From Genome to Proteome: Advances in the Practice and Application of Proteomics

From Genome to Proteome: Advances in the Practice and Application of Proteomics

Editor(s): Michael J. Dunn

Published Online: 26 DEC 2007

Print ISBN: 9783527301546

Online ISBN: 9783527613489

DOI: 10.1002/9783527613489

About this Book

As research on the human, animal, plant and microbial genomes matures towards descriptive fullness, the need for understanding the proteome has clearly emerged as the next major endeavor of life sciences. Proteomics - the quantitative analysis of all proteins working in a cell at a specific time and at specific conditions - provides deep insight into the highly organized network of expression, modification and degradation of proteins.
Compiled in this book are reviews and research articles which describe the recent advances and perspectives of this new field of research. The articles are grouped into the following sections:
- Sample Preparation and Solubilization
- Developments in Electrophoresis
- Detection and Quantitation
- Mass Spectrometry
- Proteome Data Analysis and Management
- Prokayotes and Yeast
- Biological Fluids
- Eukaryotic Cells and Tissue
- Oncology
- Plants
Proteomics is a new key for the functional analysis of living systems and of equal importance for basic as well as application oriented research.

Table of contents

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  1. Part 1: Reviews

    1. Chapter 2

      Diagnosis of cellular states of microbial organisms using proteomics (pages 17–27)

      Ruth A. Vanbogelen, Erin E. Schiller, Jeffrey D. Thomas and Frederick C. Neidhardt

    2. Chapter 4

      Proteomics for genetic and physiological studies in plants (pages 38–51)

      Hervé Thiellement, Nasser Bahrman, Catherine Damerval, Christophe Plomion, Michel Rossignol, Véronique Santoni, Dominique De Vienne and Michel Zivy

    3. Chapter 5

      Proteomics in human disease: Cancer, heart and infectious diseases (pages 52–62)

      Peter R. Jungblut, Ursula Zimny-Arndt, Evelyn Zeindl-Eberhart, Jiri Stulik, Kamila Koupilova, Klaus-Peter Pleißner, Albrecht Otto, Eva-Christina Müller, Wanda Sokolowska-Köhler, Gertrud Grabher and Georg Stöffler

  2. Part 2: Sample preparation and solubilization

    1. Chapter 11

      The potential use of laser capture microdissection to selectively obtain distinct populations of cells for proteomic analysis — Preliminary findings (pages 109–120)

      Rosamonde E. Banks, Michael J. Dunn, Mary A. Forbes, Anthea Stanley, Darryl Pappin, Tom Naven, Michael Gough, Patricia Harnden and Peter J. Selby

    2. Chapter 13

      Towards the recovery of hydrophobic proteins on two-dimensional electrophoresis gels (pages 125–131)

      Véronique Santoni, Thierry Rabilloud, Patrick Doumas, David Rouquié, Monique Mansion, Sylvie Kieffer, Jérôme Garin and Michel Rossignol

  3. Part 3: Developments in electrophoresis

    1. Chapter 16

      Modified immobilized pH gradient gel strip equilibration procedure in SWISS-2DPAGE protocols (pages 143–146)

      Jun X. Yan, Jean-Charles Sanchez, Veronique Rouge, Keith L. Williams and Denis F. Hochstrasser

    2. Chapter 17

      Microchannel networks for electrophoretic separations (pages 147–151)

      Joël S. Rossier, Alexandra Schwarz, Frédéric Reymond, Rosaria Ferrigno, François Bianchi and Hubert H. Girault

  4. Part 4: Detection and quantitation

    1. Chapter 19

      Studies of quantitative analysis of protein expression in Saccharomyces cerevisiae (pages 158–162)

      Jun X. Yan, Jean-Charles Sanchez, Luisa Tonella, Keith L. Williams and Denis F. Hochstrasser

  5. Part 5: Mass spectrometry

    1. Chapter 20

      High sensitivity mass spectrometric methods for obtaining intact molecular weights from gelseparated proteins (pages 163–168)

      Joseph A. Loo, Jeffrey Brown, Glenn Critchley, Charles Mitchell, Philip C. Andrews and Rachel R. Ogorzalek Loo

  6. Part 6: Proteome data analysis and management

    1. Chapter 22

      New algorithmic approaches to protein spot detection and pattern matching in two-dimensional electrophoresis gel databases (pages 175–185)

      Klaus-Peter Pleißner, Frank Hoffmann, Klaus Kriegel, Carola Wenk, Susan Wegner, Anders Sahlström, Helmut Oswald, Helmut Alt and Eckart Fleck

  7. Part 7: Prokaryotes and yeast

    1. Chapter 26

      Characterization of periplasmic Escherichia coli protein expression at high cell densities (pages 210–217)

      Bo Franzén, Susanne Becker, Riitta Mikkola, Kenneth Tidblad, Agneta Tjernberg and Staffan Birnbaum

    2. Chapter 31

      Comparison of yeast cell protein solubilization procedures for two-dimensional electrophoresis (pages 246–249)

      Alois Harder, Robert Wildgruber, Arek Nawrocki, Stephen J. Fey, Peter Mose Larsen and Angelika Görg

  8. Part 8: Biological Fluids

    1. Chapter 34

      Proteins of rat serum IV. Time-course of acute-phase protein expression and its modulation by indomethacine (pages 266–273)

