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In The Arabidopsis Book (American Society of Plant Biologists) http://www.bioone.org/doi/abs/10.1199/tab.0129  Acosta, I. and Farmer, E.E. (2010)

Gfeller, A., Dubugnon, L., Liechti, R. and Farmer, E.E. (16 February 2010)
Jasmonate Biochemical Pathway. Science Signaling 3 (109), cm3. [DOI: 10.1126/scisignal.3109cm3]

Gfeller, A., Liechti, R., and Farmer, E.E. (16 February 2010)
Arabidopsis Jasmonate Signaling Pathway. Science Signaling 3 (109), cm4. [DOI: 10.1126/scisignal.3109cm4]



Chauvin, A., Calderlari, D., Wolfender, J-L. and Farmer, E.E. (2013) Four 13-lipoxygenases contribute to rapid jasmonate synthesis in wounded Arabidopsis leaves: a role for LOX6 in responses to long distance wound signals. New Phytol. 197, 566-575.

Farmer, E.E. and Mueller, M.J. (2013) ROS-mediated lipid peroxidation and RES-activated signaling. Ann. Rev. Plant Biol. 64, 429-450.

Editorial overview: Farmer, E.E. and Browse, J. (2013) Physiology and Metabolism: water for thought. Curr. Opin. Plant Biol. 16, 271-273.

Dadacz-Narloch, B., Kimura, S., Kurusu, T., Farmer, E.E., Becker, D., Kuchitsu, K., Hedrich, R. (2013) On the cellular site of two-pore channel TPC1 action in the Poaceae. New Phytol. 200, 663-674.

Mousavi, S.A.R., Chauvin, A., Pascaud, F., Kellenberger, S. and Edward E. Farmer, E.E. (2013) GLUTAMATE RECEPTOR-LIKE genes mediate leaf-to-leaf wound signalling. Nature 500, 422-426.

Acosta, I.F., Gasperini, D., Chételat, A., Stolz, S., Santuari, L. and Farmer, E.E. The role of NINJA in root jasmonate signaling. (2013) Proc. Natl. Acad. Sci. USA 110, 15473-15478.



Mafli, A., Goudet, J. and Farmer, E.E. (2012) Plants and tortoises: mutations in the Arabidopsis jasmonate pathway increase feeding in a vertebrate herbivore. Mol. Ecol. 21, 2531-2541.

Schmid-Siegert, E., Loscos, J. and Farmer E.E. (2012) Inducible malondialdehyde pools in zones of cell proliferation and developing tissues in Arabidopsis. J. Biol. Chem. 287, 8954-8962.

Reeves, P.H., Ellis, C.M., Ploense, S., Wu, M-F., Yadav, V., Tholl, D., Chételat, A., Haupt, I., Kennerley, B.J., Hodgens, C., Farmer, E.E., Nagpal, P. and Reed, J.W. (2012) A regulatory network for coordinated flower maturation. PLoS Genetics 8 e1002506



Gfeller, A., Baerenfaller, K., Loscos, J., Chételat, A., Baginsky, S. and Farmer, E.E. (2011) Jasmonate controls polypeptide patterning in undamaged tissue in wounded Arabidopsis leaves. Plant Physiol. 156, 1797-1807.

Caldelari, D., Wang, G., Farmer, E.E. and Dong, X. (2011) Arabidopsis lox3 lox4 double mutants are male sterile and defective in global proliferative arrest. Plant Mol. Biol. 75, 25-33.



Rodríguez, V.M., Chételat, A., Majcherczyk P. and Farmer, E.E. (2010) Chloroplastic phosphoadenosine phosphosulfate (PAPS) metabolism regulates basal levels of the prohormone jasmonic acid in Arabidopsis leaves. Plant Physiol. 152, 1335-1345.

Gfeller, A., Dubugnon, L., Liechti, R. and Farmer, E.E. (16 February 2010)
Jasmonate Biochemical Pathway. Science Signaling 3 (109), cm3. [DOI: 10.1126/scisignal.3109cm3]

Gfeller, A., Liechti, R., and Farmer, E.E. (16 February 2010)
Arabidopsis Jasmonate Signaling Pathway. Science Signaling 3 (109), cm4. [DOI: 10.1126/scisignal.3109cm4]

Acosta, I. and Farmer, E.E. (2010) Jasmonates. In The Arabidopsis Book
(American Society of Plant Biologists) http://www.bioone.org/doi/abs/10.1199/tab.0129

Rienmüller, F., Beyhl, D., Lautner, S., Fromm, J., Al-Rasheid, K.A.S., Ache, P., Farmer, E.E., Marten, I. and Hedrich, R. (2010) Guard cell-specific calcium sensitivity of high density and activity SV/TPC1 channels. Plant Cell Physiol. 51, 1548-1554.



