Methods
A Companion to Methods in Enzymology
VOLUME 17, NUMBER I, JANUARY 1999
CONTENTS
Regulation of mRNA Stability EDITORS: Allan Jacobson and Stuart W. Peltz
1 Editorial Allan Jacobson and Stuart W. Peltz
3 Analysis of mRNA Decay Pathways in Saccharomyces cerevisiae
Weihai He and Roy Parker
11 Transcriptional Pulsing Approaches for Analysis of mRNA Turnover in Mammalian
Cells Paul T. Loflin, Chyi-Ying A. Chen, Nianhua Xu, and Ann-Bin Shyu
21 An in Vitro System Using HeLa Cytoplasmic Extracts That Reproduces Regulated
mRNA Stability Lance P. Ford and Jeffrey Wilusz
28 Linking mRNA Turnover and Translation: Assessing the Polyribosomal Association of
mRNA Decay Factors and Degradative Intermediates David A. Mangus and Allan Jacobson
38 Assaying the Polyadenylation State of mRNAs Femando J. Salles, William G. Richards, and Sidney Strickland
46 Monitoring mRNA Decapping Activity
Shuang Zhang, Carol J. Williams, Michael Wormington, Audrey Stevens, and Stuart W. Peltz
52 Assays for Analyzing Exonucleases in Vitro
Jeff Ross
60 Characterization of mRNA Endonucleases Daniel R. Schoenberg and Kristopher S. Cunningham
74 Identification and Characterization of Proteins Binding A + U-Rich Elements
Gerald M. Wilson and Gary Brewer
84 Purification and RNA Binding Properties of the Polycytidylate-Binding Proteins aCP1
and aCP2 Megerditch Kiledjian, Nancy Day, and Panayiota Trifillis
_________________________________________________________
Methods A Companion to Methods in Enzymology
VOLUME 18, NUMBER 2, JUNE 1999
CONTENTS
Preparation and Use of Brain Slices
EDITOR: Avital Schurr
85 Editorial
Avital Schurr
86 Electrophysiological Recording from Brain Slices
Kelly J. Suter, Bret N. Smith, and F. Edward Dudek
91 Use of Intrinsic Optical Signals to Monitor Physiological Changes in Brain Tissue
Slices
P. G. Aitken, D. Fayuk, G. G. Somjen, and D. A. Turner
104 Optical Methods for Probing Mitochondrial Function in Brain Slices
Thomas J. Sick and Miguel A. Perez-Pinzon
109 Use of Brain Slices to Study Long-Term Potentiation and Depression as Examples of
Synaptic Plasticity
Timothy J. Teyler
117 Study of Cerebral Energy Metabolism Using the Rat Hippocampal Slice Preparation
Avital Schurr, Ralphiel S. Payne, James J. Miller,
and Benjamin M. Rigor
127 Autoradiographic Measurements of Protein Synthesis in Hippocampal Slices from
Rats and Guinea Pigs
Peter Lipton and Kathleen M. Raley-Susman
144 Use of Ascorbate in the Preparation and Maintenance of Brain Slices
Margaret E. Rice
150 Using Hippocampal Slices to Study How Aging Alters Ion Regulation in Brain Tissue
Eugene L. Roberts, Jr.
