ROBERT C. KING
WILLIAM D. STANSFIELD
PAMELA K. MULLIGAN
OXFORD UNIVERSITY PRESS
A Dictionary of Genetics
The head of a fruitfly, Drosophila melanogaster, viewed by scanning electron microscopy. Targeted expression of the eyeless gene has induced the formation of a cluster of eye facets on the distal segment of the antenna, which lies in front of the compound eye. For further details, consult the eyeless entry. (Reprinted with permission from Walter Gehring and from Science, Vol. 267, No. 5205, 24 March 1995. Photo by Andreas Hefti and George Halder. © 1995, American Association for the Advancement of Science.)
A Dictionary of GENETICS
ROBERT C. KING
Emeritus Professor, Northwestern University
WILLIAM D. STANSFIELD
Emeritus Professor, California Polytechnic State University
PAMELA K. MULLIGAN
The field of genetics continues to advance at an astounding pace, marked by numerous extraordinary achievements in recent years. In just the past ten years, the genomic sequence of a multitude of organisms, from archaebacteria to large eukaryotes, has been determined and in many cases, comparatively analyzed in remarkable detail. Expressed sequence tags are being used for the detection of new genes and for genome annotation. DNA microarray technology has taken the study of gene expression and genetic variation to a global, genome-wide scale. Hundreds of new genes and microbial species have been identified by reconstructing the DNA sequences of entire communities of microorganisms collected in environmental samples. A wide variety of new regulatory functions have been assigned to RNA, and RNA interference has become an effective tool for creating loss of function phenotypes.
Such momentous advances in genetics have been accompanied by a deluge of new experimental techniques, computational technologies, databases and internet sites, periodicals and books, and, of course, concepts and terms. Furthermore, as new terminology emerges, many old terms inevitably recede from use or require revision. All this is reflected in the changing content of A Dictionary of Genetics, from the publication of its first edition to this seventh edition, 37 years later. This new edition has undergone an extensive overhaul, involving one or more changes (additions, deletions, or modifications of entries) on 95% of the pages of the previous one. The seventh edition contains nearly 7,000 definitions, of which 20% are revised or new, and nearly 1,100 Chronology entries, of which 30% are revised or new. Three hundred of the definitions are accompanied by illustrations or tables, and 16 of these are new. In addition, dozens of recent research papers, books, periodicals, and internet sites of genetic importance have been added to the appropriate Appendices of the current edition.
The year 2006 marks the 100th anniversary of the introduction of the term genetics by the British biologist William Bateson. In this seventh edition of A Dictionary of Genetics, the term genetics itself has been updated, reflecting progress in understanding and technique over the years, and necessitated by the convergence of classical and molecular genetics. Genetics today is no longer simply the study of heredity in the old sense, i.e., the study of inheritance and of variation of biological traits, but also the study of the basic units of heredity, i.e., genes. Geneticists of the post-genomics era identify genetic elements using forward or reverse genetics and decipher the molecular nature of genes, how they function, and how genetic variation, whether introduced in the lab or present in natural populations, affects the phenotype of the cell or the organism. The study of genes is increasingly at the core of genetic research, whether it is aimed at understanding the basis of Alzheimer disease in humans, flower development in Arabidopsis, shell pattern variation in Cepaea colonies, or speciation in Drosophila. Today’s genetics thus also unifies the biological sciences, medical sciences, and evolutionary studies.
As a broad-based reference work, A Dictionary of Genetics defines terms that fall under this expansive genetics umbrella and includes not only strictly genetic terms, but also genetics-related words encountered in the scientific literature. These include terms referring to biological and synthetic molecules (e.g., DNA polymerase, Morpholinos, and streptavidin); cellular structures (e.g., solenoid structure, spectrosome, and sponge body); medical conditions (e.g., Leber hereditary optic neuropathy [LHON], Marfan syndrome, and Tay-Sachs disease); experimental techniques (e.g., P element transformation, community genome sequencing, and yeast two-hybrid system); drugs, reagents, and media (e.g., ethyl methane sulfonate, Denhardt solution, and HAT medium); rules, hypotheses, and laws (e.g., Haldane rule, wobble hypothesis, and Hardy-Weinberg law); and acronyms (e.g., BACs, METRO, and STS). Included also are pertinent terms from such fields as geology, physics, and statistics (e.g., hot spot archipelago, roentgen, and chi-square test).
