- Email: [email protected]
Genes in the service of conservation
Resource
BOOK AND CD REVIEWS
chapters survey known mutations in cisacting transcriptional regulatory elements, somatic mutations and the growing field of epigenetics. Each chapter starts with a short survey of the characteristics of the respective protein family. Substantial space is then assigned to a detailed description of the pathophysiology of individual syndromes in context with identified mutations (which is the strongest point of the book). When possible, the author refers to mouse models, which usually provide a better approach to studying the developmental ontogeny of transcription factor defects. An extensive list of references makes it easy to track the original literature. Important credit is given to the online catalogue of Mendelian Inheritance of Man (MIM) and, throughout the text, MIM numbers are stated. The online MIM catalogue is easily accessible and will serve as a source for additional and more recent data. And here I come to some disappointing aspects of the book: that it had already become outdated by the time it went to print. To give the reader an impression about the rapid growth of research in this field, here are a few examples of diseases caused by transcription factor mutations identified
since the completion of this book: PAX8, congenital hypothyroidism (CD); SOX10, Waardenburg–Hirschsprung disease (WSCR), MIM 277580; POU4F3, autosomal dominant progressive nonsyndromic hearing loss (DFNA15), MIM 602459; FKHL7, iridogoniodysgenesis (IRID1), MIM 601631; FKHL15, congenital hypothyroidism (CD), MIM 241850; HLXB9, sacral agenesis syndrome, MIM 176450; NKX2-5, atrial septal defect (ASD), MIM 108900; CBFA1, cleidocranial dysplasia (CCD), MIM 119600; LMX1B, nail-patella syndrome (NPS), MIM 161200; CBFA2, familial platelet disorder; SIX3, holoprosencephaly 2 (HPE2), MIM 157170; FTZF1, sex reversal and adrenal failure; CRX, cone-rod dystrophy, MIM 120970; NRL, autosomal dominant retinitis pigmentosa; ZIC2, holoprosencephaly (HPE5); ZIC3, visceral heterotaxy (HTX1); PITX3, anterior segment mesenchymal dysgenesis (ASMD), MIM 107250; HESX1, septo-optic dysplasia, MIM 182230. Of course, a printed book cannot keep pace with such a rapidly expanding field, however, in a modern world one should find ways around this. One possible solution might be for publishers
Genes in the service of conservation Genetics and the extinction of species. DNA and the conservation of biodiversity edited by Laura F. Landweber and Andrew P. Dobson Princeton University Press 1999. £12.50 pbk (189 pages) ISBN 0 691 00971 6
Ross H. Crozier genrhc@ lure.latrobe.edu.au Department of Genetics and Evolution, La Trobe University, Bundoora, Victoria 3083, Australia. Current address: School of Tropical Biology, James Cook University, Townsville 4811, Australia. 234
New fields can grow from the intersections of existing ones, and theory from the restatement of practical considerations. Conservation biology was born out of concerns at the loss of biodiversity, and was constructed from the relevant aspects of demography, ecology and genetics, but it has also been gradually forming its own theory. The growth of this synthesis has been possible because of the existing theoretical maturity of mathematical demography and genetics. This book (from a 1996 meeting) underlines the importance of genetics to the development of conservation biology as a discipline and seeks to demonstrate its essential place therein. To a large extent, this goal is achieved, in a book that includes chapters by several of the leading practitioners of conservation genetics. Genetics and the extinction of species centers on the problems faced by individual species from decreasing population size, resulting from processes that include habitat destruction and that
TIG May 2000, volume 16, No. 5
yield small population size and its attendant ills. The book emphasizes that, barring restoration of most of the natural vegetation of the world, the management and prevention of endangerment must involve genetical knowledge. These problems are considered by Lande, Rodríguez-Clark, Holsinger et al. and by Amos and Freed; genetic technologies are considered by Landweber; phylogenetic demography by Harvey and Steers; disease impacts by Cann and Douglas; and Dobson summarizes the book. Lande’s opening chapter reviews the causes of endangerment and how to ameliorate and prevent it, and is a must-read chapter. Other highlights include reviews of the evolution of molecular markers and a refreshingly upbeat treatment of the prospects for successfully isolating ancient DNA. Grounds for pessimism in conservation genetics have increased over recent years, such as the realization that the long-term minimum population size
