Guide to yeast genetics: functional genomics, proteomics, and other systems analysis
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Amsterdam [u.a.]
Elsevier, Acad. Press
2010
|
| Edition: | 2. ed. |
| Series: | Methods in enzymology
470 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Item Description: | 1. Aufl. u.d.T.: Guide to yeast genetics and molecular biology, bezw.: Guide to yeast genetics and molecular and cell biology |
| Physical Description: | LII, 892 S. Ill., graph. Darst. |
| ISBN: | 9780123751720 0123751721 9780123751713 |
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| 245 | 1 | 0 | |a Guide to yeast genetics |b functional genomics, proteomics, and other systems analysis |c ed. by Jonathan Weissman ... |
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| 300 | |a LII, 892 S. |b Ill., graph. Darst. | ||
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Record in the Search Index
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| adam_text | Contents
Contributors
xv
Preface
xxiii
Volumes in Series
xxv
Section I. Functional Genomics
1
1.
Analysis of Gene Function Using
DNA Microarrays 3
Andrew P. Capaldi
1.
Introduction and Experimental Design
4
2.
Methods
8
References
16
2.
An Introduction to Microarray Data Analysis and Visualization
19
Gregg B. Whitworth
1.
Introduction
20
2.
Experimental Design: Single-Sample Versus Competitive Hybridization
23
3.
Image Analysis
26
4.
Preprocessing
29
5.
Visualizing Data Using Cluster Analysis
38
6.
Assessing the Statistical Evidence for Differential Expression
41
7.
Exploring Gene Sets
42
8.
Managing Data
44
Acknowledgments
49
References
49
3.
Genome-Wide Approaches to Monitor Pre-mRNA Splicing
51
Maki Inada
and Jeffrey A. Pleiss
1.
Introduction
52
2.
Microarray Design
53
3.
Sample Preparation
56
4.
Microarray Data Collection
68
5.
Microarray Data Analysis
69
6.
Future Methodologies
72
Acknowledgments
73
References
74
v¡
Contents
4.
ChIP-Seq:
Using High-Throughput
DNA
Sequencing for
Genome-Wide identification of Transcription Factor Binding Sites
77
Philippe
Lefrançois,
Wei Zheng, and Michael Snyder
1.
Introduction
78
2.
Protocols
81
3.
Sequencing Data Management
93
4.
Genome Analysis Pipeline
94
5.
Examining Data Quality and Parsing Barcoded Data
95
6.
Visualization in Genome Browser
95
7.
Conclusion and Future Directions
102
Acknowledgments
102
References
102
5.
Genome-Wide Mapping of Nucleosomes in Yeast
105
Oliver
).
Rando
1.
Introduction
105
2.
Isolation of Mononucleosomal
DNA 107
3.
Variation in
Titration
Level Used for Nucleosome Purification
112
4.
Labeling of Mononucleosomal
DNA
for Tiling Microarray Analysis
113
5.
Generation of Nucleosomal
DNA
Libraries for Deep Sequencing
115
References
117
6.
Genome-Wide Translational Profiling by Ribosome Footprinting
119
Nicholas T.
Ingolla
1.
Introduction
120
2.
Ribosome Footprint Generation and Purification
121
3.
Sequencing Library Preparation
128
4.
Data Analysis
133
5.
Solutions and Common Procedures
138
Acknowledgments
140
References
140
Section II. Systematic Genetic Analysis
143
7.
Synthetic Genetic Array (SGA) Analysis in
Saccharomyces cerevisiae and Schizosaccharomyces pombe
145
Anastasia
Baryshnikova, Michael Costanzo, Scott Dixon, Franco J.
Vizeacoumar, Chad L. Myers, Brenda Andrews, and Charles Boone
1.
Introduction
146
2.
Methodology
148
3.
Media and Stock Solutions
168
4.
Applications of SGA Methodology
171
References
176
Contents
vii
8.
Making Temperature-Sensitive Mutants
181
Shay Ben-Aroya, Xuewen Pan, Jef D. Boeke, and Philip Hieter
1.
Introduction
182
2.
