Eva Colla’kova'

Environmental conditions are gradually becoming unfavorable for crop production mainly because of our activities, leading to global climate change. Plants have evolved complex mechanisms (including remodeling their energy metabolism and producing stress-related protective metabolites) to cope with different stresses negatively impacting crop quality and yield. My current focus is on spaceflight-related stresses (radiation, high carbon dioxide levels, nitrogen availability, drought, and heat) and engineering crops for deep-space exploration purposes (e.g., fully edible tomato plants). These stresses are also highly relevant to field-grown crops. Our goal is also to improve nutritional quality and yield in oilseeds (soybeans, peanuts, and Camelina) under climate change-related stresses. Overall, my goal is to understand how plants alter their metabolism in response to different combinations of stresses, and use this knowledge in two major areas:

1. Crop improvement via engineering a new generation of stress-tolerant crops. We first need to identify genes that function in adaptation of plants to multiple stresses. To elucidate functions of these stress-related genes, we use a combination of multi-omics and genomic data science to probe several levels of regulation and unravel interactions of different molecules (nucleic acids, proteins, and metabolites) in plants under different stresses.
2. Method development for stress monitoring and phenotyping in crops. In collaboration with Israel and my collaborators at VT as part of digital and precision agriculture, we are developing new ways to monitor different types of stresses. These methods are based on a combination of Raman spectroscopy and near-infrared spectroscopy coupled with machine learning for stress monitoring as well as prediction of seed quality and yield in stressed crops.

• PPWS 5534: Advanced Plant Physiology and Metabolism II
• GBCB 5314: Biological Paradigms for Bioinformatics
• GBCB 5874: Problem Solving

Associate Professor | 2015 – present
School of Plant and Environmental Sciences and
Department of Plant Pathology Physiology, & Weed Science
Virginia Polytechnic Institute and State University

Assistant Professor | 2009 – 2015
Department of Plant Pathology, Physiology, & Weed Science
Virginia Polytechnic Institute and State University

Postdoctoral Fellow | 2003 – 2008
Department of Plant Biology
Michigan State University