to release a web site with constant updates in cooperation with the author, especially as this book is one of many within a whole series of monographs on medical genetics published by Oxford University Press. In general, there could have been a better use of internet resources. The author mentions some important web sites, but these are far too few and some excellent ones have been missed out [e.g. some that collect mutation data: http://www.umd.necker. fr:2003, http://www.hgu.mrc.ac.uk/ Softdata/PAX6 (or PAX2), http:// www.iarc.fr/p53/homepage.htm and http://ariel.ucs.unimelb.edu.au:80/~cotton/ mdi.htm)]. To conclude, ‘Transcription factors and human disease’ is a useful book, and I recommend it highly to the general bio-medical audience. The author has successfully taken the opportunity to bring together medical genetics and developmental biology and I am sure that the book won’t attract dust on a library shelf. For myself, it will certainly form a basis for future lectures. Publishers, however, should consider incorporating more modern publishing tools in up-and-coming similar projects.
required to protect against deleterious mutations is quite large at 5000 – a size much larger than that required to avoid inbreeding depression and comparable with sizes that significantly reduce the chances of extinguishing catastrophes. The type of genetic marker used affects how well the population’s genetic health can be monitored – none do particularly well but microsatellites outperform single-base heterozygosity. The effects of population size reduction are complex – reduction in size for several generations is needed for a substantial reduction in heterozygosity, and a consequent rise in inbreeding depression, but a bottleneck can leave heterozygosity largely unaffected while removing rare alleles and substantially reducing adaptive potential. Slow population size reduction harms less than rapid reduction, because it allows the gradual loss of deleterious alleles. The ultimate heroic measure is to take endangered populations into captivity, where the best pedigree control involves the preferential mating of the rarest lineages. The book suffers from concentrating on the problems of single species, although mention is made of the desirability of aiming for long-term rather than short-term biodiversity preservation. An agreed overall theoretical framework for maintaining biodiversity is still needed, although a suitable candidate was provided by E.O. Wilson: maximizing the information content of the world’s genomes. Not surprisingly, 0168-9525/00/$ – see front matter © 2000 Elsevier Science Ltd. All rights reserved.
BOOK AND CD REVIEWS
given the lack of this framework, little is said here about the application of genetics to preserving large-scale biodiversity (conservation’s highest goal), even though, for example in microbial communities, there is no other way to assess biodiversity. There is an apparent
contradiction between the focus of the book on the preservation of individual vertebrate and plant species, and its repeating the finding that random removal of 95% of species would still leave intact 80% of the ‘evolutionary history’. Extinction is unlikely to be
Art and architecture of proteins Introduction to Protein Structure (2nd Edn) by Carl Branden and John Tooze Garland Publishing Inc., 1999 £29.99 pbk (410 pages) ISBN 0 8153 2305 0
In his most recent book1, Max Perutz records an unattributed quotation: ‘I was so long writing my review that I never got around to reading the book’. For Introduction to Protein Structure, I had the opposite problem: I couldn’t put the book down long enough to write the review. If you have any interest in protein structure, go out and buy this book – even if you already have the first edition. I do not maintain the book is perfect, and certainly it cannot even strive to be complete, but the clarity of the text, and above all the illustrations, make it a pleasure to read. The second edition brings many updates as well as three new chapters. However, two chapters are also sadly lost – I guess so as to limit the increase in size to just over a 100 pages. These are ‘DNA Polymerase is a Multifunctional Enzyme’, and ‘Enzymes That Bind Nucleotides’. The new chapters are: ‘Folding and Flexibility’,
