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14 CALIFORNIA, SAN DIEGO moment dependence on HOOC torsion, J. Chem. Phys, 129, Sergiy Markutsya, Shankar Subramaniam, R. Dennis Vigil Dynamics Revealed by Dye-Triggered Aggregation and DA- 074316/1-074316/16 (2008). and Rodney O. Fox, On Brownian Dynamics Simulation of KAP1�-Mediated Localization in Living Cells, Chem. Biol. Jamie Matthews, Juliane L. Fry, Coleen M. Roehl, Paul O. Nanoparticle Aggregation, Ind. Eng. Chem. Res, 47, 3338- (Cambridge, MA, U. S.), 14, 1031-1042 (2007). Wennberg and Amitabha Sinha, Vibrational overtone initiated unimolecular dissociation of HOCH2OOH and HOCD2OOH: Evidence for mode selective behavior, J. Chem. Phys, 128, 184306/1-184306/12 (2008). Shuping Li, Jamie Matthews and Amitabha Sinha, Atmo- 3345 (2008). Brian Saunders, Stephen Lyon, Matthew Day, Brenda Riley, Emily Chenette and Shankar Subramaniam, The Molecule Pages database, Nucleic Acids Res, 36, D700-D706 (2008). Natarajan Kannan, Jian Wu, Ganesh S. Anand, Shibu Yooseph, Andrew F. Neuwald, J. Craig Venter and Susan S. Tay- lor, Evolution of allostery in the cyclic nucleotide binding module, GenomeBiology, 8, No pp. given (2007). Sharmin Schauble, Charles C. King, Manjula Darshi, Anspheric Hydroxyl Radical Production from Electronically Ex- tonius Koller, Kavita Shah and Susan S. Taylor, Identificacited NO2 and H2O, Science (Washington, DC, U. S.), 319, 1657-1660 (2008). Jamie Matthews, State-resolved photochemistry and spectroscopic charecterization of atmospherically relevant hydroperoxides. (D) SUBRAMANIAM, SHANKAR (b.1953) Professor. B.Sc, 1972, Osmania University; M.A.Sc, 1974, Osmania University; Ph.D, 1982, Indian Institute of Technology Kanpur. His present research focuses several important aspects of computational biology. These include web-based approaches to bioinformatics, going from protein sequence to structure and function and studying protein recognition and function. TEL: (858) 822-0986 FAX: (858) 534-5722 Web: www.chem.ucsd.edu/Faculty/bios/subramaniam. html TAUBER, MICHAEL J. Assistant Professor. B.A, 1992, Cornell University; Ph.D, 2002, University of California, Berkeley. Postdoctoral researcher, 2002-2003, University of California, Berkeley; ACS-PRF Research Associate, 2003-2006, Northwestern University. Physi- cal Chemistry. Our group investigates charge sharing and excited state dynamics in organic molecular assemblies, including self-assembled systems, by a variety of spectroscopic techniques including pump-probe Raman & resonance Raman, EPR, and transient absorption. Other topics of current research are new 3-dimensional architectures for dye-sensitized solar cells, and solvation structure/dynamics. TEL: (858) 534-7334 FAX: (858) 000-0000 Email: mtauber@ucsd.edu E. A. Weiss, M. J. Tauber, R. F. Kelley, M. J. Ahrens, M. A. Ratner and M. R. Wasielewski, Conformationally gated tion of ChChd3 as a Novel Substrate of the cAMP-dependent Protein Kinase (PKA) Using an Analog-sensitive Catalytic Subunit, J. Biol. Chem, 282, 14952-14959 (2007). Kenneth M. Humphries, Juniper K. Pennypacker and Susan S. Taylor, Redox Regulation of cAMP-dependent Protein Kinase Signaling: kinase versus phosphatase inactivation, J. Biol. Chem, 282, 22072-22079 (2007). Neal M. Alto, Andrew W. Weflen, Matthew J. Rardin, Defne Yarar, Cheri S. Lazar, Raffi Tonikian, Antonius Koller, Susan S. Taylor, Charles Boone, Sachdev S. Sidhu, San- dra L. Schmid, Gail A. Hecht and Jack E. Dixon, The type III effector EspF coordinates membrane trafficking by the spa- tiotemporal activation of two eukaryotic signaling pathways, J. Cell Biol, 178, 1265-1278 (2007). Ganesh