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Dernière mise à jour : Mai 2018

Menu Logo Principal logo Université Paris Saclay AgroParisTech

BIOGER

BIOlogie et GEstion des Risques en agriculture - Champignons Pathogènes des Plantes

Ralph Dean's sabbatical at BIOGER

photo de Ralph Dean/ Ralph Dean's picture
BIOGER hosts Dr. Ralph A. Dean, William Neal Reynolds Distinguished Professor of Plant Pathology, during his sabbatical 1st May-31st December 2016. Dr. Dean is an internationally recognized researcher who pioneered genomic approaches in fungal phytopathogens and led the genome sequencing of the rice blast fungus Magnaporthe oryzae, the first for a filamentous phytopathogen. The purpose of his sabbatical is to better understand evolutionary processes in fungal phytopathogens allowing adaptation to abiotic stresses or to host plants. This encompasses model fungal phytopathogen systems but also endophytes whose association with crop plants may be beneficial. A key factor to be investigated for adaptation to hosts is the tremendous repertoire of effector genes and their diversity within pathogen isolates. Finally, Dr. Dean will promote and facilitate discussions enabling the creation of new ideas within BIOGER connected to two of the three transversal projects of BIOGER: "Infection strategies and processes" and "Adaptation to host and control methods". For the sabbatical Prof Dean is supported by a Grant from the Crop Health and Environment department of INRA.

Ralph Dean received his undergraduate degree in botany from the University of London (England) in 1980 and his Ph.D. degree in plant pathology from the University of Kentucky in 1986. Following a postdoctoral appointment at the University of Georgia, he joined the plant pathology faculty at Clemson University where he also chaired the interdisciplinary program in genetics and was associate director of the Clemson University Genomics Institute. In 1999, he joined the Department of Plant Pathology at North Carolina State University as a professor. In 2001, he also became the founding director of the Center for Integrated Fungal Research. In 2004, he received the Secretary’s Award of Honor from the USDA and the Huxley Memorial Medal from Imperial College, London. In 2005, he was appointed as a William Neal Reynolds distinguished professor in plant pathology. He has served on numerous USDA and NSF grants panels.

Over the past 25 years, Dr. Dean has established an internationally recognized research program. He has done this through his creativity, a vision for the future direction of science, and strong leadership. Early on, he chose to focus on Magnaporthe oryzae, the rice blast fungus, as his experimental system based on the economic importance of this pathogen and its tractable genetics. Worldwide, this disease is estimated to kill enough rice annually to feed over 60 million people. In his initial work, Dr. Dean conducted elegant studies on the infection process by the fungus that led to the identification of a cAMP-dependent kinase signaling cascade necessary for infection-related development and penetration of the host tissue. Further research showed that this signaling pathway was absolutely necessary for pathogenicity and involves communication between the host and the pathogen. Dr. Dean was among the first to embrace genomic approaches for the advancement of our understanding of plant pathogenesis and is widely recognized as a leader in the microbial genomics community. Through his determination and leadership, he obtained funding from the USDA and NSF to complete the sequence of M. oryzae. These endeavors led to the release of the complete sequence and genomic organization in an article in Nature in 2005. He also has played a leading role in decoding the rice genome.

More recent efforts have focused on a functional analysis of the interaction between rice and the rice blast fungus, employing gene expression profiling, large-scale mutagenesis, and proteomics approaches to define the transcriptional networks governing the host–pathogen interaction. Active projects include; Characterization of small RNA and gene silencing mechanisms in regulating infection development and host –pathogen interactions; Interrogation of post-translational protein modifications (phosphorylation and ubiquitination) during infection; Identification and characterization of effector proteins; and Comparative genome analysis of foliar and rooting infecting members of the Magnaporthacae. This project involves comparison of the genomes and gene content of M. oryzae with closely related species Gaemanonomyces graminis tritici and M. poae.  Recently, he has embarked upon metagenome analyses to evaluate the effect of cultivar, seed age and location on the fungal and bacterial microbiomes of rice.

Dr. Dean’s portfolio includes over 180 refereed publications and numerous book chapters and reviews in prestigious journals with an h-index of 52 and an i10-index of 116. In addition to documenting his leadership in fungal genomics, many document his substantial contributions to understanding the molecular basis of fungal development, using appressorium development as a model, and his willingness to share expertise with applied programs. While he receives most of his recognition for his work with M. oryzae, he has additional genomics projects on fungi of industrial importance such as Trichoderma and Aspergillus and is also identifying host genes for resistance to Fusarium in cucurbits. He was also issued patents for a fungal diagnostic assay as well as for detection of a disease resistance gene. Evidence of his prominence in molecular plant pathology include his most recent position as panel manager for the USDA competitive grants program and his appointment to the NSF board of visitors. He serves on the steering group for the Fungal Genome Initiative hosted by the Broad Institute that is partially supported by the Human Genome Initiative at NIH. He is also a lead member of the International Rice Blast Initiative. Dean has supervised 19 graduate students and 15 post-doctoral fellows, several of whom hold faculty positions at leading research universities.

