- Email: [email protected]
A Dictyostelium anthology
358
Forum
Learning from yeast Frontiers in Molecular Biology: The Yeast Nucleus edited by Peter Fantes and Jean Beggs Oxford University Press, 2000. $55.00 pbk, (xix + 316 pages) ISBN 0 19 963772 5
The budding yeast, Saccharomyces cerevisiae, and the fission yeast, Schizosaccharomyces pombe, have long been exploited as powerful genetic systems for the dissection of metabolic and biosynthetic pathways. They have also been used for characterizing essential events in the cell cycle such as cell growth control, transcription, translation and macromolecular transport. The genetic elegance of a eukaryotic organism with a stable haploid state, combined with access to the complete genomic sequence, provide formidable tools for identifying the genes and proteins that carry out critical cellular functions. Now yeast molecular biology has entered a golden age, and the details of these mechanisms are rapidly being clarified. In this context, it is highly useful to compare the ways in which Saccharomyces and Schizosaccharomyces solve the common problems of growth and cell division. Perhaps it is not surprising that these two unicellular organisms, which are thought to have diverged some 400 million years ago, achieve similar ends in different ways. The Yeast Nucleus is an attempt to point out similarities and differences between the two most common laboratory yeasts, while summarizing our current understanding of a number of essential nuclear and cellular functions. It is both a primer for undergraduate students and a reference book for scientists in the field. By the very nature of its enterprise, however, some descriptions are already dated. The chapters cover functional genomics, replication, the cell cycle and its checkpoints, RNA pol II-mediated transcription, telomeric and centromeric silencing, splicing of messenger RNA, and nuclear transport. Depending on the background of the authors the comparison of the two http://tig.trends.com
TRENDS in Genetics Vol.17 No.6 June 2001
yeasts is successful to different degrees. Most successful, in my opinion, is the chapter by Tyers and Jorgensen, in which the cell cycles of S. cerevisiae and S. pombe are compared and contrasted with impressive lucidity. Not only are the latest details presented clearly and carefully, but the differences that are significant for understanding the cell cycles of more complex organisms are stressed, making this a useful chapter for anyone studying cell-cycle controls. The subsequent chapter on cell-cycle checkpoints (Forbes and Enoch) also makes a valiant attempt to point out the differences between the two yeast species, although in this case the field is less advanced. One cannot blame the authors, but it is striking that the information available at the time this chapter was written is already incomplete. Much the same must be said for the descriptions of repression mechanisms in S. cerevisiae and the fleeting mention of chromosome cohesins and condensins. These would merit a chapter in themselves if the book were written today. Although the editors are to be commended for their idea, there is certainly room for additional efforts in the same direction. Much more can be learned from the detailed comparison of these two model systems, and the understanding gained by such comparison surpasses the insights possible from studying only one. To overcome the inevitable bias towards the organism one works with, it would be desirable for each topic to be written as a collaborative effort between two leaders in the field, one working with fission yeast and the other with budding yeast. In this way, information will be as up to date as possible and the comparisons will probably be more comprehensive, rather than anecdotal. Despite these criticisms, The Yeast Nucleus makes valuable contributions, the most far-reaching of which may be to encourage scientists to think in comparative ways. Susan M. Gasser Dept of Molecular Biology, University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva 4, Switzerland. e-mail: [email protected]
A Dictyostelium anthology Dictyostelium: Evolution, Cell Biology and the Development of Multicellularity by Richard H. Kessin Cambridge University Press, 2001. £55.00 hbk (xiv + 294 pages) ISBN 0 521 583 640
Dictyostelium cells are intermediate in complexity between yeast cells and human cells and are proving invaluable for our understanding of processes such as cell movement, chemotaxis and phagocytosis. During development, individual Dictyostelium cells aggregate together and form themselves into a patterned structure. Thus, Dictyostelium research influences a significant fraction of modern day cell and developmental biology. Because of this wealth of potential material, the author of such a broadranging book as this faces several daunting choices and potential pitfalls. First, there is the all-important question of choice of content: should the book cover a few areas in great depth or provide a blanket coverage? Here Kessin is right on the mark. The book gives a very sound introduction but expands on those areas of Dictyostelium cell biology and developmental biology where most is known and/or where most effort is being concentrated. It is a very exciting time in the field, and this comes across extremely well. There is a lot of research in the raw here, material not yet ready for enshrinement in an undergraduate text book, but wonderful fodder for provoking further debate and generating new ideas. For this reason alone, it is just the right book to give to a newly arrived graduate student or postdoctoral fellow. The added value is that the lucky recipient of the book will also be brought up to speed with an entire field. Moreover, this will be a relatively painless learning process. The book is very well organized and beautifully written; difficult concepts are explained with panache and authority, leavened with the occasional flash of humour. Kessin has been a major figure in Dictyostelium research for more than 30 years so the reader is receiving an insider’s view that will surely prove invaluable to anyone entering the field.
