Ruth Grene

Professor

Program Focus

The focus of my program is the effects of components of climate change, such as drought, on the growth and productivity of crop plants and trees.  Drought, and other aspects of climate change, impact economic, environmental, and social aspects of life. As an example, drought affects more people than any other natural hazard.  There is increasing demand for food crops, and for renewable resources from trees, to ensure food and fiber security and to contribute to sustainable livelihoods in the coming decades.  As the world’s population grows, so will the need to cultivate and sustain crop and tree production in more hostile environments.  A better understanding of the effects of abiotic stresses such as drought and extremes of temperature on plants, especially the integration of stress-responsive events from the molecular and cellular to the whole-plant level, is vital to prepare for the genetic engineering of varieties with improved drought tolerance.

With the genomics and bioinformatics resources that are currently available for plant species, especially the model plant Arabidopsis thaliana, and, increasingly, crop and tree species, it is now possible to investigate the regulatory mechanisms that underlie relative stress tolerances among closely related genotypes.  Although individual components of stress response systems have been studied under abiotic stresses, the overall “network logic” of pathways that are operational in stress tolerant plants remains still largely unknown.  To further understand stress systems biology, the nature of regulatory control over pathways and networks must be elucidated, and other kinds of data, such as metabolomics and physiological data, and current findings from the literature, incorporated into the system.

Recent advances in network modeling have been made using the vast resources available for Arabidopsis thaliana and tools for the analysis of upstream promoter regions are increasingly available.  These integrative techniques are only beginning to be applied to crop plants and trees.

Current Projects

  • Collaboration with Dr. L. Heath (VT Computer Science) .  Beacon:  An NSF-funded project. The increasing availability of “omics” data has led to a fundamental change in the analytical tasks that challenge plant biologists. The quest for data has been augmented by the quest for meaning, with the goal of gaining insight based on a systems view of complex interactions that lay hidden in a sea of endless rows and columns. Gene expression, protein-protein interaction (PPI), metabolite, and post-transcriptional modification data sets have become the elements that comprise the Rosetta Stone of biological discovery. In response, there has been a veritable flood of bioinformatics tools developed to facilitate the task of deriving meaning from such spreadsheets, most of which are severely lacking in usability, transparency, and the presentation of results in a manner that supports an improved analytical context.

    One software system for constructing networks comes from the Beacon project, which aims to represent, simulate, and infer signal transduction pathways for plant species.  The centerpiece of the Beacon system is a network editor for capturing and visualizing signal transduction pathways in the Activity Flow language of the Systems Biology Graphical Notation (SBGN), a standardized topological description of pathways.  At a workshop held on campus in August, 2012, the Beacon editor was used to capture 12 signal transduction pathways compiled by leading plant biologists.  These “founder” pathways are stored in the Beacon database.  A simulation engine for performing in silico experiments is under development, as is an inference engine that uses omics data to infer new nodes and relationships in signal transduction pathways.  Beacon will be extended to support the visualization of time-series data through the use of pathway layers.
  • Collaboration with Dr. Eva Collakova (PPWS).  Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos .  Soybean (Glycine max) seeds are an important source of seed storage compounds, including protein, oil, and sugar used for food, feed, chemical, and biofuel production. Existence of such diversity in seed composition suggests that seed metabolism is flexible and that genetic determinants can be modified to increase the content of target seed storage compounds by metabolic engineering. The major problem in rational metabolic engineering of any metabolic phenotype is the identification of a set of genes suitable for genetic modification to obtain a specific desired metabolic phenotype. To address this problem, the first step is to understand how relevant metabolic genes are regulated and determine target biosynthetic gene-regulatory gene associations.  My role in the project is to achieve integration of diverse datasets by using a variety of existing bioinformatics tools. By this means, we aim to generate predictions about the associations and interactions of unknown regulators with the relevant pathways and steps in central carbon metabolism in soybean embryos based on “guilt-by-association” relationships. These regulators represent targets for future metabolic engineering.
  • Collaboration with Dr. Eva Collakova. In a related, NSF-funded, project, the team is taking the same approach with Arabidopsis and seed development, with the valuable addition of seeds displaying mutant phenotypes, in order to pinpoint key genes whose action affects the regulation of seed storage compound biosynthesis and the acquisition of desiccation tolerance.

