Scientific Publications 2013

Anwer, M.U. and Davis, S. J. (2013) An overview of quantitative studies in the Arabidopsis thaliana circadian clock. Sem. in Cell and Dev. Biol. (early on-line)

Archacki R., Buszewicz D., Sarnowski T. J., Sarnowska E., Rolicka A. T., Tohge T., Fernie A. R., Jikumaru Y., Kotlinski M., Iwanicka-Nowicka R., Kalisiak K., Patryn J., Halibart-Puzio J., Kamiya Y., Davis S. J., Koblowska M. K., and Jerzmanowski A. (2013) BRAHMA ATPase of the SWI/SNF Chromatin Remodeling Complex Acts as a Positive Regulator of Gibberellin-Mediated Responses in Arabidopsis. PLoS ONE 8: e58588. open access

Bujdoso, N. and Davis S. J. Mathematical modeling of an oscillating gene circuit to unravel the circadian clock network of higher plants (early on-line Frontiers in Plant Systems Biol.)

Bulgarelli, D.,  Schlaeppi, K., Spaepen, S., Ver Loren van Themaat, E. and Schulze-Lefert, P. (2013) Structure and Functions of the Bacterial Microbiota of Plants, Annual Review of Plant Biology 64, 807-838.

Chang, C., Yu, D., Jiao, J., Jing, S., Schulze-Lefert, P. and Shen, Q.-H. (2013) Direct Interference of MLA Immune Receptors with Antagonistically Acting MYB and WRKY Transcription Factors Initiates Disease Resistance Signalling, The Plant Cell, doi: 10.1105/tpc.113.109942.

Delaunois, B., Colby, T., Belloy, N., Conreux, A., Harzen, A., Baillieul, F., Clément, C., Schmidt, J., Jeandet, P. and Cordelier, S.: Large-scale proteomic analysis of the grapevine apoplastic fluid reveals mainly stress-related proteins and cell wall modifying enzymes. BMC Plant Biology 13, 24-38 (2013). open access

El-Akhal, M.R., Colby, T., Cantoral, J.M., Harzen, A., Schmidt, J. and Fernández-Acero, F.J.: Proteomic analysis of conidia germination in Colletotrichum acutatum. Archives Microbiol. 195, 227-246 (2013).

Fournier-Level, A, Wilczek, A. M., Cooper, M. D., Roe, J. L., Anderson, J., Eaton, D., Moyers, B. T., Petipas, R. H., Schaeffer, R. N., Pieper, B., Reymond, M.¸ Koornneef, M., Welch, S., Remington, D. L., Schmitt, J.: Paths to selection on life history loci in different natural environments across the native range of Arabidopsis thaliana. In: Molecular Ecology, doi 10.1111/mec.12285 (2013).

Gebhardt C, Urbany C, Stich B. Dissection of potato complex traits by linkage and association genetics as basis for developing molecular diagnostics in breeding programs. In: Advances in Genomics of Plant genetic Resources. Eds. Tuberosa R, Frison E, Graner A; in press.

Gu, C., Shannon, A., Colby, T., Wang, Z., Shabab, M., Kumari, S., Villamor, J. G., McLaughlin, C. J., Weerapana, E., Kaiser, M., Cravatt, B. F., and Van der Hoorn, R. A. L.:(2013) Chemical proteomics with sulfonyl fluoride probes reveals selective labeling of functional tyrosines in glutathione transferases. Chem. Biol. 20, 541-548 (2013).

Hacquard, S., Kracher, B., Maekawa, T., Vernaldi, S., Schulze-Lefert, P.*, Ver Loren van Themaat, E.* (2013) Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts, PNAS, doi: 10.1073/pnas.1306807110. open access
*co-corresponding authors

Huang X, Ding J, Effgen S, Turck F, Koornneef ,M. Multiple loci and genetic interactions involving flowering time genes regulate stem branching among natural variants of Arabidopsis. New Phytolgist, doi: 10.1111/nph.12306 (2013).

Kopischke, M., Westphal, L., Schneeberger,  K., Clark, R., Ossowski, S., Wewer, V., Fuchs, R., Landtag, J., Hause, G., Dörmann, P., Lipka, V., Weigel, D., Schulze-Lefert, P., Scheel, D. and Rosahl, S. (2013) Impaired sterol ester synthesis alters the response of Arabidopsis thaliana to Phytophthora infestans. The Plant Journal, 73, 456–468, DOI: 10.1111/tpj.12046.

