Human Retroviruses: Methods and Protocols PDF
Preview Human Retroviruses: Methods and Protocols
Methods in Molecular Biology 1087 Elisa Vicenzi Guido Poli Editors Human Retroviruses Methods and Protocols M M B ™ ETHODS IN OLECULAR IOLOGY Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hat fi eld, Hertfordshire, AL10 9AB, UK For further volumes: http://www.springer.com/series/7651 Human Retroviruses Methods and Protocols Edited by Elisa Vicenzi and Guido Poli Division of Immunology, Transplant, and Infectious Diseases, San Raffaele Scientific Institute, Milano, Italy Editors Elisa Vicenzi Guido Poli Division of Immunology, Transplant, Division of Immunology, Transplant, and Infectious Diseases and Infectious Diseases San Raffaele Scientific Institute San Raffaele Scientific Institute Milano , I taly Milano, Italy ISSN 1064-3745 ISSN 1940-6029 (electronic) ISBN 978-1-62703-669-6 ISBN 978-1-62703-670-2 (eBook) DOI 10.1007/978-1-62703-670-2 Springer New York Heidelberg Dordrecht London Library of Congress Control Number: 2013949423 © Springer Science+Business Media, LLC 2 014 This work is subject to copyright. 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Printed on acid-free paper Humana Press is a brand of Springer Springer is part of Springer Science+Business Media (www.springer.com) Dedication ( Excerpt from the obituary published in “Retrovirology” by Ben Berkhout et al., Retrovirology, 2013 Mar 21; 10:28 ) Our friend Kuan-Teh Jeang, “Teh” to friends and colleagues, passed away unexpectedly at the age of 54 on the evening of January 27, 2013. Great shock and sorrow rapidly spread through the scientifi c community all over the world. Teh was born in 1958 in Taiwan and went to the US in 1970. At age 16, he began col- lege at the Massachusetts Institute of Technology and, after two years, started medical school at the “Johns Hopkins” University in Baltimore, receiving both his M.D. and Ph.D. degrees by age 25. During his time at Hopkins, Teh met his wife, Diane, a graduate student in the same laboratory. They married in 1984 in Iowa, where Teh completed his medical internship. The next year, Teh started his postdoctoral work at the NIH in the laboratory of Dr. George Khoury, NCI. Teh had been working at the NIH in Bethesda for 27 years, exactly half of his life, as Chief of the Molecular Virology Section in the Laboratory of Molecular Microbiology directed by Malcolm A. Martin. His major research interest was around the human immu- nodefi ciency virus (HIV-1 ) and the human T-cell leukemia virus (HTLV-I), contributing with >300 scientifi c papers, some of which of seminal relevance and published in the best scientifi c journals. He stopped bench working only in 2004 when he became editor-in-chief of Retrovirology . In the late 1980s, Teh showed that HIV-1 uses an unprecedented mechanism of tran- scription that is dictated by an RNA-binding protein, Tat, which binds a nascent viral RNA target (TAR), the fi rst RNA enhancer element ever described. Subsequently, Teh’s group characterized cellular RNA-binding proteins that regulate HIV-1 replication, including the TAR RNA-b inding protein (TRBP) that later became known as an important factor of the cellular RNA interference machinery. In recent work, his lab completed a genome-wide screening for human cell factors that are needed for HIV-1 replication. Using novel tech- nology, Teh extended his interests in RNA-biology through the identifi cation of small RNAs (i.e., siRNAs and miRNAs) that have biologically important roles in viral infection, cellular metabolism, and virus-induced pathogenesis. In addition to all his scientifi c achievements, one of Teh’s greatest contributions to sci- ence has been his role as mentor for young scientists who have since spread across the globe, from Taiwan to China, from France to the Netherlands, and from Canada to many places in the United States. His mentoring commitment is also refl ected in his service to many professional societies and in his special interest in the area of scientifi c publication. From the earliest years, Teh was an advocate of the Open Access publishing format (“ science should be free as oxygen in the air…” was used to say presenting the initiative). In 2004 he launched, as Editor-in-Chief, the journal R etrovirology that became, in less than 10 years, among the highest cited journals in the fi eld of virology. After R etrovirology , Teh pushed vi Dedication for more journal involvement with the retroviral community … and F rontiers in Retrovirology was born in 2009 along with the fi rst and very successful conference organized by BioMed Central in Montpellier, France. Teh was also a true scientifi c leader, initiating scientifi c debate, writing editorials, sitting on many committees, orchestrating new book volumes, and organizing international meet- ings on diverse topics. For instance, he was President of the Society of Chinese Bioscientists in America (SCBA) in 2010 and voiced the strong opinion that the representation of Asian- American scientists in leadership