160 Coupling of Organotypic Brain Slice Cultures to Silicon-Based Arrays of Electrodes
Henrik Jahnsen, Bjame W. Kristensen, Pierre Thiebaud,
Jens Noraberg, Birthe Jakobsen, Marco Bove, Sergio Martinoia,
Milena Koudelka-Hep, Massimo Grattarola, and Jens Zimmer
Optical Imaging in Living Brain Slices
EDITOR: Rochelle D. Schwartz-Bloom
183 Editorial
Rochelle D. Schwartz-Bloom
185 Potential Sources of Intrinsic Optical Signals Imaged in Live Brain Slices
R. David Andrew, Cathryn R. Jarvis, and Akef S. Obeidat
197 Fluorescence Imaging of Changes in Intracellular Chloride in Living Brain Slices
Jon R. Inglefield and Rochelle D. Schwartz-Bloom
204 Simultaneous Optical Recording of Membrane Potential and Intracellular Calcium
from Brain Slices
Saurabh R. Sinha and Peter Saggau
215 Detecting Action Potentials in Neuronal Populations with Calcium Imaging
Diana Smetters, Ania Majewska, and Rafael Yuste
222 Confocal Imaging of Microglial Cell Dynamics in Hippocampal Slice Cultures
Michael E. Dailey and Marc Waite
231 Two-Photon Imaging in Living Brain Slices
Z. F. Mainen, M. Maletic-Savatic, S. H. Shi, Y. Hayashi, R. Malinow, and
kK.Svoboda
______________________________________________________________
Methods A Companion to Methods in Enzymology
VOLUME 17, NUMBER 4, APRIL 1999
CONTENTS
Editorial 273
Vincent J. Kidd
Database Search Strategies Used to Isolate Cell Death Proteins 275
Rajagopal Gururajan and Vincent J. Kidd
Isolation and Analysis of Components ofCD95 (APO-l/Fas) Death-Inducing Signaling 287
Complex
Carsten Scaffidi, Peter H. Kranimer, and Marcus E. Peter
Methods of Assaying Bcl-2 and Bax Family Proteins in Yeast 292
Qunii Xu, Juliane M. Jlirgensmeier, and John C. Reed
Use of Gene Knockouts in Cultured Cells to Study Apoptosis 305
Jill M. Lahti
Caspases: Preparation and Characterization 313
Henning R. Stennicke and Guy S. Salvesen
Irreversible Caspase Inhibitors: Tools for Studying Apoptosis 320
Joe C. Wu and Lawrence C. Fritz
Detection of DNA Fragmentation and Endonucleases in Apoptosis 329
P. Roy Walker, Julie Leblanc, Brandon Smith, Siyaram Pandey, and
Marianna Sikorska
Author Index for Volume 17 339
_____________________________________________________________
Methods A Companion to Methods in Enzymology
VOLUME 17, NUMBER 3, MARCH 1999
CONTENTS
201 Editorial
Arthur J. Sytkowski
202 Purification of Hematopoietic Stem Cells for Further Biological Study
Terry E. Thomas, Cindy L. Miller, and Connie J. Eaves
219 Monitoring Antisense Oligodeoxynucleotide Activity in Hematopoietic Cells
Deborah L. Sokol and Alan M. Gewirtz
231 Analysis of the Modulation ofTranscriptional Activity in Myelopoiesis and
Leukemogenesis
Gerhard Behre, Pu Zhang, Dong-Er Zhang, and Daniel G. Tenen
238 Thrombopoietin Signal Transduction: Studies from Cell Lines and Primary Cells
Jonathan G. Drachman, Ponlapot Rojnuckarin,
and Kenneth Kaushansky
250 Regulation of Megakaryocytopoiesis and Platelet Production by Tyrosine Kinases and
Tyrosine Phosphatases
Hava Avraham and Daniel J. Price
265 Isolation of Differentially Expressed Genes by Cloning Transcriptionally Active DNA
Fragments
Kunyuan Cui, Laurie Feidman, and Arthur J. Sytkowski
_____________________________________________________________
Methods
VOLUME: 18, NUMBER:1, MAY 1999
I Editorial
Timothy W. Nilsen
3 Identification of RNA-Protein Contacts within Functional Ribonucleoprotein Com-
plexes by RNA Site-Specific Labeling and UV Crosslinking
Robin Reed. and Maria Dolores Chiara
13 Construction of 4-Thiouridine Site-Specifically Substituted RNAs for Cross-Linking
Studies
Yi-Tao Yu
22 Site-Specific Derivatization of RNA with Photocrosslinkable Groups
Maria M. Konarska
29 Bridging Sulfur Substitutions in the Analysis of Pre-mRNA Splicing
Erik J. Sontheimer
38 'Nucleotide Analog Interference Mapping
Sean P. Ryder and Scott A. Strobel
51 Use of Circular Permutation and End Modification to Position Photoaffinity Probes for
Analysis of RNA Structure
Michael E. Harris and Eric L. Christian