Kundu, N., Dozier, U., Deslandes, L., Somssich, I.E., and Hemayet, U. Arabidopsis scaffold protein RACK1A interacts with diverse environmental stress and photosynthesis related proteins. Plant Signal. Behav. 8:5, e24012 (2013). open access

Li L, Tacke E, Hofferbert H-R, Lübeck J, Strahwald J, Draffehn AM, Walkemeier B, Gebhardt C: Validation of candidate gene markers for marker-assisted selection of potato cultivars with improved tuber quality. Theor Appl Genet, DOI 10.1007/s00122-012-2035-z (2013). open access

Logemann, E., Birkenbihl, R. P., Rawat, V., Schneeberger, K., Schmelzer, E. and Somssich, I. E. Functional dissection of the PROPEP2 and PROPEP3 promoters reveals the importance of WRKY factors in mediating microbe-associated molecular pattern-induced expression. New Phytologist. doi:10.1111/nph.12233 (2013)

Meesters C, Kombrink E . Screening for bioactive small molecules by in vivo monitoring of luciferase-based reporter gene expression in Arabidopsis thaliana. In G Hicks, S Robert, eds, Plant Chemical Biology Humana Press, New York, pp (in press).

Misas-Villamil, J. C., Toenges, G., Kolodziejek, I., Sadaghiani, A. M., Kaschani, F., Colby, T., Bogyo, M., and Van der Hoorn, R. A. L.: Activity profiling of vacuolar processing enzymes reveals a role for VPE during oomycete infection. Plant Journal 73, 689-700 (2013).

Naz, A.A., Raman, S., Martinez, C.C., Sinha, N.R., Schmitz, G., Theres, K.Trifoliate encodes an MYB transcription factor that modulates leaf and shoot architecture in tomato. Proc. Natl. Acad. Sci. USA 110:2401-2406 (2013).

Nordström; K. J. V., Albani, M. C.; Velikkakam James, G.; Gutjahr, C.; Hartwig, B.; Turck, F.; Paszkowski, U.; Coupland, G. and K. Schneeberger: Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers. Nature Biotechnology, advanced online publication 31, 325-330, doi: 10.1038/nbt.2515 (2013).

Poraty-Gavraae, L., Zimmermann, P., Haigis, S., Bednarek, P., Hazaka, O., Rogovoy Stelmakhd, O., Sadotd, E., Schulze-Lefert, P., Gruissem, W. and Yalovsky, S. The Arabidopsis ROP GTPase AtROP6 functions in developmental and pathogen response pathways, Plant Physiology 161, 1172-1188 (2013). open access

Rollins, J., Habte, E., Templer, S., Colby, T., Schmidt, J., von Korff, M.: Proteomic and Phenotypic Responses to Abiotic Stress in Barley (Hordeum vulgare L). J. Exp. Bot., in press (2013).

Schlaeppi, K., Ver Loren van Themaat, E., Bulgarelli, D. and Schulze-Lefert, P. (2013) Arabidopsis thaliana as model for studies on the bacterial root microbiota, Molecular Microbial Ecology of the Rhizosphere: Vol. 1 & 2 (ed. F. J. de Bruijn), doi: 10.1002/9781118297674.ch23.

Schön, M., Töller, A., Diezel, C., Roth, C., Westphal, L., Wiermer, M., and Somssich, I.E. Analyses of wrky18 wrky40 plants reveal critical roles of SA/EDS1 signaling and indoleglucosinolate biosynthesis for G. orontii resistance and a loss-of-resistance towards Pto AvrRPS4. Mol. Plant-Microbe Interact., doi: 10.1094/MPMI-11-12-0265-R (2013).

Sharlach, M.; Dahlbeck, D.; Liu, L.; Chiu, J.; Jiménez-Gómez, J. M.; Kimura, S.; Koenig, D.; Maloof, J. N.; Sinha, N.; Minsavage, G. V.; Jones, J. B.; Stall, R. E.; Staskawicz, B. J.: Fine genetic mapping of RXopJ4, a bacterial spot disease resistance locus from Solanum pennellii LA716. In: Theoretical and Applied Genetics 126:601-910. 1007/s00122-012-2004-6 (2013).

