Actions for Budding yeast : a laboratory manual
Budding yeast : a laboratory manual / edited by Brenda Andrews, Charles M. Boone, Trisha N. Davis, Stanley Fields
- Published
- Cold Spring Harbor, New York : Cold Spring Harbor Laboratory Press, [2016]
- Copyright Date
- ©2016
- Physical Description
- xvii, 706 pages : illustrations (chiefly color) ; 29 cm
- Additional Creators
- Andrews, Brenda, Boone, Charles M., Davis, Trisha, 1954-, Fields, Stanley, and Cold Spring Harbor Laboratory
- Contents
- Machine generated contents note: Introduction: Historical Evolution of Laboratory Strains of Saccharomyces cerevisiae -- Introduction: Classical Genetics with Saccharomyces cerevisiae / Edward J. Louis -- Introduction: Analysis of Recombination and Chromosome Structure during Yeast Meiosis / David C. Amberg / Daniel J. Burke -- Protocol 1 Analysis of Yeast Sporulation Efficiency, Spore Viability, and Meiotic Recombination on Solid Medium / G. Valentin Börner / Rita S. Cha -- Protocol 2 Induction and Analysis of Synchronous Meiotic Yeast Cultures / G. Valentin Börner / Rita S. Cha -- Protocol 3 Analysis of Meiotic Recombination and Homolog Interaction during Yeast Meiosis / G. Valentin Börner / Rita S. Cha -- Introduction: Investigating Filamentous Growth and Biofilm/Mat Formation in Budding Yeast / G. Valentin Börner / Rita S. Cha -- Protocol 1 The Plate-Washing Assay: A Simple Test for Filamentous Growth in Budding Yeast / Paul J. Cullen -- Protocol 2 Biofilm/Mat Assays for Budding Yeast / Paul J. Cullen -- Protocol 3 Evaluating Filamentous Yeast Growth at the Single-Cell Level / Paul J. Cullen -- Protocol 4 Evaluating the Activity of the Filamentous Growth Mitogen-Activated Protein Kinase Pathway in Yeast / Paull J. Cullen -- Introduction: Construction of Multifragment Plasmids by Homologous Recombination in Yeast / Paul J. Cullen -- Protocol 1 Rapid and Efficient Plasmid Construction by Homologous Recombination in Yeast / Iolanda van Leeuwen / Brenda Andrews / Charles Boone / Guihong Tan -- Introduction: Single-Molecule Analysis of Replicating Yeast Chromosomes / Jolanda van Leeuwen / Brenda Andrews / Charles Boone / Guihong Tan -- Protocol 1 Analysis of Replicating Yeast Chromosomes by DNA Combing / David Gallo / Gang Wang / Christopher M. Yip / Grant W. Brown -- Introduction: Measuring Chromatin Structure in Budding Yeast / David Gallo / Gang Wang / Christopher M. Yip / Grant W. Brown -- Protocol 1 Chromosome Conformation Capture (3C) in Budding Yeast / Jon-Matthew Belton and Job Dekker -- Protocol 2 Randomized Ligation Control for Chromosome Conformation Capture / Jon-Matthew Belton and Job Dekker -- Protocol 3 Chromosome Conformation Capture Carbon Copy (5C) in Budding Yeast / Jon-Matthew Belton and Job Dekker -- Protocol 4 Hi-C in Budding Yeast / Jon-Matthew Belton and Job Dekker -- Introduction: MX Cassettes for Knocking Out Genes in Yeast / Jon-Matthew Belton and Job Dekker -- Protocol 1 Introducing MX Cassettes into Saccharomyces cerevisiae / John H. McCusker -- Protocol 2 Popping Out MX Cassettes from Saccharomyces cerevisiae / John H. McCusker -- Introduction: Multipurpose Transposon-Insertion Libraries in Yeast / John H. McCusker -- Protocol 1 Using Yeast Transposon-Insertion Libraries for Phenotypic Screening and Protein Localization / Anuj Kumar -- Introduction: Functional