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Path to Effective Recovering of DNA from Formalin-Fixed Biological Samples in Natural History Collection: Workshop Summary Appendix B Participant Biographies STEERING COMMITTEE MEMBERS Ann C. Bucklin (Cochair) is a professor in and head of the Department of Marine Sciences and director of the Marine Sciences and Technology Center at the University of Connecticut. Before joining the University of Connecticut, she was a professor at the University of New Hampshire. Dr. Bucklin was the program manager of the Oceanic Biology Program at the Offlce of Naval Research (1988-1991). She was a Fulbright Senior Scholar in Norway (1992-1993), and she was elected a fellow of the American Association for the Advancement for Science in 1995. She served as director of the New Hampshire Sea Grant Program from 1993 to 2005. She is currently the USA Academic Delegate to the International Council for the Exploration of the Sea. Dr. Bucklin holds a B.A. in biology from Oberlin College and a Ph.D. in zoology from the University of California, Berkeley. Her research interest in spatial and temporal patterns of molecular genetic variation in marine organisms developed from her early interest in sea anemones and continues in her current work on planktonic crustaceans. She leads the Census of Marine Zooplankton, a Census of Marine Life ocean realm fleld project began in 2004, and she is a member of the International Committee for the Ocean Biogeographical Information System. Donald M. Crothers (Cochair) is Sterling Professor Emeritus of Chemistry, professor emeritus of molecular biophysics and biochemistry, and senior
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Path to Effective Recovering of DNA from Formalin-Fixed Biological Samples in Natural History Collection: Workshop Summary research scientist in chemistry at Yale University. Dr. Crothers received his doctorate in chemistry from the University of California, San Diego, and completed a National Science Foundation postdoctoral fellowship at the Max Planck Institute in Göttingen, Germany. His research focuses on the structure, dynamics, and protein-binding properties of nucleic acids. Current projects include characterization of the sequence dependence of curvature and fiexibility, and the role of those variables in determining the afflnity for core histones and regulatory proteins. Another focus is on the dynamics of protein-DNA complexes, using nuclear magnetic resonance spectroscopy and stopped-fiow methods. His research interests include the structure, properties, and function of nucleic acids, protein-DNA interactions, mechanisms of control of gene expression, and the effects of antitumor compounds on DNA, the dependence on the activation energy for DNA bending by proteins on DNA sequence, and the physical chemistry of biological polymers, particularly nucleic acids. Dr. Crothers has done theoretical and experimental work on the physical properties of nucleic acids and on their interactions with other molecules. Dr. Crothers has received numerous awards, including the Alfred P. Sloan and Guggenheim fellowships and the Alexander von Humboldt Senior Scientist Prize. He was elected into the American Academy of Arts and Sciences in 1986, inducted into the National Academy of Sciences in 1987, and named a fellow of the American Association for the Advancement of Science in 1992. He also has served on the editorial boards of numerous journals. Timothy O’Leary is director of the Biomedical Laboratory Research and Development (BLR&D) and the Clinical Science Research and Development Service (CSR&D) of the U.S. Department of Veterans Affairs. He holds a doctorate in physical chemistry from Stanford University and a medical degree from the University of Michigan. As BLR&D director, he oversees all basic biological or physiological research in humans or in animals that involves animal models or tissues, blood, or other specimens from humans. As CSR&D director, he supervises research on intact human beings as the unit of examination. He is certifled in anatomic pathology and in molecular genetic pathology by the American Board of Pathology and the American Board of Medical Genetics. For more than 15 years before joining the Department of Veterans Affairs, he chaired the Department of Cellular Pathology at the Armed Forces Institute of Pathology. He also is a reserve member of the Public Health Service Commissioned Corps. His research involves molecular changes in gastric tumors, ultrasensitive detection of
