Budding Yeast: A Laboratory Manual

by Boone, Charles; Andrews, Brenda; Fields, Stan; Davis, Trisha N.

• ISBN13: 9781621820567
• ISBN10: 1621820564
• Edition: Lab
• Format: Paperback
• Copyright: 2016-01-27
• Publisher: Cold Spring Harbor Laboratory Press
• More Book Details

Table of Contents

Preface

CHAPTER 1 Historical Evolution of Laboratory Strains of Saccharomyces cerevisiae
INTRODUCTION
Historical Evolution of Laboratory Strains of Saccharomyces cerevisiae
Edward J. Louis

CHAPTER 2 Classical Genetics with Saccharomyces cerevisiae
INTRODUCTION
Classical Genetics with Saccharomyces cerevisiae
David C. Amberg and Daniel J. Burke

CHAPTER 3 Analysis of Recombination and Chromosome Structure during Yeast Meiosis
INTRODUCTION
Analysis of Recombination and Chromosome Structure during Yeast Meiosis
G. Valentin Börner and Rita S. Cha
PROTOCOLS
1 Analysis of Yeast Sporulation Efficiency, Spore Viability, and Meiotic Recombination on Solid Medium
G. Valentin Börner and Rita S. Cha
2 Induction and Analysis of Synchronous Meiotic Yeast Cultures
G. Valentin Börner and Rita S. Cha
3 Analysis of Meiotic Recombination and Homolog Interaction during Yeast Meiosis
G. Valentin Börner and Rita S. Cha

CHAPTER 4 Investigating Filamentous Growth and Biofilm/Mat Formation in Budding Yeast
INTRODUCTION
Investigating Filamentous Growth and Biofilm/Mat Formation in Budding Yeast
Paul J. Cullen
PROTOCOLS
1 The Plate-Washing Assay: A Simple Test for Filamentous Growth in Budding Yeast
Paul J. Cullen
2 Biofilm/Mat Assays for Budding Yeast
Paul J. Cullen
3 Evaluating Filamentous Yeast Growth at the Single-Cell Level
Paul J. Cullen
4 Evaluating the Activity of the Filamentous Growth Mitogen-Activated Protein Kinase Pathway in Yeast
Paul J. Cullen

CHAPTER 5 Construction of Multi-fragment Plasmids by Homologous Recombination in Yeast
INTRODUCTION
Construction of Multi-fragment Plasmids by Homologous Recombination in Yeast
Jolanda S. van Leeuwen, Brenda J. Andrews, Charles Boone, and Guihong Tan
PROTOCOLS
1 Rapid and Efficient Plasmid Construction by Homologous Recombination in Yeast
Jolanda van Leeuwen, Brenda Andrews, Charles Boone, and Guihong Tan

CHAPTER 6 Single-Molecule Analysis of Replicating Yeast Chromosomes
INTRODUCTION
Single-Molecule Analysis of Replicating Yeast Chromosomes
David Gallo, Gang Wang, Christopher M. Yip, and Grant W. Brown
PROTOCOL
1 Analysis of Replicating Yeast Chromosomes by DNA Combing
David Gallo, Gang Wang, Christopher M. Yip, and Grant W. Brown

CHAPTER 7 Measuring Chromatin Structure in Budding Yeast
INTRODUCTION
Measuring Chromatin Structure in Budding Yeast
Jon-Matthew Belton and Job Dekker
PROTOCOLS
1 Chromosome Conformation Capture (3C) in Budding Yeast
Jon-Matthew Belton and Job Dekker
2 Randomized Ligation Control for Chromosome Conformation Capture
Jon-Matthew Belton and Job Dekker
3 Chromosome Conformation Capture Carbon Copy (5C) in Budding Yeast
Jon-Matthew Belton and Job Dekker
4 Hi-C in Budding Yeast
Jon-Matthew Belton and Job Dekker

CHAPTER 8 MX Cassettes for Knocking Out Genes in Yeast
INTRODUCTION
MX Cassettes for Knocking Out Genes in Yeast
John H. McCusker
PROTOCOLS
1 Introducing MX Cassettes into Saccharomyces cerevisiae
John H. McCusker
2 Popping Out MX Cassettes from Saccharomyces cerevisiae
John H. McCusker

