- Email: [email protected]
May all your wishes be granted
MISCELLANEA
The interactive
Acknowledgements The authors gratefully acknowledge the Dept of Computer Science at the University of British Columbia for the use of their Web server and computer equipment.
future
At present, most animations obtained from the Internet consist of a series of images that are displayed in a fixed sequence. Two new data formats will overcome this limitation, and will provide interactive control over animation playback and manipulation of 3-D objects. Of most interest to Apple Macintosh users who want to create animations from images of reconstructed 3-D specimens, QuickTime VR (an extension of Apple’s existing QuickTimeformat) permits the generation of ‘navigable objects’. In this scenario, objects are composed of different sequences of images, where each sequence shows the object from a slightly different angle. As the object is tilted up, down, left or right using a computer mouse, the software responds by displaying successive images as a QuickTime movie. This kind of interactive control can also be set up to control the playback of 2-D images. Furthermore, the format allows users to assign clickable ‘hot spots’ within an animation. The activation of these areas with a mouse can trigger a variety of actions, including launching a
May all your wishes be granted The Grant Application Writer’s Handbook by Liane Reif-Lehrer, /ones and Bartlett, 1995. $34.95 (472 pages) ISBN 0 86720 874 0 Applying for grants is a task that all scientists have to face up to eventually. Some investigators consider the preparation of a grant application to be a labour of love and an opportunity to show their stuff, whereas others treat the process as a necessary evil thatwill allow them to continue doing science. Whichever way it is viewed, writing grants is a complex process, which can be very daunting. In times such as these, when funding is difficult to come by, the way that an idea is packaged and presented is as important as the idea itself. New
78
still photograph, playing an audio clip or displaying some text. The added degree of interactivity provided by these features greatly enhances viewing of animations. Although a full-featured QuickTime VR authoring kit is commercially available from Apple to create complex navigable scenes consisting of several linked animations, software for creating much simpler navigable objects exists in the public domain (again, only for Macintosh computers). Currently, free software for viewing QuickTime VR animations is only available for Apple Macintosh and PCs running Microsoft Windows. Unlike QuickTime VR, VRML (Virtual Reality Modelling Language) describes objects as wireframe models, rather than as a sequence of images. VRML objects can be constructed from contour data of a specimen or by converting pixelbased images into polygonal format. In the case of the latter, this is only feasible for images that have clear boundaries that allow for edge detection. VRML can be used in addition to existing animation formats by providing a simplified schematic to
a more detailed visualization. Like QuickTime VR, regions within VRML objects can be linked to a Web page document so that, when a user clicks in these areas with their mouse, relevant text and other information can be displayed in a Web browser. Software for generating and viewing VRML objects is freely available for all major platforms, including Apple Macintosh, PC and Unix.
investigators, and others who ing their first grants, typically rely on the experience of their learn about packaging their the most attractive fashion and find the information relevant preparation of their application.
up of appendices. In addition, each of the eight chapters ends in a summary section that effectively focuses the reader’s attention on the critical advice given in the foregoing text. The early chapters emphasize step-by-step planning and organization of a research proposal. The component parts of a grant application are described, along with hints from experienced reviewpanel members about how to provide the information that they most need. Although the specific details aboutfilling out simple sections of applications seem unnecessary, sound advice is provided with regard to the research proposal. A good example is that reviewers want to know not only how data will be obtained but how it will be interpreted (this is important, but often omitted from proposals) and what alternative routes will be taken if the experiments do not produce the expected results. These early chapters provide important information about the review process, including who will see your application and how decisions are made to fund it or not. In addition, there is a wealth of practical
Grant Application
are writhave to peers to ideas in how to to the The
Writer’s Handbook
sets out to fill this information void by providing an outline for the preparation of a successful grant application and a guide to navigating the review process. This is a very up-to-date book that will primarily be of use to new investigators and first-time grant application writers. The focus is on the preparation of grant applications for biomedical research, with emphasis on a model for applications to the National Institutes of Health (NIH). A significant, but less detailed, section on the National Science Foundation (NSF) and a modest collection of information about other granting organizations are provided. Although this is a rather imposing-looking book, the primary text is only 123 pages long and more than half of the book is made trends
Conclusion I hope this article has given you an idea of how the Web can be used to transmit animation sequences and how you can go about putting your own animations online. To provide a starting point, a list of useful links related to animation on the Web can be found on a page at my site (http://www.cs.ubc.ca/ spider/ladic/animate.html). If you find any interesting Web pages that may be of use to other cell biologists who want to put their animations on-line, please let me know (e-mail: [email protected]). The editorial staff at trends in CELL BIOLOGY would also like to hear of useful sites ([email protected]).