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Path to Effective Recovering of DNA from Formalin-Fixed Biological Samples in Natural History Collection: Workshop Summary biological toxins, and mechanisms of formaldehyde flxation. He is credited with expanding the capacity of the Armed Forces Pathology Institute to include molecular genetics and tissue magnetic resonance microscopy. Dr. O’Leary has published more than 130 scientiflc papers since 1973 and written numerous book chapters. He edited the 2002 text Advanced Diagnostic Methods in Pathology: Principles, Practice and Protocols. He has received many awards for his work, including the 2004 Armed Forces Institute of Pathology Medallion. Christoffer Schander is professor of marine biodiversity at the University of Bergen, Norway. He received B.Sc., Ph.D., and docent degrees from Göteborg University, Sweden. His research on evolutionary forces and phylogeny in creating organism diversity uses phylogenetic analyses that integrate morphological and molecular data. His research focuses on molluscs, speciflcally the ectoparasitic pyramidellid gastropods and the shell-less, primary deep-sea aplacophorans. Alison Williams is a research staff member and lecturer in chemistry in the graduate program in molecular biophysics at Princeton University. She holds a B.S. from Wesleyan University, and she received her M.S. and Ph.D. from the University of Rochester. Dr. Williams has been a member of the Princeton Chemistry Department since 2003. She joined the department after two years as director of studies at Princeton’s Wilson College. She leads a research team investigating the properties of nucleic acids in terms of their local chemical structure and environment. Dr. Williams is a long-time member of the National Organization of Black Chemists and Chemical Engineers, and she has spoken extensively on enhancing the role of women and minorities in science. INVITED PARTICIPANTS Charles Cantor is a founder, chief scientiflc offlcer, and member of the board of directors at Sequenom, Inc. He also is founder of SelectX Pharmaceuticals, a drug-discovery company based in the Boston area, and is codirector of the Center for Advanced Biotechnology at Boston University, where he also is professor of biomedical engineering. Dr. Cantor has held positions at Columbia University and the University of California, Berkeley, and he was director of the Human Genome Center of the U.S. Department of Energy at Lawrence Berkeley National Laboratory. He has published
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Path to Effective Recovering of DNA from Formalin-Fixed Biological Samples in Natural History Collection: Workshop Summary more than 400 peer-reviewed articles and is coauthor of a three-volume textbook on biophysical chemistry and the flrst textbook on genomics, Science and Technology of the Human Genome Project. He holds more than 60 patents. He sits on the advisory boards of more than 20 national and international organizations and is a member of the National Academy of Sciences. Marvin Caruthers is a distinguished professor at the University of Colorado, Boulder. He received a Ph.D. from Northwestern University. His research interests include nucleic acid chemistry and biochemistry, and his laboratory uses nucleic acid chemistry, biochemistry, and molecular biology to study regulation and control of gene expression. Dr. Caruthers has made major contributions to the chemical synthesis of nucleic acids, culminating in development of automated DNA synthesis, and thus the availability of oligonucleotides of any desired sequence. As a result of synthesizing DNA with modifled nucleotides at deflned sites, he was able to measure the contribution of individual functional groups to DNA-protein interactions. Dr. Caruthers was named Guggenheim Fellow in 1981, and he was elected to the National Academy of Sciences in 1994. Robert DeSalle is the curator in charge of the Ambrose Monell Cryo-Collection, a curator of entomology, and codirector of molecular laboratories at the American Museum of Natural History. His flelds of specialization include molecular evolution, population genetics, molecular systematics, and developmental biology. His early research focused on the molecular systematics of the Drosophilidae, a family of fiies. His more recent work involves gene family evolution and comparative genomics in a variety of organisms, including pathogenic bacteria. Dr. DeSalle is among the founders of the museum’s Conservation Genetics Program, which applies studies at the molecular level to the conservation of wildlife and wild lands throughout the world. In 1996, Dr. DeSalle and his colleagues developed a genetic test for caviar that helped gain protection for sturgeon in the Caspian Sea basin under the Convention on the International Trade in Endangered Species of Wild Fauna and Flora. Dr. DeSalle holds a B.A. in biological sciences from the University of Chicago and a Ph.D. from Washington University. He joined the museum in 1991. He is an adjunct professor at Columbia University, New York University, the University of Connecticut, and Yale University. Dr. DeSalle is the coauthor of The Science
