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Scientific Report 2006


Molecular Biology





Chairman's Overview

Staff


Peter E. Wright, Ph.D.*
Professor and Chairman
Cecil H. and Ida M. Green Investigator in Medical Research

Ruben Abagyan, Ph.D.
Professor

Carlos F. Barbas III, Ph.D.*****
Professor
Janet and W. Keith Kellogg II Chair

Rajesh Belani, Ph.D.
Adjunct Assistant Professor

Ola Blixt, Ph.D.
Assistant Professor of Molecular Biology

Michael N. Boddy, Ph.D.
Assistant Professor

Charles L. Brooks III, Ph.D.
Professor

David A. Case, Ph.D.
Professor

Geoffrey Chang, Ph.D.*
Associate Professor

Jerold Chun, M.D., Ph.D.***
Professor

Luis De Lecea, Ph.D.**
Associate Professor
Stanford University
Palo Alto, California

Aymeric Pierre De Parseval, Ph.D.
Assistant Professor of Molecular Biology

Lluis Ribas De Pouplana, Ph.D.
Adjunct Assistant Professor
Barcelona Science Park
Barcelona, Spain

Ashok Deniz, Ph.D.
Assistant Professor

H. Jane Dyson, Ph.D.
Professor

John H. Elder, Ph.D.***
Professor

Martha J. Fedor, Ph.D.*
Associate Professor

James Arthur Fee, Ph.D.
Professor of Research

Elizabeth D. Getzoff, Ph.D.****
Professor

David B. Goodin, Ph.D.
Associate Professor

David S. Goodsell Jr., Ph.D.
Associate Professor

Joel M. Gottesfeld, Ph.D.
Professor

Jennifer Harris, Ph.D.
Assistant Professor of Biochemistry

Christian A. Hassig, Ph.D.
Adjunct Assistant Professor
Kalypsis, Inc.
San Diego, California

Peter B. Hedlund, M.D., Ph.D.
Assistant Professor of Molecular Biology

Mirko Hennig, Ph.D.**
Assistant Professor
Medical University of South Carolina
Charleston, South Carolina

John E. Johnson, Ph.D.
Professor

Gerald F. Joyce, M.D., Ph.D.*****
Professor
Dean, Faculty

Ehud Keinan, Ph.D.
Adjunct Professor

Richard A. Lerner, M.D., Ph.D.*****
President, Scripps Research
Lita Annenberg Hazen Professor of Immunochemistry
Cecil H. and Ida M. Green Chair in Chemistry

Scott Lesley, Ph.D.
Assistant Professor of Biochemistry

Tianwei Lin, Ph.D.
Associate Professor

Clare McGowan, Ph.D.
Associate Professor

Duncan E. McRee, Ph.D.
Adjunct Associate Professor
ActiveSight
San Diego, California

David P. Millar, Ph.D.
Associate Professor

Louis Noodleman, Ph.D.
Associate Professor

Arthur J. Olson, Ph.D.
Professor

James C. Paulson, Ph.D.††
Professor

Vijay Reddy, Ph.D.
Assistant Professor

Steven I. Reed, Ph.D.
Professor

Paul Russell, Ph.D.
Professor

Michel Sanner, Ph.D.
Associate Professor

Harold Scheraga, Ph.D.
Adjunct Professor
George W. and Grace L. Todd Professor of Chemistry, Emeritus
Cornell University
Ithaca, New York

Paul R. Schimmel, Ph.D.*****
Ernest and Jean Hahn Professor of Molecular Biology and Chemistry

