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E-grāmata: Guide to Yeast Genetics: Functional Genomics, Proteomics, and Other Systems Analysis

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Volume editor , Volume editor (University of California, San Francisco, U.S.A.), Volume editor (Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, U.S.A.)
  • Formāts: EPUB+DRM
  • Sērija : Methods in Enzymology
  • Izdošanas datums: 27-Feb-2010
  • Izdevniecība: Academic Press Inc
  • Valoda: eng
  • ISBN-13: 9780123751737
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Guide to Yeast Genetics: Functional Genomics, Proteomics, and Other Systems AnalysisPalielināt
  • Formāts: EPUB+DRM
  • Sērija : Methods in Enzymology
  • Izdošanas datums: 27-Feb-2010
  • Izdevniecība: Academic Press Inc
  • Valoda: eng
  • ISBN-13: 9780123751737
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This fully updated edition of the best-selling three-part Methods in Enzymology series, Guide to Yeast Genetics and Molecular Cell Biology is specifically designed to meet the needs of graduate students, postdoctoral students, and researchers by providing all the up-to-date methods necessary to study genes in yeast. Procedures are included that enable newcomers to set up a yeast laboratory and to master basic manipulations. This volume serves as an essential reference for any beginning or experienced researcher in the field.



Provides up-to-date methods necessary to study genes in yeast.
Includes proceedures that enable newcomers to set up a yeast laboratory and to master basic manipulations.
This volume serves as an essential reference for any beginning or experienced researcher in the field.

This fully updated edition of the bestselling three-part Methods in Enzymology series, Guide to Yeast Genetics and Molecular Cell Biology is specifically designed to meet the needs of graduate students, postdoctoral students, and researchers by providing all the up-to-date methods necessary to study genes in yeast. Procedures are included that enable newcomers to set up a yeast laboratory and to master basic manipulations. This volume serves as an essential reference for any beginning or experienced researcher in the field.



Provides up-to-date methods necessary to study genes in yeast.
Includes proceedures that enable newcomers to set up a yeast laboratory and to master basic manipulations.
This volume serves as an essential reference for any beginning or experienced researcher in the field.

Recenzijas

Praise for the first edition:"...this is an excellent collection of methods that is certain to be an important handbook for yeast researchers." --Will Prinz, National Institutes of Health for ANALYTICAL BIOCHEMISTRY (April 2003)