Beyhl, D., Hörtensteiner, S., Martinoia, E., Farmer, E. E., Fromm, J., Marten, I. and Hedrich, R. (2009) The fou2 mutation in the major vacuolar cation channel TPC1 confers tolerance to inhibitory luminal calcium. Plant J. 58, 715-723.

Farmer, E.E. and Dubugnon, L. (2009) Detritivorous crustaceans become herbivores on jasmonate-deficient plants. Proc. Natl. Acad. Sci. USA 106, 935-940. This work led to the development of a very simple bioassay using woodlice to screen for plants with defective JA signal pathways. The assay is in routinely used in the lab.

Glauser, G., Dubugnon, L., Mousavi, S.A.R., Rudaz, R., Wolfender, J-L. and Farmer, E.E. (2009) Velocity estimates for signal propagation leading to systemic jasmonic acid accumulation in wounded Arabidopsis. J. Biol. Chem. 284, 34506-34513. At the time of this publication groups studying long distance (systemic) defense signaling in Arabidopsis did not take interleaf vascular architecture (parastichies) into account. Doing so allowed us to improve on velocity estimates for JA accumulation in distal leaves (Glauser et al., 2008) and provide the first constrained estimate of signal velocity for a systemic wound response in plants.

Mène-Saffrané, L., Dubugnon, L., Chételat, A., Stolz, S., Gouhier-Darimont, C. and Farmer, E.E. (2009) Nonenzymatic oxidation of trienoic fatty acids contributes to reactive oxygen species management in Arabidopsis.  J. Biol. Chem. 284, 1702-1708. Proposes that omega-3 fatty acids have a primary role as sinks for ROS protecting vulnerable tissues, in particular those in light gathering structures.




Glauser, G., Grata, E., Dubugnon, L., Rudaz, S., Farmer, E.E.* and Wolfender, J-L. (2008) Spatial and temporal dynamics of jasmonate synthesis and accumulation in Arabidopsis in response to wounding. J. Biol. Chem. 283, 16400-16407 *corresponding author. This paper demonstrated that JA synthesis in leaves distal to the wounded leaf is rapid, in the region of 2-5 min after wounding and we proposed that a signal travels at at least 3 cm per min to stimulate JA synthesis distal to wounds. We also identified a new oxylipin: a highly oxidized form of jasmonoyl-isoleucine.

Schommer, C., Palatnik, J.F., Aggarwal, P., Chételat, A., Cubas, C., Farmer, E.E., Nath, U. and Weigel., D. (2008) Control of jasmonate biosynthesis and senescence by miR319 targets. Plos Biology 6, e230.

Ribot, C., Zimmerli, C., Farmer, E.E., Reymond, P. and Poirier, Y. (2008) Induction of the Arabidopsis PHO1;H10 gene by 12-oxo-phytodienoic acid but not jasmonic acid via a CORONATINE INSENSITIVE 1-dependent pathway. Plant Physiol. 147, 696-706.

Grata, E., Boccard, J., Guillarme, D., Glauser, G., Carrupt, P-A., Farmer, E.E., Wolfender, J-L. and Rudaz, S. (2008) UPLC-TOF-MS for plant metabolomics: A sequential approach for wound marker analysis in Arabidopsis thaliana. J. Chrom. B. 871, 261-270.




Mène-Saffrané, L., Davoine, C., Stolz, S., Majcherczyk, P. and Farmer, E.E. (2007) Genetic removal of tri-unsaturated fatty acids suppresses developmental and molecular phenotypes of an Arabidopsis tocopherol deficient mutant: Whole-body mapping of malondialdehyde pools in a complex eukaryote. J. Biol. Chem. 282, 35749-35756.

Bonaventure, G., Gfeller, A., Rodríguez, V.M., Armand, F. and Farmer, E.E. (2007) The fou2 gain-of-function allele and the wild-type allele of the Two Pore Channel 1 contribute to different extents or by different mechanisms to defense gene expression in Arabidopsis. . Plant Cell Physiol. 48, 1775-1789.

