVIth Plant and Animal Genomes Conference, January 12-16, Forest Tree Genomics Workshop, San Diego, CA

Neale, D.B., Lee, J., Wegrzyn, J., Nelson, D., St. Clair, B., Huber, D., Byram, T., Howe, G., Harry, D., Wheeler, N., Dean, J., McKeand, S., Whetten, R. (2008) Conifer translational genomics network. XVIth Plant and Animal Genomes Conference, January 12-16, Forest Tree Genomics Workshop, San Diego, CA

Echt, C., Whetten, R., Nelson, C.D., Peterson, D.G., Krutovsky, K., Yuceer, C., Dean J. (2008) A Proposal for New Pine Resources for Genetic Mapping and Sequencing. XVIth Plant and Animal Genomes Conference, January 12-16, Forest Tree Genomics Workshop, San Diego, CA

Nelson, C.D.,Peterson, D.G., Echt, C., Whetten, R., Krutovsky, K., Yuceer, C., Dean, J. (2008) Pine Genome Physical Mapping and Sequencing. XVIth Plant and Animal Genomes Conference, January 12-16, Forest Tree Genomics Workshop, San Diego, CA

Recent Invited Lectures

Genomics & Biotechnology of Woody Plants Symposium, October 16-17, 2003, Knoxville, TN, “Using Functional Genomics to Open New Windows on Wood Formation”

National Association of Professional Forestry Schools and Colleges/National Planning Committee (NAPFSC/NPC) Fall Conference, October 28-29, 2003, USFS Forest Products Laboratory, Madison, WI, "Recent Progress in Genetic Control of Wood Properties"

University of Maine, Forestry Program Centennial Lecture, April 29, 2004, “Will Genomics and Biotechnology Impact Forestry Practices in Your Lifetime?”

Michigan State University, Department of Forestry, October 19, 2004, "Novel drought adaptive genes in pine identified through analyses of EST libraries"

Michigan Technological University, School of Forest Resources and Environmental Sciences, March 21, 2005, "DNA Microarrays and EST databases for identifying stress response genes in pine"

Savannah River Ecology Laboratory, October 13, 2005, "Functional Genomics in Loblolly Pine: Development of Resources for Data Mining Gene Expression"

University of South Carolina, Norman J. Arnold School of Public Health, October 14, 2005,"Using Model Plant Functional Genomics to Inform Phytoremediation Approaches: Arabidopsis Gene Responses to Munitions as a Case Study"

Miami University (Ohio), Botany Department, April 21, 2006, "Transcriptional Profiling of Environmental Stress Responses in Pine"

XVth Plant and Animal Genomes Conference, January 13-17, 2007, San Diego, CA, Reduced-Representation Sequencing Workshop, “Sequencing the transcriptionally active gene space in conifers”

International Workshop on Conifer Genomics, March 18-21, 2007, Banbury Center, Cold Spring Harbor, NY, "Key Components of a Conifer Genome Program: Gene Discovery"

GROWS 2007 Forest Landowner Conference, August 2-4, 2007, Callaway Gardens, GA, "Breakout Session IV - Tree Genetics"

The Latin America and the Caribbean Meetings on Agricultural Biotechnology (REDBIO), October 22-26, 2007, Valparaiso, Chile, "The conifer genome sequence: A snapshot and a prospectus"

For more information about Dr. Dean's work see Center for Metalloenzyme Studies or The Dean Laboratory Web Page