Dictyostelium Discoideum Protocols

by Eichinger, Ludwig; Rivero, Francisco

• ISBN13: 9781588296238
• ISBN10: 1588296237
• Edition: 1st
• Format: Hardcover
• Copyright: 2006-07-30
• Publisher: Humana Pr Inc

Summary

Dictyostelium discoideum Protocols presents a comprehensive collection of cutting-edge molecular biological protocols for studying D. discoideum, with emphasis on its utility in the study of fundamental cellular processes including signal transduction, chemotaxis, cell motility, cytokinesis, phagocytosis, and aspects of development such as cell sorting, pattern formation, and cell type differentiation. Written by experts in the field, this important guide provides easy access to current methods and techniques for the study of D. discoideum. For the newcomer to the field, it offers a complete and inclusive introduction to this important model organism. The book is divided into four main parts, which include an introduction to the organism that provides integral community resources and genome-wide approaches; basic methods and available molecular genetic techniques for study of the organism; imaging and localization methods; and a discussion of D. discoideum, with emphasis on its unique advantages as a model system. This in-depth guide provides a complete introduction to and thorough handbook for the study of D. discoideum, including a discussion of the implications of the recently-completed Dictyostelium genome project in strengthening the position of D. discoideum as a model organism for studying fundamental cell processes and aspects of development. Researchers at all levels of experience will benefit from the presentations throughout of the most current, useful and innovative techniques for the study of D. discoideum from leading Dictyostelium scientists.

Table of Contents

Preface	v
Contributors	xi
PART I THE ORGANISM, COMMUNITY RESOURCES, AND GENOME-WIDE STUDIES
1 The Secret Lives of Dictyostelium
Richard H. Kessin	3	(12)
2 The Genome of Dictyostelium discoideum
Adam Kuspa and William F. Loomis	15	(16)
3 The cDNA Sequencing Project
Hideko Urushihara, Takahiro Morio, and Yoshimasa Tanaka	31	(20)
4 dictyBase and the Dicty Stock Center
Petra Fey, Pascale Gaudet, Karen E. Pilcher, Jakob Franke, and Rex L. Chisholm	51	(24)
5 Analysis of Gene Expression Using cDNA Microarrays
Marcel Kaul and Ludwig Eichinger	75	(20)
6 Proteomic Analysis of Dictyostelium discoideum
Udo Roth, Stefan Müller, and Franz-Georg Hanisch	95	(18)
PART II BASIC METHODS AND MOLECULAR GENETIC TECHNIQUES
7 Cultivation, Spore Production, and Mating
Hideko Urushihara	113	(12)
8 Parasexual Genetics Using Axenic Cells
Jason King and Robert Insall	125	(12)
9 Slug Phototaxis, Thermotaxis, and Spontaneous Turning Behavior
Paul R. Fisher and Sarah J. Annesley	137	(34)
10 Purification Techniques of Subcellular Compartments for Analytical and Preparative Purposes
Laurence Aubry and Gérard Klein	171	(16)
11 Generation of Multiple Knockout Mutants Using the Cre-IoxP System
Alan R. Kimmel and Jan Faix	187	(14)
12 Restriction Enzyme-Mediated Integration (REMI) Mutagenesis
Adam Kuspa	201	(10)
13 RNA Interference and Antisense-Mediated Gene Silencing in Dictyostelium
Markus Kuhlmann, Blagovesta Popova, and Wolfgang Nellen	211	(18)
PART III IMAGING AND LOCALIZATION METHODS
14 Application of Fluorescent Protein Tags as Reporters in Live-Cell Imaging Studies
Annette Müller-Taubenberger	229	(18)
15 Investigating Gene Expression: In Situ Hybridization and Reporter Genes
Ricardo Escalante and Leandro Sastre	247	(14)
16 Application of 2D and 3D DIAS to Motion Analysis of Live Cells in Transmission and Confocal Microscopy Imaging
Deborah Wessels, Spencer Kuhl, and David R. Soll	261	(20)
17 Using Quantitative Fluorescence Microscopy and FRET Imaging to Measure Spatiotemporal Signaling Events in Single Living Cells
Xuehua Xu, Joseph A. Brzostowski, and Tian Jin	281	(16)
18 Visualizing Signaling and Cell Movement During the Multicellular Stages of Dictyostelium Development
Dirk Dormann and Cornelis J. Weijer	297	(14)
19 Under-Agarose Chemotaxis of Dictyostelium discoideum
David Woznica and David A. Knecht	311	(16)
20 Optimized Fixation and Immunofluorescence Staining Methods for Dictyostelium Cells
Monica Hagedorn, Eva M. Neuhaus, and Thierry Soldati	327	(12)
21 Cryofixation Methods for Ultrastructural Studies of Dictyostelium discoideum
Mark J. Grimson and Richard L. Blanton	339	(30)
PART IV DICTYOSTELIUM AS MODEL ORGANISM
22 Analysis of Signal Transduction: Formation of cAMP, cGMP, and Ins(1,4,5)P3 In Vivo and In Vitro
Peter J.M. Van Haastert	369	(24)
23 Assaying Chemotaxis of Dictyostelium Cells
Michelle C. Mendoza and Richard A. Firtel	393	(14)
24 Characterization of Cross-Linked Actin Filament Gels and Bundles Using Birefringence and Polarized Light Scattering
Ruth Furukawa and Marcus Fechheimer	407	(16)
25 Quantitative and Microscopic Methods for Studying the Endocytic Pathway
Francisco Rivero and Markus Maniak	423	(16)
26 Preparation of Intact, Highly Purified Phagosomes from Dictyostelium
Daniel Gotthardt, Régis Dieckmann, Vincent Blancheteau, Claudia Kistler, Frank Reichardt, and Thierry Soldati	439	(10)
27 Assaying Cell–Cell Adhesion
Salvatore Bozzaro	449	(20)
28 Periodic Activation of ERK2 and Partial Involvement of G Protein in ERK2 Activation by cAMP in Dictyostelium Cells
Mineko Maeda	469	(10)
29 An Improved Method for Dictyostelium Centrosome Isolation
Irene Schulz, Yvonne Reinders, Albert Sickmann, and Ralph Gräf	479	(12)
30 Epigenetics in Dictyostelium
Markus Kaller, Wolfgang Nellen, and Jonathan R. Chubb	491	(16)
31 Dictyostelium discoideum as a Model to Study Host–Pathogen Interactions
Can Ünal and Michael Steinert	507	(10)
32 Pharmacogenetics: Defining the Genetic Basis of Drug Action and Inositol Trisphosphate Analysis
Kathryn E. Adley, Melanie Keim, and Robin S.B.Williams	517	(18)
33 How to Assess and Study Cell Death in Dictyostelium discoideum
Artemis Kosta, Catherine Laporte, David Lam, Emilie Tresse, Marie-Françoise Luciani, and Pierre Golstein	535	(16)
Index	551