S. Anand, Matthew Hotchko, Simon H. J. Brown, Lynn F. Ten Eyck, Elizabeth A. Komives and Susan S. Taylor, R-subunit Isoform Specificity in Protein Kinase A: Distinct Features of Protein Interfaces in PKA Types I and II by Amide H/ 2 Email: shsubramaniam@ucsd.edu Publication list has not been verified by the department. Jayesh Pandey, Mehmet Koyutuerk, Yohan Kim, Wojciech Szpankowski, Shankar Subramaniam and Ananth Grama, Functional annotation of regulatory pathways, Bioinformatics, 23, i377-i386 (2007). Mano Ram Maurya and Shankar Subramaniam, A kinetic switching between superexchange and hopping within oligop-phenylene-based molecular wires, J. Am. Chem. Soc, 127, 11842-11850 (2005). E. A. Weiss, M. J. Tauber, M. A. Ratner and M. R. Wasie- lewski, Electron spin dynamics as a probe of molecular dynamics: Temperature-dependent magnetic field effects on charge recombination within a covalent radical ion pair, J. Am. Chem. Soc, 127, 6052-6061 (2005). R. F. Kelley, M. J. Tauber and M. R. Wasielewski, Linker- H Exchange Mass Spectrometry, J. Mol. Biol, 374, 487-499 (2007). Marat Valiev, Jie Yang, Joseph A. Adams, Susan S. Taylor and John H. Weare, Phosphorylation Reaction in cAPK Protein Kinase-Free Energy Quantum Mechanical/Molecular Mechanics Simulations, J. Phys. Chem. B, 111, 13455-13464 (2007). Chinten James Lim, Jaewon Han, Nima Yousefi, Yuliang Ma, Paul S. Amieux, G. Stanley McKnight, Susan S. Taylor model for calcium dynamics in RAW 264.7 cells: 1. Mecha- controlled energy and charge transfer within chlorophyll treand Mark H. Ginsberg, �4 Integrins are type I cAMP-depen- nisms, parameters, and subpopulational variability, Biophys. foils, Angew. Chem. Int. Ed, 45, 7979-7982 (2006). dent protein kinase-anchoring proteins, Nat. Cell Biol, 9, J, 93, 709-728 (2007). M. J. Tauber, R. F. Kelley, J. M. Giaimo, B. Rybtchinski 415-421 (2007). Mano Ram Maurya and Shankar Subramaniam, A kinetic and M. R. Wasielewski, Electron hopping in pi-stacked cova- Shibu Yooseph, Granger Sutton, Douglas B. Rusch, Aaron model for calcium dynamics in RAW 264.7 cells: 2. Knock- lent and self-assembled perylene diimides observed by EN- L. Halpern, Shannon J. Williamson, Karin Remington, Jonadown response and long-term response, Biophys. J, 93, 729- DOR spectroscopy, J. Am. Chem. Soc, 128, 1782-1783 than A. Eisen, Karla B. Heidelberg, Gerard Manning, Wei- 740 (2007). (2006). zhong Li, Lukasz Jaroszewski, Piotr Cieplak, Christopher S. Andrea L. Hevener, Jerrold M. Olefsky, Donna Reichart, R. F. Kelley, M. J. Tauber and M. R. Wasielewski, Intra- Miller, Huiying Li, Susan T. Mashiyama, Marcin P. Joachim- M. T. Audrey Nguyen, Gautam Bandyopadyhay, Ho-Yin molecular electron transfer through the 20-position of a iak, Christopher van Belle, John-Marc Chandonia, David A. Leung, Matthew J. Watt, Chris Benner, Mark A. Febbraio, chlorophyll-a derivative: An unexpectedly efficient conduit Soergel, Yufeng Zhai, Kannan Natarajan, Shaun Lee, Benja- Anh-Khoi Nguyen, Brian Folian, Shankar Subramaniam, for charge transport, J. Am. Chem. Soc, 128, 4779-4791 min J. Raphael, Vineet Bafna, Robert Friedman, Steven E. Frank J. Gonzalez, Christopher K. Glass and Mercedes Ri- (2006). Brenner, Adam Godzik, David Eisenberg, Jack E. Dixon, Sucote, Macrophage PPAR� is required for normal skeletal M. J. Ahrens, M. J. Tauber and M. R. Wasielewski, Bis(n- san S. Taylor, Robert L. Strausberg, Marvin Frazier and J. muscle and hepatic insulin sensitivity and full antidiabetic ef- octylamino)perylene-3,4:9,10-bis(dicarboximide)s and their Craig Venter, The Sorcerer II global ocean sampling expedi- fects of thiazolidinediones, J. Clin. Invest, 117, 1658-1669 radical cations: Synthesis, electrochemistry, and ENDOR tion: expanding the universe of protein families, PLoS Biol, (2007). spectroscopy, J. Org. Chem, 71, 2107-2114 (2006). 