Education

Ph.D., Plant Physiology, University of California, Davis, 1972

M.A., Botany, Washington University, 1968

B.A., Biochemistry, Trinity College, Dublin, Ireland, 1965

Experience

  • June 1998 – present: Professor, Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg
  • June 1989 –  June,1998: Associate Professor, Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg
  • January 1979- June, 1988: Research Associate, Boyce Thompson Institute at Cornell University, Ithaca, NY
  • June 1985- June, 1988: Adjunct Assistant Professor, Plant Biology, Cornell University, Ithaca, NY
  • June 1977- January, 1979: Research Associate, New York Agricultural Experiment Station, Cornell University, Geneva, NY
  • June 1975- June 1977: NIH Postdoctoral Fellow, Jagendorf Lab, Cornell University, Ithaca, NY
  • June 1973- June 1975: NIH Postdoctoral Fellow, University of California, Berkeley, Ken Sauer Lab

Selected Major Awards  

  • National Science Foundation Career Advancement Award, 1992-94
  • National Research Service Award (NIH), 1975-77
  • National Institute of Health Postdoctoral Fellowship, 1973-74

Courses Taught

  • PPWS/GBCB 5314- Biological Paradigms for Bioinformatics
  • PPWS/HORT 5434- Advanced Plant Physiology and Metabolism II
  • PPWS/BIOL 5214 – Plant Stress Physiology
  • GBCB 5874 - Problem Solving GBCB