CHAPTER 9 Multi-Purpose Transposon-Insertion Libraries in Yeast
INTRODUCTION
Multi-Purpose Transposon-Insertion Libraries in Yeast
Anuj Kumar
PROTOCOL
1 Using Yeast Transposon-Insertion Libraries for Phenotypic Screening and Protein Localization
Anuj Kumar

CHAPTER 10 Functional Genomics Using the Saccharomyces cerevisiae Yeast Deletion Collections
INTRODUCTION
Functional Genomics Using the Saccharomyces cerevisiae Yeast Deletion Collections
Corey Nislow, Lai Hong Wong, Amy Huei-Yi Lee, and Guri Giaever
PROTOCOL
1 Functional Profiling Using the Yeast Deletion Collections
Corey Nislow, Lai Hong Wong, Amy Huei-Yi Lee, and Guri Giaever

CHAPTER 11 Deep Mutational Scanning: A Highly Parallel Method to Measure the Effects of Mutation on Protein Function
INTRODUCTION
Deep Mutational Scanning: A Highly Parallel Method to Measure the Effects of Mutation on Protein Function
Lea M. Starita and Stanley Fields
PROTOCOLS
1 Deep Mutational Scanning: Library Construction, Functional Selection, and High-Throughput Sequencing
Lea M. Starita and Stanley Fields
2 Deep Mutational Scanning: Calculating Enrichment Scores for Protein Variants from DNA Sequencing Output Files
Lea M. Starita and Stanley Fields

CHAPTER 12 Examination and Disruption of the Yeast Cell Wall
INTRODUCTION
Examination and Disruption of the Yeast Cell Wall
Hiroki Okada, Keiko Kono, Aaron M. Neiman, and Yoshikazu Ohya
PROTOCOLS
1 Fluorescent Labeling of Yeast Cell Wall Components
Hiroki Okada and Yoshikazu Ohya
2 Assay for Spore Wall Integrity Using a Yeast Predator
Hiroki Okada, Aaron M. Neiman, and Yoshikazu Ohya
3 Local and Acute Disruption of the Yeast Cell Surface
Keiko Kono, Hiroki Okada, and Yoshikazu Ohya

CHAPTER 13 Analyzing and Understanding Lipids of Yeast: A Challenging Endeavor
INTRODUCTION
Analyzing and Understanding Lipids of Yeast: A Challenging Endeavor
Sepp D. Kohlwein
PROTOCOLS
1 Lipid Extraction from Yeast Cells
Oskar L. Knittelfelder and Sepp D. Kohlwein
2 Thin Layer Chromatography to Separate Phospholipids and Neutral Lipids from Yeast
Oskar L. Knittelfelder and Sepp D. Kohlwein
3 Derivatization and Gas Chromatography of Fatty Acids from Yeast
Oskar L. Knittelfelder and Sepp D. Kohlwein
4 Quantitative Analysis of Yeast Phospholipids and Sterols by High-Performance Liquid Chromatography-Evaporative Light-Scattering Detection
Oskar L. Knittelfelder and Sepp D. Kohlwein

CHAPTER 14 Methods for Synchronization and Analysis of the Budding Yeast Cell Cycle
INTRODUCTION
Methods for Synchronization and Analysis of the Budding Yeast Cell Cycle
Adam P. Rosebrock
PROTOCOLS
1 Synchronization and Arrest of the Budding Yeast Cell Cycle Using Chemical and Genetic Methods
Adam P. Rosebrock
2 Synchronization of Budding Yeast by Centrifugal Elutriation
Adam P. Rosebrock
3 Analysis of the Budding Yeast Cell Cycle by Flow Cytometry
Adam P. Rosebrock

