Caenorhabditis elegans : modern biological analysis of an organism

651 Pages·1995·79.314 MB·English

by  Henry F Epstein, Diane C Shakes, American Society for Cell Biology

Series Editors
Leslie Wilson
Department of Biological Sciences
University of California, Santa Barbara
Santa Barbara. California
Paul Matsudaira
Whitehead Institute for Biomedical Research and
Department of Biology
Massachusetts Institute of Technology
Cambridge, Massachusetts
Methods in Cell Biology
Prepared under the Auspices of the American Society for Cell Biology
VOLUME 48
Cuenorhubditis elegans: Modern Biologcal Analysis
of an Organism
Edited by
Henry F. Epstein
Department of Neurology
Baylor College of Medicine
Houston, Texas
and
Diane C. Shakes
Department of Biology
University of Houston
Houston, Texas
ACADEMIC PRESS
San Diego New York Boston London Sydney Tokyo Toronto
Cover photograph (paperback edition only): Immunofluorescence image of 28-cell stage
Caenorhahditis elegans embryo stained for actin, DNA, and P granules using rhodamine-coupled
secondary antibody. See Chapter 16, Figure 1 for further details. Photograph from Evans et al, 1994;
reprinted with permission of Cell Press.
This book is printed on acid-free paper. @
Copyright 0 1995 by ACADEMIC PRESS, INC.
All Rights Reserved.
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CONTRIBUTORS
Numbers in parentheses indicate the pages on which the authors’ contributions begin.
Donna G. Albertson (339), MRC Laboratory of Molecular Biology, Cambridge CB2
2QH, England
Philip Anderson (31), Department of Genetics, University of Wisconsin, Madison,
Wisconsin 53706
Leon Avery (225,251),D epartment of Biochemistry, University of Texas southwestern
Medical Center, Dallas, Texas 75235
David L. Baillie (147), Institute of Molecular Biology and Biochemistry, Simon Fraser
University, Burnaby, Canada V5A 1S 6, British Columbia
Cornelia I. Bargmann (225), Programs in Developmental Biology, Neuroscience,
and Genetics, Department of Anatomy, The University of California, San Francisco,
California 941 43
Philip S. Birchall (339), MRC Laboratory of Molecular Biology, Cambridge CB2
2QH, England
Alan Coulson (533), The Sanger Centre, Hinxton, Cambridge CBlO lRQ, United
Kingdom
Richard Durbin (583), The Sanger Centre, Hinxton, Cambridge CBlO lRQ,
United Kingdom
Lois G. Edgar (303), Department of Molecular, Cellular, and Developmental Biology,
University of Colorado, Boulder, Colorado 80309
Mark Edgley (147), Department of Medical Genetics, University of British Columbia,
Vancouver, British Columbia, Canada V6T 123
Frank H. Eeckman (583), LBL Human Genome Center, Berkeley, California 94611
Henry F. Epstein (437), Departments of Neurology, Biochemistry, and Cell Biology,
Baylor College of Medicine, Houston, Texas 77030
Anthony Favello (551), Genome Sequencing Center, Washington University School
of Medicine, St. Louis, Missouri 63108
Andrew Fire (323, 45 l), Department of Embryology, Carnegie Institution of Washing-
ton, Baltimore, Maryland 21210
Rita M. Fishpool (339), MRC Laboratory of Molecular Biology, Cambridge CB2
2QH, England
John T. Fleming (3), Department of Pediatrics/Hematology Oncology, Massachusetts
General Hospital, Boston, Massachusetts 021 14
Lucinda L. Fulton (571), Genome Sequencing Center, Washington University School
of Medicine, St. Louis, Missouri 63108
Timothy N. Gannon (205),D epartment of Psychology, University ofBritish Columbia,
Vancouver, British Columbia, Canada V6T 124
xiii
xiv Contributors
Ed Grossman (607),B eckman Institute for Advanced Science and Technology, Urbana,
Illinois 6 180 1
David H. Hall (395),D epartment of Neuroscience, Albert Einstein College of Medicine,
Bronx, New York 10461
Robert K. Herman (123), Department of Genetics and Cell Biology, University of
Minnesota, St. Paul, Minnesota 55108
LaDeana Hillier (55 1, 571), Genome Sequencing Center, Washington University
School of Medicine, St. Louis, Missouri 63108
Linda S. Huang (97), California Institute of Technology, Pasadena, California 91 125
Chau Huynh (533), Department of Molecular and Cell Biology, University of California
at Berkeley, Berkeley, California 94720
Curt Jamison (607), Community Systems Laboratory, National Center for Supercom-
puting Applications, University of Illinois, Urbana-Campaign, Urbana, Illinois 618 01
Carl D. Johnson (187), NemaPharm, Inc., Cambridge, Massachusetts 02139
Yuko Kozono (533), Division of Rheumatology, University of Colorado, Denver,
Colorado 80262
Michael Krause (483, 513), Laboratory of Molecular Biology, National Institute of
Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda,
Maryland 20892
