Contents of other Volumes ...................................... xi
Contributors ................................................ xxiii
Preface ....................................................... xiv
PART A. IMAGING TECHNIQUES
Section 1. Light Microscopy
1. Fluorescence Microscopy ...................................... 5
WERNER BASCHONG AND LUKAS LANDMANN
2. Total Internal Reflection Fluorescent Microscopy ............ 19
DEREK TOOMRE AND DANIEL AXELROD
3. Band Limit and Appropriate Sampling in Microscopy ........... 29
RAINER HEINTZMANN
4. Optical Tweezers: Application to the Study of Motor
Proteins .................................................... 37
WALTER STEFFEN, ALEXANDRE LEWALLE, AND JOHN SLEEP
Section 2. Digital Video Microscopy
5. An Introduction to Electronic Image Acquisition during
Light Microscopic Observation of Biological Specimens ....... 49
JENNIFER С WATERS
6. Video-Enhanced Contrast Microscopy .......................... 57
DIETER G. WEISS
Section 3. Confocal Microscopy of Living Cells and Fixed
Cells
7. Spinning Disc Confocal Microscopy of Living Cells ........... 69
TIMO ZIMMERMANN AND DAMIEN BRUNNER
8. Confocal Microscopy of Drosophila Embryos ................... 77
MAITHREYI NARASIMHA AND NICHOLAS H. BROWN
9. Ultraviolet Laser Microbeam for Dissection of Drosophila
Embryos ..................................................... 87
DANIEL P. KIEHART, YOICHIRO TOKUTAKE, MING-SHIEN
CHANG, M. SHANE HUTSON, JOHN WIEMANN, XOMALIN G.
PERALTA, YUSUKE TOYAMA, ADRIENNE R. WELLS, ALICE
RODRIGUEZ, AND GLENN S. EDWARDS
Section 4. Fluorescent Microscopy of Living Cells
10.Introduction to Fluorescence Imaging of Live Cells:
An Annotated Checklist ..................................... 107
YU-LI WANG
11.Cytoskeleton Proteins ...................................... 111
KLEMENS ROTTNER, IRINA N. KAVERINA, AND THERESIA
E.B. STRADAL
12.Systematic Subcellular Localization of Novel Proteins ...... 121
JEREMY С SIMPSON AND RAINER PEPPERKOK
13.Single Molecule Imaging in Living Cells by Total
Internal Reflection Fluorescence Microscopy ................ 129
ADAM DOUGLASS AND RONALD VALE
14.Live-Cell Fluorescent Speckle Microscopy of Actin
Cytoskeletal Dynamics and Their Perturbation by
Drug Perfusion ............................................. 137
STEPHANIE L. GUPTON AND CLARE M. WATERMAN-STORER
15.Imaging Fluorescence Resonance Energy Transfer between
Green Fluorescent Protein Variants in Live Cells ........... 153
PETER J. VERVEER, MARTIN OFFTERDINGER, AND PHILIPPE
I.H. BASTIAENS
Section 5. Use of Fluorescent Dyes for Studies of
Intracellular Physiological Parameters
16.Measurements of Endosomal pH inLive Cells by Dual-
Excitation Fluorescence Imaging ............................ 163
NICOLAS DEMAUREX AND SERGIO GRINSTEIN
17.Genome-Wide Screening of Intracellular Protein
Localization in Fission Yeast .............................. 171
DA-QIAO DING AND YASUSHI HIRAOKA
18.Large-Scale Protein Localization in Yeast .................. 179
ANUJ KUMAR AND MICHAEL SNYDER
Section 6. Digital Image Processing, Analysis, Storage,
and Display
19.Lifting the Fog: Image Restoration by Decon volution ....... 187
RICHARD M. PARTON AND ILAN DAVIS
20.The State of the Art in Biological Image Analysis .......... 201
FEDERICO FEDERICI, SILVIA SCAGLIONE, AND ALBERTO DIASPRO
21.Publishing and Finding Images in the Biolmage Database,
an Image Database for Biologists ........................... 207
CHRIS CATTON, SIMON SPARKS, AND DAVID M. SHOTTON
PART B. ELECTRON MICROSCOPY
Section 7. Specimen Preparation Techniques
22.Fixation and Embedding of Cells and Tissues for
Transmission Electron Microscopy ........................... 221
ARVID B. MAUNSBACH
23.Negative Staining .......................................... 233
WERNER BASCHONG AND UELI AEBI
24.Glycerol Spraying/Low-Angle Rotary Metal Shadowing ......... 241
UELI AEBI AND WERNER BASCHONG
Section 8. Cryotechniques
25.Rapid Freezing of Biological Specimens for Freeze
Fracture and Deep Etching .................................. 249
NICHOLAS J. SEVERS AND DAVID M. SHOTTON
26.Freeze Fracture and Freeze Etching ......................... 257
DAVID M. SHOTTON
Section 9. Electron Microscopy Studies of the Cytoskeleton
27.Electron Microscopy of Extracted Cytoskeletons:
Negative Staining, Cryoelectron Microscopy, and
Correlation with Light Microscopy .......................... 267
GUENTER P. RESCH, J. VICTOR SMALL, AND KENNETH
N. GOLDIE
28.Correlative Light and Electron Microscopy of the
Cytoskeleton ............................................... 277
TATYANA M. SVITKINA AND GARY G. BORISY
Section 10. Immunoelectron Microscopy