As in previous editions, the definitions are cross-referenced and comparisons made whenever possible. For example, the maternal effect gene entry is cross-referenced to bicoid, cytoplasmic determinants, cytoplasmic localization, grandchildless genes, and maternal polarity mutants, and the reader is directed to compare it with paternal effect gene and zygotic gene entries.
In this edition of the Dictionary we have made every effort to identify the sources of the more than 120 eponyms appearing among the definitions, and following the example of Victor A. McKusick (distinguished editor of Mendelian Inheritance in Man), we have eliminated the possessive form, i.e., apostrophes, in most of the eponyms. Thus, the Creutzfeld-Jakob disease entry traces the names of the physicians who first described this syndrome in their patients and the time period when this occurred, and the Balbiani body definition identifies the biologist who first described these cellular structures and the time period during which he lived. This additional information under each eponym adds a personal, geographical, and historical perspective to the definitions and is one of the distinguishing features of this dictionary.
A Dictionary of Genetics is unique in that only 80% of the pages contain definitions. The final fifth of the Dictionary is devoted to six Appendices, which supply a wealth of useful resource material.
Appendix A, Classification, provides an evolutionary classification of the five kingdoms of living organisms. This list contains 400 words in parentheses, many of which are common names for easy identification (e.g., cellular slime molds, marine worms, and ginkgos). The italicized words in parentheses are genera which contain species notable for their economic importance (e.g., Bos taurus, Gossypium hirsutum, and Oryza sativa), for causing human diseases (e.g., Plasmodium falciparum, Staphylococcus aureus, and Trypanosoma brucei), or for being useful laboratory species (e.g., Arabidopsis thaliana, Neurospora crassa, and Xenopus laevis).
Appendix B, Domesticated Species, lists the common and scientific names of approximately 200 domesticated animal and plant species not found elsewhere in the Dictionary.
Appendix C, Chronology, is one of the most distinctive elements of the Dictionary, containing a list of notable discoveries, events, and publications, which have contributed to the advancement of genetics. The majority of entries in the Chronology report discoveries (e.g., 1865–66, Mendel’s discovery of the existence of hereditary factors; 1970, the finding of RNA-dependent DNA polymerase; 1989, the identification of the cystic fibrosis gene). In addition, there are entries that present unifying concepts and theories (e.g., 1912, the concept of continental drift; 1961, the operon hypothesis; 1974, the proposition that chromatin is organized into nucleosomes). The Chronology also includes important technological advances and techniques that have revolutionized genetic research (e.g., 1923, the building of the first ultracentrifuge; 1975, the development of Southern blotting; 1985, the development of polymerase chain reaction; 1986, the production of the first automated DNA sequencer). There are also entries that contain announcements of new terms that have become part of every geneticist’s vocabulary (e.g., 1909, gene; 1971, C value paradox; 1978, intron and exon).
Developments in evolutionary genetics figure prominently in the Chronology. Included in this category are important evolutionary breakthroughs (e.g., 1868, Huxley’s description of Archaeopteryx; 1977, the discovery of the Archaea by Woese and Fox; 2004, the proposal by Rice and colleagues that viruses evolved from a common ancestor prior to the formation of the three domains of life), and publication of books which have profoundly affected evolutionary thought (e.g., 1859, C. Darwin’s On the Origin of Species; 1963, E. Mayr’s Animal Species and Evolution; 1981, L. Margulis’s Symbiosis in Cell Evolution).
Relatively recent additions to the Chronology are entries for sequencing and analysis of the genomes of species of interest (e.g., 1996, Saccharomyces cerevisiae; 1997, Escherichia coli; 2002, Mus musculus). Finally, the Chronology lists 59 Nobel Prizes awarded to scientists for discoveries that have had a bearing on the progress of genetics (e.g., 1965, to F. Jacob, J. Monod, and A. Lwoff for their contributions to microbial genetics; 1983, to B. McClintock for her discovery of mobile genetic elements in maize; 1993, to R. J. Roberts and P. A. Sharp for discovering split genes). We hope that these and other Chronology entries, spanning the years 1590– 2005, provide students, researchers, educators, and historians alike with an understanding of the historical framework within which genetics has developed.