Steven W. L'Hernault (273), Department of Biology, Emory University, Atlanta,
Georgia 30322
James A. Lewis (3), Division of Life Sciences, University of Texas at San Antonio,
San Antonio, Texas 78249
Feizhou Liu (437), Department of Biochemistry, Baylor College of Medicine, Houston,
Texas 77030
Shawn Lockery (251), Institute of Neuroscience, University of Oregon, Eugene, Ore-
gon 97403
Craig Mello (451), University of Massachusetts Cancer Center, Biotech 11, Worcester,
Massachusetts 01605
David M. Miller (365), Department of Cell Biology, Vanderbilt University Medical
Center, Nashville, Tennessee 37232
Ronald H. A. Plasterk (59), Netherlands Cancer Institute, Division of Molecular
Biology, 1066 CX Amsterdam, The Netherlands
Kevin Powell (607), Digital Library Initiative, Grainger Engineering Library, Urbana,
Illinois 61801
David Raizen (251 ). Department of Biochemistry, University of Texas Southwestern
Medical Center, Dallas, Texas 75235
James B. Rand (187), Program in Molecular and Cell Biology, Oklahoma Medical
Research Foundation, Oklahoma City, Oklahoma 731 04
Catharine H. Rankin (205), Department of Psychology, University of British Colum-
bia, Vancouver, British Columbia, Canada V6T 124
Donald L. Riddle (147), Division of Biological Sciences, University of Missouri,
Columbia, Missouri 6521 1
Contributors xv
Thomas M. Roberts (273), Department of Biological Sciences, Florida State University,
Tallahassee, Florida 32306
Ann M. Rose (147), Department of Medical Genetics, University of British Columbia,
Vancouver, British Columbia, Canada V6T 123
Bruce R. Schatz (607), National Center for Supercomputing Applications, Beckman
Institute, University of Illinois, Urbana-Campaign, Urbana, Illinois 61 801
Geraldine Seydoux (323), Department of Embryology, Carnegie Institution of Wash-
ington, Baltimore, Maryland 2 1210
Diane C. Shakes (365), Department of Biology, University of Houston, Houston,
Texas 77204
Laura M. Shoman (607), Graduate School of Library and Information Systems, Univer-
sity of Illinois at Urbana-Champaign, Champaign, Illinois 61 820
Ratna Shownkeen (533), The Sanger Centre, Hinxton, Cambridge CBlO lRQ,
United Kingdom
Paul W. Sternberg (97), Howard Hughes Medical Institute, Research Laboratories,
California Institute of Technology, Pasadena, California 91 125
Benjamin D. Williams (81), Department of Genetics, Washington University School
of Medicine, St. Louis, Missouri 63110
Richard K. Wilson (551,571), Genome Sequencing Center and Department of Genet-
ics, Washington University School of Medicine, St. Louis, Missouri 63108
PREFACE
The choice of the title “Modern Biological Analysis of an Organism” is in-
tended to emphasize the diverse and continuously evolving methodology and
scope of Cuenorhubditis eleguns research. The volume is designed to serve the
rapidly expanding community of C. eleguns researchers, both those dedicated to
understanding the biology and genetics of the worm and the growing number
of people who would like to use C. eleguns for particular experiments relevant
to their favorite biological question. In addition, this volume is intended to serve
readers of the C. eleguns literature who are looking for a single source book that
provides detailed explanations of current C. eleguns methods.
For an introduction to the field, we recommend the 1988 work “The Nematode
Cuenorhubditis eleguns, edited by William B. Wood, which reviews the accom-
”
plishments and results generated in the first 25 years of concentrated research
efforts on C. eleguns. This first book provides reviews of major areas of C. eleguns
research and sources of frequently used C. eleguns information, such as the
neuronal “wiring diagram,” the cell lineage, and mutant strain lists. As a methods
volume, our C. eleguns book is designed to complement rather than supersede
the earlier volume. Our emphasis is on methods rather than on areas of biological
investigation, and data lists from the previous volume have been supplanted by
directions for obtaining the latest updates over the Internet.
The research approaches of both our book and the 1988 volume originated
with Sydney Brenner, then at the Medical Research Council of Molecular Biology
in Cambridge, England. Brenner had the foresight to recognize the tremendous
potential of C. eleguns as an experimental organism and pioneered research on
its genetics and neurobiology. Brenner and his fellow C. eleguns researchers at
the MRC provided a training environment for many of the principal investigators
in the field, and Brenner himself is largely responsible for promoting the multidis-
ciplinary and integrative character of C. eleguns research.