Anette Schneemann, Ph.D.
Associate Professor

Subhash C. Sinha, Ph.D.*
Associate Professor

Gary Siuzdak, Ph.D.
Adjunct Associate Professor

Vaughn V. Smider, Ph.D.
Assistant Professor of Molecular Biology

Robyn L. Stanfield, Ph.D.
Assistant Professor

James Steven, Ph.D.
Assistant Professor

Raymond C. Stevens, Ph.D.†††
Professor

Charles D. Stout, Ph.D.
Associate Professor

Peiqing Sun, Ph.D.
Associate Professor

J. Gregor Sutcliffe, Ph.D.
Professor

John A. Tainer, Ph.D.*
Professor

Fujie Tanaka, Ph.D.
Assistant Professor

Elizabeth Anne Thomas, Ph.D.
Assistant Professor

James R. Williamson, Ph.D.*****
Professor
Associate Dean, Kellogg School of Science and Technology

Ian A. Wilson, D.Phil.*
Professor

Curt Wittenberg, Ph.D.
Professor

Kurt Wüthrich, Ph.D.
Cecil H. and Ida M. Green Professor of Structural Biology

Xiang-Lei Yang, Ph.D.
Assistant Professor of Molecular Biology

Todd O. Yeates, Ph.D.
Adjunct Professor
University of California
Los Angeles, California

Qinghai Zhang, Ph.D.
Assistant Professor

Service Facilities

John Chung, Ph.D.
Manager, Nuclear Magnetic Resonance Facilities

Gerard Kroon
Assistant Manager, Nuclear Magnetic Resonance Facilities

Michael E. Pique
Director, Computer Graphics Development

Nahid Razi, Ph.D.
Assistant Core Manager, Consortium for Functional Glycomics

Peter Sobieszcsuk, Ph.D.
Core Manager, Consortium for Functional Glycomics

Senior Staff Scientist

Wayne A. Fenton, Ph.D.

Staff Scientists

Svitlana Berezhna, Ph.D.

Brian M. Lee, Ph.D.**
Southern Illinois University
Carbondale, Illinois

Maria Martinez-Yamout, Ph.D.

Garrett M. Morris, Ph.D.

Chiaki Nishimura, Ph.D.

Jeffrey Speir, Ph.D.

Manal Swairjo, Ph.D.**
Western University of Health Sciences
Pomona, California

Mutsuo Yamaguchi, Ph.D.

Xueyong Zhu, Ph.D.

Senior Research Associates

David Barondeau, Ph.D.**
Texas A&M Unversity
College Station, Texas

Kirk Beebe, Ph.D.Ryan Burnett, Ph.D.

Zhongguo Chen, Ph.D.

Brian Collins, Ph.D.**
Momenta Pharmaceuticals
Boston, Massachusetts

Adrienne Elizabeth Dubin, Ph.D.

Maria Alejandra Gamez-Abascal, Ph.D.

Reto Horst, Ph.D.

Julio Kovacs, Ph.D.

Ying Chuan Lin, Ph.D.

Mikhail Popkov, Ph.D.**
Amunix, Inc.
San Jose, California

Richard R. Rivera, Ph.D.

Kenji Sugase, Ph.D.

Koji Tamura, Ph.D.**
Tokyo University of Science
Chiba, Japan

Xiaoqin Ye, M.D., Ph.D.

Dirk M. Zajonc, Ph.D.**
La Jolla Institute for Allergy & Immunology
San Diego, California

Research Associates


Sunny Abraham, Ph.D.**
Ambit Biosciences
San Diego, California

Melanie Ann Adams, Ph.D.

Fabio Agnelli, Ph.D.

Moballigh Ahmad, Ph.D.**
University of Illinois
Urbana-Chapaign, Illinois

Alexander Ivanov Alexandrov, Ph.D.

Stephen G. Aller, Ph.D.

Marcius Da Silva Almeida, Ph.D.**
Universidade Federal do Rio de Janeiro
Rio De Janeiro, Brazil

Beatriz Gonzalez Alonso, Ph.D.

David Alvarez-Carbonell, Ph.D.**
Memorial Sloan-Kettering Cancer Center
New York, New York

Juliano Alves, Ph.D.

Yu An, Ph.D.

Brigitte Anliker, Ph.D.**
Institut für Biochemie und Molekularbiologie II
Heinrich-Heine-Universitaet
Düsseldorf, Germany

Andrew James Annalora, Ph.D.