60 Site-Specific Labeling of RNA with Fluorophores and Other Structural Probes
Peter Zhifeng Qin and Anna Marie Pyle
71 Thiol-Containing RNA for the Study of Structure and Function of Ribozymes
Snorri Th. Sigurdsson
78 Directed Cleavage of RNA with Protein-Tethered EDTA-Fe
Kathleen B. Hall and Robert 0. Fox
____________________________________________________________
Methods
VOLUME: 17, NUMBER: 2, FEBRUARY 1999
93 Editorial
William T. Garrard
95 Targeted Linearization of DNA in Vivo
Chien-Ping Liang and William T. Garrard
104 Isolation of Selected Chromatin Fragments from Yeast by Site-Specific Recombination
in Vivo
Athar Ansari, Tzu-Hao Cheng, and Marc R. Gartenberg
112 Psoralen Cross-Linking as Probe ofTorsional Tension and Topological Domain Size in
Vivo
Richard R. Sinden, Olga Bat, and Philip R. Kramer
125 Formaldehyde Cross-Linking for Studying Nucleosomal Dynamics
Vaughn Jackson
140 Histone Proteins in Vivo: Cell-Cycle-Dependent Physiological Effects of Exogenous
Linker Histones Incorporated into Physarum polycephalum
Christophe Thiriet and Jeffrey J. Hayes
151 Modeling Transcriptional Regulation Using Microinjection into Xenopus Oocytes
Carmen C. Robinett and Marietta Dunaway
161 Chromatin Assembly in Yeast Cell-Free Extracts
Michael C. Schultz
173 Functional Analysis of Chromatin Assembled in Synthetic Nuclei
Alison J. Crowe and Michelle Craig Barton
188 Electron Spectroscopic Imaging of Chromatin
David P. Bazett-Jones and Michael J. Hendzel
___________________________________________________________
METHODS
VOLUME 18, NUMBER 3, JULY 1999
CONTENTS
241 Editorial
Robert P. Erickson
244 Achieving Antisense Inhibition by Oligodeoxynucleotides Containing N(7)-Modified
2'-Deoxyguanosine Using Tumor Necrosis Factor Receptor Type 1
Joshua 0. Ojwang and Robert F. Rando
252 Controlling Gene Expression with 2-5A Antisense
Douglas W. Leaman and Hagen Cramer
266 Use of Triplex-Forming Oligonucleotides and Adenoviral Constructs for Studying the
Regulation of Gene Expression
A. T. M. Shamsul Hoque, lgor G. Panyutin, and Bruce J. Baum
273 Generation and Application of Asymmetric Hammerhead Ribozymes
Christian Hammann and Martin Tabler
281 In Situ Reverse Transcription for Detection of Hybridization between Oligonucleotides
and Their Intracellular Targets
Joan C. Politz and Robert H. Singer
286 Antisense Oligonucleotide Delivery with Polyhexylcyanoacrylate Nanoparticles as
Carriers
Andreas Zimmer
296 Inhibition of Oncogene Expression Using Vector-Generated RNA Antisense
Luke Whitesell, X, Liu, and R. Bagatell
304 Antisense Transgenics in Animals
Robert P. Erickson
311 Gene Identification by Shotgun Antisense
Richard H. Gomer
316 Utilization of Antisense Oligodeoxynucleotides with Embryonic Tissues in Culture
Raymond B, Runyan, Christopher C. Wendler, Laura A. Romano,
Angelique S. Boyer, John M. Dagle, and Daniel L. Weeks
Genetic Approaches to Eukaryotic Replication and Repair
EDITOR: Paul A. Fisher
327 Editorial
Paul A. Fisher
329 Minichromosome Maintenance as a Genetic Assay for Defects in DNA Replication
Bik K. Tye
335 Schizosaccharomyces pombe Replication and Repair Proteins: Proliferating Cell
Nuclear Antigen (PCNA)
Martha P. Arroyo and Teresa S.-F. Wang
349 Overexpression of Multisubumt Replication Factors in Yeast
Peter M. J. Burgers
356 Genetic Methods for Characterizing the cis-Acting Components of Yeast DNA Repli-
cation Origins
Joel A. Huberman
368 In Vitro DNA Replication in Yeast Nuclear Extracts
Philippe Pasero, Bernard P. Duncker, and Susan M, Gasser
377 DNA Repair Defects and Other Mustakes in Drosophila melanogaster
Daryl S, Henderson
401 Drosophila Replication and Repair Proteins: Proliferating Cell Nuclear Antigen
(PCNA)
Dmitry Ju. Mozzherin, Maeve McConnell, and Paul A. Fisher
407 Chorion Gene Amplification in Drosophila: A Model for Metazoan Origins of DNA
Replication and S-Phase Control
Brian R, Calvi and Allan C, Spradling
418 Physical and Genetic Mapping of Mammalian Replication Origins
Pieter A, Dijkwel and Joyce L. Hamlin
_______________________________________