Diploid Shuffle-Plasmid Method
183
3.
Diploid Shuffle—Chromosome Method
194
4.
Perspectives
202
References
203
9.
Quantitative Genetic Interaction Mapping Using
the
Е
-MAP
Approach
205
Sean R. Collins,
Assen
Roguev, and Nevan J. Krogan
1.
Introduction
206
2.
Selection of Mutations for Genetic Analysis
209
3.
Generation and Measurement of Double Mutant Strains
211
4.
Data Processing and Computation of Scores
221
5.
Extraction of Biological Hypotheses
224
6.
Perspective
229
References
229
10.
Exploring Gene Function and Drug Action Using
Chemogenomic Dosage Assays
233
Elke
Ericson,
Shawn
Hoon,
Robert P. St. Onge,
Guri
Giaever, and Corey Nislow
1.
Introduction
234
2.
Methodology
237
3.
Experimental Considerations
252
4.
Perspectives
253
Acknowledgments
254
References
254
Section III. Proteomics
257
11.
Yeast Expression Proteomics by High-Resolution Mass
Spectrometry
259
Tobias
С
Walther,
Jesper
V.
Olsen,
and Matthias Mann
1.
Introduction
260
2.
Background, Methods, and Applications
261
3.
Protocols
272
Acknowledgments
278
References
278
Contents
12.
High-Quality Binary
Interactome
Mapping
281
Matija
Dreze,
Dario
Monachello, Claire Lurin, Michael E. Cusick,
David E. Hill, Marc
Vidal,
and Pascal
Braun
1.
Introduction
282
2.
High-Quality Binary Interactome Mapping
283
3.
High-Throughput Y2H Pipeline
292
4.
Validation Using Orthogonal Binary Interaction Assays
309
5.
Conclusion
312
Acknowledgments
312
References
313
13.
Quantitative Analysis of Protein Phosphorylation on a
System-Wide Scale by Mass Spectrometry-Based
Proteomics
317
Bernd Bodenmiller
and Ruedi Aebersold
1.
Introduction
318
2.
Protocols
319
Acknowledgments
331
References
332
14.
A Toolkit of Protein-Fragment Complementation Assays
for Studying and Dissecting Large-Scale and Dynamic
Protein-Protein Interactions in Living Cells
335
Stephen W. Michnick,
Po Hien
Ear, Christian
Landry,
Mohan K. Malleshaiah, and Vincent Messier
1.
Introduction
336
2.
General Considerations in Using PCA
337
3.
DHFR PCA Survival-Selection for Large-Scale Analysis of PPIs
339
4.
A Life and Death Selection PCA Based on the
Prodrug-Converting Cytosine Deaminase for Dissection of PPIs
348
5.
Visualizing the Localization of PPIs with GFP Family
Fluorescent Protein PCAs
356
6.
Studying Dynamics of PPIs with Luciferase Reporter PCAs
361
References
366
15.
Yeast
Lipid
Analysis and Quantification by Mass Spectrometry
369
Xue Li Guan,
Isabelle
Riezman,
Markus
R.
Wenk,
and Howard Riezman
1.
Introduction
370
2.
Methods
373
Acknowledgments
389
References
389
Contents ix
16.
Mass
Spectrometry-Based
Metabolomics of Yeast
393
Christopher A. Crutchfield, Wenyun
Lu,
Eugene Melamud,
and Joshua D. Rabinowitz
1.
Introduction
394
2.
LC-MS Basics
395
3.
Experimental Design
395
4.
Strains
398
5.
Culture Conditions
398
6.
Metabolite Extraction
402
7.
Chemical Derivatization of Metabolites
405
8.
LC-MS for Mixture Analysis
406
9.
Liquid Chromatography
407
10.
Electrospray lonization
410
11.
Mass Spectrometry
411
12.
Targeted Data Analysis
415
13.
Untargeted Data Analysis
418
14.
Future Outlook
421
References
422
Section IV. Systems Analysis
427
17.
Imaging Single mRNA Molecules in Yeast
429
Hyun Youk, Arjun Raj, and Alexander van
Oudenaarden
1.
