Jody Puglisi's CV

JOSEPH D. PUGLISI

Curriculum Vitae

Director, Stanford Magnetic Resonance Laboratory and
Associate Professor, Department of Structural Biology

D105 Fairchild
Stanford University School of Medicine
300 Pasteur Drive
Stanford, CA 94305-5126

SMRL web page Structural Biology web page

Phone and Fax numbers:
Tel: 650/498-4397
Fax: 650/723-8464

Email: puglisi@stanford.edu

Societies/Awards	Talks/Seminars	Publications

Academic History

1980-84	B.A., Chemistry (Honors), The Johns Hopkins University
1984-89	Ph.D., Biophysical Chemistry, University of California, Berkeley
1981-84	Summer Research Scientist, Airco Central Research Laboratory, Murray Hill, NJ
1983-84	Undergraduate Research Fellow, Organic Synthesis, The Johns Hopkins University (Alex Nickon, Advisor)
1984-89	Research Assistant, University of California, Berkeley (Ignacio Tinoco, Jr., Advisor)
1989-91	Postdoctoral Fellow (EMBO Fellowship), I. B. M. C. du CNRS, Strasbourg, France (Richard Giegé, Advisor)
1991-93	Postdoctoral Fellow, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA (James R. Williamson, Advisor)
1993-96	Assistant Professor, Department of Chemistry and Biochemistry, University of California, Santa Cruz
1993-97	Affiliated Faculty, Molecular, Cellular and Developmental Biology Graduate Program, Department of Biology, University of California, Santa Cruz
1997	Associate Professor, Department of Chemistry and Biochemistry, Universiy of California, Santa Cruz
1997+	Associate Professor, Department of Structural Biology and Director, Stanford Magnetic Resonance Laboratory, Stanford University

Societies and Awards

1984, '85, '87 - Outstanding Graduate Teaching Assistant, Department of Chemistry, UC Berkeley
1988 - Bruce Mahan Memorial Teaching Award, Department of Chemistry, UC Berkeley
1989 - Sigma Xi Honor Society
1989 - Thesis nominated for J. T. Baker Award in Chemistry
1993 - Camille and Henry Dreyfus Teacher-Scholar Award
1994 - David and Lucille Packard Fellowship
1997 - Alfred P. Sloan Research Fellowship
1998 - Rhône-Poulenc Rorer Grant: "RNA as a Potential Drug Target"

Invited Talks and Seminars

1989
Biophysical Seminar, Department of Chemistry, University of California, Berkeley
Gordon Conference-Nucleic Acids, New Hampton, NH
Institut de Biologie Moleculaire et Cellulaire du CNRS, Strasbourg, France
1990
EMBO Workshop: DNA-Protein Interactions, Autrans, France
Department of Biochemistry, University of Dundee, UK
1991
Minisymposium on RNA Structure, University of Leiden, The Netherlands
Biomolecular Structure/Function Seminar, Massachusetts Institute of Technology
1992
Structural Tools for the Analysis of Protein-Nucleic Acid Complexes, Wildbad-Kreuth, Germany
Biomolecular Structure/Function Seminar, Massachusetts Institute of Technology
1993
Bay Area RNA Club, San Francisco, CA
Department of Chemistry, University of Berkeley, CA
1994
Keystone Symposium, Nucleic Acid-Protein Interactions, Tamarron, CO
Institute of Microbiology, University of Brescia Medical School, Brescia, Italy
Biophysics Group, University of California, San Francisco, CA
1995
International Translation Workshop, Victoria, BC, Canada
Gordon Conference-Nucleic Acids, New Hampton, NH
York College, NY
1996
Department of Biochemistry, University of Utah
Department of Chemistry, University of California, Riverside
Department of Molecular Biology and Biophysics, Yale University
Buffalo Medicinal Chemistry Conference, NY
Gordon Conference-Biopolymers, Newport, RI
Structural Biology Seminar, University of California, Berkeley
Department of Chemistry, California Institute of Technology
Department of Structural Biology and Stanford Magnetic Resonance Laboratory, Stanford University
1997
Department of Pharmaceutical Chemistry, University of California, Berkeley
NMR and Molecular Biology Conference, Taos, NM
3rd Course: Protein Dynamics, Function and Design, International School of Structural Biology and Magnetic Resonance, Erice, Italy
Departments of Chemistry and Computer Science, Stanford University