Yan, Y., Stolz, S., Chételat, A., Reymond, P., Pagni, M., Dubugnon, L., and Farmer, E.E. (2007) A Downstream Mediator in the Growth Repression Limb of the Jasmonate Pathway. Plant Cell, 19, 2470-2483.

Farmer, E.E. (2007) Jasmonate perception machines. Nature 448, 659-660.

Grata, E., Bocard, J., Carrupt, P-A., Farmer, E.E., Wolfender, J-L., and Rudaz, S. (2007) Development of a two-step screening ESI-TOF-MS method for rapid determination of significant stree-induced metabolome modifications in plant leaf extracts: The wound response in arabidopsis thiana as a case study. J. Sep. Sci. 30, 2268-2278.

Farmer, E.E. and Davoine, C. (2007) Reactive electrophile species. Curr. Opin. Plant Biol. 10, 380-386.

Bonaventure, G., Gfeller, A., Proebsting, W.M., Hoerstensteiner, S., Chélat, A., Martinoia, E. and Farmer, E.E. A gain of founction allele of TPC1 activates oxylipin biogenesis after leaf wounding in Arabidopsis. Plant J. 49,889-898




Mueller, M.J., Mène-Saffrané, L., Grun, C., Karg, K. and Farmer, E.E. (2006) Oxylipin analysis methods. Plant J. 45, 472-489.

Musser, R.O., Farmer, E.E., Peiffer, M., Williams, S.A. and Felton, G.A. (2006) Ablation of caterpillar labial salivary glands: Technique for determinating the role of saliva in insect-plant interactions. J.Chem. Ecol. 32.981-922.

Sattler, S.E., Mène-Saffrané, L., Farmer, E.E., Krischke, M., Mueller, M.J. and DellaPenna, D. (2006) Non-enzymatic lipid peroxidation reprogams gene expression and activates defense markers in tocopherol deficient mutants. Plant Cell 18,3706-3720.



Armand, F., Bucher, P., Jongeneel, C.V., and Farmer, E.E., (2005) Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge. Bioinformatics, 21, 2906-2908.

Schulze-Lefert, P., and Farmer, E.E. (2005) Biotic interactions: From molecular networks to interorganismal communities (Editorial overview). Curr. Opin. Plant Biol. 8, 343-345.

Nagpal, P., Ellis, C.M., Weber, H., Ploense, S., Barkawi, L.S., Guilfoyle, T.J., Hagen, G., Alonso, J.M., Cohen, J.D., Farmer, E.E., Ecker, J.R. and Reed, J.W. (2005) Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation. Development, 132, 4107-4118.



Gfeller, A., Farmer, E.E, (2004) Keeping the Leaves Green Above Us. Science. 316, 1515-1516.

Bariola, P.A., Retelska, D., Stasiak, A., Kammerer, R.A., Fleming, A., Hijri, M., Frank, S. and Farmer, E.E. (2004) Remorins form a novel family of coiled coil-forming oligomeric and filamentous proteins associated with apical, vascular and embryonic tissues in plants. Plant Mol. Biol. 55: 579-594. The work supports the idea that remorin is an important part of the membrane skeleton.

See videos of remorin localisation.
video 1
video 2

Previous publications on remorin from our work :

  • J. Biol. Chem. 266, 3140-3145
  • Plant Physiol. 103, 1393-1397
  • Plant Cell 8, 2265-2276
  • Proc. Natl. Acad. Sci. USA 92, 4145-4149

Reymond, P., Bodenhausen, N., Van Poecke, R.M.P., Krishnamurthy, V., Dicke, M. and Farmer, E.E. (2004) A conserved transcript pattern in response to a specialist and a generalist herbivore. Plant Cell, 16, 3132-3147.
Demonstrates that between 67 to 84 % of insect activated gene expression depends, directly or indirectly on the jasmonate signal pathway.

Weber, H., Chételat, A, Reymond, P. and Farmer, E.E. (2004) Selective and powerful stress gene expression in Arabidopsis in response to malondialdehyde. Plant J. 37, 877-888.
Demonstrates that malondialdehyde (MDA) can have potent biological activtiy at low concentation in an intact eukaryote thus confirming predictions made in Alméras et al.