Genomics Using the Saccharomyces cerevisiae Yeast Deletion Collections / Anuj Kumar -- Protocol 1 Functional Profiling Using the Yeast Deletion Collections / Corey Nislow / Lai Hong Wong / Amy Huei-Yi Lee / Guri Giaever -- Introduction: Deep Mutational Scanning: A Highly Parallel Method to Measure the Effects of Mutation on Protein Function / Corey Nislow / Lai Hong Wong / Amy Huei-Yi Lee / Guri Giaever -- Protocol 1 Deep Mutational Scanning: Library Construction, Functional Selection and High-Throughput Sequencing / Lea M. Starita / Stanley Fields -- Protocol 2 Deep Mutational Scanning: Calculating Enrichment Scores for Protein Variants from DNA Sequencing Output Files / Lea M. Starita / Stanley Fields -- Introduction: Examination and Disruption of the Yeast Cell Wall / Lea M. Starita / Stanley Fields -- Protocol 1 Fluorescent Labeling of Yeast Cell Wall Components / Hiroki Okada / Keiko Kono / Aaron M. Neiman / Yoshikazu Ohya -- Protocol 2 Assay for Spore Wall Integrity Using a Yeast Predator / Hiroki Okada / Yoshikazu Ohya -- Protocol 3 Local and Acute Disruption of the Yeast Cell Surface / Hiroki Okada / Aaron M. Neiman / Yoshikazu Ohya -- Introduction: Analyzing and Understanding Lipids of Yeast: A Challenging Endeavor / Keiko Kono / Hiroki Okada / Yoshikazu Ohya -- Protocol 1 Lipid Extraction from Yeast Cells / Sepp D. Kohlwein -- Protocol 2 Thin Layer Chromatography to Separate Phospholipids and Neutral Lipids from Yeast / Oskar L. Knittelfelder / Sepp D. Kohlwein -- Protocol 3 Derivatization and Gas Chromatography of Fatty Acids from Yeast / Oskar L. Knittelfelder / Sepp D. Kohlwein -- Protocol 4 Quantitative Analysis of Yeast Phospholipids and Sterols by High-Performance Liquid Chromatography-Evaporative Light-Scattering Detection / Oskar L. Knittelfelder / Sepp D. Kohlwein -- Introduction: Methods for Synchronization and Analysis of the Budding Yeast Cell Cycle / Oskar L. Knittelfelder / Sepp D. Kohlwein -- Protocol 1 Synchronization and Arrest of the Budding Yeast Cell Cycle Using Chemical and Genetic Methods / Adam P. Rosebrock -- Protocol 2 Synchronization of Budding Yeast by Centrifugal Elutriation / Adam P. Rosebrock -- Protocol 3 Analysis of the Budding Yeast Cell Cycle by Flow Cytometry / Adam P. Rosebrock -- Introduction: High-Throughput Microscopy-Based Screening in Saccharomyces cerevisiae / Adam P. Rosebrock -- Protocol 1 Liquid Growth of Arrayed Fluorescently Tagged Saccharomyces cerevisiae Strains for Live-Cell High-Throughput Microscopy Screens / Erin B. Styles / Helena Friesen / Charles Boone / Brenda Andrews -- Protocol 2 Quantification of Cell, Actin and Nuclear DNA Morphology with High-Throughput Microscopy and CalMorph / Michael J. Cox / Yolanda T. Chong / Charles Boone / Brenda Andrews -- Introduction: Single-Molecule Total Internal Reflection Fluorescence Microscopy / Hiroki Okada / Shinsuke Ohnuki / Yoshikazu Ohya -- Protocol 1 Coverslip Cleaning and Functionalization for Total Internal Reflection Fluorescence Microscopy / Emily M. Kudalkar / Trisha N. Davis / Charles L. Asbury -- Protocol 2 Preparation of Reactions for Imaging with Total Internal Reflection Fluorescence Microscopy / Emily M. Kudalkar / Yi Deng / Trisha N. Davis / Charles L. Asbury -- Protocol 3 Data Analysis for Total Internal Reflection Fluorescence Microscopy / Emily M. Kudalkar / Trisha