Encyclopedia of Genetics, Genomics, Proteomics And Bioinformatics: 8 Volume Set - Rilegato

Rilegato

ISBN 10: 0470849746 ISBN 13: 9780470849743

Casa editrice: John Wiley & Sons Inc, 2005

Riassunto

Available in print and online, this unique reference brings together all four fields of genetics, genomics, proteomics, and bioinformatics to meet your dynamic research requirements. It brings together the latest concepts in these vibrant areas and ensures a truly multidisciplinary approach. Topics include genetic variation and evolution, epigenetics, the human genome, expression profiling, proteome families, structural proteomics, gene finding/gene structure, protein function and annotation, and more. The work incorporates a vast amount of topical information, profiles cutting-edge techniques, and presents the very latest findings from an international team of over five hundred contributors. With articles for both students and more experienced scientists, this is a key reference source for everyone.

• Contains more than 450 articles covering all aspects of genomics, proteomics, bioinformatics and related technologies
• Includes a glossary containing over 550 clear and concise definitions

"I am pleased to recommend it heartily as a essential reference tool...should remain the definitive work...for many years to come."
THE CHEMICAL EDUCATOR

"Jorde...and co-editors have done a remarkable job in coordinating this information, distilling it into a package that is both easy to navigate and over-flowing in discovery."
ELECTRIC REVIEW

Su questo libro

Informazioni sull?autore

Volume Editors:
Dr. Lynn Jorde is a Professor in the Department of Human Genetics at the University of Utah School of Medicine, USA.
Dr. Jorde's laboratory is actively involved in studies of human genetic variation and in studies of the genetic basis of human limb malformations. He has published more than 150 scientific articles and is the lead author of Medical Genetics, a textbook that is used widely in North America and elsewhere.
Dr. Jorde has served on several advisory panels for the National Science Foundation and the National Institutes of Health. He recently completed a 4-year term as a member of the Mammalian Genetics review panel at the National Institutes of Health. He is on the Board of Directors of the American Society of Human Genetics and has served on the editorial boards of Human Biology, the American Journal of Human Biology, and the American Journal of Human Genetics.

Peter Little is the Professor of Medical Biochemistry and Head of the School of Biotechnology and Biomolecular Sciences at the University of New South Wales, Sydney, Australia.
Peter Little obtained his PhD in 1976 from Edinburgh University, studying with Edwin Southern and Peter Walker. He carried out postdoctoral research between 1976 and 1980 at St. Mary's Hospital Medical School, from 1980 to 1981 at the California Institute of Technology and from 1981 to 1982 at Harvard University. From 1982-1987 he was a staff scientist at the Institute of Cancer Research, London and from 1987 to 2000 a Lecturer, then Reader, at the Imperial College of Science Technology and Medicine. He accepted his current position and moved to Australia in 2000.
Peter Little's research has been at the interface of molecular genetics, genetics and computational biology and he has published over 100 papers in these areas. He is a widely read commentator on molecular genetics and genomics and has a present research interest in the effects of genetic variation upon transcription.
He has a long experience in the administration of science, working with national and international agencies and corporations and is on the editorial board of a number of Genomics and Biochemistry journals.

Dr. Michael J. Dunn is?SFI Research Professor of Biomedical Proteomics at University College Dublin, Ireland.
Dr Mike Dunn has recently been appointed Professor of Proteomics at the Institute of Psychiatry, King's College, London, UK. His research team have moved to the new state-of-the-art proteomics facility that has been established as a joint facility between the Institute of Psychiatry and Proteome Sciences Plc. Before this move, Dr Dunn was a senior staff member in the National Heart and Lung Institute Division of Imperial College of Science, Technology and Medicine, London, UK for 13 years (1988-2001). His proteomics research group was based in the Heart Science Centre at Harefield Hospital, London, where research focused on laboratory and clinical studies of heart disease and transplantation. Dr Dunn's group has considerable experience in applying the proteomics approach to characterise alterations in protein expression associated with myocardial dysfunction in heart disease and to investigate processes of acute and chronic rejection following cardiac transplantation. Since the move to the Institute of Psychiatry, Dr Dunn's research focus includes neuroscience, with emphasis on the application of proteomics to the study of neurodegenerative disease.
Dr Dunn has used gel electrophoretic techniques for many years, beginning with his post-doctoral studies of erythrocyte membrane proteins at the University of Edinburgh (1970-1976), and then applied to the study of alterations in protein expression in muscular dystrophy (1978-1988) and heart disease (since 1988). Much of his research has involved the use of two-dimensional gel electrophoresis combined with quantitative computer analysis of protein expression profiles, followed by protein identification and characterisation using a range of techniques including Western immunoblotting, N-terminal microsequencing, amino acid compositional analysis and, more recently, mass spectrometry.
Dr Dunn is the current President of the British Electrophoresis Society and a former President of the international Electrophoresis society (1984-1986). He has an extensive bibliography and has contributed to many texts in the area of gel electrophoretic and proteomics technologies and applications. Dr Dunn was for many years a Senior Deputy Editor of Electrophoresis and he is now Editor in Chief of the journal, Proteomics, launched in 2001 and published by Wiley-VCH. This monthly journal is devoted to all areas of proteomic technology and applications.