in CELL BIOLOGY
(Vol.
6) February
1996
MISCELLANEA
advice, such as knowing the study section that the grant is most likely to be given to and how to direct your application to the study section where it will have the greatest opportunity for success. Finally, a chapter describes how the summary ‘pink sheets’ for a grant application can be interpreted and what the investigator’s options are if the grant is not funded. A collection of sample summary sheets, from both successful and unsuccessful applications, provides helpful insights into what review panels are looking for in an application, but I thought that 24 examples was more than necessary.
Super Cooper! Oncogenes
(2nd edn)
by Geoffrey M. Cooper, /ones and Bartlett, 7995. $52.50 (384 pages) lSBN 0 86720 937 2 With the current volume of output on cancer genetics, keeping abreast with the advances has become a formidable task for any student of the subject. Geoffrey Cooper’s attempt to condense the large body of work on cancer genetics in an updated version of his monograph is therefore commendable. With its vivid and concise recounting of the major discoveries in cancer genetics, this monograph has remained the best of its kind for graduate students or clinicians wishing to get a quick glimpse of oncogenes. In the original definition, ‘oncogenes’ were unique to tumorigenic viruses. Since the discovery that some retroviruses actually borrowed their oncogenes from the host genome, the definition has blurred. The ‘oncogenes’ described in this monograph are a collection of viral and cellular genes of diverse physiological functions. Despite a number of favourite models, there is not as yet a satisfactory explanation for the contribution of any of these genes to tumour development. The author included some of the current models for the action of the more popular oncogenes, but did not attempt to integrate them -this is an accurate reflection of the current status of the field. trends
in CELL BIOLOGY
(Vol.
6) February
The most useful aspects of this book are the extensive appendices that provide an up-to-date compilation of useful addresses and sources of information, both hard copy and on-line, about where funding is available and how to get help from the specific agencies when preparing an application (particularly useful in the early stages, when you have to consider if your idea matches the mission of the agency you are applying to). Although considerably less extensive, there is also an appendix providing information about scientific services that may be very useful for boosting
your productivity (antibody production, cell-culture services and a variety of on-line information listings). Veteran scientists will likely have little to gain from The Grant Application Writer’s Handbook. However, for new principal-investigators and postdoctoral fellows who are approaching independence, I highly recommend this book, in part as a guide for the preparation of a research proposal and also as a resource-book to help find out what you can apply for and how to access a wealth of information that will help with preparing a successful application.