CHAPTER 15 High Throughput Microscopy-based Screening in Saccharomyces cerevisiae
INTRODUCTION
High Throughput Microscopy-based Screening in Saccharomyces cerevisiae
Erin B. Styles, Helena Friesen, Charles Boone, and Brenda Andrews
PROTOCOLS
1 Liquid Growth of Arrayed Fluorescently Tagged Saccharomyces cerevisiae Strains for Live-Cell High-Throughput Microscopy Screens
Michael J. Cox, Yolanda T. Chong, Charles Boone, and Brenda Andrews
2 Quantification of Cell, Actin, and Nuclear DNA Morphology with High-Throughput Microscope and CalMorph
Hiroki Okada, Shinsuke Ohnuki, and Yoshikazu Ohya

CHAPTER 16 Single-Molecule Total Internal Reflection Fluorescence Microscopy
INTRODUCTION
Single-Molecule Total Internal Reflection Fluorescence Microscopy
Emily M. Kudalkar, Trisha N. Davis, and Charles L. Asbury
PROTOCOLS
1 Coverslip Cleaning and Functionalization for Total Internal Reflection Fluorescence Microscopy
Emily M. Kudalkar, Yi Deng, Trisha N. Davis, and Charles L. Asbury
2 Preparation of Reactions for Imaging with Total Internal Reflection Fluorescence Microscopy
Emily M. Kudalkar, Trisha N. Davis, and Charles L. Asbury
3 Data Analysis for Total Internal Reflection Fluorescence Microscopy
Charles L. Asbury

CHAPTER 17 Building Cell Structures in Three Dimensions: Electron Tomography Methods for Budding Yeast
INTRODUCTION
Building Cell Structures in Three Dimensions: Electron Tomography Methods for Budding Yeast
Eileen T. O'Toole, Thomas H. Giddings, Jr., and Mark Winey
PROTOCOL
1 Cryopreparation and Electron Tomography of Yeast Cells
Eileen T O'Toole, Thomas H. Giddings, Jr., and Mark Winey

CHAPTER 18 The Yeast Two-Hybrid System: A Tool for Mapping Protein-Protein Interactions
INTRODUCTION
The Yeast Two-Hybrid System: A Tool for Mapping Protein-Protein Interactions
Jitender Mehla, J. Harry Caufield, and Peter Uetz
PROTOCOL
1 Mapping Protein-Protein Interactions Using Yeast Two-Hybrid Assays
Jitender Mehla, J. Harry Caufield, and Peter Uetz

CHAPTER 19 Membrane Yeast Two-Hybrid (MYTH) Mapping of Full-length Membrane Protein Interactions
INTRODUCTION
Membrane Yeast Two-Hybrid (MYTH) Mapping of Full-length Membrane Protein Interactions
Jamie Snider and Igor Stagljar
PROTOCOLS
1 Generation and Validation of MYTH Baits: iMYTH and tMYTH Variants
Jamie Snider and Igor Stagljar
2 MYTH Screening: iMYTH and tMYTH Variants
Jamie Snider and Igor Stagljar

CHAPTER 20 Protein-Fragment Complementation Assays for Large-Scale Analysis, Functional Dissection, and Spatiotemporal Dynamic Studies of Protein-Protein Interactions in Living Cells
INTRODUCTION
Protein-Fragment Complementation Assays for Large-Scale Analysis, Functional Dissection, and Spatiotemporal Dynamic Studies of Protein-Protein Interactions in Living Cells
Stephen W. Michnick, Christian R. Landry, Emmanuel D. Levy, Guillaume Diss, Po Hien Ear, Jacqueline Kowarzyk, Mohan K. Malleshaiah, Vincent Messier, and Emmanuelle Tchekanda
PROTOCOLS
1 The Dihydrofolate Reductase Protein-Fragment Complementation Assay: A Survival-Selection Assay for Large-Scale Analysis of Protein-Protein Interactions
Stephen W. Michnick, Emmanuel D. Levy, Christian R. Landry, Jacqueline Kowarzyk, and Vincent Messier
2 Combining the Dihydrofolate Reductase Protein-Fragment Complementation Assay with Gene Deletions to Establish Genotype-to-Phenotype Maps of Protein Complexes and Interaction Networks
Guillaume Diss and Christian R. Landry
3 Dissecting the Contingent Interactions of Protein Complexes with the Optimized Yeast Cytosine Deaminase Protein-Fragment Complementation Assay
Po Hien Ear, Jacqueline Kowarzyk, and Stephen W. Michnick
4 Real-Time Protein-Fragment Complementation Assays for Studying Temporal, Spatial, and Spatiotemporal Dynamics of Protein-Protein Interactions in Living Cells
Mohan Malleshaiah, Emmanuelle Tchekanda, and Stephen W. Michnick