Scientific Publications

1986

Tinoco, I., Jr., Cruz, P., Davis, P., Hall, K., Hardin, C.C., Mathies, R.A., Puglisi, J.D., Trulson, M.O., Johnson, W.C. and Neilson, T. (1986) "Z-RNA: A left-handed double helix." In: Structure and Dynamics of RNA, Plenum Press, NY, pp. 55-68.
Cruz, P., Hall, K., Puglisi, J., Davis, P., Hardin, C., Trulson, M., Mathies, R., Tinoco, I., Jr., Johnson, W., Jr. and Neilson, T. (1986) "The left-handed Z-form of double-stranded RNA." In: Biomolecular Stereodynamics IV, Adenine Press, NY, pp. 179-200.

1987

Hardin, C.C., Zarling, D.A., Puglisi, J.D., Trulson, M.O., Davis, P.D. and Tinoco, I., Jr. (1987) "Stabilization of Z-RNA by chemical bromination and its recognition by anti-Z-DNA anitbodies." Biochemistry 2, 5191-5199.
Trulson, M.O., Cruz, P., Puglisi, J.D., Tinoco, I., Jr. and Mathies, R.A. (1987) "Raman spectroscopic study of left-handed Z-RNA." Biochemistry 26, 8624-8630.
Tinoco, I., Jr., Davis, P.W., Hardin, C.C., Puglisi, J.D., Walker, G.T. and Wyatt, J.R. (1987) "RNA structure from A to Z." Cold Spring Harbor Sym. Quant. Biol. 52, 135-146.

1988

Wyatt, J.R., Puglisi, J.D. and Tinoco, I., Jr. (1988) "Pseudoknotted RNA characterization of a simple RNA tertiary structure." J. Cell Biol. 107(6 part 3), 11A.
Wyatt, J.R., Puglisi, J.D. and Tinoco, I., Jr. (1988) "Pseudoknotted RNA oligonucleotides." In: Molecular Biology of RNA, (T. Cech, ed.) UCLA Symposia Series 94, Alan R. Liss, Inc., New York, NY, pp. 25-32.
Puglisi, J.D., Wyatt, J.R. and Tinoco, I., Jr. (1988) "A pseudoknotted RNA oligonucleotide." Nature 331, 283-286.

1989

Puglisi, J.D. and Tinoco, I., Jr. (1989) "Absorbance melting curves of RNA." In: Methods in Enzymology, RNA Processing 180, (J.E. Dahlberg and J.N. Abelson, eds.), Academic Press, NY.
Tinoco, I., Jr., Aboul-ela, F., Hardin, C.C., Puglisi, J.D., Varani, G., Walker, G.T., Wolk, S. and Wyatt, J.R. (1989) "Nucleic acids from A to Z." In: Frontiers of Macromolecular Science. (T. Saegusa, T. Higashimura and A. Abe, eds.), Blackwell Scientific Publications, Oxford, UK, pp. 519-524.
Wyatt, J.R., Puglisi, J.D. and Tinoco, I., Jr. (1989) "RNA folding: Pseudoknots, loops and bulges." Bioassays 11, 100-106.