Part I of the book provides a brief summary on the biology of cancer cells and gives some of the experimental criteria for the definition of ‘neoplastic transformation’. Table 1 .l, in which terminologies used by biologists and oncologists are correlated, may be quite helpful to basic researchers interested in human cancer. Part II, which includes three chapters on viral oncogenes, is the gem of the book. In particular, the two chapters on retroviral oncogenes are clear, concise and comprehensive. Anyone interested in teaching this topic at either the undergraduate or graduate level should take advantage of these two chapters, including their figures and tables. The seven chapters of Part Ill describe the identification of cellular oncogenes and tumour suppressor genes. The rediscovery of retroviral oncogenes by four other routes is described in Chapters 5-8. Of course, each of the four routes has also led to the identification of other genes, not previously transduced by retroviruses. These genes are tabulated in each chapter, based on the method of their discovery by: gene transfer (Chapter 5), the identification of integration sites of retroviruses that do not carry an oncogene (Chapter 6), the characterization of breakpoints of chromosomal translocations (Chapter 7) and the study of amplicons in cancer cells (Chapter 8). There is significant redundancy in the tables of these four chapters. It seems to me that such tabulation serves only one useful purpose - that is, to keep the record straight concerning who isolated the various oncogenes from the variety of human
cancers. Chapters 9 and 10 discuss the concept of tumour suppressor genes by using Rb, the retinoblastoma susceptibility gene, as a model. Relative to the treatment given to oncogenes, tumour suppressors were shortchanged in this book. Chapter 11 describes a few experimental systems that have implicated the importance of oncogenes and tumour suppressor genes in the development of cancer in animals and humans. The central theme here is the ‘multistep and multiple mutations’ hypothesis that is the current consensus. However, this hypothesis does not explain how oncogenic retroviruses, most of which carry only one oncogene, induce tumours in animals with the kind of efficiency and ferocity that alerted virologists to consider the existence of oncogenes in the first place. Part IV (8 chapters) is a rather loose collection of summaries on the function of the oncogene products. The first six chapters are organized to reflect another consensus view, that is, that oncoproteins drive cell proliferation. Thus, there are chapters on receptor tyrosine growth factors, kinases, guanine-nucleotide-binding proteins, Ser/Thr protein kinases, transcription factors and the pathway of mitogenic signal transduction. These are followed by two brief considerations of cell-cycle regulation (Chapter 18) and the regulation of development, differentiation and programmed cell death (Chapter 19). The emphasis on mitogenic signal transduction reflects the emphasis of the field in the past decade. Mitogenic stimulation is obviously required for tumour growth, but it is doubtful
1996
David Dept
Stuart of Molecular
Biology, North
10666 Torrey
Pines Road, La
Jolla, CA 92037, USA.
79
The interactive
Acknowledgements The authors gratefully acknowledge the Dept of Computer Science at the University of British Columbia for the use of their Web server and computer equipment.
future
At present, most animations obtained from the Internet consist of a series of images that are displayed in a fixed sequence. Two new data formats will overcome this limitation, and will provide interactive control over animation playback and manipulation of 3-D objects. Of most interest to Apple Macintosh users who want to create animations from images of reconstructed 3-D specimens, QuickTime VR (an extension of Apple’s existing QuickTimeformat) permits the generation of ‘navigable objects’. In this scenario, objects are composed of different sequences of images, where each sequence shows the object from a slightly different angle. As the object is tilted up, down, left or right using a computer mouse, the software responds by displaying successive images as a QuickTime movie. This kind of interactive control can also be set up to control the playback of 2-D images. Furthermore, the format allows users to assign clickable ‘hot spots’ within an animation. The activation of these areas with a mouse can trigger a variety of actions, including launching a
May all your wishes be granted The Grant Application Writer’s Handbook by Liane Reif-Lehrer, /ones and Bartlett, 1995. $34.95 (472 pages) ISBN 0 86720 874 0 Applying for grants is a task that all scientists have to face up to eventually. Some investigators consider the preparation of a grant application to be a labour of love and an opportunity to show their stuff, whereas others treat the process as a necessary evil thatwill allow them to continue doing science. Whichever way it is viewed, writing grants is a complex process, which can be very daunting. In times such as these, when funding is difficult to come by, the way that an idea is packaged and presented is as important as the idea itself. New
78
still photograph, playing an audio clip or displaying some text. The added degree of interactivity provided by these features greatly enhances viewing of animations. Although a full-featured QuickTime VR authoring kit is commercially available from Apple to create complex navigable scenes consisting of several linked animations, software for creating much simpler navigable objects exists in the public domain (again, only for Macintosh computers). Currently, free software for viewing QuickTime VR animations is only available for Apple Macintosh and PCs running Microsoft Windows. Unlike QuickTime VR, VRML (Virtual Reality Modelling Language) describes objects as wireframe models, rather than as a sequence of images. VRML objects can be constructed from contour data of a specimen or by converting pixelbased images into polygonal format. In the case of the latter, this is only feasible for images that have clear boundaries that allow for edge detection. VRML can be used in addition to existing animation formats by providing a simplified schematic to
a more detailed visualization. Like QuickTime VR, regions within VRML objects can be linked to a Web page document so that, when a user clicks in these areas with their mouse, relevant text and other information can be displayed in a Web browser. Software for generating and viewing VRML objects is freely available for all major platforms, including Apple Macintosh, PC and Unix.