CHAPTER 21 Protein Complex Purification by Affinity Capture
INTRODUCTION
Protein Complex Purification by Affinity Capture
John LaCava, Javier Fernandez-Martinez, Zhanna Hakhverdyan, and Michael P. Rout
PROTOCOLS
1 Optimized Affinity Capture of Yeast Protein Complexes
John LaCava, Javier Fernandez-Martinez, Zhanna Hakhverdyan, and Michael P. Rout
2 Native Elution of Yeast Protein Complexes Obtained by Affinity Capture
John LaCava , Javier Fernandez-Martinez, and Michael P. Rout
3 Density Gradient Ultracentrifugation to Isolate Endogenous Protein Complexes After Affinity Capture
Javier Fernandez-Martinez, John LaCava , and Michael P. Rout

CHAPTER 22 Proteomic Analysis of Protein Posttranslational Modifications by Mass Spectrometry
INTRODUCTION
Proteomic Analysis of Protein Posttranslational Modifications by Mass Spectrometry
Danielle L Swaney and Judit Villen
PROTOCOLS
1 Enrichment of Phosphopeptides via Immobilized Metal Affinity Chromatography
Danielle L Swaney and Judit Villen
2 Enrichment of Modified Peptides via Immunoaffinity Precipitation with Modification-Specific Antibodies
Danielle L Swaney and Judit Villen

CHAPTER 23 Protein Microarrays: Flexible Tools for Scientific Innovation
INTRODUCTION
Protein Microarrays: Flexible Tools for Scientific Innovation
Johnathan P Neiswinger, Ijeoma Uzoma, Eric Cox, HeeSool Rho, Guang Song, Corry Paul, Jun Seop Jeong, Kuan-Yi Lu, Chien-Sheng Chen, and Heng Zhu
PROTOCOLS
1 Characterization of Protein-Protein Interactions Using Protein Microarrays
Corry Paul, HeeSool Rho, Johnathan Neiswinger, and Heng Zhu
2 Characterization of RNA-Binding Proteins Using Protein Microarrays
Guang Song, Johnathan Neiswinger, and Heng Zhu
3 Characterization of Lipid-Protein Interactions Using Nonquenched Fluorescent Liposomal Nanovesicles and Yeast Proteome Microarrays
Kuan-Yi Lu, Chien-Sheng Chen, Johnathan Neiswinger, and Heng Zhu
4 Posttranslational Modification Assays on Functional Protein Microarrays
Johnathan Neiswinger, Ijeoma Uzoma, Eric Cox, HeeSool Rho, Jun Seop Jeong, and Heng Zhu

CHAPTER 24 Synthetic Genetic Arrays: Automation of Yeast Genetics
INTRODUCTION
Synthetic Genetic Arrays: Automation of Yeast Genetics
Elena Kuzmin, Michael Costanzo, Brenda Andrews, and Charles Boone
PROTOCOL
1 Synthetic Genetic Array Analysis
Elena Kuzmin, Michael Costanzo, Brenda Andrews, and Charles Boone

CHAPTER 25 Systematic Mapping of Chemical-Genetic Interactions in Saccharomyces cerevisiae
INTRODUCTION
Systematic Mapping of Chemical-Genetic Interactions in Saccharomyces cerevisiae
Sundari Suresh, Ulrich Schlecht, Weihong Xu, Walter Bray, Molly Miranda, Ronald W. Davis, Corey Nislow, Guri Giaever, R. Scott Lokey, and Robert P. St.Onge
PROTOCOLS
1 A High-Throughput Yeast Halo Assay for Bioactive Compounds
Walter Bray and R. Scott Lokey
2 Identification of Chemical-Genetic Interactions via Parallel Analysis of Barcoded Yeast Strains
Sundari Suresh, Ulrich Schlecht, Weihong Xu, Molly Miranda, Ronald W. Davis, Corey Nislow, Guri Giaever, and Robert P. St.Onge

