Plant Systems Biology Group Oak Ridge National Laboratory January 2010 Nancy L. Engle – B.A. Rollins College, Florida Research interests include quantifying plant and microbe responses to perturbations using mass spectrometry-based metabolomics, structural elucidation of unknown metabolites, and natural product synthesis. Structured pedigrees and natural genotypic variation are used to identify genetic and environmental effects on metabolite production, to which advanced mass-spectometry based analysis using ion trapping and Time-of-Flight analyzers are used to aid in identification of unknowns. Results are used to better understand the metabolic effects of alterations and to develop synthesis strategies for confirmation of unknown metabolites Lee E. Gunter – M.S. University of Georgia Research interests include the biology and evolution of Populus; the discovery and characterization of genes involved in plant cell wall biosynthesis through bioinformatics, association studies and mapping; effect of phytochrome expression on crown architecture; and abiotic stress response in plants. Results are applied to design and assessment of transgenic poplar and gene expression and evolution. Sara S. Jawdy – M.S., University of Tennessee Research interests include transcriptomics and expression analysis of plants, both wild-type and genetically modified, that have been subjected to various experimental treatments. Various tools such as microarray analysis, 454 sequencing and quantitative PCR are used to identify individual genes and gene networks involved in controlling response(s) to treatment. The results are used to understand how both herbaceous and woody plant species respond under certain conditions. This knowledge can be used to modify plants such that they are better suited for carbon sequestration or biomass production, or to elucidate previously unknown functions of specific genes and gene networks. Udaya C. Kalluri – Ph. D. Michigan Technological University Research interests include molecular and phenotypic characterization and modeling of biological phenomenon across single cell to whole plant levels. Current projects involve studies of plant processes such as cell wall biosynthesis, hormone signaling, developmental biology, plant-microbe interactions under the larger research contexts of bioenergy and carbon biosequestration. Abhijit A. Karve - Ph.D. Clemson University Research interests include molecular characterization of plant responses to heat stress and understanding the role of plant-microbe interactions in plant adaptation to environmental stresses. The environmental stress responses are characterized by using enzyme activity assay, proteomic analysis and protoplast based transient expression assays. The role of protein interactions in plant adaptation is studied by recombinant protein expression in bacteria and protein-protein interaction assays. The results help better understand the cellular processes that are involved in determining the adaptation to environmental stresses. Madhavi Z. Martin – Ph.D. University of California, Los Angeles Research interests are to pursue R&D in the design, fabrication, and testing of environmental sensors specifically for biomass characterization and forensic applications. Specific examples include the evaluation of a laser-induced breakdown spectroscopy (LIBS) system capable of rapid and simultaneous elemental analysis for dendrochemistry, detection of total carbon and nitrogen in soils, including heavy metal and radionuclide detection in the environment. Results are applied to the advanced development of bioenergy crops, to understand soil carbon cycle processes, and to correlate the environmental response to fire and climate. Forensic applications have led to solving murder cases and criminal lawsuits. Priya Ranjan – Ph.D. Michigan Technological University Research interests include bioinformatics analysis of high throughput “omics” data, focusing on next-generation sequencing technologies, genetic association studies using single nucleotide polymorphisms (SNPs), identification of candidate genes from QTL studies related to cell wall traits. Results are applied to genetic improvement of bioenergy crops. Timothy J. Tschaplinski – Ph.D. University of Toronto Research interests include characterizing gene function by analysis of transgenic plants and microbes with mass spectrometry-based metabolomics, plant response to environmental stress, and linking phenotypic traits to underlying molecular mechanisms. Structured pedigrees and natural genotypic variation are used to identify genetic and environmental effects on metabolite production, drought tolerance, carbon partitioning and allocation. Results are applied for the accelerated domestication of bioenergy crops, to