‘Specific Transcription Factors Belong to a Few Families’ and ‘Fibrous Proteins’. All three are, without doubt, excellent additions. The philosophy behind the volume is clear: to extract from the known structures general principles of protein architecture and function and to present them in an exquisitely clear and elegant fashion. Indeed, the artwork is of such high quality that Garland Press have made it available on a separate CDROM. Another characteristic of the book that brings the subject to life is the frequent inclusion of the names and institutions of those scientists who have made major contributions. However, one thing that is inescapable is that this second edition is, after all, just an update. Indeed, my few complaints about the book all stem from this fact. For instance, the chapter on DNA structure does not reflect our current understanding of DNA struc-
Embryology on CD ROM Interactive Embryology: The Human Embryo Program by Jay Lash Sinauer, 1999. $29.95 CD-ROM ISBN 0 87893 448 0
The Embryonic Disk by J.E. Cook and M.K. Osmond University College London, 1999. £12.22*
The process of morphological change that takes place between fertilization of the secondary oocyte and formation of the human fetus is highly complex, making embryology a difficult subject to teach and learn. Clearly the ideal way to illustrate embryogenesis is by animated sequences. An excellent and detailed film showing normal human heart development, and the generation of congenital heart defects, was produced by the British Medical Association many years ago, but so far
*Details are on the website: http://www.ucl.ac.uk/innovations/embryonic 0168-9525/00/$ – see front matter © 2000 Elsevier Science Ltd. All rights reserved.
as I am aware, nothing equivalent has been produced for other systems. This is hardly surprising, given the time, skill and knowledge required. Recently, two CD ROMs have been produced that attempt to fill this need, but also combine many of the features of a textbook with click-on information boxes. The CD by Jay Lash shows animated sequences of each developing system, as well as a brief summary overview. Much of it is enjoyable to watch, although there are some significant inaccuracies and omissions that limit its usefulness. Each animated sequence can either be followed at the built-in pace, or the speed can be con-
Resource
phylogenetically random but will fall on distinctive communities and kinds of species. However, the book does very well within its focus and is an essential reference for all wishing to enter genetical theory and technology as applied to conservation. ture – especially in terms of local variations in structure and flexibility of this important molecule. The technique of electron diffraction really deserves to be discussed at greater length and moved into the main methods chapter. This chapter itself would have benefited from an update, and perhaps mention of multidimensional nuclear magnetic resonance, for instance. My biggest complaint however, is that there is still one chapter missing from the volume: ‘structure and function of macromolecular complexes’. If we set the date based on the cover structure of the volume (the potassium ion channel), then the authors have chosen not to include two of the most impressive structures: the nucleosome and F1 ATPase. It is clear that protein complexes are the future of structural biology (consider the recent ribosome and RNA polymerase structures). So it is a shame that these have been omitted. I guess I must save up for the third edition!
Reference 1 Perutz, M. (1998) I wish I’d made you angrier earlier, Oxford University Press
trolled by mouse; neurulation is particularly good fun when taken fast and the anatomical shapes are not scrutinized too carefully. The heart section is excellent for understanding lateral folding, but there are serious flaws in the aortic arches section: the second-formed arch is shown to add on rostral to the first, and the ductus arteriosus (left sixth aortic arch) is shown as a narrow vessel, when it is in fact the main channel from the pulmonary trunk to the aorta. Division of the atria is well done, but division of the outflow tract, which is conceptually more difficult, is not shown. The urogenital system sequence integrates several simultaneous events that are usually separated in textbooks to avoid visual overload. The complexity of this sequence is not a problem because it can be repeated as many times as necessary to take everything in. Some of the other sections seem to me to have no advantages over static textbook illustrations; there are some poor drawings, for instance, pharyngeal arches that are uniform in size and shape.
TIG May 2000, volume 16, No. 5
John W.R. Schwabe jws2@ mrc-lmb.cam.ac.uk MRC Laboratory of Molecular Biology, Hills Road, Cambridge, UK CB2 2QH.