5, 432-466 (2007). Jin Sun, Francine Battaglia and Shankar Subramaniam, Richard F. Kelley, Michael J. Tauber, Thea M. Wilson and Natarajan Kannan, Susan S. Taylor, Yufeng Zhai, J. Craig Hybrid two-fluid DEM simulation of gas-solid fluidized Michael R. Wasielewski, Controlling energy and charge Venter and Gerard Manning, Structural and functional diverbeds, J. Fluids Eng, 129, 1394-1403 (2007). transfer in linear chlorophyll dimers, Chem. Commun. (Cam- sity of the microbial kinome, PLoS Biol, 5, 467-478 (2007). Robert W. Byrnes, Eoin Fahy and Shankar Subramaniam, bridge, U. K.), 42, 4407-4409 (2007). Natarajan Kannan, Nina Haste, Susan S. Taylor and An- A laboratory information management system for high- Christina M. Stuart, Michael J. Tauber and Richard A. Ma- drew F. Neuwald, The hallmark of AGC kinase functional dithroughput experimental lipidomics: Minimal information re- thies, Structure and Dynamics of the Solvated Electron in Al- vergence is its C-terminal tail, a cis-acting regulatory mod- quired for the analysis of lipidomics experiments (MIALE), cohols from Resonance Raman Spectroscopy, J. Phys. Chem. ule, Proc. Natl. Acad. Sci. U. S. A, 104, 1272-1277 (2007). JALA, 12, 230-238 (2007). A, 111, 8390-8400 (2007). Rahul Das, Veronica Esposito, Mona Abu-Abed, Ganesh Kara Schmelzer, Eoin Fahy, Shankar Subramaniam and S. Anand, Susan S. Taylor and Giuseppe Melacini, cAMP ac- Edward A. Dennis, The lipid maps initiative in lipidomics, Methods Enzymol, 432, 171-183 (2007). Eoin Fahy, Dawn Cotter, Robert Byrnes, Manish Sud, Andrea Maer, Joshua Li, David Nadeau, Yihua Zhau and Shankar Subramaniam, Bioinformatics for lipidomics, Methods Enzymol, 432, 247-273 (2007). Purnima Guda, Shankar Subramaniam and Chittibabu Guda, Mitoproteome: human heart mitochondrial protein sequence database, Methods Mol. Biol. (Totowa, NJ, U. S.), 357, 375-383 (2007). Joelle R. Zavzavadjian, Sam Couture, Wei Sun Park, James Whalen, Stephen Lyon, Genie Lee, Eileen Fung, Qingli Mi, Jamie Liu, Estelle Wall, Leah Santat, Kavitha Dhandapani, Christine Kivork, Adrienne Driver, Xiaocui Zhu, Mi Sook Chang, Baljinder Randhawa, Elizabeth Gehrig, Heather Bryan, Mary Verghese, Andreia Maer, Brian Saunders, Yuhong Ning, Shankar Subramaniam, Tobias Meyer, Melvin I. Simon, Nancy O’Rourke, Grischa Chandy and Iain D. C. Fraser, The alliance for cellular signaling plasmid collection: a flexible resource for protein localization studies and signaling pathway analysis, Mol. Cell. Proteomics, 6, 413-424 (2007). Manish Sud, Eoin Fahy, Dawn Cotter, Alex Brown, Edward A. Dennis, Christopher K. Glass, Alfred H. Merrill, Jr., Robert C. Murphy, Christian R. H. Raetz, David W. Russell and Shankar Subramaniam, LMSD: LIPID MAPS structure database, Nucleic Acids Res, 35, D527-D532 (2007). Ying Xu and Shankar Subramaniam, Consistent modeling TAYLOR, SUSAN S. (b.1942) Professor. B.A, 1964, University of Wisconsin; Ph.D, 1968, The Johns Hopkins University. Postdoctoral Fellowship, 1969-1971, Laboratory of Molecular Biology, Cambridge, England; Postdoctoral Fellowship, 1971-1972, University of California, San Diego. Biochemistry; Crystallography. CAMP-dependent Protein Kinase: Dynamics of Structures and Localization cAMP-dependent protein kinase (cAPK) serves as a prototype for the entire protein kinase superfamily. Crystal structures of the RIa and RIIb cAMP binding domains of the R subunits show clear isoform differences. From these structures we can more fully