1990

Tinoco, I., Jr., Puglisi, J.D. and Wyatt, J.R. (1990) "RNA folding." In: Nucleic Acids and Molecular Biology 4, (F. Eckstein and D. Lilley, eds. ), Springer-Verlag, Berlin, pp. 205-226.
Puglisi, J.D., Wyatt, J.R. and Tinoco, I., Jr. (1990) "Solution conformation of an RNA hairpin loop." Biochemistry 29, 4215-4226.
Puglisi, J.D., Wyatt, J.R. and Tinoco, I., Jr. (1990) "Conformation of an RNA pesudoknot." J. Mol. Biol. 214, 437-453.
Wyatt, J.R., Puglisi, J.D. and Tinoco, I., Jr. (1990) "RNA pseudoknots: Stability and loop size requirements." J. Mol. Biol. 214, 455-470.
Giegé, R., Florentz, C., Garcia, A., Grosjean, H., Perret, V., Puglisi, J., Theobald-Dietrich, A. and Ebel, J.-P. (1990) "Exploring the animoacylation function of transfer RNA by macromolecular engineering approaches. Involvement of conformation features in the charging process of yeast tRNA^Asp." Biochimie 72, 453-462.
Perret, V., Garcia, A., Puglisi, J., Grosjean, H., Ebel, J.-P. and Giegé, R. (1990) "Conformation in solution of tRNA^Asp transcripts deprived of modified nucletides." Biochimie 72, 735-744.

1991

Puglisi, J.D., Wyatt, J.R. and Tinoco, I., Jr. (1991) "RNA pseudoknots." Accts. Chem. Res. 24, 152-158.
Pütz, J., Puglisi, J.D., Florentz, C. & Giegé, R. (1991) "Identity elements for specific aminoacylation of yeast tRNA^Asp by cognate aspartyl-tRNA synthetase." Science 252, 1696-1699.
Wyatt, J.R., Chastain, M. and Puglisi, J.D. (1991) "Synthesis and purification of large amounts of RNA oligonucleotides." BioTechniques 11, 764-769.

1992

Rudinger, J., Puglisi, J.D., Pütz, J., Schatz, D., Eckstein, F., Florentz, C. and Giegé, R. (1992) "Determinant nucleotides of yeast tRNA^Asp interact directly with aspartyl-tRNA synthetase." Proc. Natl. Acad. Sci. USA 89, 5882-5886.
Perret, V., Florentz, C., Puglisi, J.D. and Giegé, R. (1992) "Effect of conformational features on the aminoacylation of tRNAs and consequences on the permutation of tRNA specificities." J. Mol. Biol. 226, 323-333.
Puglisi, J.D., Tan, R., Calnan, B.J., Frankel, A.D. and Williamson, J.R. (1992) "Conformation of the TAR RNA-arginine complex by NMR spectroscopy." Science 257, 76-80.
Batey, R.T., Inada, M., Kujawinski, E., Puglisi, J.D. and Wiliamson, J.R. (1992) "Preparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy of RNA." Nucleic Acids Res. 20, 4515-4523.
Puglisi, J.D., Tan, R., Frankel, A.D., Williamson, J.R. (1992) "Structure and Function of HIV TAR RNA." In: Structural Tools for the Analusis of Protein-Nucleic Acid Complexes. Advances in Life Sciences. (D.M.J. Lilley, H. Heumann, D. Suck, eds.), Birkhauser, Basel, pp. 269-285.

1993

Giegé, R., Florentz, C. and Puglisi, J.D. (1993) "tRNA structure and aminoacylation efficiency." Prog. Nucl. Acids Res. Molec. Biol. 45, 129-206.
Puglisi, J.D., Pütz, J., Florentz, C. and Giegé, R. (1993) "Influence of tRNA tertiary structure and stability on aminoacylation by yeast aspartyl-tRNA synthetase." Nucleic Acids Res. 21, 41-49.
Pütz, J., Puglisi, J.D., Florentz, C. and Giegé, R. (1993) "Additive, cooperative and anticooperative effects between identity nucleotides of a tRNA." EMBO J. 12, 2949-2957.
Puglisi, J.D., Chen, L., Frankel, A.D. and Williamson, J.R. (1993) "The role of RNA structure in arginine binding to TAR RNA." Proc. Natl. Acad. Sci. USA 90, 3680-3684.
Puglisi, J.D., Tan, R., Calnan, B.J., Frankel, A.D. and Williamson, J.R. (1993) "RNA protein interactions in model systems for HIV tar-tat recognition." Biophys. J. 64(2 part 2), A1.