investigators, and others who ing their first grants, typically rely on the experience of their learn about packaging their the most attractive fashion and find the information relevant preparation of their application.
up of appendices. In addition, each of the eight chapters ends in a summary section that effectively focuses the reader’s attention on the critical advice given in the foregoing text. The early chapters emphasize step-by-step planning and organization of a research proposal. The component parts of a grant application are described, along with hints from experienced reviewpanel members about how to provide the information that they most need. Although the specific details aboutfilling out simple sections of applications seem unnecessary, sound advice is provided with regard to the research proposal. A good example is that reviewers want to know not only how data will be obtained but how it will be interpreted (this is important, but often omitted from proposals) and what alternative routes will be taken if the experiments do not produce the expected results. These early chapters provide important information about the review process, including who will see your application and how decisions are made to fund it or not. In addition, there is a wealth of practical
Grant Application
are writhave to peers to ideas in how to to the The
Writer’s Handbook
sets out to fill this information void by providing an outline for the preparation of a successful grant application and a guide to navigating the review process. This is a very up-to-date book that will primarily be of use to new investigators and first-time grant application writers. The focus is on the preparation of grant applications for biomedical research, with emphasis on a model for applications to the National Institutes of Health (NIH). A significant, but less detailed, section on the National Science Foundation (NSF) and a modest collection of information about other granting organizations are provided. Although this is a rather imposing-looking book, the primary text is only 123 pages long and more than half of the book is made trends
Conclusion I hope this article has given you an idea of how the Web can be used to transmit animation sequences and how you can go about putting your own animations online. To provide a starting point, a list of useful links related to animation on the Web can be found on a page at my site (http://www.cs.ubc.ca/ spider/ladic/animate.html). If you find any interesting Web pages that may be of use to other cell biologists who want to put their animations on-line, please let me know (e-mail: [email protected]). The editorial staff at trends in CELL BIOLOGY would also like to hear of useful sites ([email protected]).
in CELL BIOLOGY
(Vol.
6) February
1996
MISCELLANEA
advice, such as knowing the study section that the grant is most likely to be given to and how to direct your application to the study section where it will have the greatest opportunity for success. Finally, a chapter describes how the summary ‘pink sheets’ for a grant application can be interpreted and what the investigator’s options are if the grant is not funded. A collection of sample summary sheets, from both successful and unsuccessful applications, provides helpful insights into what review panels are looking for in an application, but I thought that 24 examples was more than necessary.
Super Cooper! Oncogenes
(2nd edn)
by Geoffrey M. Cooper, /ones and Bartlett, 7995. $52.50 (384 pages) lSBN 0 86720 937 2 With the current volume of output on cancer genetics, keeping abreast with the advances has become a formidable task for any student of the subject. Geoffrey Cooper’s attempt to condense the large body of work on cancer genetics in an updated version of his monograph is therefore commendable. With its vivid and concise recounting of the major discoveries in cancer genetics, this monograph has remained the best of its kind for graduate students or clinicians wishing to get a quick glimpse of oncogenes. In the original definition, ‘oncogenes’ were unique to tumorigenic viruses. Since the discovery that some retroviruses actually borrowed their oncogenes from the host genome, the definition has blurred. The ‘oncogenes’ described in this monograph are a collection of viral and cellular genes of diverse physiological functions. Despite a number of favourite models, there is not as yet a satisfactory explanation for the contribution of any of these genes to tumour development. The author included some of the current models for the action of the more popular oncogenes, but did not attempt to integrate them -this is an accurate reflection of the current status of the field. trends
in CELL BIOLOGY
(Vol.