appreciate the conformational versatility of this ancient signaling module that binds cAMP and mediates a biological response. This stable module binds with high affinity to scaffold proteins. The molecular basis for targeting has been elucidated by solving high-resolution structures of two D/D domains by hetero nuclear NMR in collaboration with Dr. Patricia Jennings. Isoform differences in PKA targeting are being explored. We have identified two novel AKAPs that bind to both RIa and RIIb. Both target cAPK to mitochondria. We are beginning to elucidate the molecular basis for this targeting. TEL: (858) 534-3677 FAX: (858) 534-8193 Web: susantaylorlab.ucsd.edu/ Email: staylor@ucsd.edu tivation of PKA defines an ancient signaling mechanism, Proc. Natl. Acad. Sci. U. S. A, 104, 93-98 (2007). Jian Wu, Simon H. J. Brown, Sventja von Daake and Su- san S. Taylor, PKA Type II� Holoenzyme Reveals a Combinatorial Strategy for Isoform Diversity, Science (Washington, DC, U. S.), 318, 274-279 (2007). Susan S. Taylor, Choel Kim, Cecilia Y. Cheng, Simon H. J. Brown, Jian Wu and Natarajan Kannan, Signaling through cAMP and cAMP-dependent protein kinase: Diverse strategies for drug design, Biochim. Biophys. Acta, Proteins Pro- teomics, 1784, 16-26 (2008). Lynn F. Ten Eyck, Susan S. Taylor and Alexandr P. Kornev, Conserved spatial patterns across the protein kinase family, Biochim. Biophys. Acta, Proteins Proteomics, 1784, 238-243 (2008). Natarajan Kannan, Andrew F. Neuwald and Susan S. Tay- lor, Analogous regulatory sites within the �C-�4 loop re- gions of ZAP-70 tyrosine kinase and AGC kinases, Biochim. Biophys. Acta, Proteins Proteomics, 1784, 27-32 (2008). Natarajan Kannan and Susan S. Taylor, Rethinking pseu- dokinases, Cell (Cambridge, MA, U. S.), 133, 204-205 (2008). Yuliang Ma and Susan S. Taylor, A Molecular Switch for Targeting between Endoplasmic Reticulum (ER) and Mito- chondria: Conversion of a mitochondria-targeting element into an er-targeting signal in DAKAP1, J. Biol. Chem, 283, 11743-11751 (2008). Alexandr P. Kornev, Susan S. Taylor and Lynn F. Ten of interphase turbulent kinetic energy transfer in particle-laden turbulent flows, Phys. Fluids, 19, 085101/1-085101/9 Publication list has not been verified by the department. Eyck, A generalized allosteric mechanism for cis-regulated cyclic nucleotide binding domains, PLoS Comput. Biol, 4, (2007). Ganesh Anand, Susan S. Taylor and David A. Johnson, No pp. given (2008). Srinivasan Ramachandran, Lai-Hua Xie, Scott A. John, Cyclic-AMP and Pseudosubstrate Effects on Type-I A-Ki- Alexandr P. Kornev, Susan S. Taylor and Lynn F. Ten Shankar Subramaniam and Ratnesh Lal, A novel role for nase Regulatory and Catalytic Subunit Binding Kinetics, Bio- Eyck, A helix scaffold for the assembly of active protein kiconnexin hemichannel in oxidative stress and smoking-in- chemistry, 46, 9283-9291 (2007). nases, Proc. Natl. Acad. Sci. U. S. A, 105, 14377-14382 duced cell injury, PLoS One, 2, No pp. given (2007). Choel Kim, Cecilia Y. Cheng, S. Adrian Saldanha and Su- (2008). Colin T. Walsh, Julie Radeff-Huang, Rosalia Matteo, Al- san S. Taylor, PKA-I holoenzyme structure reveals a mecha- Larry R. Masterson, Alessandro Mascioni, Nathaniel J. bert Hsiao, Shankar Subramaniam, Dwayne Stupack and nism for cAMP-dependent activation, Cell (Cambridge, MA, Traaseth, Susan S. Taylor and Gianluigi Veglia, Allosteric Joan Heller Brown, Thrombin receptor and RhoA mediate U. S.), 130, 1032-1043 (2007). cooperativity in protein kinase A, Proc. Natl. Acad. Sci. U. S. cell proliferation through integrins and cysteine-rich protein Brent R. Martin, Thomas J. Deerinck, Mark H. Ellisman, A, 105, 506-511 (2008). 61, FASEB J, 22, 4011-4021 (2008). Susan S. Taylor and Roger Y. Tsien, Isoform-Specific PKA Ali Torkamani, Natarajan Kannan, Susan S. Taylor and
