Encyclopedia of Genetics, Genomics, Proteomics, and Informatics

Transcription

1 George P. Rédei Encyclopedia of Genetics, Genomics, Proteomics, and Informatics 3rd Edition Volume 1 A L With 1914 figures and 94 tables

2 George P. Rédei Encyclopedia of Genetics, Genomics, Proteomics, and Informatics 3rd Edition Volume 2 M Z With 1914 figures and 94 tables

3 Author: George P. Rédei Professor Emeritus, University of Missouri, Columbia 3005 Woodbine Ct. Columbia, MO USA A C.I.P. Catalog record for this book is available from the Library of Congress ISBN: This publication is available also as: Electronic publication under ISBN and Print and electronic bundle under ISBN This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in other ways, and storage in data banks. Duplication of this publication or parts thereof is only permitted under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer Verlag. Violations are liable for prosecution under the German Copyright Law. Springer is part of Springer Science+Business Media springer.com George P. Rédei 2008 The use of registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Product liability: The publishers cannot guarantee the accuracy of any information about the application of operative techniques and medications contained in this book. In every individual case the user must check such information by consulting the relevant literature. Printed on acid free paper SPIN:

4 Acknowledgements I thank my wife Magdi for her patience during writing and for critical reading of the text. My daughter Mari introduced me into word processing. My son-in-law, Kirk has been very supportive. Granddaughters, Grace, Paige and Anne are most inspirational. I am grateful to countless numbers of colleagues on whose work this material is based and to whom I could not refer because of limitations of space. I am indebted to colleagues, especially to Dr. Csaba Koncz, Max-Planck-Institut, Cologne, Germany for many useful discussions. My students at the University of Missouri, Columbia, MO, and students and colleagues, particularly Dr. András Fodor, at the Eötvös Lóránd University of Basic Sciences, Budapest, provided purpose for undertaking this project. I am also indebted to Jane D Phillips, Director of Development for Life Sciences at the University of Missouri for her interest and encouragement. Some of the chemical formulas are based on the Merck Index, on the Aldrich Catalog and Fluka Catalog. During the preparation of the third edition, Mark Jarvis has been most helpful in resolving a variety of computer problems. I appreciated the comments from the readers on the first and second editions. The first from Dr. SLC said: Thank you for assembling such concise explanations of all genetic concepts in a single volume. Similar letters came from many others, which for reasons of space, I cannot quote here. I am thankful to the public reviews for the constructive comments and suggestions. Author is much indebted to Anil Chandy for expert advice, friendship, cooperation and understanding during all phases of the production of this book. Cudweed by Konrad von Gessner (1597), the famous Swiss savant and zoological and botanical illustrator. Von Gessner's work has been borrowed by many, among them the German Joachim Camerarius ( ) of Tübingen, a great authority on classics, religion and science and whose descendant Rudolph Jacob Camerarius ( ) would become the first experimental geneticist, and discover the love life of plants.

5 Preface to the First Edition The primary goal of this Manual is the facilitation of communication and understanding across the wide range of biology that is now called genetics. The emphasis is on recent theoretical advances, new concepts, terms and their applications. The book includes about 18 thousand concepts and over 650 illustrations (graphs, tables, equations and formulas). Most of the computational procedures are illustrated by worked-out examples. A list of about 900, mainly recent books, is provided at the end of the volume, and additional references are located at many entries and illustrations. The most relevant databases are also listed. The cross-references following the entries connect to a network within the book, so this is not just a dictionary or glossary. By a sequential search, comprehensive, integrated information can be obtained as you prepare for exams, or lectures, or develop or update a course, or need to review a manuscript, or just wish to clarify some problems. In contrast to standard encyclopedias, I have used relatively short but greater variety of entries in order to facilitate rapid access to specific topics. This Manual was designed for students, teachers, scientists, physicians, reviewers, environmentalists, lawyers, administrators, and to all educated persons who are interested in modern biology. Concise technical information is available here on a broad range of topics without a need for browsing an entire library. This volume can always be at your fingertips without leaving the workbench or desk. Despite the brevity of the entries, the contents are clear even for the beginner. Herbert Macgregor made the remarkable statement that in 1992 about 7,000 articles related just to chromosomes were scattered among 627 journals. Since then, the situation has become worse. Many publications beyond a person s specialization are almost unreadable because of the multitude of unfamiliar acronyms and undefined terms. Students and colleagues have encouraged me to undertake this effort to facilitate reading of scientific and popular articles and summarize briefly the current status of important topics. According to Robert Graves (a good poem) makes complete sense and says all that it has to say memorably and economically. I hope you will appreciate the sense and economy of this Manual. I will be much indebted for any comment, suggestion and correction. GPR 3005 Woodbine Ct. Columbia, MO , USA Telephone: (573) , redeig@missouri.edu or redeia@mchsi.com I almost forgot to say that genetics will disappear as a separate science because, in the 21st century, everything in biology will become gene-based, and every biologist will be a geneticist. Sydney Brenner, 1993