Introduction
429
2.
RNA
FISH Protocol
432
3.
Example: STLl mRNA Detection in Response to NaCl Shock
444
4.
Conclusions
445
Acknowledgments
445
References
445
18.
Reconstructing Gene Histories in Ascomycota Fungi
447
lian
Wapinski and Aviv Regev
1.
Introduction
448
2.
Synergy
451
3.
Evaluating Orthogroup Quality
459
4.
Biological Analysis of Gene Histories
466
5.
Analysis of Paralogous Genes
478
6.
Discussion and General Applicability
480
References
482
Contents
19.
Experimental
Evolution In
Yeast: A Practical Guide
487
Wiaitreya
).
Dunham
1.
Introduction
488
2.
Experiment Rationale
488
3.
Experimental Evolution Approaches
490
4.
Experimental Design
493
5.
Practical Considerations
496
6.
Analysis Techniques
500
7.
Example Protocol
502
8.
Conclusions
504
Acknowledgments
505
References
505
20.
Enhancing Stress Resistance and Production Phenotypes
Through
Transcriptome
Engineering
509
Felix H. Lam, Franz S. Hartner, Gerald R. Fink, and Gregory Stephanopoulos
1.
Introduction
510
2.
Transcription Factor Selection
511
3.
Plasmid Library Construction
512
4.
Assessment of Phenotypic Diversity
519
5.
Selecting for Phenotypes of Interest
524
6.
Validation
528
7.
Concluding Remarks
529
References
530
Section V. Advances in Cytology/ Biochemistry
533
21.
Visualizing Yeast Chromosomes and Nuclear Architecture
535
Peter
Meister,
Lutz R. Gehlen,
Elisa Varela,
Véronique
Kalek,
and
Susan
M.
Gasser
1.
Introduction
536
2.
Strain Constructions and Image Acquisition for Nuclear Architecture
Analysis in Living Cells
537
3.
Data Analysis and Quantitative Measurements
547
4.
IF and FISH on Fixed Samples
557
References
566
22.
Quantitative Localization of Chromosomal Loci by
Immunofluorescence
569
Donna Garvey Brickner, William Light, and Jason H. Brickner
1.
Yeast Strain Construction
570
2.
Immunofluorescence
572
Contents xi
3.
Fixing
Celts
573
4.
Spheroplasting
574
5.
Preparing Slides
574
6.
Antibody Incubations
575
7.
Mounting and Storage of Slides
575
8.
Microscopy and Analysis
576
Acknowledgments
578
References
579
23.
Spinning-Disk Confocal Microscopy of Yeast
581
Kurt Thorn
1.
Introduction
582
2.
Building a Spinning-Disk Confocal Microscope
583
3.
Sample Preparation
594
Acknowledgments
600
References
600
24.
Correlative GFP-lmmunoelectron Microscopy in Yeast
603
Christopher
Buser
and Kent McDonald
1.
Introduction
604
2.
Recent Advances in High-Pressure Freezing
and Freeze-Substitution
605
3.
How to Prepare Yeast by HPF/FS
606
4.
Immunolabeling
612
5.
Conclusions
613
6.
Protocols
614
Acknowledgments
617
References
617
25.
Analyzing P-Bodies and Stress Granules in
Saccharomyces cerevisiae
619
J. Ross
Buchán,
Tracy Nissan, and Roy Parker
1.
Introduction
620
2.
Determining If a Specific Protein can Accumulate in
P-Bodies or Stress Granules
622
3.
Monitoring Messenger
RNA
in P-Bodies
630
4.
Determining If a Mutation/Perturbation Affects P-Body
or Stress Granule Size and Number
631
5.
Quantification of P-Body Size and Number
635
Acknowledgments
637
References
637
xii Contents
26.
Analyzing mRNA Expression Using Single mRNA
Resolution Fluorescent In Situ Hybridization
641
Daniel Zenklusen and Robert H. Singer
1.
Introduction
642
2.
Probe Design
643
3.
Probe Labeling
645
4.
Cell Fixation, Preparation, and Storage
647
5.