29.Immunoelectron Microscopy with Lowicryl Resins ............. 289
ARVID B. MAUNSBACH
30.Use of Ultrathin Cryo- and Plastic Sections for
Immunocytochemistry ........................................ 299
NORBERT ROOS, PAUL WEBSTER, AND GARETH GRIFFITHS
31.Direct Immunogold Labeling of Components within
Protein Complexes .......................................... 307
JULIE L. HODGKINSON AND WALTER STEFFEN
PART C. SCANNING PROBE AND SCANNING ELECTRON MICROSCOPY
Section 11. Scanning Probe and Scanning Electron Microscopy
32.Atomic Force Microscopy in Biology ......................... 317
DIMITRIOS FOTIADIS, PATRICK L.T.M. FREDERIX, AND
ANDREAS ENGEL
33.Field Emission Scanning Electron Microscopy and
Visualization of the Cell Interior ......................... 325
TERENCE ALLEN, SANDRA RUTHERFORD, STEVE MURRAY,
SIEGFREID REIPERT, AND MARTIN GOLDBERG
PART D. MICRODISSECTION
Section 12. Tissue and Chromosome Microdissection
34.Laser Capture Microdissection .............................. 339
VIRGINIA ESPINA AND LANCE LIOTTA
35.Chromosome Microdissection Using Conventional Methods ...... 345
NANCY WANG, LIQIONG LI, AND HARINDRA R. ABEYSINGHE
36.Micromanipulation of Chromosomes and the Mitotic Spindle
Using Laser Microsurgery (Laser Scissors) and Laser-
Induced Optical Forces (Laser Tweezers) .................... 351
MICHAEL W. BERNS, ELLIOT BOTVINICK, LIH-HUEI LIAW,
CHUNG-HO SUN, AND JAGESH SHAH
PART E. TISSUE ARRAYS
Section 13. Tissue Arrays
37.Tissue Microarrays ......................................... 369
RONALD SIMON, MARTINA MIRLACHER, AND GUIDO SAUTER
PART F. CYTOGENETICS AND IN SITU HYBRIDIZATION
Section 14. Cytogenetics
38.Basic Cytogenetic Techniques: Culturing, Slide Making,
and G Banding .............................................. 381
KIM SMITH
39.A General and Reliable Method for Obtaining High-Yield
Metaphasic Preparations from Adherent Cell Lines:
Rapid Verification of Cell Chromosomal Content ............. 387
DORIS CASSIO
Section 15. In Situ Hybridization
40.Mapping Cloned DNA on Metaphase Chromosomes Using
Fluorescence in Situ Hybridization ......................... 395
MARGARET LEVERSHA
41.Human Genome Project Resources for Breakpoint Mapping ...... 403
DEBORAH С BURFORD, SUSAN M. GRIBBLE, AND ELENA
PRIGMORE
42.Fine Mapping of Gene Ordering by Elongated Chromosome
Methods .................................................... 409
THOMAS HAAF
43.In Situ Hybridization Applicable to mRNA Species in
Cultured Cells ............................................. 413
ROELAND W. DIRKS
44.In Situ Hybridization for Simultaneous Detection of DNA,
RNA, and Protein ........................................... 419
NOELIA CUSTODIO, CELIA CARVALHO, T. CARNEIRO, AND
MARIA CARMO-FONSECA
45.Fluorescent Visualization of Genomic Structure and DNA
Replication at the Single Molecule Level ................... 429
RONALD LEBOFSKY AND AARON BENSIMON
PART G. GENOMICS
Section 16. Genomics
46.Genomic DNA Microarray for Comparative Genomic
Hybridization .............................................. 445
ANTOINE M. SNIJDERS, RICHARD SEGRAVES, STEPHANIE
BLACKWOOD, DANIEL PINKEL, AND DONNA G. ALBERTSON
47.Genotyping of Single Nucleotide Polymorphisms by
Minisequencing Using Tag Arrays ............................ 455
LOVISA LOVMAR, SNAEVAR SIGURDSSON, AND ANN-CHRISTINE
SYVANEN
48.Single Nucleotide Polymorphism Analysis by Matrix-
Assisted Laser Desorption / Ionization Time-of-Flight
Mass Spectrometry .......................................... 463
PAMELA WHITTAKER, SUZANNAH BUMPSTEAD, KATE DOWNES,
JILUR GHORI, AND PANOS DELOUKAS
49.Single Nucleotide Polymorphism Analysis by ZipCode-
Tagged Microspheres ........................................ 471
J. DAVID TAYLOR, J. DAVID BRILEY, DAVID P. YARNALL,
AND JINGWEN CHEN
50.Polymerase Chain Reaction-Based Amplification Method
of Retaining the Quantitative Difference between Two
Complex Genomes ............................................ 477
GANG WANG, BRENDAN D. PRICE, AND G. MIKE MAKRIGIORGOS
PART H. TRANSGENIC, KNOCKOUTS, AND KNOCKDOWN METHODS
Section 17. Transgenic, Knockouts and Knockdown Methods
51.Production of Transgenic Mice by Pronuclear
Microinjection ............................................. 487
JON W. GORDON
52.Gene Targeting by Homologous Recombination in Embryonic
Stem Cells ................................................. 491
AHMED MANSOURI
53.Conditional Knockouts: Cre-lox Systems ..................... 501
DANIEL METZGER, MEI LI, ARUP KUMAR INDRA, MICHAEL
SCHULER, AND PIERRE CHAMBON
54.RNAi-Mediated Gene Silencing in Mammalian Cells ............ 511
DEREK M. DYKXHOORN
55.Antisense Oligonucleotides ................................. 523
ERICH KOLLER AND NICHOLAS M. DEAN
|