      Ivano Eberini, Ingrid Miller, Valeria Zancan, Chiara Bolego, Lina Puglisi, Manfred Gemeiner and Elisabetta Gianazza

    2. Chapter 35

      Improved two-dimensional gel electrophoresis representation of serum proteins by using ProtoClear™ (pages 274–279)

      Bridget A. Lollo, Sheryl Harvey, Jane Liao, Anthony C. Stevens, Raymond Wagenknecht, Rick Sayen, Justine Whaley and Fereydoun G. Sajjadi

  9. Part 9: Eukaryotic cells and tissue

    1. Chapter 41

      A two-dimensional electrophoresis database of rat heart proteins (pages 311–317)

      Xin Ping Li, Klaus-Peter Pleißner, Christian Scheler, Vera Regitz-Zagrosek, Johann Salnikow and Peter R. Jungblut

    2. Chapter 42

      Bovine dilated cardiomyopathy: Proteomic analysis of an animal model of human dilated cardiomyopathy (pages 318–326)

      John Weekes, Colin H. Wheeler, Jun X. Yan, Joachim Weil, Thomas Eschenhagen, Günter Scholtysik and Michael J. Dunn

    3. Chapter 43

      Two-dimensional map of human brain proteins (pages 327–336)

      Hanno Langen, Peter Berndt, Daniel Röder, Nigel Cairns, Gert Lubec and Michael Fountoulakis

    4. Chapter 46

      A proteome analysis of livers from obese (ob/ob) mice treated with the peroxisome proliferator WY14,643 (pages 355–362)

      Ulrika Edvardsson, Maria Alexandersson, Helena Brockenhuus Von Löwenhielm, Ann-Christin Nyström, Bengt Ljung, Fredrik Nilsson and Björn Dahllöf

    5. Chapter 47

      Regional protein alterations in rat kidneys induced by lead exposure (pages 363–371)

      Frank A. Witzmann, Carla D. Fultz, Raymond A. Grant, Linda S. Wright, Steven E. Kornguth and Frank L. Siegel

    6. Chapter 48

      Functional proteomics of signal transduction by membrane receptors (pages 372–381)

      Jasminka Godovac-Zimmermann, Vukic Soskic, Slobodan Poznanovic and Federico Brianza

    7. Chapter 49

      Modulation of signal transduction pathways and global protein composition of macrophages by ionizing radiation (pages 382–388)

      Jiří Stulík, Kamila Koupilová, Lenka Hernychová, Aleš Macela, Václav Bláha, Claudia Baaske, Walter Kaffenberger and Dirk Van Beuningen

    8. Chapter 54

      A two-dimensional protein map of Chinese hamster ovary cells (pages 414–420)

      Kathleen M. Champion, David Arnott, William J. Henzel, Sam Hermes, Stefanie Weikert, John Stults, Martin Vanderlaan and Lynne Krummen

    9. Chapter 55

      Two-dimensional gel electrophoresis as analytical tool for identifying Candida albicans immunogenic proteins (pages 421–430)

      Aida Pitarch, Mercedes Pardo, Antonio Jiménez, Jesús Pla, Concha Gil, Miguel Sánchez and César Nombela

    10. Chapter 57

      A computer-assisted two-dimensional gel electrophoresis approach for studying the variations in protein expression related to an induced functional repression of NFkB in lymphoblastoid cell lines (pages 437–446)

      Raymond Joubert-Caron, Jean Feuillard, Sylvie Kohanna, Florence Poirier, Jean-Pierre Le Caër, Marino Schuhmacher, Georg W. Bornkamm, Axel Polack, Michel Caron, Dominique Bladier and Martine Raphaël

    11. Chapter 59

      Active dissociation of the fluorescent dye Hoechst 33342 from DNA in a living cell: Who could do it? (pages 453–458)

      Stanislav N. Naryzhny, Vera V. Levina, Elena Y. Varfolomeeva, Eugeny A. Drobchenko and Michael V. Filatov

  10. Part 10: Oncology

    1. Chapter 63

      Protein changes associated with ionizing radiation-induced apoptosis in human prostate epithelial tumor cells (pages 485–494)

      Sarada C. Prasad, Viatcheslav A. Soldatenkov, Michael R. Kuettel, Peter J. Thraves, Xiaojun Zou and Anatoly Dritschilo

    2. Chapter 66

      Glial fibrillary acidic protein and its fragments discriminate astrocytoma from oligodendroglioma (pages 507–512)

      Theo M. Luider, Johan M. Kros, Peter A. E. Sillevis Smitt, Martin J. Van den Bent and Charles J. Vecht

    3. Chapter 67

      Identification of HSP-60 as the specific antigen of IgM produced by BRG-Iymphoma cells (pages 512–517)

      Luca Musante, Massimo Ulivi, Giovanna Cutrona, Nicholas Chiorazzi, Silvio Roncella, Giovanni Candiano and Manlio Ferrarini

  11. Part 11: Plants

    1. Chapter 68

      Separation and characterization of needle and xylem maritime pine proteins (pages 518–528)

      Paulo Costa, Cédric Pionneau, Guy Bauw, Christian Dubos, Nasser Bahrmann, Antoine Kremer, Jean-Marc Frigerio and Christophe Plomion

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