Postdoctoral—Michigan State University, Biochemical Mass Spectrometry
Ph.D.—Michigan State University, Plant Biochemistry
M.S.—San Diego State University, Plant Physiology
B.S.—University of California-Riverside, Microbiology
Plant biochemistry; Cellular and molecular biology related to the regulation of plant growth and development; System biology approaches (metabolomics and proteomics) to understanding complex processes
Cell signaling and growth regulation: The primary signal transduction systems in plants involve hormonal messengers that translate developmental, positional and environmental information into optimized growth and development. The levels of the hormone messengers in plant tissues are determined by four general processes: biosynthesis, conjugation reactions, catabolism and transport. Each of these processes must be under close regulation because the levels of the phytohormone are critical for the regulation of growth and developmental processes. It is one of the fundamental goals of this laboratory to understand in precise detail how the levels of auxin (indole-3-acetic acid, IAA), the first discovered plant hormone, are regulated in specific cells and tissues within plants.
Why study auxin and what might it do for horticulture? Auxins are most well known for their two uses: 1) They form the active ingredient in rooting hormone mixtures, and 2) they are used for the selective control of broadleaf weeds in lawns and pastures. However, auxins control a wide variety of plant processes from early embryo growth to the regulation of plant senescence. In fact, they control the size of every plant cell, are part of the system that defines plant size and shape and control the growth of fruit as well as the formation of wood and vascular tissues.
The laboratory is widely recognized for research aimed at understanding auxin biosynthesis and metabolism. Previous work from our group have shown 1) that indole-3-butryic acid is a native auxin in plants; 2) that multiple pathways are present in plants, including one that is independent of the amino acid tryptophan, and the use of these pathways is under environmental and developmental regulation, 3) that auxins exist in plant both as the free form as well as conjugated to various other compounds including proteins, and 4) that auxins control the rate of ripening in some fruit tissues. We continue to expand on these findings and develop new ways to use our knowledge of auxin biology to improve and develop new plant materials.
Toward single cell biology: One of the major limiting factors in plant metabolomics is the absence of effective methods for measuring spatial distributions of metabolites. There have been some reports of success using microsampling techniques but few reports regarding low level compounds such as plant hormones. For example, laser microdissection has been used to sample small clusters of cells and microcapillary needles have been used for aspirating cellular contents for nanoelectrospraying directly into a mass spectrometer. We are currently evaluating many microsampling techniques for targeted metabolomics and metabolic flux analysis, especially for indolic metabolites and stress-related compounds in plants.
Communication between plants and insects: The deposition of antimicrobial plant resins in honey bee nests has important physiological benefits, however resin foraging is difficult to approach experimentally because resin composition is highly variable among and between plant families, the environmental and plant-genotypic effects on resins are unknown, and resin foragers are relatively rare and often forage in unobservable tree canopies. Subsequently, little is known about the botanical origins of resins in many regions or the benefits of specific resins to bees. We use metabolomic methods as a type of environmental forensics to track individual resin forager behavior through comparisons of global resin metabolite patterns. The resin from a single bee was sufficient to identify that resin's botanical source such that antimicrobial compounds can be studied in detail.
Metabolomics and metabolic flux analysis: The flow of matter through an organism’s network of metabolic pathways is the most direct molecular indicator of an organism’s phenotype. Together with Dr. Hegeman’s laboratory, our goals are to improve the applicability of dynamic metabolic flux analysis to intact plants by optimizing methods for measurement of dynamic metabolic fluxes in intact plant systemsusing timed stable isotope labeled nutrient incorporation, LC and GC-MS analysis, and automated data extraction and calculation of dynamic fluxes. We are also developing and testing a procedure for finding additional connectivity and pathway components of genome derived metabolic network models using dynamic flux information. The method will be tested using a publically available metabolic network model for Arabidopsis thaliana with flux data collected from Arabidopsis plants subjected to multiple stress conditions. 3) We will create and distribute computational and bioinformatics resources for metabolic flux analysis workflows.
Useful web sites that are derived from work from our group and our close collaborators:
http://13carbon.com Web site for our growth system for plant labeling with 13CO2
http://www.hplcsimulator.org Web-based high-performance liquid chromatography simulation developed by Dr. Paul Boswell and collaborators.
http://www.retentionprediction.org Retention Predictor is an open-source Java application that uses the gradient retention times of a set of "instrument calibration solutes" to back-calculate the effective gradient and flow rate profiles produced by a user's instrument developed by Dr. Paul Boswell and members of his group.
http://plantmetabolomics.cfans.umn.edu/index.htm Project website for our NSF funded research in collaboration with Dr. Adrian Hegeman.
We also maintain extensive collaborations with academic, industry and commercial grower colleagues.