6) February
The most useful aspects of this book are the extensive appendices that provide an up-to-date compilation of useful addresses and sources of information, both hard copy and on-line, about where funding is available and how to get help from the specific agencies when preparing an application (particularly useful in the early stages, when you have to consider if your idea matches the mission of the agency you are applying to). Although considerably less extensive, there is also an appendix providing information about scientific services that may be very useful for boosting
your productivity (antibody production, cell-culture services and a variety of on-line information listings). Veteran scientists will likely have little to gain from The Grant Application Writer’s Handbook. However, for new principal-investigators and postdoctoral fellows who are approaching independence, I highly recommend this book, in part as a guide for the preparation of a research proposal and also as a resource-book to help find out what you can apply for and how to access a wealth of information that will help with preparing a successful application.
Part I of the book provides a brief summary on the biology of cancer cells and gives some of the experimental criteria for the definition of ‘neoplastic transformation’. Table 1 .l, in which terminologies used by biologists and oncologists are correlated, may be quite helpful to basic researchers interested in human cancer. Part II, which includes three chapters on viral oncogenes, is the gem of the book. In particular, the two chapters on retroviral oncogenes are clear, concise and comprehensive. Anyone interested in teaching this topic at either the undergraduate or graduate level should take advantage of these two chapters, including their figures and tables. The seven chapters of Part Ill describe the identification of cellular oncogenes and tumour suppressor genes. The rediscovery of retroviral oncogenes by four other routes is described in Chapters 5-8. Of course, each of the four routes has also led to the identification of other genes, not previously transduced by retroviruses. These genes are tabulated in each chapter, based on the method of their discovery by: gene transfer (Chapter 5), the identification of integration sites of retroviruses that do not carry an oncogene (Chapter 6), the characterization of breakpoints of chromosomal translocations (Chapter 7) and the study of amplicons in cancer cells (Chapter 8). There is significant redundancy in the tables of these four chapters. It seems to me that such tabulation serves only one useful purpose - that is, to keep the record straight concerning who isolated the various oncogenes from the variety of human
cancers. Chapters 9 and 10 discuss the concept of tumour suppressor genes by using Rb, the retinoblastoma susceptibility gene, as a model. Relative to the treatment given to oncogenes, tumour suppressors were shortchanged in this book. Chapter 11 describes a few experimental systems that have implicated the importance of oncogenes and tumour suppressor genes in the development of cancer in animals and humans. The central theme here is the ‘multistep and multiple mutations’ hypothesis that is the current consensus. However, this hypothesis does not explain how oncogenic retroviruses, most of which carry only one oncogene, induce tumours in animals with the kind of efficiency and ferocity that alerted virologists to consider the existence of oncogenes in the first place. Part IV (8 chapters) is a rather loose collection of summaries on the function of the oncogene products. The first six chapters are organized to reflect another consensus view, that is, that oncoproteins drive cell proliferation. Thus, there are chapters on receptor tyrosine growth factors, kinases, guanine-nucleotide-binding proteins, Ser/Thr protein kinases, transcription factors and the pathway of mitogenic signal transduction. These are followed by two brief considerations of cell-cycle regulation (Chapter 18) and the regulation of development, differentiation and programmed cell death (Chapter 19). The emphasis on mitogenic signal transduction reflects the emphasis of the field in the past decade. Mitogenic stimulation is obviously required for tumour growth, but it is doubtful
1996
David Dept
Stuart of Molecular
Biology, North
10666 Torrey
Pines Road, La
Jolla, CA 92037, USA.
79