Roger Armen, Ph.D.

Joseph W. Arndt, Ph.D.

Karunesh Arora, Ph.D.

Mabelle Ashe, Ph.D.

Wojciech Augustyniak, Ph.D.

Jamie Mitchell Bacher, Ph.D.

Sung-Hun Bae, Ph.D.

Manidipa Banerjee, Ph.D.

Christopher Baskerville, Ph.D.**
Veterans Administration Medical Center
San Diego, California

Lipika Basummalick, Ph.D.**
current employer unknown
relocated to Bay Area

Konstantinos Beis, Ph.D.

Per Bengston, Ph.D.**
Lund University
Lund, Sweden

Christine, Beuck, Ph.D.

William Henry Bisson, Ph.D.**
Burnham Institute
La Jolla, California

David Boehr, Ph.D.

David Bostick, Ph.D.

Ronald M. Brudler, Ph.D.††††

Lintao Bu, Ph.D.

Tommy Bui, Ph.D.

Rosa Maria Cardoso, Ph.D.

Justin E. Carlson, Ph.D.

Andrew Barry Carmel, Ph.D.

Qing Chai, M.D., Ph.D.

Eli Chapman, Ph.D.

Amarnath Chatterjee, Ph.D.

Anju Chatterji, Ph.D.**
Bayer Healthcare, Diagnostics Division
Berkeley, California

Susana Chaves, Ph.D.

Anton Vladislavovich Cheltsov, Ph.D.**
Burnham Institute
La Jolla, California

Jianhan Chen, Ph.D.

Yen-Ju Chen, Ph.D.

Zhiyong Chen, Ph.D.

Srinivas Chittaboina, Ph.D.

Jungwoo Choe, Ph.D.

Chung Jen Chou, Ph.D.

Li-Chiou Chuang, Ph.D.

Jean-Pierre Clamme, Ph.D.**
Université Louis Pasteur Strasbourg
Strasbourg, France

Linda Maria Columbus, Ph.D.

Stephen Connelly, Ph.D.

Adam Corper, Ph.D.

Qizhi Cui, Ph.D.††††

la P. Da Costa, Ph.D.

Sanjib Das, Ph.D.**
Takeda
San Diego, California

Surya Kanta De, Ph.D.

Robert De Bruin, Ph.D.

Sohela De Rozieres, Ph.D.**
Biomatrica
San Diego, California

Qingdong Deng, Ph.D.**
Klypsy, Inc.
San Diego, California

Paula Desplats, Ph.D.

Claire Louise Dovey, Ph.D.

Zhanna Druzina, Ph.D.

Li-Lin Du, Ph.D.

Michelle Duquette-Huber, Ph.D.

Scott Eberhardy, Ph.D.**
Schering-Plough
Union, New Jersey

Stephen Edgcomb, Ph.D.

Susanna V. Ekholm-Reed, Ph.D.

Li Fan, Ph.D.

Daniel Felitsky, Ph.D.

Allan Chris Merrera Ferreon, Ph.D.

Josephine Chu Ferreon, Ph.D.

Pierre Henri Gaillard, Ph.D.**
Centre National de la Recherche Scientifique
Marseille, France

Yann Gambin, Ph.D.

Hui Gao, Ph.D.**
Arena Pharmaceuticals
San Diego, California

Elsa D. Garcin, Ph.D.

Shannon E. Gardell, Ph.D.

Joshua Gill, Ph.D.

Edith Caroline Glazer, Ph.D.

Bettina Groschel, Ph.D.

Fang Guo, Ph.D.**
Department of Immonology
Scripps Research

Min Guo, Ph.D.

Mahender Gurram, Ph.D.

Bong Kwan Han, Ph.D.**
University of California
San Diego, Calfornia

Byung Woo Han, Ph.D.

Shoufa Han, Ph.D.