In addition to his core research activities, funded from a variety of federal (NIH, NSF and USDA) and industrial sources, Dr. Dean has been instrumental in creating outreach programs. He and his research group have developed an innovative outreach program on genomics that is coordinated by Science House, an educational outreach program at NC State. This includes programs for students and teachers.  Dean’s research group is also active in exhibits such as the genomics program at the NC Museum of Natural History and at the NC State Fair. One of the most innovative outreach programs developed by Dr. Dean and his group is the Summer College for Biotechnology and the Life Sciences (SCIBLS). SCIBLS is an opportunity for talented high school students to learn about molecular biology through hands on experience with cutting edge techniques and to interact with college students and faculty on a daily basis. In addition to experiencing the university environment, students tour research facilities in the nearby Research Triangle Park where they hear first hand about careers in science.

Representative publications: Total 186

Franck, W, E. Gokce, S. Randall, Y. Oh, A.  Eyre, D. Muddiman, RA. Dean. Phosphoproteome analysis links protein phosphorylation to cellular remodeling and metabolic adaptation during  appressorium development. Journal of Proteome Research 2015 Apr 30. [Epub ahead of print]

Oh, Y.; Franck, W.L.; Han, S.O.; Shows, A.; Gokce, E.; Muddiman, D.C.; Dean, R.A. 2012. Polyubiquitin Is Required for Growth, Development and Pathogenicity in the Rice Blast Fungus Magnaporthe oryzae, PloS One,7,8,e42868.

Dean, R.; Van Kan, J.A.L.; Pretorius, Z.A.; Hammond-Kosack, K.E.; Di Pietro, A.; Spanu, P.D.; Rudd, J.J.; Dickman, M.; Kahmann, R.; Ellis, J. 2012.  The Top 10 fungal pathogens in molecular plant pathology, Molecular Plant Pathology,13,4,414-430.

Sailsbery JK, Atchley W, Dean RA. 2011. Phylogenetic Analysis and Classification of the Fungal bHLH Domain. Mol Biol Evol. 2011 Nov 22. [Epub ahead of print]

Nunes, C. C., Gowda, M., Sailsbery, J., Xue, M., Chen, F., Brown, D. E., Oh, Y. Y., Mitchell, T. K., Dean, R. A. 2011. Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae. BMC Genomics, 12:288 doi:10.1186/1471-2164-12-288

Gowda, M., Nunes, C.C., Sailsbery, J., Xue, M., Chen, F., Nelson, C.A., Brown, D.E., Oh, Y., Meng, S., Mitchell, T., Hagedorn, C.H., Dean, R.A.  2010. Genome-wide characterization of methylguanosine-capped and polyadenylated small RNAs in the rice blast fungus Magnaporthe oryzae. Nucleic Acids Research 38(21):7558-69.

Dean, R.A., Talbot, N.J., Ebbole, D.J., Farman, M.L., Mitchell, T., Orbach, M.J., Thon, M., Kulkarni, R., Xu, J-R.,Pan, H., Read, N.D., Lee, Y-H., Carbone, I., Brown, D., Oh, Y.Y., Donofrio, N., Soanes, D.M., Djonovic, S., Kolomiets, E., Rehmeyer, C., Li, W., Harding, M., Soonok, K., Lebrun M-H., Bohnert, H., Coughlin, S., Butler, J., Calvo, S., Ma, L-J., Nicol, R., Purcell, S., Nusbaum, C., Galagan, J.E., Birren, B.W. (2005).  The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434:890-896.

Kulkarni, R.D., Kelkar, H.S., Dean, R.A. (2003). An eight-cysteine containing CFEM domain unique to a group of fungal membrane proteins. Trends in Biochemical Sciences 28:118-121.

Goff, S.A., Ricke, D., Lan, T.H., Presting, G., Wang, R., Dunn, M., Glazebrook, J., Sessions, A., Oeller, P., Varma, H., Hadley, D., Hutchison, D., Martin, C., Katagiri, F., Lange, B.M., Moughamer, T., Xia, Y., Budworth, P., Zhong, J., Miguel, T., Paszkowski, U., Zhang, S., Colbert, M., Sun, W.L., Chen, L., Cooper, B., Park, S., Wood, T.C., Mao, L., Quail, P., Wing, R., Dean, R.A., Yu, Y., Zharkikh, A., Shen, R., Sahasrabudhe, S., Thomas, A., Cannings, R., Gutin, A., Pruss, D., Reid, J., Tavtigian, S., Mitchell, J., Eldredge, G., Scholl, T., Miller, R.M., Bhatnagar, S., Adey, N., Rubano, T., Tusneem, N., Robinson, R., Feldhaus, J., Macalma, T., Oliphant, A., Briggs, S. (2002). A draft sequence of the rice genome. Science 296: 92-100.

Zhu, H., Bilgin, M., Bangham, R., Hall, D., Casamayor, A., Bertone, P., Lan, N., Jansen, R., Bidlingmaier, S., Houfek, T.D., Mitchell, T., Miller, P., Dean, R.A., Gerstein, M., Snyder, M. (2001). Global analysis of protein activities using proteome chips. Science 293: 2101-2105.