Wright, A.D., Sampson, M.B., Neuffer, M.G., Michalczuk, L., Slovin, J.P. and Cohen, J.D. Indole-3-acetic acid biosynthesis in the mutant maize orange pericarp, a tryptophan auxotroph. Science 254:998-1000 (1991)
Zhao Y., Christensen S.K., Fankhauser C., Cashman J.R., Cohen J.D., Weigel D. and Chory J. A role for flavin monooxygenase-like enzymes in auxin biosynthesis. Science 291:306-309 (2001) (pdf)
Culler AH, Quint M, Slovin JP and Cohen JD. Plant Hormones, Auxins. In Comprehensive Natural Products II Chemistry and Biology; Mander, L., Lui, H.-W., Eds.; Elsevier: Oxford, 2010; Vol 4, pp.13–24 (2010)
Negi S, Sukumar P, Liu X, Cohen JD, Muday GK Genetic dissection of the role of ethylene in regulating auxin dependent lateral and adventitious root formation in tomato. Plant J 61:3-15 (2010)
Ludwig-Müller J, Denk K, Cohen JD, Quint M An inhibitor of tryptophan-dependent biosynthesis of indole-3-acetic acid alters seedling development in Arabidopsis. J Plant Growth Regul 29:242-248 (2010)
Yang X-Y, Chen W-P, Rendahl AK, Hegeman AD, Gray WM, Cohen JD Measuring the turnover rates of Arabidopsis proteins using deuterium oxide: an auxin signaling case study. Plant J 63:680-695 (2010)
Liu F, Jiang H, Ye S, Chen W-P, Liang W, Xu Y, Sun B, Sun J, Wang Q, Cohen JD and Li C The Arabidopsis P450 protein CYP82C2 modulates jasmonate-induced root growth inhibition, defense gene expression, and indole glucosinolate biosynthesis. Cell Research 20:539-552 (2010)
Park S, Ozga JA, Cohen JD, Reinecke DM Evidence of 4-Cl-IAA- and IAA-bound to proteins in pea fruit and seeds. J Plant Growth Regul 29:184-193 (2010)
Chen W-P, Yang X-Y, Hegeman AD, Gray WM, Cohen JD Microscale analysis of amino acids using gas chromatography-mass spectrometry after methyl chloroformate derivatization. J. Chromatogr B 878:2199-2208 (2010)
Barkawi LS, Cohen JD A method for concurrent diazomethane synthesis and substrate methylation in a 96-sample format. Nature Protocols 5:1619–1626 (2010)
Barkawi LS, Tam YY, Tillman JA, Normanly J, Cohen JD A high throughput method for the quantitative analysis of auxins. Nature Protocols 5:1619–1626 (2010)
Ge L, Peer W, Robert S, Swarup R, Ye S, Prigge M, Cohen JD, Friml J, Murphy A, Tang D, Estelle M Arabidopsis ROOT UVB SENSITIVE2/WEAK AUXIN RESPONSE1 is required for polar auxin transport. Plant Cell 22:1749-1761 (2010)
Qi Y, Tsuda K, Joe A, Sato M, Nguyen LV, Glazebrook J, Alfano JR, Cohen JD, Katagiri F A putative RNA-binding protein positively regulates salicylic acid-mediated immunity in Arabidopsis. Molecular Plant-Microbe Interactions 23:1573-1583 (2010)
Strader LC, Culler AH, Cohen JD, Bartel B Conversion of endogenous indole-3-butyric acid to indole-3-acetic acid drives cell expansion in Arabidopsis seedlings. Plant Physiol 153:1577-1586 (2010)
Nonhebel H, Yuan Y, Al-Amier H, Pieck M, Akor E, Ahamed A, Cohen JD, Celenza JL, Normanly J Redirection of tryptophan metabolism in tobacco by ectopic expression of an Arabidopsis indolic glucosinolate biosynthetic gene. Phytochemistry 72:37-48 (2011)
Strader LC, Wheeler DL, Christensen SE, Berens JC, Cohen JD, Rampey RA and Bartel B Multiple facets of Arabidopsis seedling development require indole-3-butyric acid-derived auxin. Plant Cell 23: 984–999 (2011)
Phillips KA, Skirpan AL, Liu X, Christensen A, Slewinski TL, Hudson C, Barazesh S, Cohen JD, Malcomber S and McSteen P vanishing tassel2 encodes a grass-specific tryptophan aminotransferase required for vegetative and reproductive development in maize. Plant Cell 23: 550–566 (2011)
Cheng N, Liu JZ, Liu X, Wu Q, Thompson SM, Lin J, Chang J, Whitham SA, Park S, Cohen JD, Hirschi KD Arabidopsis monothiol glutaredoxin, AtGRXS17, is essential for temperature-dependent postembryonic growth and development via modulating auxin response. J Biol Chem 286:20398-20406 (2011)
Chen W-P, Yang X-Y, Harms GL, Gray WM, Hegeman AD, Cohen JD An automated growth enclosure for metabolic labeling of Arabidopsis thaliana with 13C-carbon dioxide - an in vivo labeling system for proteomics and metabolomics research. Proteome Science 9:9; doi: 10.1186/1477-5956-9-9 (2011)