CALIFORNIA, SAN DIEGO 15 Nicholas J. Schork, Congenital disease SNPs target lineage Email: mht@chem.ucsd.edu of a transcriptional terminator, Nucleic Acids Research, 34, specific structural elements in protein kinases, Proc. Natl. mthiemens@ucsd.edu 6461-6471 (2006). Acad. Sci. U. S. A, 105, 9011-9016 (2008). S. A. Aireau, J. Farquhar, M. H. Thiemens, L. A. Leshin, K. S. Keating, N. Toor and A. M. Pyle, The GANC tetra- Natarajan Kannan, Nina Haste, Susan S. Taylor and An- H. Bao and E. Young, Planetesimal sulfate and aqueous al- loop receptor interaction, Journal of Molecular Biology, 383, drew F. Neuwald, The hallmark of AGC kinase functional di- teration in CM and CI carbonaceous chondrites, Geochinica 475-481 (2008). vergence is its C-terminal tail, a cis-acting regulatory mod- Cosmochimica Acta, 69, 4166-4171 (2005). N. Toor, K. Rajashankar, K. S. Keating and A. M. Pyle, ule. [Erratum to document cited in CA146:333062], Proc. R. Jost, G. Michalski and M. H. Thiemens, Comparison of Structural basis of exon recognition by a group II intron, Na- Natl. Acad. Sci. U. S. A, 105, 9130 (2008). rovibronic density of symmetric versus symmetric NO2 iso- ture Structural and Molecular Biology, 15, 1221-1222 topologues at dissociation threshold: Broken symmetry ef- (2008). TEZCAN, F. AKIF (b.1972) Assistant Professor. A.B, fects, J. (Chemistry). Physics, 123, 054230 (2005). N. Toor, K. S. Keating, S. D. Taylor and A. M. Pyle, Crys- 1995, Macalester College; Ph.D, 2001, Caltech. Re- J. R. McCabe, C. S. Boxe, A. J. Colussi, M. R. Hoffmann tal structure of a self-spliced group II intron, Science, 320, search Fellow, 2001-2005, Caltech. Bioinorganic Chem- and M. H. Thiemens, Oxygen isotopic fractionation in the 77-82 (2008). istry. Metal-Protein and Protein-Protein Interactions photochemistry of nitrate and ice, J. Geophys. Res, 110, D15- Metal-Directed Protein Self-Assembly Biological Nitro- D15310 (2005). TOR, YITZHAK (b.1960) Professor. B.Sc, 1982, Telgen Fixation. TEL: (858) 534-4862 FAX: (858) 534- B. Alexander, R. J. Park, D. J. Jacob, Q. B. Li, R. M. Yan- Aviv University, Israel; Ph.D, 1990, The Weizmann In- 6157 tosca, J. Savarino, C. C. W. Lee and M. H. Thiemens, Sulfate stitute of Science, Israel. Weizmann Postdoctoral Fel- Web: tezcan.ucsd.edu formation in sea-salt aerosols: Constraints from oxygen iso- lowship, 1990-1993, California Institute of Technology. topes, J. Geophys. Res. Atmospheres). J. Geophys. Res, 110, Email: tezcan@ucsd.edu Bioorganic Chemistry; Organic Chemistry. RNA–small D10307 (2005). Eric N. Salgado, Jasmin Faraone-Mennella and F. Akif V. K. Rai, T. L. Jackson and M. H. Thiemens, Photochem- molecule interactions; antiviral and antibacterial agents; Tezcan, Controlling Protein-Protein Interactions through ical mass independent sulfur isotopes in achondritic meteornew emissive nucleosides and oligonucleotides; novel Metal Coordination: Assembly of a 16-Helix Bundle Protein, ites, Science, 309, 1062-1065 (2005). cellular delivery agents. TEL: (858) 534-6401 FAX: J. Am. Chem. Soc, 129, 13374-13375 (2007). Mark H. Thiemens, History and applications of mass inde- (858) 534-0202 Eric N. Salgado, Richard A. Lewis, Jasmin Faraone-Men- pendent isotope effects, Annual Reviews of Earth and Plane- Web: www-chem.ucsd.edu/research/profile.cfm?cid= nella and F. Akif Tezcan, Metal-Mediated Self-Assembly of tary Sciences, 34, 217-262 (2006). C02218 Protein Superstructures: Influence of Secondary Interactions