6 Preface to the Second Edition The majority of the users of the first edition considered this book as an encyclopedia because the cross-references tied the short entries into comprehensive reviews of the topics. In contrast to big encyclopedias in this work only a few entries exceed a couple of thousand words and that make it much faster to find the specific concept or term of interest. Unlike multi-author works this is practically free of redundancy and it is compact in size but not in depth of information. One of the reviewers pointed out that many of the topics covered could not be found in any other single book, including encyclopedias, dictionaries or glossaries. Another reviewer appreciated it as a broad resource of information that may take a lengthy search to uncover without it. Since the publication of the 1st edition, I have steadily updated and improved on the topics. I have added many new concepts, illustrations, books and database addresses. (The database addresses are in an unfortunate flux and some may be out existence by the time you wish to log in; therefore I provided several to minimize the problem beyond my control.) This second edition contains about 50% more information and more than twice as many illustrations than the 1st edition. A new feature is the predominantly current, over 7,000 text references to journal articles. Their bibliographies may help to locate additional key and classical papers. The General References at the end include about 2,000 books. For additional medical genetics references I suggest the use of OMIM at The National Center for Biotechnology Information ( see also Grivell, L EMBO Rep. 3:200). I have greatly expanded the cross-references among the entries because the users found this feature especially useful. Color plates were added to the end of the book. At the end of the files there are some historical vignettes. Since the publication of the first edition the need for such a book became even more evident. In the literature unexplained concepts, terms and acronyms are on the increase and even a name DAS (dreaded abbreviation syndrome) has been coined for the malaise (Science, 283:1118). The users of the first edition agreed with the Nobellaureate geneticist, HJ Muller who posed and answered the still current problem: Must we geneticists become bacteriologists, physiological chemists and physicists, simultaneously with being zoologists and botanists? Let us hope so. (Amer. Nat. 1922, 56:32). The vision of genetics today is not less than the complete understanding how cells and organisms are built, how they function metabolically and developmentally, and how they have evolved. This requires the integration of previously separate disciplines, based on diverse concepts and tongues. Whatever is your specialization or interest, I hope you will find this single volume helpful and affordable. Although I had the aim of comprehensiveness beyond all the available compendiums, there were hard decisions of what to include and what to pass. The same science may appear different depending on who, how and when looks at it (up or down) as Gerald H Fisher's art above (man or woman or both) illustrates the point.* Thank you for the appreciation of the first edition. I will be much indebted for your comments and suggestions. GPR redeia@mchsi.com *By permission of Perception and Psychophysics 4:189 (1968).