1994

Puglisi, E.V., Puglisi, J.D., Williamson, J.R. and RajBhandary, U.L. (1994) "NMR analysis of tRNA acceptor stem microhelices: Discriminator base changes affect tRNA conformation at the 3'-end." Proc. Natl. Acad. Sci. USA 91, 11467-11471.
Publisi, J.D. and Williamson, J.R. (1994) "NMR studies of HIV TAR RNA." In: Structural Biology: The State of the Art, vol. 2. (R.H. Sarma and M.H. Sarma, eds.), Adenine Press, Schenectady, New York, pp. 285-291.

1995

Puglisi, J.D. and Wyatt, J.R. (1995) "Biochemical and NMR studies of RNA conformation." Methods in Enzymology 261, 323-350.
Puglisi, J.D. (1995) "Welcome guests to the RNA world: Proteins that interact with RNA." (Book Review) Chemistry and Biology 2, 581.
Puglisi, J.D., Chen, L., Blanchard, S. and Frankel, A.D. (1995) "Solution structure of a bovine immunodeficiency virus Tat-TAR Peptide-RNA complex." Science 270, 1200-1203.

1996

Recht, M.I., Fourmy, D., Blanchard, S.C., Dahlquist, K.D. and Puglisi, J.D. (1996) "RNA sequence determinants for aminoglycoside binding to an A-site rRNA model oligonucleotide." J. Mol. Biol. 262, 421-436.
Fourmy, D., Recht, M.I., Blanchard, S.C. and Puglisi, J.D. (1996) "Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic." Science 274, 1367-1371.

1997

Puglisi, E.V. and Puglisi, J.D. (1997) "RNA Structure." In: mRNA Metabolism and Post-Transcriptional Gene Regulation. (J.B. Harford and D.R. Morris, eds.), Wiley-Liss, NY.
Puglisi, E.V., Green, R., Noller, H.F. and Puglisi, J.D. (1997) "Structure of a conserved RNA component of the peptidyl transferase centre." Nature Struct. Biol. 4, 775-778.
Puglisi, J.D., Fourmy, D., Recht, M.I., Yoshizawa, S., Blanchard, S.C. and Eason, R.G. (1997) "Structural basis of aminoglycoside antibiotic action." Abstracts of Papers Am. Chem. Soc. 213(1-3), CARB 72.

1998

Puglisi, E.V. and Puglisi, J.D. (1998) "Nuclear magnetic resonance spectroscopy of RNA." In: RNA Structure and Function, (R.W. Simons and M. Grunberg-Manago, eds.), Cold Spring Harbor Press, NY, pp. 117-146.
Fourmy, D., Yoshizawa, S. and Puglisi, J.D. (1998) "Paromomycin binding induces a local conformational change in the A-site of 16 S rRna." J. Mol. Biol. 277, 333-345.
Fourmy, D., Recht, M.I. and Puglisi, J.D. (1998) "Binding of neomycin-class animoglycoside antibiotics to the A-site of 16 S rRna." J. Mol. Biol. 277, 347-362.
Blanchard, S.C., Fourmy, D., Eason, R.G. and Puglisi, J.D. (1988) "rRNA chemical groups required for aminoglycoside binding." Biochemistry 37, 7716-7724.
Yoshizawa, S. and Puglisi, J.D. (1998) "NMR structure determination of an antibiotic-RNA complex." In: Protein Dynamics, Function and Design, (J.-F. Lefevre and O. Jardetzky, eds.), Plenum Press, NY, in press.

Academic History	Societies/Awards	Talks/Seminars

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