T. A. Mather, J. R. McCabe, V. K. Rai, M. K. Thiemens, Email: ytor@ucsd.edu on Protein Oligomerization and Aggregation, J. Am. Chem. D. M. Pyle, T. H. E. Heaton, H. J. Sloane and G. Fern, Oxy- Soc, 130, 6082-6084 (2008). Lev Elson-Schwab and Yitzhak Tor, Targeting HIV-1 gen and sulfur isotopic composition of volcanic sulfate aero- RNA with aminoglycoside antibiotics and their derivatives, sol at the point of emission, J. Geophys. Res, 111, D18205 Aminoglycoside Antibiot, 267-287, 2 plates (2007). THEODORAKIS, EMMANUEL A. (b.1964) Pro- (2006). Christopher M. Barbieri, Malvika Kaul, Melanie Bozzafessor. B.S, 1987, University of Athens, Greece; M.S, J. Savarino, J. Kaiser, S. Morin, D. M. Sigman and M. H. Hingos, Fang Zhao, Yitzhak Tor, Thomas Hermann and Dan- 1989, University of Paris XI, France; Ph.D, 1993, Uni- Thiemens, Nitrogen and oxygen isotopic constraints on the iel S. Pilch, Defining the molecular forces that determine the versity of Paris XI, France. Postdoctoral, 1993-1995, origin of atmospheric nitrate in coastal Antarctica, Atmos. impact of neomycin on bacterial protein synthesis: impor- Scripps Research Institute. Bioorganic Chemistry; Or- Chem. Phys, 7, 1925-1945 (2007). tance of the 2’-amino functionality, Antimicrob. Agents Cheganic Chemistry. Synthesis of natural products; develop- M. De Angelis, M. H. Thiemens, J. Savarino and J. R. Pet- mother, 51, 1760-1769 (2007). it, Contributions of an ancient evaporitic-type reservoir to ment of synthetic methodology; and interaction of organ- Seergazhi G. Srivatsan and Yitzhak Tor, Fluorescent Py- Lake Vostok chemistry, Earth and Planetary Science Letters, ic molecules with biomolecules. TEL: (858) 822-0456 rimidine Ribonucleotide: Synthesis, Enzymatic Incorpora- 222, 751-765 (2007). FAX: (858) 822-0386 Tetsuya Yokoyama, Vinai K. Rai, Conel M. O’D. Alexantion, and Utilization, J. Am. Chem. Soc, 129, 2044-2053 Web: www.chem-faculty.ucsd.edu/Theodorakis/index. der, Roy S. Lewis, Richard W. Carlson, Steven B. Shirey, (2007). html Mark H. Thiemens and Richard J. Walker, Osmium isotope Victor K. Tam, Denise Kwong and Yitzhak Tor, Fluores- Email: etheodor@ucsd.edu evidence for uniform distribution of s- and r-process compo- cent HIV-1 Dimerization Initiation Site: Design, Properties, nents in the early Solar system, Earth Planet. Sci. Lett, 259, and Use for Ligand Discovery, J. Am. Chem. Soc, 129, 3257- Gianni Guizzunti, Thomas P. Brady, Vivek Malhotra and 567-580 (2007). 3266 (2007). Emmanuel A. Theodorakis, Trifunctional norrisolide probes Vinai K. Rai and Mark H. Thiemens, Mass independently Edith C. Glazer, Douglas Magde and Yitzhak Tor, Ruthefor the study of Golgi vesiculation, Bioorg. Med. Chem. Lett, fractionated sulfur components in chondrites, Geochim. Cosnium Complexes That Break the Rules: Structural Features 17, 320-325 (2007). mochim. Acta, 71, 1341-1354 (2007). Controlling Dual Emission, J. Am. Chem. Soc, 129, 8544- Derek Fischer and Emmanuel A. Theodorakis, Studies on M. A. Tyra, J. Farquhar, B. A. Wing, G. K. Benedix, A. J. 8551 (2007). the synthesis of Schisandraceae natural products: exploring a T. Jull, T. Jackson and M. H. Thiemens, Terrestrial alteration Lev Elson-Schwab, Omai B. Garner, Manuela Schuksz, cyclopropylcarbinol ring expansion strategy, Eur. J. Org. of Antarctic CM chondrite meteorites in a suite of Antarctic Brett E. Crawford, Jeffrey D. Esko and Yitzhak Tor, Guani- Chem, 4193-4196 (2007). CM chondrites: Evidence from oxygen and carbon isotopes, dinylated Neomycin Delivers Large, Bioactive Cargo into Paqui G. Traves, Sonsoles Hortelano, Miriam Zeini, Ta- Geochimica Cosmochimica Acta, 71, 782-795 (2007). Cells through