Forum
What, though, of the cognoscenti? Herein, I am afraid, lies the hidden danger of such an ambitious enterprise. The obvious potential pitfall is that of false omniscience. The author has read a large fraction of the 6000 extant Dictyostelium papers, but has he integrated, analysed and presented them accurately? Unfortunately, in Kessin’s description of my area of interest, Dictyostelium pattern formation, I found a number of inaccuracies. Because of these, I cannot now judge whether the section on the cytoskeleton, for example, gives a completely accurate picture. For those wanting a detailed insight into a particular process outside their area of expertise, it is a case of ‘let the buyer beware’; you would be well advised to read the Kessin book first, then go away and read the relevant review articles. An illuminating comparison can be made with the previous two ‘standard’ Dictyostelium books. In 1975, Loomis published a sole-author work, Dictyostelium discoideum: A Developmental System1, and in 1982 he edited a multi-author volume, The Development of Dictyostelium discoideum2. Both covered the same general areas. In the latter book, experts in the field reviewed specific areas. Although both were invaluable when published, the 1975 sole-author book sometimes lacked in detail, and the 1982 multi-author book lacked consistency of presentation. In Kessin’s publication, we have gone full circle. Some parts of the book have been checked over by experts in particular areas and those are, I am sure, accurate. If the entire book had been pre-filtered in the same way, then this would have been the ideal compromise – multiple native speakers translated by one interpreter. I don’t want to end on a negative note because I give my strong endorsement to the book. It is a major achievement and will serve the field well for several years to come. The inaccuracies of detail should not detract from a well balanced and comprehensive review of a vibrant field. They will hopefully be weeded out before the next edition, and I, for one, greatly look forward to reading it. Jeffrey Williams School of Biological Sciences, University of Dundee, Dundee, UK DD1 5EH. e-mail: [email protected] References 1 Loomis, W.F. (1975) Dictyostelium discoideum: A Developmental System, Academic Press 2 Loomis, W.F. ed. (1982) The Development of Dictyostelium discoideum, Academic Press http://tig.trends.com
TRENDS in Genetics Vol.17 No.6 June 2001
Making the most of phage display Phage Display: A Laboratory Manual edited by C.F. Barbas III, D.R. Burton, J.K. Scott and G.J. Silverman Cold Spring Harbor Laboratory Press, 2001. $135.00 hbk (xvi + 736 pp) ISBN 0 87969 546 3
Originally conceived in 1985 (Ref. 1), phage display is now a fundamental tool of both basic research and the drug discovery process. It has provided a rich source of applications from the detection of protein– protein interactions to molecular evolution. During phage display, a protein or peptide is expressed as a fusion product with a phage coat protein and ‘displayed’on the surface of the phage particle. The phage has a phenotype associated with the fusion protein, and the gene encoding the foreign protein is contained within the phage particle. Very large libraries of fusion partners can be cloned into phage and individual phage can be rescued from the libraries by the interaction of the displayed protein with a binding partner. Although the concept of phage display is elegant in its simplicity, putting the technique to practical use can be a complex and challenging process requiring significant technical expertise. Phage Display: A Laboratory Manual is a comprehensive collection of protocols and background information designed to address these practical challenges. The manual was assembled from the output of Cold Spring Harbor phage display laboratory courses held annually since 1992. It benefits, therefore, from the practical experiences of students attending the course. The first section gives a theoretical overview of phage display, including a chapter on the biology of filamentous phage that is indispensable for a full understanding of the field. The Ff class of filamentous phage (f1, fd and M13) is used in phage display systems and is ideal because such phage do not kill their host during productive infection. These bacteriophage also use the E. coli F conjugative pilus as a receptor, thus infecting only bacteria containing the F plasmid and not other lab strains. The remaining sections of the manual are most valuable as they cover the practical aspects of the subject. The second section is a guide to the construction, screening and analysis of antibody libraries on the phage surface. The third section gives a similar treatment to peptide libraries and the fourth
359