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Path to Effective Recovering of DNA from Formalin-Fixed Biological Samples in Natural History Collection: Workshop Summary of Jurassic Park and the Lost World, and he was curator of the museum’s 1999 landmark exhibition “Epidemic! The World of Infectious Disease.” Miral Dizdaroglu is the leader of the DNA Measurements Group in the Biochemical Science Division of the National Institute of Standards and Technology. He is also an adjunct professor at the University of Maryland, Baltimore County. His research concerns oxidative stress and DNA damage and repair. Oxidative stress is produced in cells by oxygen-derived species resulting from cellular metabolism and from interaction with cells of exogenous sources, such as carcinogenic compounds, redox-cycling drugs, and ionizing radiations. DNA damage caused by oxygen-derived species, including free radicals, is the most frequent type encountered by aerobic cells. Oxidative DNA damage can produce DNA modiflcations that include base and sugar lesions, strand breaks, DNA-protein cross-links, and base-free sites. Accurate measurement of those modiflcations is essential for explaining the mechanisms and biological effects of oxidative DNA damage. Dr. Dizdaroglu received a diploma in chemical engineering from the University of Ankara, Turkey, and a Ph.D. in physical chemistry from the University of Karlsruhe, West Germany. Catherine Fenselau is a professor at the University of Maryland, College Park. She conducts biomolecular studies using mass spectrometry, rapid characterization of microorganisms by mass spectrometry, and new methods for proteomics. She is a past president of the American Society for Mass Spectrometry and the recipient of numerous awards, including the Garvan Medal of the American Chemical Society and of Spectroscopy Society of Pittsburgh Award. Dr. Fenselau holds an A.B. from Bryn Mawr College and a Ph.D. from Stanford University. Neil Hall is an assistant investigator at the Institute for Genomic Research. He has a B.S. in genetics and a Ph.D. in molecular biology from the University of Liverpool. Before joining the institute, he was a project manager in bioinformatics at the Sanger Institute. His major research is on the genomics of infectious diseases, using bioinformatics analysis to elucidate the evolution of pathogenic organisms, how they respond to selective forces acting upon them, and how the ability to infect humans originates. He recently has become interested in using genomic data to study pathogen populations, and he has begun projects to develop databases and methods that will assist in that research.
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Path to Effective Recovering of DNA from Formalin-Fixed Biological Samples in Natural History Collection: Workshop Summary Timothy Harris is the director of sequencing technology at Helicos BioSciences Corporation. Until 2004, Dr. Harris was director of research at Prealux, a wholly owned subsidiary of Amersham Biosciences, where his work involved single-molecule DNA sequencing technology. He originated the design and led the development for the Amersham IN Cell Analyzer. From 1978 to 1996, Dr. Harris worked for Bell Laboratories where his work led to the flrst report of single-molecule imaging, spectroscopy, and lifetimes. His work resulted in more than 80 publications, 100 invited talks, the IR Award in 1982 for the development of an intracavity laser spectrometer, and the 1992 Williams-Wright Award for his contributions to vibrational spectroscopy. Dr. Harris holds a B.S. in chemistry from California Polytechnic State University and a Ph.D. in analytical chemistry from Purdue University. Dr. Harris holds two patents. Matthias Hofer is a postdoctoral fellow at Harvard Medical School. He received his M.D. from the University of Ulm Medical School in Ulm, Germany. His residency was in the Department of Urology at the University Hospital of Ulm. He joined Mark Rubin’s laboratory at Brigham and Women’s Hospital in Boston as postdoctoral research fellow. His research is on molecular proflles of prostate cancer and on the metastasis-associated gene 1. He was a 2003 recipient of a U.S. Department of Defense postdoctoral fellowship. Steven Hofstadler is vice president of research for the Ibis Division of Isis Pharmaceuticals. He heads the mass spectrometry program and coordinates the company’s basic research activities. He also is responsible for primary high-throughput screening activities and for the development of advanced mass spectrometric instrumentation and methods to support the company’s diagnostics and proteomics research. He has worked on several initiatives of the Defense Advanced Research Projects Agency and with a continuing program for the U.S. Centers for Disease Control and Prevention. Dr. Hofstadler has a Ph.D. in analytical chemistry from the University of Texas, Austin. He is the author of more than 100 scientiflc publications and holds several U.S. patents. He received R&D Magazine’s R&D 100 Award in 2000 for “Multitarget Afflnity/Speciflcity Screening” and was the recipient of the Society for Biomolecular Screening’s 2004 Perkin Elmer Life Sciences Award for innovations in high-throughput screening. Dr. Hofstadler serves on the scientiflc committee of the Association for Laboratory Automation, the editorial board for the American Chemical