understand the metabolic consequences of genetic manipulation, to unravel plant-microbe signaling pathways, and to improve microbial bioprocessing to overcome the recalcitrance of lignocellulosic biomass for bioenergy production. Gerald A. Tuskan – Ph.D. Texas A&M University Over 18 years of experience in leading and working with the Department of Energy and the larger scientific community on the development of woody perennial bioenergy feedstocks. Currently the co-lead for the Joint Genome Institute Plant Genomic effort and the Activity Lead for the BioEnergy Science Center Populus Biosynthesis team. In addition, he is the co-lead PI on DOE research related to poplar genetics and genomics, and plant-microbe interactions. His research focuses on the accelerated domestication of poplar through direct genetic manipulation of targeted genes and gene families, with focus on cell wall biosynthesis. Published more that 118 peer-reviewed articles since 1990 in the areas of genetic and genomics of perennial plants; including 15 publications with nearly 550 citations exclusively related to genomics and bioenergy. David J. Weston – Ph.D. Clemson University The main goal of our research is to discover and validate mechanisms driving plant adaptive traits. We use a comparative systems biology approach, whereby genes, metabolites and proteins are modeled using network theory across multiple species and linked to traits of interest. Both species - conserved and - diverse aspects of the network are confirmed at molecular levels (usually reverse genetics), and scaled to higher levels of biological organization through collaborations. Current projects include linking physiological traits (especially photosynthetic properties) to the heat shock response and plant - microbe interactions. Stan D. Wullschleger – Ph.D. University of Arkansas Research interests include quantifying plant response to environmental stress and linking phenotypic traits to underlying molecular mechanisms. Structured pedigrees and natural genotypic variation are used to identify genetic and environmental controls on carbon partitioning and biomass distribution above- and below- ground. Results are applied to the advanced development of bioenergy crops, to understand soil carbon cycle processes, and to characterize interactions between physiology and genetics in determining plant adaptation to climate. Xiaohan Yang – Ph.D. Cornell University Major research interests include discovery of genes involved in plant cell wall biosynthesis, algal oil production, stress response, and intercellular signal transduction, with a focus on small protein genes. Sequencing of transcriptome and proteome is used to profile gene expression. The sequencing data are analyzed using bioinformatics to identify candidate genes, which are then characterized at biochemical, physiological, and morphological levels using molecular genetics. Radio bio-imaging technology is pursued to monitor the movement of small signaling proteins. Other interests include new genome sequencing, evolutionary dynamics, gene annotation, and phylogenetic analysis. Knowledge gained is relevant to bioethanol and biodiesel production and carbon sequestration. Tara Hall – Administrative Assistant Sara Allen – Intern Zackary Moore – Student Intern University of Tennessee Maya Strahl – Student Intern Alina Campbell – M.S. Graduate Student University of Tennessee Whitney McNutt – HERE Intern University of Tennessee Alyssa Deleon – Student Intern Rhonda Egidy – Student Intern Plant Systems Biology Group 2009 Citations Chatterjee A., R. Lal, L. Wielopolski, M. Z. Martin, and M. H. Ebinger. 2009. Evaluation of different soil carbon determination methods. Plant Sciences. Cheng, Z., and G. A. Tuskan. 2009. Populus community mega-genomics: coming of age. Critical Reviews in Plant Science 28: 1-3. Islam-Faridi, M. N., C. D. Nelson, S. P. DiFazio, L. E. Gunter, and G. A. Tuskan. 2009. Cytogenetic analysis of Populus Trichocarpa-Ribosomal DNA, telomere repeat sequence, and marker-selected BACs. Cytogenetic and Genome Research 125: 74-80. Jung, H. W., T. J. Tschaplinski, L. Wang, J. Glazebrook, J. T. Greenberg. 2009. Priming in systemic plant immunity. Science 324: 89-91. Kalluri U. C., G. B. Hurst, P. K. Lankford, P. Ranjan, and D. A. Pelletier. 2009. Shotgun proteome profile of Populus developing xylem. Proteomics 9: 4871-4880. Kang, B., L. Osburn, D. Kopsell, G. A. Tuskan, and Z. Cheng. 2009. Micropropagation of Populus trichocarpa ‘Nisqually-1’: the genotype deriving the Populus reference genome. Plant Cell Tissue and Organ Culture 99: 251-257. Karve, A., and B. D. Moore. 2009. Function of Arabidopsis hexokinase-like1 as a negative regulator of plant growth. Journal of Experimental Botany 10: 1-13. Leakey, A. D. B., E.