to other libraries containing gene fragments and cDNAs. This last section also deals with affinity selection of libraries and with more complex selection targets. In vivo selection, which involves injecting a phage library into a whole organism and collecting phage that localize to a target organ or tissue, is detailed. This technique has been used to select organ-specific peptides in mice2 and could be developed further to select for agents specifically targeting diseased human tissue. Selection of antibodies from phage libraries by capture on cell surfaces and selection using cell sorting are also discussed. Again, such antibody or peptide reagents have potential as therapeutic agents. Finally, the reader is provided with detailed appendices containing a range of useful information including recipes, suppliers and some general procedures. The book’s raison d’être is as a source of detailed protocols. These are clearly written, and include ideas for experimental controls and useful trouble-shooting notes. Jargon is generally avoided, and the protocols are up to date. However, they occasionally lack detail on the context in which they should be applied. Being experienced with phage display, I maintain that the keys to successful application are a good-quality phage library, and a selection and screening strategy tailored to reflect the eventual use of the selected moiety. Cell-based or in vivo selection strategies are more appropriate for the generation of cell- or organ-specific peptides or antibodies that can be used as general research tools, such as immunocytochemistry reagents, or as targeting reagents. Selection strategies using purified antigen or ligand can be used to generate pools of binding reagents for screening on the basis of affinity, sequence diversity, or ability to recognize antigen on a western blot or a cell surface. Phage Display: A Laboratory Manual has been written with this is mind and is a much-needed and wellexecuted attempt at theoretical and practical support to any researcher, established or novice, using phage display. Jane K. Osbourn Display Technology, Cambridge Antibody Technology, The Science Park, Melbourn, UK SG8 6JJ. References 1 Smith, G.P. (1985) Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228, 1315–1317 2 Pasqualini, R. and Ruoslahti, E. (1996) Organ targeting in vivo using phage display peptide libraries. Nature 380, 364–366
Forum
Learning from yeast Frontiers in Molecular Biology: The Yeast Nucleus edited by Peter Fantes and Jean Beggs Oxford University Press, 2000. $55.00 pbk, (xix + 316 pages) ISBN 0 19 963772 5
The budding yeast, Saccharomyces cerevisiae, and the fission yeast, Schizosaccharomyces pombe, have long been exploited as powerful genetic systems for the dissection of metabolic and biosynthetic pathways. They have also been used for characterizing essential events in the cell cycle such as cell growth control, transcription, translation and macromolecular transport. The genetic elegance of a eukaryotic organism with a stable haploid state, combined with access to the complete genomic sequence, provide formidable tools for identifying the genes and proteins that carry out critical cellular functions. Now yeast molecular biology has entered a golden age, and the details of these mechanisms are rapidly being clarified. In this context, it is highly useful to compare the ways in which Saccharomyces and Schizosaccharomyces solve the common problems of growth and cell division. Perhaps it is not surprising that these two unicellular organisms, which are thought to have diverged some 400 million years ago, achieve similar ends in different ways. The Yeast Nucleus is an attempt to point out similarities and differences between the two most common laboratory yeasts, while summarizing our current understanding of a number of essential nuclear and cellular functions. It is both a primer for undergraduate students and a reference book for scientists in the field. By the very nature of its enterprise, however, some descriptions are already dated. The chapters cover functional genomics, replication, the cell cycle and its checkpoints, RNA pol II-mediated transcription, telomeric and centromeric silencing, splicing of messenger RNA, and nuclear transport. Depending on the background of the authors the comparison of the two http://tig.trends.com
TRENDS in Genetics Vol.17 No.6 June 2001
yeasts is successful to different degrees. Most successful, in my opinion, is the chapter by Tyers and Jorgensen, in which the cell cycles of S. cerevisiae and S. pombe are compared and contrasted with impressive lucidity. Not only are the latest details presented clearly and carefully, but the differences that are significant for understanding the cell cycles of more complex organisms are stressed, making this a useful chapter for anyone studying cell-cycle controls. The subsequent chapter on cell-cycle checkpoints (Forbes and Enoch) also makes a valiant attempt to point out the differences between the two yeast species, although in this case the field is less advanced. One cannot blame the authors, but it is striking that the information available at the time this chapter was written is already incomplete. Much the same must be said for the descriptions of repression mechanisms in S. cerevisiae and the fleeting mention of chromosome cohesins and condensins. These would merit a chapter in themselves if the book were written today. Although the editors