a Heparan Sulfate-dependent Pathway, J. Biol. Hsiang Chao, Thanh Lam, Saskia T. Neuteboom, Emmanuel S. A. Ewing, G. Michalski, M. Thiemens, R. C. Quinn, J. Chem, 282, 13585-13591 (2007). A. Theodorakis, Michael A. Palladino, Antonio Castrillo and L. Macalady, S. Kohl, S. D. Wankel, C. Kendall, C. P. Seergazhi G. Srivatsan and Yitzhak Tor, Synthesis and en- Lisardo Bosca, Selective activation of liver X receptors by McKay and R. Amundson, Rainfall limit of the N cycle on zymatic incorporation of a fluorescent pyrimidine ribonuacanthoic acid-related diterpenes, Mol. Pharmacol, 71, 1545- Earth, Global Biogeochemical Cycles, 21, GB3009 (2007). cleotide, Nat. Protoc, 2, 1547-1555 (2007). 1553 (2007). Justin R. McCabe, Mark H. Thiemens and Joel Savarino, A Nicholas J. Greco and Yitzhak Tor, Synthesis and site-spe- Derek Fischer, Emmanuel A. Theodorakis and Mark A. record of ozone variability in South Pole Antarctic snow: role cific incorporation of a simple fluorescent pyrimidine, Nat. Haidekker, Synthesis and use of an in-solution ratiometric of nitrate oxygen isotopes, J. Geophys. Res., [Atmos.], 112, Protoc, 2, 305-316 (2007). fluorescent viscosity sensor, Nat. Protoc, 2, 227-236 (2007). D12303/1-D12303/9 (2007). Renatus W. Sinkeldam and Yitzhak Tor, To D or not to D? Mark A. Haidekker and Emmanuel A. Theodorakis, Mo- N. Patris, S. S. Cliff, P. K. Quinn, M. Kasem and M. H. On estimating the microenvironment polarity of biomoleculecular rotors-fluorescent biosensors for viscosity and flow, Thiemens, Isotopic analysis of aerosol sulfate and nitrate durlar cavities, Org. Biomol. Chem, 5, 2523-2528 (2007). Org. Biomol. Chem, 5, 1669-1678 (2007). ing ICT-2k2: Determination of different formation pathways Nicholas J. Greco and Yitzhak Tor, Furan decorated nucle- Ayse Batova, Thanh Lam, Veit Wascholowski, Alice L. as a function of particle size, J. Geophysical Research, 112, oside analogues as fluorescent probes: synthesis, photophysi- Yu, Athanassios Giannis and Emmanuel A. Theodorakis, D23301 (2007). cal evaluation, and site-specific incorporation, Tetrahedron, Synthesis and evaluation of caged Garcinia xanthones, Org. Yuki Kimura, Joseph A. Nuth, III, Subrata Chakraborty 63, 3515-3527 (2007). Biomol. Chem, 5, 494-500 (2007). and Mark H. Thiemens, Non-mass-dependent oxygen isoto- Seergazhi G. Srivatsan and Yitzhak Tor, Using an emissive Matthew E. Nipper, Sheereen Majd, Michael Mayer, James pic fractionation in smokes produced in an electrical disuridine analogue for assembling fluorescent HIV-1 TAR con- C.-M. Lee, Emmanuel A. Theodorakis and Mark A. Hai- charge, Meteorit. Planet. Sci, 42, 1429-1439 (2007). structs, Tetrahedron, 63, 3601-3607 (2007). dekker, Characterization of changes in the viscosity of lipid Melanie Baroni, Mark H. Thiemens, Robert J. Delmas and Yitzhak Tor, Susan Del Valle, David Jaramillo, Seergazhi membranes with the molecular rotor FCVJ, Biochim. Bio- Joel Savarino, Mass-independent sulfur isotopic composi- G. Srivatsan, Andro Rios and Haim Weizman, Designing phys. Acta, Biomembr, 1778, 1148-1153 (2008). tions in stratospheric volcanic eruptions, Science (Washingnew isomorphic fluorescent nucleobase analogues: the thieno Alba Diaz-Rodriguez, Susana Fernandez, Yogesh S. ton, DC, U. S.), 315, 84-87 (2007). [3,2-d]pyrimidine core, Tetrahedron, 63, 3608-3614 (2007). Sanghvi, Emmanuel A. Theodorakis, Vicente Gotor and Mi- Gerardo Dominguez, Terri Jackson, Burton Brothers, Seergazhi Srivatsan, Nicholas J. Greco and Yitzhak Tor, A guel Ferrero, Synthesis of 2’,3’-cyclohexene bicyclic nucleo- Bryan Nguyen and Mark H. Thiemens, Discovery and meahighly emissive fluorescent nucleoside that signals the activiside analogues as antiviral compounds, Nucleic Acids Symp. surement of an isotopically distinct source of sulfate in ty of toxic ribosome-inactivation proteins, Angew. Chem., Ser, 52, 99-100 (2008). Earth’s atmosphere, Proc. Natl. Acad. Sci. U. S. A, 105, Int. Ed, 47, 6661-6665 (2008). 