Boswell PG, Schellenberg JR, Carr PW, Cohen JD, Hegeman AD A study on retention “projection” as a supplementary means for compound identification by liquid chromatography-mass spectrometry capable of predicting retention with different gradients, flow rates, and instruments. J Chromatogr A 1218:6732-6741 (2011)
Boswell PG, Schellenberg JR, Carr PW, Cohen JD, Hegeman AD Easy and accurate high-performance liquid chromatography retention prediction with different gradients, flow rates, and instruments by back-calculation of gradient and flow rate profiles. J Chromatogr A 1218:6742-6749 (2011)
Liu X, Cohen JD, Gardner G Low fluence red light increases the transport and biosynthesis of auxin. Plant Physiology 157:891-904 (2011)
Justen VL, Cohen JD, Gardner GM, Fritz VA Seasonal variation in glucosinolate accumulation in turnip cultivars grown with colored plastic mulches. HortScience 46:1608-1614 (2011)
Franklin KA, Lee SH, Patel D, Kumar SV, Spartz AK, Gu C, Ye S, Yu P, Breen G, Cohen JD, Wigge PA, Gray WM PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) regulates auxin biosynthesis at high temperature. Proc Nat Acad Sci USA 108: 20231-20235 (2011)
Menzel WI, Chen W-P, Hageman AD, Cohen JD Qualitative and quantitative screening of amino acids in plant tissues. In: High Throughput Phenotyping in Plants: Methods and Protocols [Methods in Molecular Biology Series #918], Normanly J, ed. Humana Press/Springer, New York, pp 165-178 (2012)
Keller CP, Grundstad ML, Evanoff MA, Keith JD, Lentz DS, Wagner SL, Culler AH, Cohen JD Auxin-induced leaf blade expansion in Arabidopsis requires both wounding and detachment. Plant Signaling & Behavior 6:1-11 (2011)
Dal Bosco C, Dovzhenko A, Liu X, Wörner N, Rensch T, Eismann M, Eimer S, Hegermann J, Paponov IA, Ruperti B, Heberle-Bors E, Touraev A, Cohen JD, Palme K The endoplasmic reticulum localized PIN8 is a pollen specific auxin carrier involved in intracellular auxin homeostasis. Plant Journal 71:860–870 (2012)
Liu X, Barkawi L, Gardner G, Cohen JD Transport of indole-3-butyric acid and indole-3-acetic acid in Arabidopsis hypocotyls using stable isotope labeling. Plant Physiology 158:1988-2000 (2012)
Liu X, Hegeman AD, Gardner G, Cohen JD Protocol: High-throughput and quantitative assays of auxin and auxin precursors from minute tissue samples. Plant Methods 8:31 (2012)
Boswell PG, Carr PW, Cohen JD, Hegeman AD Easy and accurate calculation of programmed temperature gas chromatographic retention times by back-calculation of temperature and hold-up time profiles. Journal of Chromatography A 1263:179-188 (2012)
Li W, Zhou Y, Liu X, Yu P, Cohen JD, Meyerowitz EM Flower development master regulator LEAFY controls auxin response pathways in floral primordia formation. Science Signaling 6: ra23 (2013)
DeMason DA, Chetty V, Barkawi LS, Liu X, Cohen JD Unifoliata-Afila interactions in pea leaf morphogenesis. American J Botany 100:478-495 (2013)
Yu H, Karampelias M, Robert S, Peer WA, Swarup R, Ye S, Ge L, Cohen JD, Murphy A, Friml J, Estelle M ROOT ULTRAVIOLET B-SENSITIVE1/WEAK AUXIN RESPONSE3 is essential for polar auxin transport in Arabidopsis. Plant Physiology 162:965-976 (2013)
Mazhar S, Cohen JD, Hasnain S Auxin producing non-heterocystous Cyanobacteria and their impact on the growth and endogenous auxin homeostasis of wheat. Journal of Basic Microbiology 53:996-1003 (2013) DOI: 10.1002/jobm.201100563.
Wilson MB, Spivak M, Hegeman AD, Rendahl A, Cohen JD Metabolomics reveals the origins of antimicrobial plant resins collected by honey bees. PLoS ONE 8(10): e77512. doi:10.1371/journal.pone.0077512 (2013)
Tivendale ND, Ross JJ, Cohen JD The shifting paradigms of auxin biosynthesis. Trends in Plant Science 19:44-51 (2014) (http://dx.doi.org/10.1016/j.tplants.2013.09.012)
Roe MR, Cohen JD, and Hegeman AD Targeted deuteration of polyphenolics for their qualitative and quantitative metabolomic analysis in plant-derived extracts, Sriram G. Ed. Methods Mol Biol.1083:17-29. doi: 10.1007/978-1-62703-661-0_2. (2014)
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