1. Zhang X, Tubergen P, Agorsor I, Khadka P, Tempe C, Collakova E, Pilot G, Danna CH (2022) Elicitors of plant defense induce the accumulation of amino acids that suppress both bacterial virulence and growth. Plant Physiol (in revision)
2. Zhao C, Pratelli R, Yu S, Shelley B, Collakova E, Pilot G (2021) Detailed characterization of the UMAMIT proteins provides insight into their evolution, amino acid transport properties, and role in the plant. J Exp Bot 72: 6400-6417. doi: 10.1093/jxb/erab288
3. Besnard J, Sonawala U, Maharjan B, Collakova E, Finlayson SA, Pilot G, McDowell J, Okumoto S (2021) Increased expression of UMAMIT amino acid transporters results in activation of salicylic acid dependent stress response. Front Plant Sci 11: 606386. doi: 10.3389/fpls.2020.606386
4. Lott AA, Freed CP, Dickinson CC, Whitehead SR, Collakova E, Jelesko JG (2020) Poison ivy hairy root cultures enable a stable transformation system suitable for detailed investigation of urushiol metabolism. Plant Direct 4: e00243. doi: 10.1002/pld3.243
5. Tanniche I, Collakova E, Denbow C, Senger RS (2020) Characterizing glucose, illumination, and nitrogen-deprivation phenotypes of Synechocystis PCC6803 with Raman spectroscopy. PeerJ 8: e8585. doi: 10.7717/peerj.8585
6. Tanniche I, Collakova E, Denbow C, Senger RS (2020) Characterizing metabolic stress-induced phenotypes of Synechocystis PCC6803 with Raman spectroscopy. PeerJ 8: e8535. doi: 10.7717/peerj.8535
7. Lott AA, Baklajian ER, Dickinson CC, Collakova E, Jelesko JG (2019) Accession-level differentiation of urushiol levels, and identification of cardanols in nascent emerged poison ivy seedlings. Molecules 24: 4213. doi: 10.3390/molecules24234213
8. Clermont K, Wang Y, Liu S, Yang Z, dePamphilis CW, Yoder JI, Collakova E, Westwood JH (2019) Comparative metabolomics of early development of the parasitic plants Phelipanche aegyptiaca and Triphysaria versicolor. Metabolites 9: 114. doi: 10.3390/metabo9060114
9. Aziz M, Sturtevant D, Winston J, Collakova E, Jelesko JG, Chapman KD (2017) MALDI-MS imaging of urushiol in poison ivy stems. Molecules 22: article# E711. doi: 10.3390/molecules22050711
10. Gupta C, Krishnan A, Collakova E, Wolinski P, Pereira A. (2017) SANe: The seed active network for mining transcriptional regulatory programs of seed development. bioRxiv. doi: 10.1101/165894
11. 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. doi: 10.3389/fpls.2016.01936
12. Besnard J, Pratelli R, Zhao C, Sonawala U, Collakova E, Pilot G, Okumoto S (2016) UMAMIT14 is an amino acid exporter involved in phloem unloading in Arabidopsis roots. J Exp Bot 67: 6385-6397. doi: 10.1093/jxb/erw412
13. Aghamirzaie D, Collakova E, Li S, Grene R (2016) CoSpliceNet: A framework for co-splicing network inference from transcriptomics data. BMC Genomics 17: 845. doi: 10.1186/s12864-016-3172-6
14. Schneider A, Aghamirzaie D, Elamarakeby 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 J 85: 305-319. doi: 10.1111/tpj.13106
15. 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. doi: 10.1186/s12864-015-2108-x
16. Nourbakhsh A, Collakova E, Gillaspy GE (2015) Characterization of the inositol monophosphatase gene family in Arabidopsis. Front Plant Sci 5: Article 725 (1-14). doi: 10.3389/fpls.2014.00725
17. Zu TNK, Athamneh AIM, Collakova E, Robertson J, Aardema C, Senger RS (2015) Assessment of ex vivo perfused liver health by Raman spectroscopy. J Raman Spectrosc 46:551-558. doi: 10.1002/jrs.4688
18. Zu TNK, Athamneh AIM, Wallace RS, Collakova E, Senger RS (2014) Near real-time analysis of the phenotypic responses of Escherichia coli to 1-butanol exposure using Raman spectroscopy. J Bacteriol 196:3983-3991. doi: 10.1128/JB.0159014
19. Singh D, Balota M, Isleib TG, Collakova E, Welbaum GE (2014) Suitability of canopy temperature depression, specific leaf area, and SPAD chlorophyll reading for genotypic comparison of peanut grown in a sub-humid environment. Peanut Sci 41:100-110. doi: 10.3146/PS13-11.1
20. Singh D, Collakova E, Isleib TG, Welbaum GE, Tallury SP, Balota M (2014) Differential physiological and metabolic responses to drought stress of peanut cultivars and breeding lines. Crop Sci 54:2262-2274. doi:10.2135/cropsci2013.09.0606
21. 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 Biol 13:72-87. doi: 10.1186/1471-2229-13-72
22. Collakova E, Aghamirzaie D, Fang Y, Klumas C, Tabataba F, Kakumanu A, Myers E, Heath L, Grene R (2013) Metabolic and transcriptional reprogramming in developing soybean (Glycine max) embryos. Metabolites 3: 347-372. doi: 10.3390/metabo3020347
23. 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 2: 1311-1337. doi: 10.3390/biology2041311
24. 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 3 (241):1-14. doi: 10.3389/fpls.2012.00241
25. Collakova E, Yen JY, Senger R (2012) Are we ready for genome-scale modeling in plants? Plant Sci 191-192: 53-70. doi: 10.1016/j.plantsci.2012.04.010