Shin, J., Anwer, M. U., and Davis, S. J. (2013) Phytochrome-interacting factors (PIFs) as bridges between environmental signals and the circadian clock: diurnal regulation of growth and development. Mol. Plant (early on-line)

Shin, J. Du, S., Bujdoso, N., Hu. Y., and Davis, S. J. (2013) Overexpression and loss-of-function at TIME FOR COFFEE results in similar phenotypes in diverse growth and physiological responses. J. Plant Biol. (in press)

Tintor N, Ross A, Kanehara K, Yamada K, Fan L, Kemmerling B, Nürnberger T, Tsuda K, Saijo Y.: Layered pattern receptor signaling via ethylene and endogenous elicitor peptides during Arabidopsis immunity to bacterial infection. In: Proceedings of the National Academy of Sciences 110, 6211-6216 (2013).

Tomanov, K., Hardtke, C., Budhiraja, R., Hermkes, R., Coupland, G. and Bachmair, A.: Small Ubiquitin-Like Modifier Conjugating Enzyme with Active Site Mutation Acts as Dominant Negative Inhibitor of SUMO Conjugation in Arabidopsis. Journal of Integrative Plant Biology, 55: 75–82. doi: 10.1111/jipb.12016 (2013). open access

Wang Z, Cao H, Sun Y, Li X, Chen F, Carles A, Li Y, Ding M, Zhan C, Deng X, Soppe WJJ, and Liu Y. Arabidopsis paired amphipathic helix proteins SNL1 and SNL2 redundantly regulate primary seed dormancy via the ABA-ethylene antagonism mediated by histone deacetylation. Plant Cell 25:149-166 (2013).

Xing, S., Salinas, M., Garcia-Molina, A., Höhmann, S., Berndtgen, R. and Huijser, P. (2013), SPL8 and miR156-targeted SPL genes redundantly regulate Arabidopsis gynoecium differential patterning. The Plant Journal. doi: 10.1111/tpj.12221. open access

Yamaguchi, N., Wu, M.-F., Winter, C.M., Berns, M.C., Nole-Wilson, S., Yamaguchi, A., Coupland, G., Krizek, B.A. and Wagner, D. A Molecular Framework for Auxin-Mediated Initiation of Flower Primordia. Developmental Cell 24, 271-282 (2013).

Yun, H.S., Kwaaitaal, M., Kato, N., Yi, C., Park, S., Sato M.H., Schulze-Lefert, P.* and Kwon, C.*  Requirement of vesicle-associated membrane protein 721 and 722 for sustained growth during immune responses in Arabidopsis. Mol. Cells Vol. 35, 6 (2013).
*co-corresponding authors

Zbierzak, A.M., Porfirova, S., Griebel, T., Melzer, M., *Parker, J.E. and *Dörmann, P. 2013. A TIR-NBS protein encoded by Arabidopsis Chilling Sensitive 1 (CHS1) limits chloroplast damage and cell death at low temperature. Plant J., doi: 10.1111/tpj.12219. *Corresponding authors.

Zech, H., Hensler, M., Koßmehl, S., Drüppel, K., Wöhlbrand, L., Trautwein, K., Hulsch, R., Maschmann, U., Colby, T., Schmidt, J., Reinhardt, R., Schreiber, K., Schomburg, D., Rabus, R.: Adaptation of Phaeobacter gallaeciensis DSM 17395 to growth with complex nutrients. Proteomics, in press (2013).

Zech, H., Hensler, M., Koßmehl, S., Drüppel, K., Wöhlbrand, L., Trautwein, K., Colby, T., Schmidt, J., Reinhardt, R., Schmidt-Hohagen, K.., Schomburg, D., Rabus, R.: Dynamics of amino acid utilization in Phaeobacter gallaeciensis DSM 17395. Proteomics, in press (2013).

Zografou, T and Turck, F.: Epigenetic Control of Flowering Time. In: Epigenetic Memory and Control in Plants. Heidelberg, Springer 2013 (Signaling and Communication in Plants Vol. 18) pp 77-105. http://dx.doi.org/10.1007/978-3-642-35227-0_5