Wenge Han, Ph.D.

Jason W. Harger, Ph.D.**
Illumina, Inc.
San Diego, California

Rodney Harris, Ph.D.

David M. Herman, Ph.D.

Deron Herr, Ph.D.

Joreg Hinnerwisch, Ph.D.

Kenichi Hitomi, Ph.D.

Wen-Xu Hong, Ph.D.

Yunfeng Hu, Ph.D.

Kwan Hoon Hyun, Ph.D.

Wonpil Im, Ph.D.**
University of Kansas
Lawrence, Kansas

Masanori Imai, Ph.D.

Veli-Pekka Jaakola, Ph.D.

Kai Jenssen, Ph.D.

Glenn C. Johns, Ph.D.
Ionian Technologies
Upland, California

Eric C. Johnson, Ph.D.**
Bruker BioSpin Corporation
Fremont, California

Hope Johnson, Ph.D.

Margaret Alice Johnson, Ph.D.

Susanna Juraja, Ph.D.

Christian Kannemeier, Ph.D.

Mili Kapoor, Ph.D.

Andrey Aleksandrovich Karyakin, Ph.D.

Yang Khandogin, Ph.D.

Ilja V. Khavrutskii, Ph.D.

Reza Khayat, Ph.D.

Dae Hee Kim, Ph.D.

Eda Koculi, Ph.D.

Bethany Koehntop, Ph.D.

Milka Kostic, Ph.D.

Irina Kufareva, Ph.D.

Shantanu Kumar, Ph.D.

Sharon Kwan, Ph.D.

Bianca Lam, Ph.D.

Emma Langley, Ph.D.

Jason Lanman, Ph.D.

Chang-Wook Lee, Ph.D.

Chul Won Lee, Ph.D.

Jinhyuk Lee, Ph.D.**
University of Kansas
Lawrence, Kansas

June Hyung Lee, Ph.D.

Kelly Lee, Ph.D.

Edward Lemke, Ph.D.

Chenglong Li, Ph.D.**
Ohio State University
Columbus, Ohio

Liao Liang, Ph.D.

Vasco Liberal, Ph.D.

William M. Lindstrom, Ph.D.

Hui-Yue Christine Lo, Ph.D.††††

Kunheng Luo, Ph.D.

Ann MacLaren, Ph.D.

Darly Joseph Manayani, Ph.D.

Jeff Mandell, Ph.D.

Maria Victoria Martin-Sanchez, Ph.D.**
University of Geneva
Geneva, Switzerland

Santiago Cavero Martinez, Ph.D.

Hanna-Stina Martinsson Ahlzén, Ph.D.

Tsutomu Matsui, Ph.D.

Derrick Meinhold, Ph.D.

Elena Menichelli, Ph.D.

Jonathan Mikolosko, Ph.D.

Peter J. Mikulecky, Ph.D.

Mauro Mileni, Ph.D.

Susumu Mitsumori, Ph.D.**
Shionogi Research Laboratories
Osaka, Japan

Marissa Mock, Ph.D.

Seongho Moon, Ph.D.**
Samsung Electronic
Seoul, South Korea

Samrat Mukhopadhyay, Ph.D.

Tetsuji Mutoh, Ph.D.

Sujatha Narayan, Ph.D.

Hung Nguyen, Ph.D.

George Nicola, Ph.D.

Tadateru Nishikawa, Ph.D.

Kyoko Noguchi, Ph.D.

Wataru Nomura, Ph.D.

Brian V. Norledge, Ph.D.
Severn School
Severna Park, Maryland

Wendy Fernandez Ochoa, Ph.D.**
University of California
San Diego, California

Amy Odegard, Ph.D.

Lisa Renee Olano, Ph.D.

Brian L. Olson, Ph.D.

Mary O’Reilly, Ph.D.

Brian Paegel, Ph.D.

Sandeep Patel, Ph.D.**
University of Delaware
Newark, Delaware

Stephanie Pebernard, Ph.D.