Gillian Morriss-Kay gillian morriss-kay@ human-anatomy. oxford.ac.uk Department of Human Anatomy, University of Oxford, South Parks Road, Oxford UK OX1 3QX. 235
BOOK AND CD REVIEWS
chapters survey known mutations in cisacting transcriptional regulatory elements, somatic mutations and the growing field of epigenetics. Each chapter starts with a short survey of the characteristics of the respective protein family. Substantial space is then assigned to a detailed description of the pathophysiology of individual syndromes in context with identified mutations (which is the strongest point of the book). When possible, the author refers to mouse models, which usually provide a better approach to studying the developmental ontogeny of transcription factor defects. An extensive list of references makes it easy to track the original literature. Important credit is given to the online catalogue of Mendelian Inheritance of Man (MIM) and, throughout the text, MIM numbers are stated. The online MIM catalogue is easily accessible and will serve as a source for additional and more recent data. And here I come to some disappointing aspects of the book: that it had already become outdated by the time it went to print. To give the reader an impression about the rapid growth of research in this field, here are a few examples of diseases caused by transcription factor mutations identified
since the completion of this book: PAX8, congenital hypothyroidism (CD); SOX10, Waardenburg–Hirschsprung disease (WSCR), MIM 277580; POU4F3, autosomal dominant progressive nonsyndromic hearing loss (DFNA15), MIM 602459; FKHL7, iridogoniodysgenesis (IRID1), MIM 601631; FKHL15, congenital hypothyroidism (CD), MIM 241850; HLXB9, sacral agenesis syndrome, MIM 176450; NKX2-5, atrial septal defect (ASD), MIM 108900; CBFA1, cleidocranial dysplasia (CCD), MIM 119600; LMX1B, nail-patella syndrome (NPS), MIM 161200; CBFA2, familial platelet disorder; SIX3, holoprosencephaly 2 (HPE2), MIM 157170; FTZF1, sex reversal and adrenal failure; CRX, cone-rod dystrophy, MIM 120970; NRL, autosomal dominant retinitis pigmentosa; ZIC2, holoprosencephaly (HPE5); ZIC3, visceral heterotaxy (HTX1); PITX3, anterior segment mesenchymal dysgenesis (ASMD), MIM 107250; HESX1, septo-optic dysplasia, MIM 182230. Of course, a printed book cannot keep pace with such a rapidly expanding field, however, in a modern world one should find ways around this. One possible solution might be for publishers
Genes in the service of conservation Genetics and the extinction of species. DNA and the conservation of biodiversity edited by Laura F. Landweber and Andrew P. Dobson Princeton University Press 1999. £12.50 pbk (189 pages) ISBN 0 691 00971 6
Ross H. Crozier genrhc@ lure.latrobe.edu.au Department of Genetics and Evolution, La Trobe University, Bundoora, Victoria 3083, Australia. Current address: School of Tropical Biology, James Cook University, Townsville 4811, Australia. 234
New fields can grow from the intersections of existing ones, and theory from the restatement of practical considerations. Conservation biology was born out of concerns at the loss of biodiversity, and was constructed from the relevant aspects of demography, ecology and genetics, but it has also been gradually forming its own theory. The growth of this synthesis has been possible because of the existing theoretical maturity of mathematical demography and genetics. This book (from a 1996 meeting) underlines the importance of genetics to the development of conservation biology as a discipline and seeks to demonstrate its essential place therein. To a large extent, this goal is achieved, in a book that includes chapters by several of the leading practitioners of conservation genetics. Genetics and the extinction of species centers on the problems faced by individual species from decreasing population size, resulting from processes that include habitat destruction and that
TIG May 2000, volume 16, No. 5
yield small population size and its attendant ills. The book emphasizes that, barring restoration of most of the natural vegetation of the world, the management and prevention of endangerment must involve genetical knowledge. These problems are considered by Lande, Rodríguez-Clark, Holsinger et al. and by Amos and Freed; genetic technologies are considered by Landweber; phylogenetic demography by Harvey and Steers; disease impacts by Cann and Douglas; and Dobson summarizes the book. Lande’s opening chapter reviews the causes of endangerment and how to ameliorate and prevent it, and is a must-read chapter. Other highlights include reviews of the evolution of molecular markers and a refreshingly upbeat treatment of the prospects for successfully isolating ancient DNA. Grounds for pessimism in conservation genetics have increased over recent years, such as the realization that the long-term minimum population size
