Postdoctoral Fellow

Timothy J. Durfee Genome Center/Biotechnology Center Faculty Supervisor: Fred Blattner Email: durf@genome.wisc.edu 262-8552

The major focus of my research is to develop a predictive model describing how changes in growth rate affect global transcription in E. coli and what role guanine tetraphosphate, (p)ppGpp (also known as “magic spot”), plays in that process. The biological component of the work consists of determining growth rates, ppGpp levels and gene expression profiles from both wild type MG1655 cells and various relA spoT mutant strains under conditions that affect growth rate. Computationally, a probabilistic model based on a learned Bayesian network will be developed that, based on the experimental data, computes the likelihood that any given gene will be expressed at a particular growth rate. Additional computational methods will be developed to assess promoter regions for elements that allow positive or negative regulation by (p)ppGpp. .

CV

CV 2004 (Word document)

Publications (selected)

Durfee, T., Becherer, K., Chen, P.L., Yeh, S.H., Zhu, Y.Z., Kilburn, A., Lee, W.H., Elledge, S.J., 1993. The Retinoblastoma Protein Associates with the Protein Phosphatase Type 1 Catalytic Subunit. Genes Dev. 7, 555-569.

Durfee, T., Mancini, M., Jones, D., Elledge, S.J., Lee, W.H., 1994. The Amino-Terminal Region of the Retinoblastoma Gene Product Binds a Novel Nuclear Matrix Protein that Co-localizes to Centers for RNA Processing. J. Cell Biol. 127, 609-622.

Shan, B., Durfee, T., Lee, W.H., 1996. Disruption of the Rb/E2F-1 Interaction by Single-Point Mutations in E2F-1 Enhances S Phase Entry and Apoptosis. Proc. Natl. Acad. Sci. USA 93, 679-684.
Roe, J.R. *, Durfee, T. *, Zupan, J.R., Repetti, P., McLean, B.G., Zambryski, P.C., 1997. TOUSLED is a Nuclear Serine/Threonine Protein Kinase that Requires a Coiled-Coil Region for Oligomerization and Catalytic Activity. J. Biol. Chem. 272, 5838-5845.

Plunkett III, G., Rose, D.J., Durfee, T., Blattner, F.R., 1999. Sequence of Shiga Toxin 2 Phage 933W from Escherichia coli O157:H7: Shiga Toxin as a Phage Late-Gene Product. J. Bacteriol. 181(6): 1767-1778.

Durfee, T., Draper, O., Zupan, J., Conklin, D., Zambryski, P.C., 1999. New Tools for Protein Linkage Mapping and General Two-Hybrid Screening. Yeast. 15, 1761-1768.

Durfee, T., Feiler, H., Gruissem, W., 2000. Rb Related Proteins in Plants: Homologs or Orthologs of Their Mammalian Counterparts. Plant Mol. Biol., 43: 635-642.

Durfee, T., Roe, J.L., Sessions, R.A., Inouye, C., Serikawa, K., Weigel, D., Zambryski, P.C., 2003. The F-box Protein UFO and AGAMOUS Participate in Antagonistic Pathways Regulating Early Petal Development in Arabidopsis. Proc. Natl. Acad. Sci. USA, 100, 8571-8576.

Ehsan, H., Reichheld, J.-P., Durfee, T., and Roe, J.L. (2004) TOUSLED kinase activity oscillates during the cell cycle and interacts with chromatin regulators. Plant Physiol., 134, 1488-1499.

Chauhan, R.S., Durfee, T., Holt, J., Blattner, F.R. and Leong, S. 2004. Rice Blast Resistance Locus, Pi-CO39(t) is Embedded in a Hypervariable Region Rich in NBS-LRR and Serpin Genes. Mol. Gen. Genet., in press.

Kang, Y. *, Durfee*, T., Glasner, J.D., Qiu, Y., Frisch, D., Winterberg, K.M. and Blattner, F.R. 2004. Systematic Mutagenesis of the Escherichia coli Genome. J. Bacteriol., 186, 4921-30.

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File last modified: August 13, 2003
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