12769-12773 (2008). Renatus W. Sinkeldam, Nicholas J. Greco and Yitzhak Derek A. Fischer, Synthetic studies toward complex natu- Subrata Chakraborty, Musahid Ahmed, Teresa L. Jackson Tor, Polarity of major grooves explored by using isosteric ral products. (D) and Mark H. Thiemens, Experimental Test of Self-Shielding emissive nucleoside, ChemBioChem, 9, 706-709 (2008). Fatima R. Rivas, Synthetic studies towards the total synin Vacuum Ultraviolet Photodissociation of CO, Science Seergazhi G. Srivatsan, Haim Weizman and Yitzhak Tor, thesis of norzoanthamine. (D) (Washington, DC, U. S.), 321, 1328-1331 (2008). A highly fluorescent nucleoside analog based on thieno[3,4- Thanh T. Lam, synthetic studies towards diterpenes; synd]pyrimidine senses mismatched pairing, Org. Biomol. thetic studies towards the caged garcinia xanthones. (D) Chem, 6, 1334-1338 (2008). Thomas Patrick Brady, Total synthesis of norrisolide, syn- TOOR, NAVTEJ SINGH (b.1973) Assistant Profes- Manuela Schuksz, Mark M. Fuster, Jillian R. Brown, Brett thesis of norrisolide analogues, and biological evaluation of sor. B.Sc, 1996, University of Calgary; Ph.D, 2004, Uni- E. Crawford, David P. Ditto, Roger Lawrence, Charles A. norrisolide probes. (D) versity of Calgary. Howard Hughes Medical Institute Glass, Lianxhun Wang, Yitzhak Tor and Jeffrey D. Esko, Postdoctoral Fellow, 2004-2009, Yale University. Bio- Surfen, a small molecule antagonist of heparan sulfate, Proc. THIEMENS, MARK H. (b.1950) Professor and chemistry; Structural Biology. Group II introns are self- Natl. Acad. Sci. U. S. A, 105, 13075-13080 (2008). Dean. B.S, 1972, University of Miami; M.S, 1974, Old splicing RNAs which are thought to be the ancestors of Dominion University; Ph.D, 1977, Florida State Univer- both retrotransposons and spliceosomal introns, which Nicholas J. Greco, Design, synthesis and application of sity. Postdoctoral Fellowship, 1977-1980, University of together make up more than 50% of the human genome. novel fluorescent nucleosides. (D) Chicago. Atmospheric Chemistry; Physical Chemistry. My research interests include studying the structure and Victor K. Tam, Targeting unique nucleic acid structures Measurement of isotope ratios in atmospheric species; function of group II introns, as well as the spliceosome, with small molecules. (D) application of high precision stable isotope ratio mea- using a combination of x-ray crystallography and surement to resolve quantum chemical astrophysical and biochemistry. TEL: (858) 534-3211 FAX: (858) 534- TROGLER, WILLIAM C. Professor. B.A, 1974, atmospheric processes; studies on the evolution of the 6255 Johns Hopkins; M.A, 1974, Johns Hopkins; Ph.D, 1977, solar system and nucleosynthesis. Paleoclimatology and Email: ntoor@ucsd.edu California Institute of Technology. Materials Chemistry; ice core studies. Investigations of the origin and evolu- N. Toor, A. R. Robart, J. Christianson and S. Zimmerly, Nanochemistry. Inorganic polymers and nanoparticles as tion of planets and life. TEL: (858) 534-6882 FAX: Self-splicing of a group IIC intron: 5’ exon recognition and luminescent and electronic sensors for explosives. Char- (858) 822-0389 alternative 5’ splicing events implicate the stem-loop motif acterization of the chemoselectivity of field effect tran-
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