to release a web site with constant updates in cooperation with the author, especially as this book is one of many within a whole series of monographs on medical genetics published by Oxford University Press. In general, there could have been a better use of internet resources. The author mentions some important web sites, but these are far too few and some excellent ones have been missed out [e.g. some that collect mutation data: http://www.umd.necker. fr:2003, http://www.hgu.mrc.ac.uk/ Softdata/PAX6 (or PAX2), http:// www.iarc.fr/p53/homepage.htm and http://ariel.ucs.unimelb.edu.au:80/~cotton/ mdi.htm)]. To conclude, ‘Transcription factors and human disease’ is a useful book, and I recommend it highly to the general bio-medical audience. The author has successfully taken the opportunity to bring together medical genetics and developmental biology and I am sure that the book won’t attract dust on a library shelf. For myself, it will certainly form a basis for future lectures. Publishers, however, should consider incorporating more modern publishing tools in up-and-coming similar projects.
required to protect against deleterious mutations is quite large at 5000 – a size much larger than that required to avoid inbreeding depression and comparable with sizes that significantly reduce the chances of extinguishing catastrophes. The type of genetic marker used affects how well the population’s genetic health can be monitored – none do particularly well but microsatellites outperform single-base heterozygosity. The effects of population size reduction are complex – reduction in size for several generations is needed for a substantial reduction in heterozygosity, and a consequent rise in inbreeding depression, but a bottleneck can leave heterozygosity largely unaffected while removing rare alleles and substantially reducing adaptive potential. Slow population size reduction harms less than rapid reduction, because it allows the gradual loss of deleterious alleles. The ultimate heroic measure is to take endangered populations into captivity, where the best pedigree control involves the preferential mating of the rarest lineages. The book suffers from concentrating on the problems of single species, although mention is made of the desirability of aiming for long-term rather than short-term biodiversity preservation. An agreed overall theoretical framework for maintaining biodiversity is still needed, although a suitable candidate was provided by E.O. Wilson: maximizing the information content of the world’s genomes. Not surprisingly, 0168-9525/00/$ – see front matter © 2000 Elsevier Science Ltd. All rights reserved.
BOOK AND CD REVIEWS
given the lack of this framework, little is said here about the application of genetics to preserving large-scale biodiversity (conservation’s highest goal), even though, for example in microbial communities, there is no other way to assess biodiversity. There is an apparent
contradiction between the focus of the book on the preservation of individual vertebrate and plant species, and its repeating the finding that random removal of 95% of species would still leave intact 80% of the ‘evolutionary history’. Extinction is unlikely to be
Art and architecture of proteins Introduction to Protein Structure (2nd Edn) by Carl Branden and John Tooze Garland Publishing Inc., 1999 £29.99 pbk (410 pages) ISBN 0 8153 2305 0
In his most recent book1, Max Perutz records an unattributed quotation: ‘I was so long writing my review that I never got around to reading the book’. For Introduction to Protein Structure, I had the opposite problem: I couldn’t put the book down long enough to write the review. If you have any interest in protein structure, go out and buy this book – even if you already have the first edition. I do not maintain the book is perfect, and certainly it cannot even strive to be complete, but the clarity of the text, and above all the illustrations, make it a pleasure to read. The second edition brings many updates as well as three new chapters. However, two chapters are also sadly lost – I guess so as to limit the increase in size to just over a 100 pages. These are ‘DNA Polymerase is a Multifunctional Enzyme’, and ‘Enzymes That Bind Nucleotides’. The new chapters are: ‘Folding and Flexibility’,