Shankar Subramaniam is a Professor of Bioengineering, Chemistry and Biochemistry and Biology and Director of the Bioinformatics Graduate Program at the University of California at San Diego, USA.
He also has adjunct Professorships at the Salk Institute for Biological Studies and the San Diego Supercomputer Center. Prior to moving to UC San Diego, Dr. Subramaniam was a Professor of Biophysics, Biochemistry, Molecular and Integrative Physiology, Chemical Engineering and Electrical and Computer Engineering at the University of Illinois at Urbana-Champaign (UIUC). He was also the Director of the Bioinformatics and Computational Biology Program at the National Center for Supercomputing Applications and the Co-Director of the W.M. Keck Center for Comparative and Functional Genomics at UIUC. He is a fellow of the American Institute for Medical and Biological Engineering and is a recipient of Smithsonian Foundation and Association of Laboratory Automation Awards.

Estratto. © Ristampato con autorizzazione. Tutti i diritti riservati.

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

John Wiley & Sons

Copyright © 2005 Michael J. Dunn
All right reserved.
ISBN: 978-0-470-84974-3

Chapter One

Introductory Review

99. Separation-dependent approaches for protein expression profiling

Michael J. Dunn and Stephen R. Pennington Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland

1. Introduction

Intense efforts over the last few years have resulted in the availability, at the time of writing (February 2005), of complete genome sequences for 256 organisms (21 archael, 203 bacterial, 32 eukaryotic), including man. This wealth of information is an invaluable resource that will allow comprehensive studies of gene expression that will in turn lead to new insights into cellular functions that determine biologically relevant phenotypes in health and disease. The understanding that one gene can encode more than a single protein has led to a realization that the functional complexity of an organism far exceeds that indicated by its genome sequence alone. While powerful techniques such as DNA microarrays and serial analysis of gene expression (SAGE) make it possible to undertake rapid, global transcriptomic profiling of mRNA expression, processes including alternative mRNA splicing, RNA editing, and co- and posttranslational protein modification make it essential to undertake expression studies at the protein level. The concept of mapping the human complement of protein expression was first proposed more than 25 years ago (Anderson and Anderson, 1982), with the development of a technique in which large numbers of proteins could be separated simultaneously by two-dimensional polyacrylamide gel electrophoresis (2-DE) (O'Farrell, 1975). The term "proteome" was not established until the mid-1990s (Wasinger et al., 1995) when it was proposed to define the protein complement of a genome. This article will give an introduction to expression profiling in which the individual proteins in a complex sample are separated prior to semiquantitative analysis, and then identified usually using techniques of mass spectrometry. For an introduction to alternative strategies for expression profiling of unresolved complex protein samples, see article 99, Separation-independent approaches for protein expression profiling, Volume 0.

2. Two-dimensional gel electrophoresis (2-DE)

The technique of two-dimensional gel electrophoresis (2-DE) in which proteins are separated in the first dimension according to their charge properties (isoelectric point, pI) under denaturing conditions, followed by their separation in the second dimension according to their relative molecular mass ([M.sub.r]) by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) was developed more than 25 years ago (O'Farrell, 1975). Nevertheless, it remains the core technology of choice for the majority of applied proteomic projects (Grg et al., 2004; see article 99, Two-dimensional gel electrophoresis (2-DE), Volume 0, article 99, Two-dimensional gel electrophoresis, Volume 0) due to its ability to separate simultaneously thousands of proteins and to indicate posttranslational modifications that result in alterations in protein pI and/or [M.sub.r]. Large-format (24 21 cm) 2-D gels can routinely separate around 2000 protein spots. Moreover, recent developments including the use of narrow range "zoom" gels (see article 99, Two-dimensional gel electrophoresis (2-DE), Volume 0, article 99, Two-dimensional gel electrophoresis, Volume 0) and fluorescent dyes that facilitate the multiplex analysis of samples (see article 99, 2D DIGE, Volume 0, article 99, 2-D Difference Gel Electrophoresis - an accurate quantitative method for protein analysis, Volume 0) make it possible to achieve greater proteomic coverage combined with more accurate differential expression analysis. Additional advantages of 2-DE are the high-sensitivity visualization of the resulting 2-D separations (see article 99, Detecting protein posttranslational modifications using small molecule probes and multiwavelength imaging devices, Volume 0), compatibility with quantitative computer analysis to detect differentially regulated proteins (Dowsey et al., 2003; see article 99, Image analysis, Volume 0), and the relative ease with which proteins from 2-D gels can be identified and characterized by mass spectrometry (see article 99, MS-based methods for identification of 2-DE-resolved proteins, Volume 0).