CHAPTER 26 Prions
INTRODUCTION
Prions
Dmitry Kryndushkin, Herman K. Edskes, Frank P. Shewmaker, and Reed B. Wickner
PROTOCOLS
1 Genetic Methods for Studying Yeast Prions
Reed B. Wickner, Herman K. Edskes, Dmitry Kryndushkin, and Frank P. Shewmaker
2 Prion Transfection of Yeast
Herman K. Edskes, Dmitry Kryndushkin, Frank P. Shewmaker, and Reed B. Wickner
3 Isolation and Analysis of Prion and Amyloid Aggregates from Yeast Cells
Dmitry Kryndushkin, Natalia Pripuzova, and Frank P. Shewmaker

CHAPTER 27 Gene-Centered Yeast One-Hybrid Assays
INTRODUCTION
Gene-Centered Yeast One-Hybrid Assays
Juan I. Fuxman Bass, John S. Reece-Hoyes, and Albertha J.M. Walhout
PROTOCOLS
1 Generating Bait Strains for Yeast One-Hybrid Assays
Juan I. Fuxman Bass, John S. Reece-Hoyes, and Albertha J.M. Walhout
2 Performing Yeast One-Hybrid Library Screens
Juan I. Fuxman Bass, John S. Reece-Hoyes, and Albertha J.M. Walhout
3 Colony Lift Colorimetric Assay for ß-Galactosidase Activity
Juan I. Fuxman Bass, John S. Reece-Hoyes, and Albertha J.M. Walhout
4 Zymolase-Treatment and Polymerase Chain Reaction Amplification from Genomic and Plasmid Templates from Yeast
Juan I. Fuxman Bass, John S. Reece-Hoyes, and Albertha J.M. Walhout

CHAPTER 28 Transposon Calling Cards
INTRODUCTION
Transposon Calling Cards
David Mayhew and Robi D. Mitra
PROTOCOL
1 Calling Card Analysis in Budding Yeast
David Mayhew and Rob D. Mitra

CHAPTER 29 Transcription Factor-DNA Binding Motifs in Saccharomyces cerevisiae: Tools and Resources
INTRODUCTION
Transcription Factor-DNA Binding Motifs in Saccharomyces cerevisiae: Tools and Resources
Joshua L. Schipper and Raluca M. Gordan

CHAPTER 30 The Saccharomyces Genome DatabaseA Tool for Discovery
INTRODUCTION
The Saccharomyces Genome Database--A Tool for Discovery
J. Michael Cherry
PROTOCOLS
1 The Saccharomyces Genome Database--Exploring Biochemical Pathways and Mutant Phenotypes
J. Michael Cherry
2 The Saccharomyces Genome Database--Advanced Searching Methods and Data Mining
J. Michael Cherry
3 The Saccharomyces Genome Database--Gene Product Annotation of Function, Process, and Component
J. Michael Cherry
4 The Saccharomyces Genome Database--Exploring Genome Features and Their Annotations
J. Michael Cherry

CHAPTER 31 BioGRID: A Tool for Studying Biological Interactions in Yeast
INTRODUCTION
BioGRID: A Tool for Studying Biological Interactions in Yeast
Rose Oughtred, Andrew Chatr-aryamontri, Bobby-Joe Breitkreutz, Christie S. Chang, Jennifer M. Rust, Chandra L. Theesfeld, Sven Heinicke, Ashton Breitkreutz, Daici Chen, Jodi Hirschman, Nadine Kolas, Michael S. Livstone, Julie Nixon, Lara O'Donnell, Lindsay Ramage, Andrew Winter, Teresa Reguly, Adnane Sellam, Chris Stark, Lorrie Boucher, Kara Dolinski, and Mike Tyers
PROTOCOL
1 Use of the BioGRID Database for Analysis of Yeast Protein and Genetic Interactions
Rose Oughtred, Andrew Chatr-aryamontri, Bobby-Joe Breitkreutz, Christie S. Chang, Jennifer M. Rust, Chandra L. Theesfeld, Sven Heinicke, Ashton Breitkreutz, Daici Chen, Jodi Hirschman, Nadine Kolas, Michael S. Livstone, Julie Nixon, Lara O'Donnell, Lindsay Ramage, Andrew Winter, Teresa Reguly, Adnane Sellam, Chris Stark, Lorrie Boucher, Kara Dolinski, and Mike Tyers