Farmer E.E, Almeras E. and Krisnamurthy V., (2003) Jasmonates and related oxylipins in plant responses to pathogenesis and herbivory. Curr. Op. Plant Biol 6, 372-378.

Alméras E., Stolz S., Vollenweider S., Reymond P., Mène-Saffrané L., and Farmer, E.E., (2003) Reactive electrophile species activate defense gene expression in Arabidopsis. Plant J. 34, 205-216. Shows that the ubiquitous non-enzymatic lipid oxidation product MDA can regulate survival- and defense-related genes



Liechti, R., Farmer, E.E., (2002) The jasmonate pathway. Science 296 (5573): 1649-50.

Weber, H. (2002) Fatty acid-derived signals in plants. TRENDS in Plant Science 7, 217-224




Farmer, E. E. (2001) Surface-to-air signals. Nature 411, 854-856. Proposed the term 'reactive eclectrophile species' (RES).

Stintzi, A., Weber, H., Reymond, P., Browse, J. and Farmer, E.E. (2001) Plant defense in the absence of jasmonic acid: the role of cyclopentenones. Proc. Natl. Acad. Sci. USA, 98, 12837-12842. Details. See commentary by Gregg A. Howe. Showed that cyclopentenone jasmonates (OPDA and dnOPDA) can signal as electrophphiles. Also suggests that cyclopentenone jasmonates can also signal through the jasmonate pathway.



Vollenweider, S., Weber, H., Stolz, S., Chételat, A. and Farmer, E.E. (2000) Fatty acid ketodienes and fatty acid ketotrienes : Michael addition acceptors that accumulate in wounded and diseased Arabidopsis leaves. Plant J. 24, 467-476. We show that a variety of pathogenesis-associated lipids including fatty acid ketotrienes activate the GST1 gene in Arabidopsis and that this is structure-dependent. The structure in question is the a,b-unsaturated carbonyl group. Introduces a protocol with which to volatilize malondialdehyde.

Reymond, P., Weber H., Damond M. and Farmer E.E. (2000) Differential gene expression in response to mechanical wounding and insect feeding in Arabidopsis. Plant Cell 12, 707-719. Details This microarray analysis of responses to herbivory in Arabidopsis supported an important role for jasmonates in gene expression following insect damage. Interestingly, genes that are strongly upregulated in mechanically crushed tissues and also induced during dehydration were less activated by insects. The implication is that insect feeding strategies might minimise the cut leaf surface exposed to the air. This, of course, might help explain why insects often cut circles and semi-circles in leaves.
New (March 2002): Selected as New Hot Paper by ISI Essential Science Indicator here
Farmer, E.E. (2000) Adding injury to insult:pathogen detection and responses. Genome Biology 1, reviews 1012.1-1012.3



Weber, H., Chételat, A., Caldelari, D. and Farmer, E.E. (1999) Divinyl ether fatty acid synthesis in late blight diseased potato leaves. Plant Cell 11, 485-493.
Many studies on antibiotics (phytoalexins) made in potato in response to the devastating pathogen Phytophora infestans have concentrated on tubers. We looked at the primary infection sites, leaves, and were surprised to find very high levels of fatty acid divinyl ethers which we describe as "phytoalexin-like compounds".



Caldelari, D. and Farmer, E.E. (1998) Rapid assays for the coupled cell free generation of oxylipins. Phytochem. 47, 599-604. These assays were used successfully to isolate new oxylipin synthesis mutants ('fou' mutants) by Bonaventure et al. 2007.

Reymond, P and Farmer, E.E. (1998) Jasmonate and salicylate as global signals for defense gene expression. Curr. Op. Plant Biol. 1, 404-411.



Weber, H., Vick, B.A. and Farmer, E.E. (1997) Dinor-oxo-phytodienoic acid: a new hexadecanoid signal in the jasmonate family. Proc. Natl. Acad. Sci. USA 94, 10473-10478. Introduces the concept of the "oxylipin signature" whereby more than one jasmonate family member is responsible for the fine-tuning of gene expression and that different jasmonates might play diferent biological roles. Presents a new method for the discovery and quantification of jasmonates and describes a new sixteen carbon jasmonate, dinor-OPDA.
Farmer, E.E. (1997) New fatty acid-based signals: A lesson from the plant world. (Perspective) Science 276, 912-913.


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