7 Preface to the Third Edition When I acquired the right words, it was easier for me to understand what I was thinking: it is difficult to reason through a problem if you cannot articulate what the problem is. (John F Bruzzi 2006 New England J. Med. 354:665). This volume is essentially an improved and enlarged new version of the previous, much-acclaimed book. The third edition has over 1,000 pages more of new material than the second. The latest progress in current hot topics such as stem cells, gene therapy, small RNAs, transcription factories, chromosomal territories, networks, genetic networks, ENCODE project, epigenetics, histone and protein biology, prions, hereditary diseases, and even patents are covered. The number of illustrations increased to nearly 2,000 and several hundreds are in four-color. The old entries have been revised, updated and expanded. Cross-references among entries have been increased. Retractions and corrigenda are pointed out. Nearly 1,800 database and web server addresses, about 14,000 journal paper references and more than 3,000 current book titles are included. Interesting historical vignettes lend some insight into the lighter sides of biology. I hope the reader finds the absence of laboratory jargon refreshing. The encyclopedia will equip its reader to prepare journal papers, write or review research proposals or help organize a new course or update a current course. Students will find the topics useful for preparing for exams or for writing term papers. It may also appeal to basic and applied biologists and to practitioners of many other fields. The readers of previous editions appreciated the clarity of the basics in this book. A sample of what professional reviewers wrote about the book is carried for the reader's reference. In addition, about the current publications in general, the Editor of Science had the following comment. Each specialty has focused in to a point at which even the occupants of neighboring fields have trouble understanding each others papers The language used in Reports and Research Articles is sufficiently technical and arcane that they are hard to understand, even for those in related disciplines. (Kennedy, D 2007 Science 318:715). One of the most fascinating features of science is its continuous evolution. My goal was to emphasize the principles, provide numerical data and guide to resources that are more difficult to access from other publications. The book can assist the reader to make better use of the Internet but the Internet and textbooks are no substitutes for this book. Unlike the majority of books, this Encyclopedia will not be outdated because the continuously renewed and updated databases and web sites listed assure its usefulness even in the distant future. Describing individual genes in different organisms with some exceptions is no longer practical in a single book or even with the aid of an excellent resource such as PubMed due to the multitude of abstracts (more than 15,000,000 entries from more than 19,000 journals). The web sites listed in this book can however, provide great help in identifying many genes, their synonyms, functions and interacting partners as well as critical references to them. Although basic statistical concepts are explained in simple terms, most of the theoretical mathematical models or detailed laboratory procedures are not included because of the difficulties of describing the techniques within the limited space available in a single book. The abundance of references can lead the reader in the right direction. Selection of papers for inclusion is also a continuous challenge. During 1992 to ,061 journals published more than 3.47 million peer-reviewed articles in health-related areas alone (Paraje, G et al Science 308:959). Although this book is quite complex, integrated, and referenced, it does not include everything but it might be a useful guide to almost everything one needs in biology. For a proof of principle, I suggest that you look up any concept what you know or what you are uncertain or have doubts about. I welcome all readers and I promise to respond to questions or comments. GPR redeia@mchsi.com

8 First to Read for the Third Edition The organization of the expanded and revised third edition is slightly different from that of the previous ones. The material is still in alphabetical order but in a somewhat different style. Numbers involved with the entries do not affect the order. Entries beginning with Greek letters are sorted as if they would be in Roman or the Greek letter follows the term. Words followed by a comma and another word precede entry words without comma, e.g., antibody, secondary is followed by antibody detection. Hyphenated entries are sorted as single words. The spelling of some terms vary because in the scientific literature some technical terms are written either with a c or k or with an e or ae. Some abbreviations are used in the literature as e.g., PGD or P.G.D. and both may not be used in this book. Here the most common usage is favored. Some entries are qualified by another word added after and in others the qualifier comes first. Most entries are followed by cross-references that guide to relevant topics. In particular cross-references qualifiers are not separated by comma even when they are with comma in the main list. In case you make electronic searches it is frequently more practical to use only part of the words because in the alphabetical list their ending may be different, e.g., maximum or maximal. An attempt has been made to guide the reader to the desired entry when necessary. In rare instances the reader may need to search for synonyms or related terms to find the desired entry. Thank you for your patience. This book contains a large number of Internet addresses under the heading of databases and even more after many entries. Every effort has been made to keep the web addresses current. Unfortunately, they are altered frequently and it is likely that some will cease to exist or will change by the time the book gets to your hands. In some instances Word alone may not open the URL site directly, but Internet Explorer or Safari or even the search engines Google, Yahoo, AltaVista or others can be used to access the sites. It must be remembered that data are not knowledge. The data must be integrated into science and the aim of the author has been the facilitation of such integration. The contents of the entries are based on the best information available in the literature at the time of the completion of the writing. As sources of information like most human products, are not always perfect, the author and publishers cannot claim perfection or assume legal responsibility for errors beyond their control. Knowledge built on opinion only, will not stand. Linnaeus, 1735