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Nina Fedoroff
 ••Telephone: (814) 863-4576 *****E-mail: nvf1@psu.edu

           Arabidopsis
                                            Arabidopsis

  • Evan Pugh Professor of Biology
  • Willaman Professor of Life Sciences, Biology Department
  • External Faculty, Santa Fe Institute
Education:
B.S., Syracuse University, Biology and Chemistry, summa cum laude (1966)
Ph.D., The Rockefeller University, Molecular Biology (1972)

Research Interests:

• Plant stress response
• Hormone signaling
• Transposable elements
• Epigenetic mechanisms

Plant stress response: A major project in the laboratory is investigating the responses of plants to biotic (pathogens) and abiotic (ozone, temperature, chemicals) stresses using DNA microarray gene expression profiling and reverse genetics. We have identified more than 1200 stress-modulated Arabidopsis genes and studying their expression under various conditions. The illustration shows the change in gene expression of 366 genes that are induced (red) or repressed (green) by ozone. Among the genes induced by various stresses are signaling genes, transcription factors, and effector genes that include enzymes that alter the cells structure and properties in response to stress. The signaling molecules include MAP kinases and receptor-like kinases. We are suppressing and overexpressing potential regulatory genes to identify the genes under their control. We want to understand the structure of the stress-response gene networks and to explores molecular genetic approaches to modifying the stress response (see Holter et al, 2000, 2001).

Hormone responses: The hyl1 Arabidopsis mutant (right) has a transposon insertion mutation in a gene that is involved in several hormonal signaling pathways, including those for abscisic acid, auxin and cytokinin. The mutant is affected in many growth parameters, including graviperception. It is not as sensitive to exogenous auxins and cytokinins as the wiltype, but it is hypersensitive to abscisic acid. The HYL1 protein binds to double-stranded RNA and localizes to the nucleus. The mutant is described in Lu and Fedoroff (2000). We are investigating how this protein affects hormone signaling.

Transposable elements: transposable elements or transposons were discovered in corn (maize) plants by the famous geneticist Barbara McClintock through classical genetic analysis of unstable mutations (for a brief history, see http://www.ergito.com or Fedoroff 2001). Maize transposons were cloned in our laboratory almost 20 years ago and are now widely used for insertional mutagenesis. We have created a database of several hundred Arabidopsis transposon insertion lines using a transposon tagging system developed in the laboratory (Smith et al., 1996; Raina et al., 2001). A map of the insertions is shown and the database can be searched at: http://sgio2.biotec.psu.edu/sr.

Epigenetic mechanisms: The maize Suppressor-mutator (Spm) transposon is epigenetically inactivated by methylation and encodes a protein, TnpA, which is capable of reversing the inactivation (Schläppi et al., 1994; Fedoroff et al., 1995). Using an inducible promoter to express TnpA, current experiments seek to understand how it demethylates the Spm promoter. Some ideas about plant transposon evolution are explored in Fedoroff (2000).

 

 


DNA microarray data


Maize kernel
 

MENDEL IN THE KITCHEN: A Scientist's View of Genetically Modified Foods
Nina Fedoroff and Nancy Marie Brown.
Joseph Henry, (352p) ISBN 0-309-09505-1


Reviews

 

Additional Links:
http://www.science.psu.edu/alert/Fedoroff10-2004.html
http://www.nap.edu/catalog/11000.html
http://thinks.com/cgi-bin/books/books.pl/item-0309092051/shop.htm



 

National Science Board Awards Dinner

May 7, 2002
U.S. Department of State

Eamon Kelly, NSB Chair; (left) Rita Colwell, NSF Director; (center) Nina Fedoroff, NSB member (right)

 

Some technical references:

  • Fedoroff, N. V. (2000). Transposons and genome evolution in plants. Proc. Natl. Acad. Sci. USA 97: 7002-7007 (download pdf file).
  • Holter, N. S., Mitra, M., Maritan, A, Cieplak, M., Banavar, J. R. and N. Fedoroff (2000) Fundamental patterns underlying gene expression profiles: simplicity from complexity. Proc. Natl. Acad. Sci. USA 97: 8409-8414 (download pdf file).
  • Lu, C. and N. Fedoroff (2000). HYL1, a dsRNA-binding nuclear regulatory protein in plant hormone signaling. Plant Cell 12: 1-15 (download pdf file).
  • Holter, N. S., Maritan, A., Cieplak, M., Fedoroff, N. V., and J. R. Banavar (2001). Dynamic modeling of gene expression data. Proc. Natl. Acad. Sci. USA, 98: 1693-1698 (download pdf file).
  • Fedoroff, N. V. (2001) How transposition was discovered. Nature Struct. Biol. 8: 300-301 (download pdf file).
  • Fedoroff, N. V. (2002).  RNA-binding proteins in plants: the tip of an iceberg?  Curr. Op. Plant Biol., 5:452-459 (download pdf file).
  • Raina, S., Mahalingam, R., Chen, F., and N. Fedoroff (2002). A collection of sequenced and mapped Ds transposon insertion sites in Arabidopsis thaliana.   Plant Mol.Biol. 50:93-110 (download pdf file).
  • Fedoroff, N. V. and W. Fontana (2002) Small numbers of large molecules.  Science 297:1129-1130 (download pdf file).
  • Cui, H., and Fedoroff, N. V. (2002) Inducible DNA demethylation mediated by the maize Spm transposon-encoded TnpA protein.  Plant Cell 14:1-17 (download pdf file).
  • Lu, C., Han, M.-H., Guevara-Garcia, A., and Fedoroff, N.  (2002) Mitogen-activated protein kinase signaling in post-germination arrest of development by abscisic acid. Proc. Natl. Acad. Sci. USA 99:15812-15817 (download pdf file).
  • Mahalingam, R., Buitrago, A. M., Eckardt, N.,  Shah, N., Guevara-Garcia, A., Day, P, Raina, R., and Fedoroff, N (2003). Charactarizing the stress/defense transcriptome of Arabidopsis.  Genome Biology  4: R20 (download pdf file).
  • Mahalingam, R., and Fedoroff, N (2003).  Stress response, cell death and signaling:  the many faces of ROS.  Physiologia Plantarum, 119:56-68 (download pdf file).
  • Racunas, S.A., N. Shah & N.V. Fedoroff (2003). A contradiction-based framework for testing gene regulation hypotheses. In IEEE Bioinformatics. Stanford University, Palo Alto, California: IEEE Computer Society (download pdf file).
  • Shah, N. H., King, D. C., Shah, P. N. and Fedoroff, N. V. (2003) A tool-kit for cDNA microarray and promoter analysis.  Bioinformatics, 19: 1848-8.
  • Zhang, S. Raina, S., Li, H., Li, J. Ma, H., Huang, H., and N. Fedoroff (2003). Resources for targeted insertional and deletional mutagenesis in Arabidopsis. Plant Mol. Biol. 53: 133-150 (download pdf file).
  • Han, M.-H., Goud, S., Song, L., and Fedoroff, N. (2004) The Arabidopsis dsRNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proc. Natl. Acad. Sci. USA, 101: 1093-1098 (download pdf file).
  • Racunas, S.A., Shah, N. H., Albert I. and Fedoroff N. V. (2004).  HyBrow: A prototype system for computer-aided hypothesis evaluation.  Bioinformatics, in press (download pdf file).

Websites and non-technical publications:

  • Fedoroff, N. V. (2001). The genomicist's tool kit: DNA cloning and sequencing, the polymerase chain reaction, and DNA microarrays. At http://www.science.psu.edu. http://www.science.psu.edu/alert/frontiers/Fedoroff1-HTML/index.htm
  • Fedoroff, N. V. (2001). Monsters or miracles? Genetically modified organisms in our food. At http://www.science.psu.edu.
  • Fedoroff, N. (1992). Barbara McClintock: the geneticist, the genius, the woman. Cell, 71, 181-182.
  • Fedoroff, N. (1996). Two women geneticists. American Scholar 65,587-592.
  • Fedoroff, N. (1997). Food for a hungry world: we must find ways to increase agricultural productivity. The Chronicle of Higher Education 43: 84-85.
  • Fedoroff, N. V. and J. E. Cohen (1999). Plants and population: Is there time? Proc. Natl. Acad. Sci USA 96: 5903-5907 (download pdf file).
  • Fedoroff, N. V. (2001). What is the future of GMOs? In: 2001 AAAS Science and Technology Policy Yearbook. A. H. Teich, S. D. Nelson, C. McEnaney, and S. J. Lita, eds. (AAAS, Washington, D.C.) pp. 165-172.
  • Fedoroff, N. (2001). Biotechnology and agriculture: promise and peril. In: Proceedings of a conference titled: “The Role of New Technologies in Poverty Alleviation and Sustainable Development,” NAS, in press.
  • Fedoroff, N. (2003) Prehistoric GM corn.  Science 302:1158-59 (download pdf file). Responses to letters to the editor. Science 303.1765 (download pdf file).
  • Fedoroff, N. V., and N. M. Brown (2004)  Mendel in the Kitchen:  A Scientist's View of Genetically Modified Foods  (NAS Joseph Henry Press: Washington, DC), http://www.nap.edu/catalog/11000.html
 
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