Papildus informācija

An essential volume featuring updated, time-tested methods dealing with genes in yeast
Contributors xv
Preface xxiii
Volumes in Series xxv
Section I. Functional Genomics
1(142)
Analysis of Gene Function Using DNA Microarrays
3(16)
Andrew P. Capaldi
Introduction and Experimental Design
4(4)
Methods
8(11)
References
16(3)
An Introduction to Microarray Data Analysis and Visualization
19(32)
Gregg B. Whitworth
Introduction
20(3)
Experimental Design: Single-Sample Versus Competitive Hybridization
23(3)
Image Analysis
26(3)
Preprocessing
29(9)
Visualizing Data Using Cluster Analysis
38(3)
Assessing the Statistical Evidence for Differential Expression
41(1)
Exploring Gene Sets
42(2)
Managing Data
44(7)
Acknowledgments
49(1)
References
49(2)
Genome-Wide Approaches to Monitor Pre-mRNA Splicing
51(26)
Maki Inada
Jeffrey A. Pleiss
Introduction
52(1)
Microarray Design
53(3)
Sample Preparation
56(12)
Microarray Data Collection
68(1)
Microarray Data Analysis
69(3)
Future Methodologies
72(5)
Acknowledgments
73(1)
References
74(3)
ChIP-Seq: Using High-Throughput DNA Sequencing for Genome-Wide Identification of Transcription Factor Binding Sites
77(28)
Philippe Lefrancois
Wei Zheng
Michael Snyder
Introduction
78(3)
Protocols
81(12)
Sequencing Data Management
93(1)
Genome Analysis Pipeline
94(1)
Examining Data Quality and Parsing Barcoded Data
95(1)
Visualization in Genome Browser
95(7)
Conclusion and Future Directions
102(3)
Acknowledgments
102(1)
References
102(3)
Genome-Wide Mapping of Nucleosomes in Yeast
105(14)
Oliver J. Rando
Introduction
105(2)
Isolation of Mononucleosomal DNA
107(5)
Variation in Titration Level Used for Nucleosome Purification
112(1)
Labeling of Mononucleosomal DNA for Tiling Microarray Analysis
113(2)
Generation of Nucleosomal DNA Libraries for Deep Sequencing
115(4)
References
117(2)
Genome-Wide Translational Profiling by Ribosome Footprinting
119(24)
Nicholas T. Ingolia
Introduction
120(1)
Ribosome Footprint Generation and Purification
121(7)
Sequencing Library Preparation
128(5)
Data Analysis
133(5)
Solutions and Common Procedures
138(5)
Acknowledgments
140(1)
References
140(3)
Section II. Systematic Genetic Analysis
143(114)
Synthetic Genetic Array (SGA) Analysis in Saccharomyces cerevisiae and Schizosaccharomyces pombe
145(36)
Anastasia Baryshnikova
Michael Costanzo
Scott Dixon
Franco J. Vizeacoumar
Chad L. Myers
Brenda Andrews
Charles Boone
Introduction
146(2)
Methodology
148(20)
Media and Stock Solutions
168(3)
Applications of SGA Methodology
171(10)
References
176(5)
Making Temperature-Sensitive Mutants
181(24)
Shay Ben-Aroya
Xuewen Pan
Jef D. Boeke
Philip Hieter
Introduction
182(1)
Diploid Shuffle---Plasmid Method
183(11)
Diploid Shuffle---Chromosome Method
194(8)
Perspectives
202(3)
References
203(2)
Quantitative Genetic Interaction Mapping Using the E-MAP Approach
205(28)
Sean R. Collins
Assen Roguev
Nevan J. Krogan
Introduction
206(3)
Selection of Mutations for Genetic Analysis
209(2)
Generation and Measurement of Double Mutant Strains
211(10)
Data Processing and Computation of Scores
221(3)
Extraction of Biological Hypotheses
224(5)
Perspective
229(4)
References
229(4)
Exploring Gene Function and Drug Action Using Chemogenomic Dosage Assays
233(24)
Elke Ericson
Shawn Hoon
Robert P. St. Onge
Guri Giaever
Corey Nislow
Introduction
234(3)
Methodology
237(15)
Experimental Considerations
252(1)
Perspectives
253(4)
Acknowledgments
254(1)
References
254(3)
Section III. Proteomics
257(170)
Yeast Expression Proteomics by High-Resolution Mass Spectrometry
259(22)
Tobias C. Walther
Jesper V. Olsen
Matthias Mann
Introduction
260(1)
Background, Methods, and Applications
261(11)
Protocols
272(9)
Acknowledgments
278(1)
References
278(3)
High-Quality Binary Interactome Mapping
281(36)
Matija Dreze
Dario Monachello
Claire Lurin
Michael E. Cusick
David E. Hill
Marc Vidal
Pascal Braun
Introduction
282(1)
High-Quality Binary Interactome Mapping
283(9)
High-Throughput Y2H Pipeline
292(17)
Validation Using Orthogonal Binary Interaction Assays
309(3)
Conclusion
312(5)
Acknowledgments
312(1)
References
313(4)
Quantitative Analysis of Protein Phosphorylation on a System-Wide Scale by Mass Spectrometry-Based Proteomics