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Path to Effective Recovering of DNA from Formalin-Fixed Biological Samples in Natural History Collection: Workshop Summary Society journal Analytical Chemistry, and the National Institutes of Health Special Emphasis Review Panel. Charles Lydeard is a program director in the Directorate for Biological Sciences at the National Science Foundation and a professor in the Department of Biological Sciences at the University of Alabama. His research is in systematics, conservation, and evolution of invertebrates. He, his students, and his collaborators have been focusing attention on freshwater mollusks, particularly unionid bivalves and pleurocerid gastropods and more recently terrestrial gastropods. Dr. Lydeard has a Ph.D. from Auburn University. Juan Carlos Morales is a program director in the Directorate for Biological Sciences at the National Science Foundation and an associate research scientist in the Center for Environmental Research and Conservation at Columbia University. His research is in systematics, biogeography, and conservation genetics of mammals. He is particularly interested in the use of molecular markers to determine evolutionary relationships, distributional patterns, areas of genetic endemism, and population structure in several mammalian groups. Mark Rubin is an associate professor of pathology and director of genito-urinary pathology at Brigham and Women’s Hospital, Harvard Medical School. He has been closely involved in the National Institutes of Health’s development of protocols for recovering high-quality DNA from formalin-flxed material. Daniel Ryan is a senior scientist in the Genomics/Location Analysis R&D group at Agilent Technologies, Inc. His research is on improved methods for recovery of genomic DNA from formalin-flxed samples, including formalin-flxed cells for ChIP-on-chip analysis (a type of “location analysis”) and formalin-flxed paraffln-embedded samples. Before joining Agilent in 2005, Dr. Ryan was a senior investigator in the Biochemistry Department at the University of California, San Francisco where he worked on integrating data from published studies of yeast and mammalian spliceosomes into a 3-dimensional molecular model of a spliceosome at the flrst step of chemistry. From 1995 to 2002, Dr. Ryan was a Division of Biology fellow and senior scientist at the California Institute of Technology, working to elucidate the structure-function relationships in putative catalytic RNA in spliceosomes. As a postdoctoral fellow at Columbia University, his research
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Path to Effective Recovering of DNA from Formalin-Fixed Biological Samples in Natural History Collection: Workshop Summary involved studies of the natural cross-linking products and oxidation-reduction chemistries of quinone/hydroquinone-functionalized peptides in marine animals called tunicates, or “sea squirts.” He has a Ph.D. in organic chemistry from Princeton University. Steven Salzberg is director of the Center for Bioinformatics and Computational Biology and Horvitz Professor in the Department of Computer Science at the University of Maryland, College Park. He holds a Ph.D. from Harvard University, and he is a fellow of the American Association for the Advancement of Science. His research is in bioinformatics, genomics, gene flnding, and genome assembly. REPRESENTATIVES OF SPONSORING AGENCIES Tom Evans is a senior scientist at New England Biolabs, Inc. Gonzalo Giribet is a curator of invertebrate zoology at the Museum of Comparative Zoology and a professor in the Department of Organismic and Evolutionary Biology at Harvard University. Evon Hekkala is a postdoctoral scientist at the U.S. Environmental Protection Agency’s Environmental Monitoring and Assessment Program. Scott Miller is a senior program offlcer in the Offlce of the Under Secretary for Science at the Smithsonian Institution and a research entomologist at the National Museum of Natural History. Ernest Mueller is the R&D principal investigator in molecular biology at Sigma-Aldrich. Benjamin Rosenthal is a molecular systematist in the U.S. Department of Agriculture’s Agricultural Research Service. David Schindel is executive secretary of the Consortium for the Barcode of Life.
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Path to Effective Recovering of DNA from Formalin-Fixed Biological Samples in Natural History Collection: Workshop Summary NRC STAFF Fran Sharples, Director, Board on Life Sciences Evonne P.Y. Tang, Senior Program Offlcer Tova Jacobovits, Senior Program Assistant
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