Bill Francesco Pedrini, Ph.D.

Robert Pejchal, Ph.D.

Vladimir Pelmenschikov, Ph.D.

Jefferson Perry, Ph.D.

Suzanne Peterson, Ph.D.

Jessica Petrillo, Ph.D.

oran Pljevaljcic, Ph.D.

Stephanie Pond, Ph.D.

Owen Pornillos, Ph.D.**
Celgene Corporation
San Diego, California

Daniel Joseph Price, Ph.D.**
GlaxoSmithKline
Research Triangle Park, North Carolina

John Prudden, Ph.D.

Grazia Daniela Raffa, Ph.D.**
Università di Roma La Sapienza
Rome, Italy

Christopher L. Reyes, Ph.D.
Biogen Idec Research
San Diego, California

Alim Seit-Nebi, Ph.D.

Riturparna Sinha Roy, Ph.D.

Stanislav Rudyak, Ph.D.††††

Sean Ryder, Ph.D.**
University of Massachusetts Medical School
Worcester, Massachusetts

Manami R. Saha, Ph.D.††††

Sanjay Adrian Saldanha, Ph.D.

Andre Schiefner, Ph.D.

Lauren J. Schwimmer, Ph.D.

Jennifer S. Scorah, Ph.D.

Pedro Serrano-Navarro, Ph.D.

Craig McLean Shepherd, Ph.D.

David S. Shin, Ph.D.

Develeena Shivakumar, Ph.D.

David A. Shore, Ph.D.

Daniela Andrea Slavin, Ph.D.

Elisabetta Soragni, Ph.D.

Holly Heaslet Soutter, Ph.D.**
Pfizer Global Research & Development
Ann Arbor, Michigan

Greg Springsteen, Ph.D.
Furman University
Greenville, South Carolina

S.V. Ramasastry Sripada, Ph.D.

Thomas Steinbrecher, Ph.D.

Gudrun Stengel, Ph.D.**
University of Lund
Lund, Sweden

Shih-Che Su, Ph.D.

Magnus Sundstrom, Ph.D.

Blair R. Szymczyna, Ph.D.

Florence Muriel Tama, Ph.D.**
University of Arizona
Tucson, Arizona

Nardos Tassew, Ph.D.**
University of Toronto
Toronto, Canada

Hiroaki Tateno, Ph.D.

Rebecca E. Taurog, Ph.D.

Ewan Richardson Taylor, Ph.D.

Hua Tian, Ph.D.

Mauricio Carrillo Tripp, Ph.D.

Ulrich Ignaz Tschulena, Ph.D.

Julie L. Tubbs, Ph.D.

Naoto Utsumi, Ph.D.

Frank van Drogen, Ph.D.**
Institute für Biochemie
Zürich, Switzerland

Ajay Vashisht, Ph.D.

Philip Arno Venter, Ph.D.

Petra Verdino, Ph.D.

William Frederick Waas, Ph.D.

Shun-ichi Wada, Ph.D.††††

Ross Walker, Ph.D.
San Diego Supercomputer
La Jolla, California

Jessica Williams, Ph.D.

Robert Scott Williams, Ph.D.

Eric L. Wise, Ph.D.

Jonathan Wojciak, Ph.D.

Vance Wong, Ph.D.

Timothy I. Wood, Ph.D.**
Walter Reed Army Medical Center
Washington, D.C

Eugene Wu, Ph.D.**
Duke University Medical Center
Durham, North Carolina

Wei Xie, Ph.D.

Lan Xu, Ph.D.

Yoshiki Yamada, Ph.D.

Atsushi Yamagata, Ph.D.

Qi Yan, Ph.D.**
Miramar College
San Diego, California

Yong Yao, Ph.D.**
Burnham Institute
La Jolla, California

Yongjun Ye, Ph.D.

Kye Sook Yi, Ph.D.

Yong Yin, Ph.D.

Kenji Yoshimoto, Ph.D.