N. Davis / Charles L. Asbury -- Introduction: Building Cell Structures in Three Dimensions: Electron Tomography Methods for Budding Yeast / Charles L. Asbury -- Protocol 1 Cryopreparation and Electron Tomography of Yeast Cells / Eileen T. O'Toole / Thomas H. Giddings Jr / Mark Winey -- Introduction: The Yeast Two-Hybrid System: A Tool for Mapping Protein-Protein Interactions / Eileen T. O'Toole / Thomas H. Giddings Jr / Mark Winey -- Protocol 1 Mapping Protein-Protein Interactions Using Yeast Two-Hybrid Assays / Jitender Mehla / J. Harry Caufield / Peter Uetz -- Introduction: Membrane Yeast Two-Hybrid (MYTH) Mapping of Full-Length Membrane Protein Interactions / Jitender Mehla / J. Harry Caufield / Peter Uetz -- Protocol 1 Generation and Validation of MYTH Baits: iMYTH and tMYTH Variants / Jamie Snider / Igor Stagljar -- Protocol 2 MYTH Screening: iMYTH and tMYTH Variants / Jamie Snider / Igor Stagljar -- Introduction: Protein-Fragment Complementation Assays for Large-Scale Analysis, Functional Dissection and Spatiotemporal Dynamic Studies of Protein-Protein Interactions in Living Cells / Jamie Snider / Igor Stagljar -- Protocol 1 The Dihydrofolate Reductase Protein-Fragment Complementation Assay: A Survival-Selection Assay for Large-Scale Analysis of Protein-Protein Interactions / Stephen W. Michnick / Christian R. Landry / Emmanuel D. Levy / Guillaume Diss / Po Hien Ear / Jacqueline Kowarzyk / Mohan K. Malleshaiah / Vincent Messier / Emmanuelle Tchekanda -- Protocol 2 Combining the Dihydrofolate Reductase Protein-Fragment Complementation Assay with Gene Deletions to Establish Genotype-to-Phenotype Maps of Protein Complexes and Interaction Networks / Stephen W. Michnick / Emmanuel D. Levy / Christian R. Landry / Jacqueline Kowarzyk / Vincent Messier -- Protocol 3 Dissecting the Contingent Interactions of Protein Complexes with the Optimized Yeast Cytosine Deaminase Protein-Fragment Complementation Assay / Guillaume Diss / Christian R. Landry -- Protocol 4 Real-Time Protein-Fragment Complementation Assays for Studying Temporal, Spatial and Spatiotemporal Dynamics of Protein-Protein Interactions in Living Cells / Po Hien Ear / Jacqueline Kowarzyk / Stephen W. Michnick -- Introduction: Protein Complex Purification by Affinity Capture / Mohan Malleshaiah / Emmanuelle Tchekanda / Stephen W. Michnick -- Protocol 1 Optimized Affinity Capture of Yeast Protein Complexes / John LaCava / Javier Fernandez-Martinez / Zhanna Hakhverdyan / Michael P. Rout -- Protocol 2 Native Elution of Yeast Protein Complexes Obtained by Affinity Capture / John LaCava / Javier Fernandez-Martinez / Zhanna Hakhverdyan / Michael P. Rout -- Protocol 3 Density Gradient Ultracentrifugation to Isolate Endogenous Protein Complexes after Affinity Capture / John LaCava / Javier Fernandez-Martinez / Michael P. Rout -- Introduction: Proteomic Analysis of Protein Posttranslational Modifications by Mass Spectrometry / Javier Fernandez-Martinez / John LaCava / Michael P. Rout -- Protocol 1 Enrichment of Phosphopeptides via Immobilized Metal Affinity Chromatography / Danielle L. Swaney / Judit Villén -- Protocol 2 Enrichment of Modified Peptides via Immunoaffinity Precipitation with Modification-Specific Antibodies / Danielle L. Swaney / Judit Villen -- Introduction: Protein Microarrays: Flexible Tools for Scientific Innovation / Danielle L. Swaney / Judit Villén -- Protocol 1 Characterization of Protein-Protein Interactions Using Protein Microarrays / Johnathan Neiswinger / Ijeoma Uzoma / Eric Cox / HeeSool Rho / Guang Song / Corry Paul / Jun Seop Jeong / Kuan-Yi Lu / Chien-Sheng Chen / Heng Zhu -- Protocol 2 Characterization of RNA-Binding Proteins Using Protein Microarrays / Corry Paul / HeeSool Rho / Johnathan Neiswinger / Heng Zhu -- and Contents note continued: Protocol 3 Characterization of Lipid-Protein Interactions Using Nonquenched Fluorescent Liposomal Nanovesicles and Yeast Proteome Microarrays / Guang Song / Johnathan Neiswinger / Heng Zhu -- Protocol 4 Posttranslational Modification Assays on Functional Protein Microarrays / Kuan-Yi Lu / Chien-Sheng Chen / Johnathan Neiswinger / Heng Zhu -- Introduction: Synthetic Genetic Arrays: Automation of Yeast Genetics / Jun Seop Jeong / HeeSool Rho / Heng Zhu / Eric Cox / Ijeoma Uzoma / Johnathan Neiswinger -- Protocol 1 Synthetic Genetic Array Analysis / Elena Kuzmin / Michael Costanzo / Brenda Andrews / Charles Boone -- Introduction: Systematic Mapping of Chemical-Genetic Interactions in Saccharomyces cerevisiae / Charles Boone / Brenda Andrews / Elena Kuzmin / Michael Costanzo -- Protocol 1 A High-Throughput Yeast Halo Assay for Bioactive Compounds / R. Scott Lokey / Robert P. St.Onge / Ronald W. Davis / Sundari Suresh / Corey Nislow / Guri Giaever / Molly Miranda / Walter Bray / Weihong Xu / Ulrich Schlecht -- Protocol 2 Identification of Chemical-Genetic Interactions via Parallel Analysis of Barcoded Yeast Strains / R. Scott Lokey / Walter Bray -- Introduction: Prions / Sundari Suresh / Ulrich Schlecht / Weihong Xu / Molly Miranda / Ronald W. Davis / Corey Nislow / Guri Giaever / Robert P. St.Onge -- Protocol 1 Genetic Methods for Studying Yeast Prions / Dmitry Kryndushkin / Herman K. Edskes / Frank P. Shewmaker / Reed B. Wickner -- Protocol 2 Priori Transfection of Yeast / Reed B. Wickner / Herman K. Edskes / Dmitry Kryndushkin / Frank P. Shewmaker -- Protocol 3 Isolation and Analysis of Prion and Amyloid Aggregates from Yeast Cells / Herman K. Edskes / Dmitry Kryndushkin / Frank P. Shewmaker / Reed B. Wickner -- Introduction: Gene-Centered Yeast One-Hybrid Assays / Dmitry Kryndushkin / Natalia Pripuzova / Frank P. Shewmaker -- Protocol 1 Generating Bait Strains for Yeast One-Hybrid Assays / Juan I. Fuxman Bass / John S. Reece-Hoyes / Albertha J.M. Walhout -- Protocol 2 Performing Yeast One-Hybrid Library Screens / Juan I. Fuxman Bass / John S. Reece-Hoyes / Albertha I.M. Walhout -- Protocol 3 Colony Lift Colorimetric Assay for β-Galactosidase Activity / Juan I. Fuxman Bass / John S. Reece-Hoyes / Albertha I.M. Walhout -- Protocol 4 Zymolase-Treatment and Polymerase Chain Reaction Amplification from Genomic and Plasmid Templates from Yeast / Juan I. Fuxman Bass / John S. Reece-Hoyes / Albertha I.M. Walhout -- Introduction: Transposon Calling Cards / Juan I. Fuxman Bass / John S. Reece-Hoyes / Albertha I.M. Walhout -- Protocol 1 Calling Card Analysis in Budding Yeast / David Mayhew / Robi D. Mitra -- Introduction: Transcription Factor-DNA Binding Motifs in Saccharomyces cerevisiae: Tools and Resources / David Mayhew / Robi D. Mitra -- Introduction: The Saccharomyces Genome Database: A Tool for Discovery / Joshua L. Schipper / Raluca M. Gordân -- Protocol 1 The Saccharomyces Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes / J. Michael Cherry -- Protocol 2 The Saccharomyces Genome Database: Advanced Searching Methods and Data Mining / J. Michael Cherry -- Protocol 3 The Saccharomyces Genome Database: Gene Product Annotation of Function, Process and Component / J. Michael Cherry -- Protocol 4 The Saccharomyces Genome Database: Exploring Genome Features and Their Annotations / J. Michael Cherry -- Introduction: BioGRID: A Resource for Studying Biological Interactions in Yeast / J. Michael Cherry -- 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 / Cara O'Donnell / Lindsay Ramage / Andrew Winter / Teresa Reguly / Adnane Sellam / Chris Stark / Lorrie Boucher / Kara Dolinski / Mike Tyers -- Protocol 1 Exploratory Analysis of Biological Networks through Visualization, Clustering and Functional Annotation in Cytoscape / 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 SeIlam / Chris Stark / Lorrie Boucher / Kara Dolinski / Mike Tyers -- Introduction: Metabolomics in Yeast / Anastasia Baryshnikova -- Protocol 1 Metabolite Extraction from Saccharomyces cerevisiae for Liquid, Chromatography-Mass Spectrometry / Amy A. Caudy / Michael Mülleder / Markus Raiser -- Protocol 2 A High-Throughput Method for the Quantitative Determination of Free Amino Acids in Saccharomyces cerevisiae by Hydrophilic Interaction Chromatography, Tandem Mass Spectrometry / Adam P. Rosebrock / Amy A. Caudy -- Protocol 3 Spectrophotometric Analysis of Ethanol and Glucose Concentrations in Yeast Culture Media / Michael Mülleder / Katharina Bluemlein / Markus Raiser -- Introduction: High-Throughput Yeast Strain Sequencing / Amy A. Caudy -- Protocol 1 Preparation of Yeast DNA Sequencing Libraries / Katja Schwartz / Gavin Sherlock -- Introduction: Budding Yeast Strains and Genotype-Phenotype Mapping / Gavin Sherlock / Katja Schwartz -- Protocol 1 Isolation and Laboratory Domestication of Natural Yeast Strains / Gianni Liti / Jonas Warringer / Anders Blomberg -- Protocol 2 Mapping Quantitative Trait Loci in Yeast / Gianni Liti / Jonas Warringer / Anders Blomberg -- Protocol 3 Yeast Reciprocal Hemizygosity to Confirm the Causality of a Quantitative Trait Loci-Associated Gene / Gianni Liti / Jonas Warringer / Anders Blomberg -- Introduction: Genetic Analysis of Complex Traits in Saccharomyces cerevisiae / Jonas Warringer / Gianni Liti / Anders Blomberg -- Protocol 1 Genetic Dissection of Heritable Traits in Yeast Using Bulk Segregant Analysis / Ian M. Ehrenreich / Paul M. Magwene -- Introduction: Chemostat Culture for Yeast Physiology and Experimental Evolution / Ian M. Ehrenreich / Paul M. Magwene -- Protocol 1 Assembly of a Mini-Chemostat Array / Maitreya J. Dunham / Emily O. Kerr / Aaron W. Miller / Celia Payen -- Protocol 2 Chemostat Culture for Yeast Physiology / Aaron W. Miller / Emily O. Kerr / Maitreya J. Dunham -- Protocol 3 Chemostat Culture for Yeast Experimental Evolution / Emily O. Kerr / Maitreya I. Dunham -- Protocol 1 Methods to Synthesize Large DNA Fragments for a Synthetic Yeast Genome / Celia Payen / Maitreya J. Dunham.
- Subject(s)
- ISBN
- 9781621820550 (hardcover)
1621820556 (hardcover)
9781621820567 (paperback)
1621820564 (paperback) - Bibliography Note
- Includes bibliographical references and index.
View MARC record | catkey: 17502797