Plants as “green factories” offer a solution to growing food and energy needs. From an agronomic perspective, seeds are the lowest cost/highest volume biological producers of protein and oils, which are valuable sources of food and chemicals. To obtain high oil content in seeds, rational metabolic engineering strategies are needed based on the knowledge of the corresponding regulatory mechanisms. Systems biology approaches such as transcriptomics, metabolomics, and fluxomics allow better understanding of metabolic regulation by globally investigating cellular interactions in seed composition. At VT, this interdisciplinary research falls within three key College of Agriculture and Life Sciences initiatives: Agricultural and Environmental Sustainability, Biodesign and Bioprocessing, and the Green Industry.
- “A systems biology approach to cellular regulation of seed filling” is a project funded by the National Science Foundation (NSF). This project focuses on understanding the regulation of seed metabolism in the weed Arabidopsis thaliana by using reverse genetics and systems biology approaches.
- “Enabling Phenotype Predictions of Cyanobacteria” is another interdisciplinary NSF-funded project focusing of predicting metabolic phenotypes in the blue-green alga Synechocystis sp. PCC6803 to predict metabolic engineering strategies for high hydrogen and lipid production in cyanobacteria. This project uses both experimental and computational approaches (including metabolomics, genome-scale modeling, and 13C-based metabolic flux analysis) to achieve this goal.
- “Predicting high-oil phenotypes for seed rational metabolic engineering using genome-scale modeling” is an USDA CSREES-funded project (via the Biodesign and Bioprocessing Research Center at VT) focusing on prediction of metabolic engineering strategies by using genome-scale modeling that would enable engineering soybean seed accumulating high oil levels.
Ph.D., Plant Biology, Michigan State University, 2003
B.S., Biochemistry, University of P.J. Safarik, Kosice, Slovak Republic, 1995
- January 2009 – present: Assistant Professor, Department of Plant Pathology, Physiology, and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg
- May 2003 – December 2008: Postdoctoral Researcher, Michigan State University, East Lansing
- PPWS 5534 - Advanced Plant Physiology & Metabolism II
- PPWS/GBCB 5314 - Paradigms for Bioinformatics
- PPWS 5004 - Seminar
- ALS 5014 - Seminar
Other Teaching and Advising
I am a member of the Translational Plant Science (TPS) graduate program that provides interdisciplinary plant-related research opportunities for graduate students. The TPS program fosters interdisciplinary collaborations among student of the plant science community at VT.
Undergraduate and graduate students have more opportunities to participate in research than high school students. Most laboratory learning experiences before college do not engage students in asking their own research questions or designing their own experiments with unknown outcomes. My outreach program involves collaborations with several high schools in VA via the Partnership for Research and Education in Plants program to foster their critical thinking and inspire them to become scientists by engaging these high school students in real research. Mutual communication and active engagement of scientists, high school students and their teachers in a meaningful research strengthens student’s interest and skills in science and at the same time may provide publishable results for the scientists.
I participate in the PREP program that provides genuine research opportunities for high school students and their teachers. These students design and conduct their own experiments to determine how previously uncharacterized Arabidopsis mutants with one or more disabled genes differ from the wild type in response to various environmental stresses. We have identified a number of Arabidopsis mutants with altered seed composition phenotype that need to be tested for sensitivity to environmental stresses. High school students conduct experiments with our mutants and I provide expertise for them to be successful so they will learn as much as they can from the process.
- Collakova, E., Aghamirzaie, D., Fang, Y., Klumas, C., Tabataba, F., Kakumanu, A., Myers, E., Heath, L., and Grene, R. (2013) Metabolic and transcriptional reprogramming in developing soybean (Glycine max) embryos. Metabolites, submitted.
- Collakova, E., Klumas, C., Suren, H., Myers, E., Heath, L.S., Holliday, J.A., and Grene, R. (2013). Evidence for extensive heterotrophic metabolism, antioxidant action, and associated regulatory events during winter hardening in Sitka spruce. BMC Plant Biol, in press.
- Grene, R., Klumas, C., Suren, H., Yang, K., Collakova, E., Myers, E., Heath, L.S., and Holliday, J.A. (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 3: 1-14
- Collakova, E., Yen, J.Y., and Senger, R. (2012). Are we ready for genome-scale modeling in plants? Plant Sci 191-192: 53-70
- Collakova, E., Goyer, A., Naponelli, V., Krassovskaya, I., Gregory, J.F. III, Hanson, A.D., and Shachar-Hill, Y. (2008). Arabidopsis 10-formyl tetrahydrofolate deformylases are essential for photorespiration. Plant Cell 20: 1818-1832
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