The Chronology in Appendix C is followed by an alphabetical List of the Scientists cited in it, together with the dates of these citations. This list includes Francis Crick, Edward Lewis, Maurice Wilkins, and Hampton Carson (who all died late in 2004), and Ernst Mayr (who died early in 2005), and it provides the dates of milestones in their scientific careers. Finally, Appendix C includes a Bibliography of 170 titles, and among the most recent books are four that give accounts of the lives of David Baltimore, George Beadle, Sidney Brenner, and Rosalind Franklin. Also listed is a video collection (Conversations in Genetics) of interviews with prominent geneticists.
Appendix D, Periodicals, lists the titles and addresses of 500 periodicals related to genetics, cell biology, and evolutionary studies, from Acta Virologica to Zygote.
Appendix E, Internet Sites, contains 132 prominent web site addresses to facilitate retrieval of the wealth of information in the public domain that can be accessed through the World Wide Web. These include addresses for “master” sites (e.g., National Center for Biotechnology Information [NCBI], National Library of Medicine, National Institutes of Health), for individual databases (e.g., GenBank, Single Nucleotide Polymorphisms [SNPs], and Protein Data Bank [PDB]), and for species web sites (e.g., Agrobacterium tumefaciens, Chlamydomonas reinhardii, and Gossypium species).
Appendix F, Genome Sizes and Gene Numbers, tabulates the genome sizes and gene numbers for 49 representative organisms, viruses, or cell organelles that appear in the Dictionary. These are listed in order of complexity. The smallest genome listed is that of the MS2 virus, with 3.6 × 103 base pairs encoding just 4 proteins, and the largest listed is that of man, consisting of 3.2 × 109 base pairs of DNA encoding 31,000 genes. Between these entries appear the genome sizes and gene numbers of other viruses, organelles, and a diverse range of organisms representing all five kingdoms. This is but a small representation of the larger and increasingly complex collections of genomic data which are being generated at an exponential rate and transforming the way we look at relationships between organisms that inhabit this planet. A quick glance at Appendix F raises some intriguing questions. For example, why does Streptomyces, a prokaryote, have more genes than Saccharomyces, a eukaryote, whose genome size is 28% larger? And why do the genomes of the puffer fish, Takifugu rubripes, and man encode roughly the same number of protein-coding genes, even though the puffer fish genome is nearly 88% smaller than the human? Such questions and others are at the forefront of current whole-genome research, as the massive sequence data are evaluated and the information encoded within them extracted. Comparative genomic analyses promise new insights into the evolutionary forces that shape the size and structure of genomes. Furthermore, the intertwining of genetics, genomics, and bioinformatics makes for a strong force for identifying new genetic elements and for unraveling the mysteries of cellular processes in the most minute detail.
Appendix Cross-References. Whenever possible, cross references to the Appendices appear under the appropriate definition. The cross references provide information which complements that in the definition. For example, nucleolus is cross-referenced to entries in Appendix C, which indicate that this structure was first observed in the nucleus in 1838, that it was first shown to be divisible into subunits in 1934, that in 1965 the sex chromosomes of Drosophila melanogaster were found to contain multiple rRNA genes in their nucleolus organizers, and that in 1967 amplified rDNA was isolated from Xenopus oocytes. Furthermore, nucleolar Miller trees were discovered in 1969, in 1976 ribosomal proteins were found to attach to precursor rRNAs in the nucleolus, and in 1989 the cDNA for human nucleolin was isolated. Another example is Streptomyces, which is cross-referenced to Appendices A, E, and F. In this case, the material in the Appendices indicates that this organism is a prokaryote belonging to the phylum Actinobacteria, that there is web-based information pertaining to S. coelicolor at http://www.sanger.ac.uk, and that the genome of this species has 12.07 × 106 base pairs and contains 7,825 predicted genes. The cross-referenced information in the Appendices thus greatly broadens the reader’s perspective on a particular term or concept.
Genetics has clearly entered an exciting new era of exploration and expansion. It is our sincere hope that A Dictionary of Genetics will become a helpful companion for those participating in this marvelous adventure.