317(18)
Bernd Bodenmiller
Ruedi Aebersold
Introduction
318(1)
Protocols
319(16)
Acknowledgments
331(1)
References
332(3)
A Toolkit of Protein-Fragment Complementation Assays for Studying and Dissecting Large-Scale and Dynamic Protein-Protein Interactions in Living Cells
335(34)
Stephen W. Michnick
Po Hien Ear
Christian Landry
Mohan K. Malleshaiah
Vincent Messier
Introduction
336(1)
General Considerations in Using PCA
337(2)
DHFR PCA Survival-Selection for Large-Scale Analysis of PPIs
339(9)
A Life and Death Selection PCA Based on the Prodrug-Converting Cytosine Deaminase for Dissection of PPIs
348(8)
Visualizing the Localization of PPIs with GFP Family Fluorescent Protein PCAs
356(5)
Studying Dynamics of PPIs with Luciferase Reporter PCAs
361(8)
References
366(3)
Yeast Lipid Analysis and Quantification by Mass Spectrometry
369(24)
Xue Li Guan
Isabelle Riezman
Markus R. Wenk
Howard Riezman
Introduction
370(3)
Methods
373(20)
Acknowledgments
389(1)
References
389(4)
Mass Spectrometry-Based Metabolomics of Yeast
393(34)
Christopher A. Crutchfield
Wenyun Lu
Eugene Melamud
Joshua D. Rabinowitz
Introduction
394(1)
LC-MS Basics
395(1)
Experimental Design
395(3)
Strains
398(1)
Culture Conditions
398(4)
Metabolite Extraction
402(3)
Chemical Derivatization of Metabolites
405(1)
LC-MS for Mixture Analysis
406(1)
Liquid Chromatography
407(3)
Electrospray lonization
410(1)
Mass Spectrometry
411(4)
Targeted Data Analysis
415(3)
Untargeted Data Analysis
418(3)
Future Outlook
421(6)
References
422(5)
Section IV. Systems Analysis
427(106)
Imaging Single mRNA Molecules in Yeast
429(18)
Hyun Youk
Arjun Raj
Alexander van Oudenaarden
Introduction
429(3)
RNA Fish Protocol
432(12)
Example: STL1 mRNA Detection in Response to NaCl Shock
444(1)
Conclusions
445(2)
Acknowledgments
445(1)
References
445(2)
Reconstructing Gene Histories in Ascomycota Fungi
447(40)
Ilan Wapinski
Aviv Regev
Introduction
448(3)
Synergy
451(8)
Evaluating Orthogroup Quality
459(7)
Biological Analysis of Gene Histories
466(12)
Analysis of Paralogous Genes
478(2)
Discussion and General Applicability
480(7)
References
482(5)
Experimental Evolution in Yeast: A Practical Guide
487(22)
Maitreya J. Dunham
Introduction
488(1)
Experiment Rationale
488(2)
Experimental Evolution Approaches
490(3)
Experimental Design
493(3)
Practical Considerations
496(4)
Analysis Techniques
500(2)
Example Protocol
502(2)
Conclusions
504(5)
Acknowledgments
505(1)
References
505(4)
Enhancing Stress Resistance and Production Phenotypes Through Transcriptome Engineering
509(24)
Felix H. Lam
Franz S. Hartner
Gerald R. Fink
Gregory Stephanopoulos
Introduction
510(1)
Transcription Factor Selection
511(1)
Plasmid Library Construction
512(7)
Assessment of Phenotypic Diversity
519(5)
Selecting for Phenotypes of Interest
524(4)
Validation
528(1)
Concluding Remarks
529(4)
References
530(3)
Section V. Advances in Cytology/Biochemistry
533(202)
Visualizing Yeast Chromosomes and Nuclear Architecture
535(34)
Peter Meister
Lutz R. Gehlen
Elisa Varela
Veronique Kalck
Susan M. Gasser
Introduction
536(1)
Strain Constructions and Image Acquisition for Nuclear Architecture Analysis in Living Cells
537(10)
Data Analysis and Quantitative Measurements
547(10)
If and FISH on Fixed Samples
557(12)
References
566(3)
Quantitative Localization of Chromosomal Loci by Immunofluorescence
569(12)
Donna Garvey Brickner
William Light
Jason H. Brickner
Yeast Strain Construction
570(2)
Immunofluorescence
572(1)
Fixing Cells
573(1)
Spheroplasting
574(1)
Preparing Slides
574(1)
Antibody Incubations
575(1)
Mounting and Storage of Slides
575(1)
Microscopy and Analysis
576(5)
Acknowledgments
578(1)
References
579(2)
Spinning-Disk Confocal Microscopy of Yeast
581(22)
Kurt Thorn
Introduction
582(1)
Building a Spinning-Disk Confocal Microscope
583(11)
Sample Preparation
594(9)
Acknowledgments
600(1)
References
600(3)
Correlative GFP-Immunoelectron Microscopy in Yeast
603(16)
Christopher Buser
Kent McDonald
Introduction
604(1)
Recent Advances in High-Pressure Freezing and Freeze-Substitution
605(1)
How to Prepare Yeast by HPF/FS
606(6)
Immunolabeling
612(1)
Conclusions
613(1)
Protocols
614(5)
Acknowledgments
617(1)
References
617(2)