are to be commended for their idea, there is certainly room for additional efforts in the same direction. Much more can be learned from the detailed comparison of these two model systems, and the understanding gained by such comparison surpasses the insights possible from studying only one. To overcome the inevitable bias towards the organism one works with, it would be desirable for each topic to be written as a collaborative effort between two leaders in the field, one working with fission yeast and the other with budding yeast. In this way, information will be as up to date as possible and the comparisons will probably be more comprehensive, rather than anecdotal. Despite these criticisms, The Yeast Nucleus makes valuable contributions, the most far-reaching of which may be to encourage scientists to think in comparative ways. Susan M. Gasser Dept of Molecular Biology, University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva 4, Switzerland. e-mail: [email protected]
A Dictyostelium anthology Dictyostelium: Evolution, Cell Biology and the Development of Multicellularity by Richard H. Kessin Cambridge University Press, 2001. £55.00 hbk (xiv + 294 pages) ISBN 0 521 583 640
Dictyostelium cells are intermediate in complexity between yeast cells and human cells and are proving invaluable for our understanding of processes such as cell movement, chemotaxis and phagocytosis. During development, individual Dictyostelium cells aggregate together and form themselves into a patterned structure. Thus, Dictyostelium research influences a significant fraction of modern day cell and developmental biology. Because of this wealth of potential material, the author of such a broadranging book as this faces several daunting choices and potential pitfalls. First, there is the all-important question of choice of content: should the book cover a few areas in great depth or provide a blanket coverage? Here Kessin is right on the mark. The book gives a very sound introduction but expands on those areas of Dictyostelium cell biology and developmental biology where most is known and/or where most effort is being concentrated. It is a very exciting time in the field, and this comes across extremely well. There is a lot of research in the raw here, material not yet ready for enshrinement in an undergraduate text book, but wonderful fodder for provoking further debate and generating new ideas. For this reason alone, it is just the right book to give to a newly arrived graduate student or postdoctoral fellow. The added value is that the lucky recipient of the book will also be brought up to speed with an entire field. Moreover, this will be a relatively painless learning process. The book is very well organized and beautifully written; difficult concepts are explained with panache and authority, leavened with the occasional flash of humour. Kessin has been a major figure in Dictyostelium research for more than 30 years so the reader is receiving an insider’s view that will surely prove invaluable to anyone entering the field.
Forum
What, though, of the cognoscenti? Herein, I am afraid, lies the hidden danger of such an ambitious enterprise. The obvious potential pitfall is that of false omniscience. The author has read a large fraction of the 6000 extant Dictyostelium papers, but has he integrated, analysed and presented them accurately? Unfortunately, in Kessin’s description of my area of interest, Dictyostelium pattern formation, I found a number of inaccuracies. Because of these, I cannot now judge whether the section on the cytoskeleton, for example, gives a completely accurate picture. For those wanting a detailed insight into a particular process outside their area of expertise, it is a case of ‘let the buyer beware’; you would be well advised to read the Kessin book first, then go away and read the relevant review articles. An illuminating comparison can be made with the previous two ‘standard’ Dictyostelium books. In 1975, Loomis published a sole-author work, Dictyostelium discoideum: A Developmental System1, and in 1982 he edited a multi-author volume, The Development of Dictyostelium discoideum2. Both covered the same general areas. In the latter book, experts in the field reviewed specific areas. Although both were invaluable when published, the 1975 sole-author book sometimes lacked in detail, and the 1982 multi-author book lacked consistency of presentation. In Kessin’s publication, we have gone full circle. Some parts of the book have been checked over by experts in particular areas and those are, I am sure, accurate. If the entire book had been pre-filtered in the same way, then this would have been the ideal compromise – multiple native speakers translated by one interpreter. I don’t want to end on a negative note because I give my strong endorsement to the book. It is a major achievement and will serve the field well for several years to come. The inaccuracies of detail should not detract from a well balanced and comprehensive review of a vibrant field. They will hopefully be weeded out before the next edition, and I, for one, greatly look forward to reading it. Jeffrey Williams School of Biological Sciences, University of Dundee, Dundee, UK DD1 5EH. e-mail: [email protected] References 1 Loomis, W.F. (1975) Dictyostelium discoideum: A Developmental System, Academic Press 2 Loomis, W.F. ed. (1982) The Development of Dictyostelium discoideum, Academic Press http://tig.trends.com