Newcomers to the C. eleguns field frequently remark upon the frequent use
of the word “community” by C. eleguns researchers. There is a great deal of
communication among laboratories, and a tradition of sharing dominates the
field. These exchanges include mutants and DNA clones, databases and DNA
sequences, physical DNA and genetic linkage maps, and prepublication data
publicized in the “Worm Breeder’s Gazette” (although one of us has reservations
about nonrefereed communications). This philosophy of sharing is tied to the
dominant theme of considering the integrated organism and its life cycle in
analyzing specific pathways, stages, structures, and cell types. Because C. eleguns
is a multicellular organism with characteristic nervous, muscle, digestive, and
reproductive systems, research in the field involves a wide range of biological
xvii
xviii Preface
disciplines including informatics, neurobiology, pharmacology, psychology, and
the triad molecular, cell, and developmental biology.
This volume is divided into four sections that evolved as the book was assem-
bled. The diversity of the chapters and sections serves to emphasize the multitude
of biological approaches currently employed in C. elegans as well as the evolution
of the field from one centered almost exclusively around genetics and neurobiol-
ogy to one that also sits at the forefront of genomics research.
In the first section, the chapters deal with basic culture methods and the
classical strength of the C. elegans system, namely its use as a genetic organism.
The chapter by Lewis and Fleming on basic culture methods will be useful to
new investigators as well as to those who want to employ large-scale culturing
methods. The chapter by Huang and Sternberg manages to put much of C.
elegans research in perspective as the authors explain the methods by which
genetics can be used to dissect regulatory pathways. For those interested in
classical genetic methods, three chapters (mutagenesis techniques, mosaic analy-
sis, and genetic balancers) uniquely integrate a vast amount of useful information
that had not until now been pulled together into single articles. Finally, chapters
by Williams and Plasterk describe new approaches of combining molecular and
classical genetic techniques that greatly expand the power of C. elegans ge-
netic analysis.
In the second section, the breadth of the current research in C. elegans neurobi-
ology is revealed. The earlier triumphs of the field, the elucidation of the complete
C. elegans “wiring diagram” based on the reconstruction of transmission EM
serial section and the collection of a vast number of neurological mutants, provide
the groundwork for many of these new approaches. Chapters on laser ablation
and electrophysiology show how the function of single neurons can be analyzed
in the context of the entire worm. The other chapters describe methods by which
C. elegans is being employed in neuropharmacological studies as well as those
of learning and memory.
The third section provides a compilation of a wide variety of techniques that
are useful for analyzing cell biological problems in C. elegans. Chapters on sperm
and blastomere culture describe the method for handling two general cell types
that are particularly amenable to cell biological analysis. Other chapters deal
with general microscopy techniques and the localization and analysis of both
mRNA and protein in C. elegans embryos and worms. Also included are chapters
on transformation techniques and methods for analyzing transcription and trans-
lation, two areas that were still in development when the 1988 volume was written
but which have now become standard techniques in the field.
The final section is devoted to the ever-growing importance of genomics and
the use of computer databases in C. elegans research. For those interested in C.
elegans as a model organism in genomics research, the methodology underlying
the large-scale genomics research is described. For the growing number of people
who need access to this genomic information and other C. elegans information,
two chapters describe the most widely used C. elegans databases. The tremendous
Preface xix
success of ACeDB, originally developed for C. elegans, has led to its adoption
by genomic researchers in other systems. WCS is a broader database that contains
not only the information in ACeDB but also additional information and added
mechanisms of information exchange.
At some level a scientific methods volume is always a “snap-shot” in time,
but we hope that the nature of most of the chapters is such that the volume will
continue to be a useful reference source for years to come. Nevertheless, we
have also listed C. elegans information sources in the appendixes, which readers
can consult for up-to-the-minute information.
In closing, we sincerely thank the various chapter authors who agreed to
contribute to this important community resource as well as the many reviewers
whose valuable comments helped ensure that this book would serve as a useful
resource for C. elegans aficionados as well as newcomers to the field. As editors,
we strived to have each chapter reviewed by both C. eleguns and non C. eleguns
researchers to ensure that the chapters would be accessible and useful to a
wide audience.
Henry F. Epstein
Diane C. Shakes
ACKNOWLEDGMENTS
We acknowledge the following persons who critically reviewed the various
chapters: Chris Bauer, Kate Beckingham, Hugo Bellen, Alan Coulson, Anne
Delcour, Monica Driscoll, Bonnie Dunbar, Patrick Dunne, Gregor Eichele,
Arnold Eskin, George Fox, Richard Gibbs, Andy Golden, Richard Gomer,
Iva Greenwald, Wade Harper, Ralph Hecht, David Hirsh, Sandra Honda, Ken-
neth Kemphues, Deborah Kimbrell, James Kramer, Michael Krause, Steve
L’Hernault, Don Moerman, James Pries, Mary Rayborn, Gary Ruvkun,
Amy Sater, Tim Schedl, Heinke Schnabel, Robert Schwartz, Michael Siciliano,
Michael Stern, Susan Strome, Kevin van Doren, Michael Wagner, Samuel Ward,
and Richard Wilson.