‘Specific Transcription Factors Belong to a Few Families’ and ‘Fibrous Proteins’. All three are, without doubt, excellent additions. The philosophy behind the volume is clear: to extract from the known structures general principles of protein architecture and function and to present them in an exquisitely clear and elegant fashion. Indeed, the artwork is of such high quality that Garland Press have made it available on a separate CDROM. Another characteristic of the book that brings the subject to life is the frequent inclusion of the names and institutions of those scientists who have made major contributions. However, one thing that is inescapable is that this second edition is, after all, just an update. Indeed, my few complaints about the book all stem from this fact. For instance, the chapter on DNA structure does not reflect our current understanding of DNA struc-
Embryology on CD ROM Interactive Embryology: The Human Embryo Program by Jay Lash Sinauer, 1999. $29.95 CD-ROM ISBN 0 87893 448 0
The Embryonic Disk by J.E. Cook and M.K. Osmond University College London, 1999. £12.22*
The process of morphological change that takes place between fertilization of the secondary oocyte and formation of the human fetus is highly complex, making embryology a difficult subject to teach and learn. Clearly the ideal way to illustrate embryogenesis is by animated sequences. An excellent and detailed film showing normal human heart development, and the generation of congenital heart defects, was produced by the British Medical Association many years ago, but so far
*Details are on the website: http://www.ucl.ac.uk/innovations/embryonic 0168-9525/00/$ – see front matter © 2000 Elsevier Science Ltd. All rights reserved.
as I am aware, nothing equivalent has been produced for other systems. This is hardly surprising, given the time, skill and knowledge required. Recently, two CD ROMs have been produced that attempt to fill this need, but also combine many of the features of a textbook with click-on information boxes. The CD by Jay Lash shows animated sequences of each developing system, as well as a brief summary overview. Much of it is enjoyable to watch, although there are some significant inaccuracies and omissions that limit its usefulness. Each animated sequence can either be followed at the built-in pace, or the speed can be con-
Resource
phylogenetically random but will fall on distinctive communities and kinds of species. However, the book does very well within its focus and is an essential reference for all wishing to enter genetical theory and technology as applied to conservation. ture – especially in terms of local variations in structure and flexibility of this important molecule. The technique of electron diffraction really deserves to be discussed at greater length and moved into the main methods chapter. This chapter itself would have benefited from an update, and perhaps mention of multidimensional nuclear magnetic resonance, for instance. My biggest complaint however, is that there is still one chapter missing from the volume: ‘structure and function of macromolecular complexes’. If we set the date based on the cover structure of the volume (the potassium ion channel), then the authors have chosen not to include two of the most impressive structures: the nucleosome and F1 ATPase. It is clear that protein complexes are the future of structural biology (consider the recent ribosome and RNA polymerase structures). So it is a shame that these have been omitted. I guess I must save up for the third edition!
Reference 1 Perutz, M. (1998) I wish I’d made you angrier earlier, Oxford University Press
trolled by mouse; neurulation is particularly good fun when taken fast and the anatomical shapes are not scrutinized too carefully. The heart section is excellent for understanding lateral folding, but there are serious flaws in the aortic arches section: the second-formed arch is shown to add on rostral to the first, and the ductus arteriosus (left sixth aortic arch) is shown as a narrow vessel, when it is in fact the main channel from the pulmonary trunk to the aorta. Division of the atria is well done, but division of the outflow tract, which is conceptually more difficult, is not shown. The urogenital system sequence integrates several simultaneous events that are usually separated in textbooks to avoid visual overload. The complexity of this sequence is not a problem because it can be repeated as many times as necessary to take everything in. Some of the other sections seem to me to have no advantages over static textbook illustrations; there are some poor drawings, for instance, pharyngeal arches that are uniform in size and shape.
TIG May 2000, volume 16, No. 5
John W.R. Schwabe jws2@ mrc-lmb.cam.ac.uk MRC Laboratory of Molecular Biology, Hills Road, Cambridge, UK CB2 2QH.
Gillian Morriss-Kay gillian morriss-kay@ human-anatomy. oxford.ac.uk Department of Human Anatomy, University of Oxford, South Parks Road, Oxford UK OX1 3QX. 235