Other Teaching, Advising, and Outreach

  • Member of a group of founding faculty of Doctoral Program in Genetics, Bioinformatics, and Computational Biology (GBCB) at VT; Faculty Liaison for the VT-AMP program to retain and promote success of underrepresented groups in the STEM fields, 2005-2009; Vice-Chair, then Chair of the VT Commission for Equal Opportunity and Diversity, 2006-2008; Co-PI of Science Mentoring Program for retention of first generation and underrepresented groups in the life sciences, Office of Inclusion and Diversity, 2016-2018;  Member of the VT Molecular Plant Sciences Faculty; Co-Founder of the Molecular Cell Biology and Biotechnology Option at VT, 1990
  •  Thesis Advisor and Postdoctoral Mentor, (10 graduate students, 4 post-doctoral fellows).  Alfred Hausladen, Duke University: Andreas Doulis, Mediterreanan Agronomic Institute: Neval Erturk, Converse College: Camellia Moses Okpodu, Norfolk State University: Cecilia Vasquez Robinet, Ludwigs Maximillian Universitat: Shrinivasrao Mane, Dow: James V. Anderson, USDA: Ashima Sen Gupta, USDA: NR Madamanchi, University of North Carolina; Hiromi Tasaki, Cornell University; Akshay Kakumanu, Pennsylvania State University, Mae Rose Sumugat, Hiromi Tasaki, Cornell University, Delasa Aghamirzaie, University of Washington, Ying Ni, Deustche Bank
  • Aghamirzaie D, Batra D, Heath LS, Schneider A, Grene R, Collakova E (2015) Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos. BMC Genomics 16: 928
  • Aghamirzaie D, Collakova E, Li S, Grene R (2016) CoSpliceNet: a framework for co-splicing network inference from transcriptomics data. BMC Genomics 17: 845
  • Aghamirzaie D, Nabiyouni M, Fang Y, Klumas C, Heath LS, Grene R, Collakova E (2013) Changes in RNA Splicing in Developing Soybean (Glycine max) Embryos. Biology (Basel) 2: 1311-1337
  • Collakova E, Aghamirzaie D, Fang Y, Klumas C, Tabataba F, Kakumanu A, Myers E, Heath LS, Grene R (2013) Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos. Metabolites 3: 347-372
  • Ni Y, Aghamirzaie D, Elmarakeby H, Collakova E, Li S, Grene R, Heath LS (2016) A Machine Learning Approach to Predict Gene Regulatory Networks in Seed Development in Arabidopsis. Front Plant Sci 7: 1936
  • Nilsen ET, Freeman J, Grene R, Tokuhisa J (2014) A rootstock provides water conservation for a grafted commercial tomato (Solanum lycopersicum L.) line in response to mild-drought conditions: a focus on vegetative growth and photosynthetic parameters. PLoS One 9: e115380
  • Schneider A, Aghamirzaie D, Elmarakeby H, Poudel AN, Koo AJ, Heath LS, Grene R, Collakova E (2016) Potential targets of VIVIPAROUS1/ABI3-LIKE1 (VAL1) repression in developing Arabidopsis thaliana embryos. Plant Journal 85: 305-319    
  • Collakova E, Klumas C, Suren H, Myers E, Heath LS, Holliday JA, Grene R (2013) Evidence for extensive heterotrophic metabolism, antioxidant action, and associated regulatory events during winter hardening in Sitka spruce. BMC Plant Biology, in press
  • Zhou L, Franck C, Yang K, Pilot G, Heath LS, Grene R (2012). Mining for meaning: visualization approaches to deciphering Arabidopsis stress responses in roots and shoots. OMICS. 2012 Apr;16(4):208-28. Epub 2012 Mar 14.
  • Grene R, Klumas C, Suren H, Yang K, Collakova E, Myers E, Heath LS, Holliday JA (2012) Mining and visualization of microarray and metabolomic data reveal extensive cell wall remodeling during winter hardening in Sitka spruce (Picea sitchensis). Front Plant Sci. 2012; 3:241.
  • Kakumanu A, Ambavaram MM, Klumas C, Krishnan A, Batlang U, Myers E, Grene R, Pereira A. (2012). Effects of drought on gene expression in maize reproductive and leaf meristem tissue revealed by RNA-Seq. Plant Physiol. 160:846-67.
  • Grene R, Vasquez-Robinet C, Bohnert H, (2011) Molecular Biology and Physiological Genomics of Dehydration Stress in Plant Desiccation Tolerance Ecological Studies 215: 255-287
  • Vásquez-Robinet C, Watkinson, JI, Sioson AA, Ramakrishnan N, Heath LS, Grene R (2010) Differential Expression Of Heat Shock Protein Genes In Preconditioning For Photosynthetic Acclimation In Water-Stressed Loblolly Pine. Plant Physiology and Biochemistry. 48: 256-264.
  • Goff S. et al., (2011). The iPlant collaborative: cyberinfrastructure for plant biology. Frontiers in Plant Genetics and Genomics doi: 10.3389/fpls.2011.000
  • Sumugat M., J. Donahue, D. Cortes Bermudez, V. Stromberg, R. Grene, V. Shulaev, G. Welbaum. (2010). Seed development and germination in an Arabidopsis thaliana line antisense to glutathione reductase. Journal of New Seeds 11:104-126.
  • Mane SP, Vasquez Robinet C, Ulanov A, Schafleitner R, Tincopa L, Gaudin A, Nomberto G, Alvarado C, Solis C, Avila Bolivar L, Blas R, Ortega J, Solis J, Panta A, Rivera C, Samolski I, Carbajulca DH, Bonierbale M, Pati A, Heath LS, Bohnert HJ, Grene R (2008) Molecular and physiological adaptation to prolonged drought stress in the leaves of two Andean potato genotypes Functional Plant Biology,. 35: 669 – 688.
Ruth Grene
  • (540) 231-6761
  • grene@vt.edu
  • 101H Price Hall
    Mail code: 0331
    170 Drillfield Drive
    Blacksburg, VA 24061