3. Alternatives to 2-DE

Despite the many advantages of 2-DE, there are alternative protein separation strategies. Perhaps the simplest alternative to 2-DE is the use of one-dimensional SDS-PAGE to separate proteins in the sample, on the basis of their [M.sub.r] followed by protein identification by tandem mass spectrometry (MS/MS), such that several proteins comigrating in a single band can be identified. This method is limited by the complexity of the protein mixture that can be analyzed but is well suited for the analysis of membrane proteins, and has also been successfully applied to the study of protein complexes (Figeys et al., 2001). Other approaches avoid the use of gels altogether by combining liquid chromatography (LC) and MS. In these so-called shotgun approaches, a tryptic digest of the sample is separated by one or more dimensions (typically ion-exchange combined with reverse-phase) of LC to reduce the complexity of peptide fractions. These are subsequently introduced (either on-or off-line) into a tandem mass spectrometer for sequence-based identification. For example, the so-called MudPIT approach (Wolters et al., 2001) identified around 1500 yeast proteins in a single analysis (Washburn et al., 2001). An alternative to this approach that is more robust than multidimensional chromatography, while still allowing complex samples to be analyzed, has been termed GeLC-MS/MS (Schirle et al., 2003). Here, tryptic digests of protein bands excised from the SDS-PAGE gel are separated by one-dimensional RP-HPLC prior to on- or off-line MS/MS analysis. However, a major limitation of such approaches is that unless combined with some form of stable isotope labeling or "mass tagging", they provide no information on semiquantitative abundance of proteins and are very limited in their ability to detect posttranslational modifications.

The former problem is currently being addressed by the development of a range of MS-based techniques in which stable isotopes are used to differentiate between two or more populations of proteins (Han et al., 2001). In general, this approach consists of four steps: (1) differential isotopic labeling of the two (or more) protein mixtures, (2) digestion of the combined labeled samples with a protease such as trypsin or Lys-C, (3) separation of the peptides by multidimensional LC, and (4) semiquantitative analysis and identification of the peptides by MS/MS. Currently, the most widely used method is the isotope-coded affinity tag (ICAT) (Han et al., 2001; see article 99, ICAT and other labeling strategies for semiquantitative LC-based expression profiling, Volume 0), but there are a variety of other approaches involving labeling with stable isotopes at the whole cell, intact protein, or tryptic peptide level (Julka and Regnier, 2004; Ross et al., 2004; see article 99, ICAT and other labeling strategies for semiquantitative LC-based expression profiling, Volume 0). Although these approaches are promising, there are caveats: (1) their quantitative reproducibility needs to be established, (2) the dynamic range of the these techniques may be little better than 2-DE, and (3) there is evidence that they can be complementary to a 2-DE approach in identifying a different subset of proteins from a given sample (Kubota et al., 2003).

4. Conclusion

The current array of proteomic techniques makes it possible to characterize global alterations in protein expression associated with the progression of many different biological processes, including human disease. However, there is still no one method that is suitable for the analysis of all samples, and for many projects it is likely that a combination of proteomic platforms, both gel and nongel based, will have to be applied to provide the required depth of proteomic coverage.

Acknowledgments

MJD is the recipient of a Science Foundation Ireland Research Professorship, and is grateful to SFI for the generous support of research in his laboratory. The Proteome Research Centre established by SRP has been supported by grants from the Higher Education Authority in Ireland.

(Continues...)

Excerpted from Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics Copyright © 2005 by Michael J. Dunn. Excerpted by permission.
All rights reserved. No part of this excerpt may be reproduced or reprinted without permission in writing from the publisher.
Excerpts are provided by Dial-A-Book Inc. solely for the personal use of visitors to this web site.

Dettagli dell'edizione

• Editore: John Wiley & Sons Inc
• Data di pubblicazione: 2005
• Lingua: Inglese
• ISBN 10: 0470849746
• ISBN 13: 9780470849743
• Rilegatura: Copertina rigida
• Numero edizione: 1
• Numero di pagine: 3897
• Redattore: Jorde Lynn B.
• Contatto del produttore: non disponibile
• Persona responsabile: non disponibile