positions should be increased. Teh was the recipient of many awards, most recently the International Retrovirology Association’s Dale McFarlin Award in 2011, BioMed Central’s Open Access “Editor of the Year” in 2010 and the Johns Hopkins University Woodrow Wilson Award in 2009. Teh was also elected to membership in prestigious societies such as the Academia Sinica in Taiwan, Fellow of the American Academy of Microbiology, and Fellow of the American Association for the Advancement of Science. Teh had an infectious enthusiasm and winner’s mentality both at work and play. He was a skilled tennis and chess player, a gifted writer, and a great debater with strong opinions on virtually all subjects of science and life. Additionally, he had a passion for current events and a love for travel, movies, food, and music. Teh’s death is a blow to the retrovirus research community and we will sorely miss his scientifi c leadership. He has been central to so much of what we have accomplished together as well as being a supportive and generous friend to many of us individually. Teh’s life was much too short, but his legacy and our memories of him will last forever. Our hearts and condolences are with his wife Diane and his three children David (23), Diana (20), and John (15). This book is dedicated to him and his untamed enthusiasm for science and life. In the Deserved Honor of Kuan-Teh Jeang, a Visionary in Science and Communication By Jean-Luc Darlix Dear Teh, We’ll miss you Yes, we’ll miss you so much, We’ll miss your ideas and unforgettable dedications In Science while constantly advocating for novel communications, Debating with enthusiasm for worldwide free open access, So brightly, straightforwardly with fairness. Yes, Dear Teh We’ll miss all of these original views of Yours At the very same time We’ll miss the man Yes, the Man Dedication vii viii Dedication 1 . Ajit Kumar, Teh, Michael Bukrinski and Rakesh Kumar at George Washington University, Washington DC, ca. January 19, 2013. 2. Juang Jeng-Tse, Teh, Jeremy Luban and Guido Poli, San Raffaele Scientific Institute, Milano, 2008. 3. Teh and Jean Luc Darlix in Lyon Fourvière, France, June 2011. 4. Teh and Anne Napoly in Lyon Fourvière, France, June 2011. 5. Teh giving giving the Retrovirology Achievement Award to JL Darlix, June 2011. 6. Anna Cereseto and Teh, San Raffaele Scientific Institute, Milano, 2008. 7. Teh presenting the Open Access experience as Editor-in-Chief of “Retrovirology.” 8. Gabriella Scarlatti and Teh at the International Conference on HIV/AIDS in Vienna, Austria, 2010. 9. Diane Havlir and Teh at the International Conference on HIV/AIDS in Vienna, Austria, 2010. 10. Teh and the Editors of Retrovirology Monsef Benkirane (left) and Ben Berkhout (right) at the International Conference on HIV/AIDS in Vienna, Austria, 2010. Pref ace There are several books on HIV/AIDS and retrovirology dedicated to either basic virology, immunology or the clinical and social aspects of this pandemic infectious disease. So, why another book on this subject! Because, this is the fi rst collection of articles dedicated to the key experimental protocols that are at the basis of all the major discoveries of the fi eld since pathogenic human retroviruses came under the limelight with human T-cell leukemia/ lymphoma virus type 1 (HTLV-1) in 1980—a virus causing the rare adult T cell leukemia and tropical spastic paraparesis—and, especially, with the discovery of the human immuno- defi ciency virus type 1 (HIV-1) in 1983–1984 and HIV-2 (1986) as the etiological agents of the acquired immunodefi ciency syndrome (AIDS), still a major threat to mankind with more than 34 millions infections worldwide and 7,500 new infections daily. The current book is organized in 5 blocks of chapters focusing on the following: “Mapping the HIV life cycle” (14 chapters), “Isolation, co-receptor use, and cell tropism of HIV-1” (5 chapters), “In vivo quantifi cation of HIV-1” (2 chapters), “Biological aspects of HIV-1” (2 chapters) and, last, but not least, to “HTLVs” (3 chapters). Of course, most of the chapters are dedicated to HIV-1, the big killer, but there are also issues dedicated to HIV-2 and to the HTLVs, including the still “disease-less” HTLV-2. In addition, some articles explore “assay and function of accessory genes,” largely involving the interface between retroviral and host factors, the extracellular role of Tat and Tax, resembling the function of cytokines, and the biotechnological exploitation of HIV as len- tiviral vector to carry foreign genes with therapeutic value. Although the “core business” of the book and of its individual chapters is to provide state-of-art methodological protocols from world leaders in human retrovirology, the book is not meant to be a just a collection of “cook-book recipes.” In fact, each chapter provides an updated, though synthetic, review of the fundamental knowledge concerning a single retroviral life step. Enjoy reading! Milano, Italy Elisa Vicenzi Guido Poli ix
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