Naoto Yoshizuka, Ph.D.

Veronica Yu, Ph.D.††††

Yuan Yuan, Ph.D.

Markus Zeeb, Ph.D.

Ying Zeng, Ph.D.

Haile Zhang, Ph.D.

Qing Zhang, Ph.D.

Wei Zhang, Ph.D.**
Southwest Medical Center
Houston, Texas

Yong Zhao, Ph.D.

Peizhi Zhu, Ph.D.**
University of Michigan
Arbor, Michigan

Scientific Associates

Enrique Abola, Ph.D.

Andrew S. Arvai, M.S.

Ognian V. Bohorov, Ph.D.

Dennis Carlton, B.S.

Vadim Cherezov, Ph.D.

Ellen Yu-Lin Tsai Chien, Ph.D.

Xiaoping Dai, Ph.D.

Marc Deller, D.Phil.

Gye Won Han, Ph.D.

Michael Allen Hanson, Ph.D.

Marcy A. Kingsbury, Ph.D.

Diane Marie Kubitz, B.A.

Padmaja Natarajan, Ph.D.

Marianne Patch, Ph.D.**
Qualcomm
San Diego, California

Gabriela Perez-Alvarado, Ph.D.**
Southern Illinois University
Carbondale, Illinois

Nicholas Preece, Ph.D.††††

Lin Wang, Ph.D.

Visiting Investigators

Stephen J. Benkovic, Ph.D.
Pennsylvania State University
University Park, Pennsylvania

Astrid Graslund, Ph.D.
Stockholm University
Stockholm, Sweden

Arne Holmgren, M.D., Ph.D.
Karolinska Institutet
Stockholm, Sweden

Barry Honig, Ph.D.
Columbia University
New York, New York

Arthur Horwich, M.D.
Yale University
New Haven, Connecticut

Shie-Liang Hsieh, Ph.D.
National Yang-Ming University
Taipei, Taiwan

Tai-Huang Huang, Ph.D.
Academica Sinica
Taipei, Taiwan

Sunghoon Kim, Ph.D.
Seoul National University
Seoul, Korea

Ayori Mitsutake, Ph.D.
Keio University
Yokohama, Japan

Joseph David Ng, Ph.D.
University of Alabama, Huntsville
Huntsville, Alabama

Victoria A. Roberts, Ph.D.
University of California
San Diego, California

Robert D. Rosenstein, Ph.D.
Lawrence Berkeley National Laboratory
Berkeley, California

Lincoln Scott, Ph.D.
Cassia, LLC
San Diego, California

Deborah Tahmassebi, Ph.D.
University of San Diego
San Diego, California

* Joint appointment in The Skaggs Institute for Chemical Biology
** Appointment completed; new location shown
*** Joint appointment
in the Molecular and Integrative Neurosciences Department
**** Joint appointments in the Department of Immunology and The Skaggs Institute for Chemical Biology
***** Joint appointments in the Department of Chemistry and The Skaggs Institute for Chemical Biology
† Joint appointment in the Department of Cell Biology
†† Joint appointment in the Department of Molecular and Experimental Medicine
††† Joint appointment in the Department of Chemistry
†††† Appointment completed

 


Depiction of the P22 bacteriophage virion as solved by electron cryomicroscopy. This structure reveals the major components of the infection machinery, as well as the manner in which DNA is spooled coaxially within the icosahedral capsid. The contour level is set so that the cross section of individual dsDNA strands can be seen with only the outer, most ordered shell of DNA visible. A dodecameric structure at the center of the infection machinery functions as a pressure sensor, which during the packaging of DNA during virus maturation, sends a termination signal to the packaging machinery once the capsid has been fully packaged. Reconstruction and graphics by graduate student Gabriel Lander. Work done in the laboratory of John E. Johnson, Ph.D., in collaboration with Bridget Carragher and Clint Potter, Department of Cell Biology, National Research Resource for Automated Microscopy.