CHAPTER 32 Exploratory Analysis of Biological Networks Through Visualization, Clustering, and Functional Annotation in Cytoscape
PROTOCOL
Exploratory Analysis of Biological Networks Through Visualization, Clustering, and Functional Annotation in Cytoscape
Anastasia Baryshnikova

CHAPTER 33 Metabolomics in Yeast
INTRODUCTION
Metabolomics in Yeast
Amy A. Caudy, Michael Mulleder, and Markus Ralser
PROTOCOLS
1 Metabolite Extraction from Saccharomyces cerevisiae for Liquid Chromatography-Mass Spectrometry
Adam P. Rosebrock and Amy A. Caudy
2 A High-Throughput Method for the Quantitative Determination of Free Amino Acids in Saccharomyces cerevisiae by Hydrophilic Interaction Chromatography-Tandem Mass Spectrometry
Michael Mulleder, Katharina Bluemlein, and Markus Ralser
3 Spectrophotometric Analysis of Ethanol and Glucose Concentrations in Yeast Culture Media
Amy A. Caudy

CHAPTER 34 High-Throughput Yeast Strain Sequencing
INTRODUCTION
High-Throughput Yeast Strain Sequencing
Katja Schwartz and Gavin Sherlock
PROTOCOL
1 Preparation of Yeast DNA Sequencing Libraries
Katja Schwartz and Gavin Sherlock

CHAPTER 35 Budding Yeast Strains and Genotype-Phenotype Mapping
INTRODUCTION
Budding Yeast Strains and Genotype-Phenotype Mapping
Gianni Liti, Jonas Warringer, and Anders Blomberg
PROTOCOLS
1 Isolation and Laboratory Domestication of Natural Yeast Strains
Gianni Liti, Jonas Warringer, and Anders Blomberg
2 Mapping Quantitative Trait Loci in Yeast
Gianni Liti, Jonas Warringer, and Anders Blomberg
3 Yeast Reciprocal Hemizygosity to Confirm the Causality of a QTL-Associated Gene
Jonas Warringer, Gianni Liti, and Anders Blomberg

CHAPTER 36 Genetic Analysis of Complex Traits in Saccharomyces cerevisiae
INTRODUCTION
Genetic Analysis of Complex Traits in Saccharomyces cerevisiae
Ian M. Ehrenreich and Paul M. Magwene
PROTOCOL
Genetic Dissection of Heritable Traits in Yeast Using Bulk Segregant Analysis
Ian M. Ehrenreich and Paul M. Magwene

CHAPTER 37 Chemostat Culture for Yeast Physiology and Experimental Evolution
INTRODUCTION
Chemostat Culture for Yeast Physiology and Experimental Evolution
Maitreya J. Dunham, Emily O. Kerr, Aaron W. Miller, and Celia Payen
PROTOCOLS
1 Assembly of a Mini-Chemostat Array
Aaron W. Miller, Emily O. Kerr, and Maitreya J. Dunham
2 Chemostat Culture for Yeast Physiology
Emily O. Kerr and Maitreya J. Dunham
3 Chemostat Culture for Yeast Experimental Evolution
Celia Payen and Maitreya J. Dunham

CHAPTER 38 Methods to Synthesize Large DNA Fragments for a Synthetic Yeast Genome
PROTOCOL
Methods to Synthesize Large DNA Fragments for a Synthetic Yeast Genome
Yizhi Cai and Junbiao Dai

APPENDIX General Safety and Hazardous Material Information

INDEX