Analyzing P-Bodies and Stress Granules in Saccharomyces cerevisiae
619(22)
J. Ross Buchan
Tracy Nissan
Roy Parker
Introduction
620(2)
Determining If a Specific Protein can Accumulate in P-Bodies or Stress Granules
622(8)
Monitoring Messenger RNA in P-Bodies
630(1)
Determining If a Mutation/Perturbation Affects P-Body or Stress Granule Size and Number
631(4)
Quantification of P-Body Size and Number
635(6)
Acknowledgments
637(1)
References
637(4)
Analyzing mRNA Expression Using Single mRNA Resolution Fluorescent In Situ Hybridization
641(20)
Daniel Zenklusen
Robert H. Singer
Introduction
642(1)
Probe Design
643(2)
Probe Labeling
645(2)
Cell Fixation, Preparation, and Storage
647(3)
Hybridization
650(3)
Image Acquisition
653(1)
Image Analysis
654(3)
Summary and Perspectives
657(4)
Acknowledgments
658(1)
References
658(3)
The Use of In Vitro Assays to Measure Endoplasmic Reticulum-Associated Degradation
661(20)
Jeffrey L. Brodsky
Introduction
662(3)
In Vitro ERAD Assays Using a Soluble Substrate, pαF
665(8)
In Vitro Assays for Integral Membrane Proteins that are ERAD Substrates
673(8)
References
677(4)
A Protein Transformation Protocol for Introducing Yeast Prion Particles into Yeast
681(14)
Motomasa Tanaka
Introduction
682(1)
Purification of Bacterially Expressed Sup-NM
683(1)
Preparation of Different Conformations of In Vitro Sup-NM Amyloid
684(1)
Preparation of In Vivo Prions from Yeast
685(1)
Preparation of Lyticase
686(1)
Protein Transformation
686(2)
Determination of Prion Conversion Efficiency and Prion Strain Phenotypes
688(7)
Acknowledgments
692(1)
References
692(3)
Overexpression and Purification of Integral Membrane Proteins in Yeast
695(14)
Franklin A. Hays
Zygy Roe-Zurz
Robert M. Stroud
Introduction
696(1)
General Considerations
696(1)
Protocol---Molecular Biology
697(2)
Protocol---Cell Growth
699(1)
Protocol---Membrane Preparation and Solubilization
699(2)
Protocol---Protein Purification
701(4)
Protocol---Protein Characterization
705(1)
Conclusion
706(3)
Acknowledgments
706(1)
References
706(3)
Biochemical, Cell Biological, and Genetic Assays to Analyze Amyloid and Prion Aggregation in Yeast
709(26)
Simon Alberti
Randal Halfmann
Susan Lindquist
Introduction
710(2)
Methods
712(19)
Concluding Remarks
731(4)
References
731(4)
Section VI. Other Fungi
735(132)
Genetics and Molecular Biology in Candida albicans
737(22)
Aaron. D. Hernday
Suzanne. M. Noble
Quinn. M. Mitrovich
Alexander. D. Johnson
Homozygous Gene Disruption in C. albicans
738(5)
C. albicans DNA Transformation
743(2)
C. albicans Total RNA Purification
745(1)
C-Terminal Epitope Tagging in C. albicans
746(4)
C. albicans Chromatin Immunoprecipitation
750(9)
References
758(1)
Molecular Genetics of Schizosaccharomyces pombe
759(38)
Sarah A. Sabatinos
Susan L. Forsburg
Introduction
760(1)
Biology, Growth, and Maintenance of Fission Yeast
761(6)
Genetics and Physiology
767(9)
Molecular Analysis
776(9)
Cell Biology
785(6)
Conclusion
791(6)
References
793(4)
Applying Genetics and Molecular Biology to the Study of the Human Pathogen Cryptococcus neoformans
797(36)
Cheryl D. Chun
Hiten D. Madhani
Introduction
798(1)
Serotypes, Strains, and Sequences
799(1)
Life Cycle
800(2)
Techniques for Basic Culture
802(2)
Basic Molecular Biology Techniques
804(13)
Methods for Assaying Pathogenesis
817(11)
Concluding Remarks
828(5)
Acknowledgments
829(1)
References
829(4)
The Fungal Genome Initiative and Lessons Learned from Genome Sequencing
833(24)
Christina A. Cuomo
Bruce W. Birren
Introduction: Yeast Genomes and Beyond
834(7)
Computational Prediction of Genes and Noncoding Elements
841(2)
Mechanisms of Genome Evolution
843(4)
Genomic Potential for Sex
847(1)
Gene Family Conservation and Evolution
848(1)
Impact of Next-Generation Sequencing
849(2)
Future Directions
851(6)
Acknowledgments
852(1)
References
853(4)
Ultradian Metabolic Cycles in Yeast
857(10)
Benjamin P. Tu
Introduction
857(1)
Induction of Ultradian Cycles of Oxygen Consumption Using a Chemostat
858(3)
Long-Period Cycles
861(1)
Short-Period Cycles
862(1)
Significance of Ultradian Cycles
863(4)
Acknowledgments
865(1)
References
865(2)
Author Index 867(12)
Subject Index 879
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