TRENDS in Genetics Vol.17 No.6 June 2001
Making the most of phage display Phage Display: A Laboratory Manual edited by C.F. Barbas III, D.R. Burton, J.K. Scott and G.J. Silverman Cold Spring Harbor Laboratory Press, 2001. $135.00 hbk (xvi + 736 pp) ISBN 0 87969 546 3
Originally conceived in 1985 (Ref. 1), phage display is now a fundamental tool of both basic research and the drug discovery process. It has provided a rich source of applications from the detection of protein– protein interactions to molecular evolution. During phage display, a protein or peptide is expressed as a fusion product with a phage coat protein and ‘displayed’on the surface of the phage particle. The phage has a phenotype associated with the fusion protein, and the gene encoding the foreign protein is contained within the phage particle. Very large libraries of fusion partners can be cloned into phage and individual phage can be rescued from the libraries by the interaction of the displayed protein with a binding partner. Although the concept of phage display is elegant in its simplicity, putting the technique to practical use can be a complex and challenging process requiring significant technical expertise. Phage Display: A Laboratory Manual is a comprehensive collection of protocols and background information designed to address these practical challenges. The manual was assembled from the output of Cold Spring Harbor phage display laboratory courses held annually since 1992. It benefits, therefore, from the practical experiences of students attending the course. The first section gives a theoretical overview of phage display, including a chapter on the biology of filamentous phage that is indispensable for a full understanding of the field. The Ff class of filamentous phage (f1, fd and M13) is used in phage display systems and is ideal because such phage do not kill their host during productive infection. These bacteriophage also use the E. coli F conjugative pilus as a receptor, thus infecting only bacteria containing the F plasmid and not other lab strains. The remaining sections of the manual are most valuable as they cover the practical aspects of the subject. The second section is a guide to the construction, screening and analysis of antibody libraries on the phage surface. The third section gives a similar treatment to peptide libraries and the fourth
359
to other libraries containing gene fragments and cDNAs. This last section also deals with affinity selection of libraries and with more complex selection targets. In vivo selection, which involves injecting a phage library into a whole organism and collecting phage that localize to a target organ or tissue, is detailed. This technique has been used to select organ-specific peptides in mice2 and could be developed further to select for agents specifically targeting diseased human tissue. Selection of antibodies from phage libraries by capture on cell surfaces and selection using cell sorting are also discussed. Again, such antibody or peptide reagents have potential as therapeutic agents. Finally, the reader is provided with detailed appendices containing a range of useful information including recipes, suppliers and some general procedures. The book’s raison d’être is as a source of detailed protocols. These are clearly written, and include ideas for experimental controls and useful trouble-shooting notes. Jargon is generally avoided, and the protocols are up to date. However, they occasionally lack detail on the context in which they should be applied. Being experienced with phage display, I maintain that the keys to successful application are a good-quality phage library, and a selection and screening strategy tailored to reflect the eventual use of the selected moiety. Cell-based or in vivo selection strategies are more appropriate for the generation of cell- or organ-specific peptides or antibodies that can be used as general research tools, such as immunocytochemistry reagents, or as targeting reagents. Selection strategies using purified antigen or ligand can be used to generate pools of binding reagents for screening on the basis of affinity, sequence diversity, or ability to recognize antigen on a western blot or a cell surface. Phage Display: A Laboratory Manual has been written with this is mind and is a much-needed and wellexecuted attempt at theoretical and practical support to any researcher, established or novice, using phage display. Jane K. Osbourn Display Technology, Cambridge Antibody Technology, The Science Park, Melbourn, UK SG8 6JJ. References 1 Smith, G.P. (1985) Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228, 1315–1317 2 Pasqualini, R. and Ruoslahti, E. (1996) Organ targeting in vivo using phage display peptide libraries. Nature 380, 364–366