Hybridization
650
6.
Image Acquisition
653
7.
Image Analysis
654
8.
Summary and Perspectives
657
Acknowledgments
658
References
658
27.
The Use of In Vitro Assays to Measure Endoplasmic
Reticulum-Associated Degradation
661
Jeffrey L.
Brodsky
1.
Introduction
662
2.
In Vitro
ERAD
Assays Using a Soluble Substrate,
pcď
665
3.
In Vitro Assays for Integral Membrane Proteins that are
ERAD
Substrates
673
References
677
28.
A Protein Transformation Protocol for Introducing
Yeast Prion Particles into Yeast
681
Motomasa Tanaka
1.
Introduction
682
2.
Purification of Bacterially Expressed Sup-NM
683
3.
Preparation of Different Conformations of In Vitro Sup-NM Amyloid
684
4.
Preparation of In Vivo
Prions
from Yeast
685
5.
Preparation of Lyticase
686
6.
Protein Transformation
686
7.
Determination of Prion Conversion Efficiency and
Prion Strain Phenotypes
688
Acknowledgments
692
References
692
29.
Overexpression and Purification of Integral Membrane
Proteins in Yeast
695
Franklin A. Hays, Zygy Roe-Zurz, and Robert M. Stroud
1.
Introduction
696
2.
General Considerations
696
Contents
xiii
3.
Protocol—
Molecular
Biology
697
4.
Protocol—Cell Growth
699
5.
Protocol—Membrane Preparation and Solubilization
699
6.
Protocol—Protein Purification
701
7.
Protocol—Protein Characterization
705
8.
Conclusion
706
Acknowledgments
706
References
706
30.
Biochemical, Cell Biological, and Genetic Assays to
Analyze Amyloid and Prion Aggregation in Yeast
709
Simon
Alberti,
Randal
Halfmann,
and Susan Lindquist
1.
Introduction
710
2.
Methods
712
3.
Concluding Remarks
731
References
731
Section VI. Other Fungi
735
31.
Genetics and Molecular Biology in Candida albicans
737
Aaron. D. Hernday, Suzanne. M. Noble, Quinn. M. Mitrovich,
and Alexander. D. Johnson
1.
Homozygous Gene Disruption in C. albicans
738
2.
С
albicans
DNA
Transformation
743
3.
С
albicans Total
RNA
Purification
745
4.
C-Terminal
Epitope Tagging in
С
albicans
746
5.
С
albicans Chromatin Immunopredpitation
750
References
758
32.
Molecular Genetics of Schizosaccharomyces pombe
759
Sarah
A. Sabatinos
and Susan L.
Forsburg
1.
Introduction
760
2.
Biology, Growth, and Maintenance of Fission Yeast
761
3.
Genetics and Physiology
767
4.
Molecular Analysis
776
5.
Cell Biology
785
6.
Conclusion
791
References
793
xiv
Contents
33.
Applying Genetics and Molecular Biology to the Study
of the Human Pathogen Cryptococcus neoformans
797
Cheryl D. Chun and
Hiten
D.
Madhani
1.
Introduction
798
2.
Serotypes, Strains, and Sequences
799
3.
Life Cycle
800
4.
Techniques for Basic Culture
802
5.
Basic Molecular Biology Techniques
804
6.
Methods for Assaying Pathogenesis
817
7.
Concluding Remarks
828
Acknowledgments
829
References
829
34.
The Fungal Genome Initiative and Lessons Learned
from Genome Sequencing
833
Christina A. Cuomo and Bruce W. Birren
1.
Introduction: Yeast Genomes and Beyond
834
2.
Computational Prediction of Genes and Noncoding Elements
841
3.
Mechanisms of Genome Evolution
843
4.
Genomic Potential for Sex
847
5.
Gene Family Conservation and Evolution
848
6.
Impact of Next-Generation Sequencing
849
7.
Future Directions
851
Acknowledgments
852
References
853
35.
Ultradian Metabolic Cycles in Yeast
857
Benjamin P.
Tu
1.
Introduction
857
2.
Induction of Ultradian Cycles of Oxygen Consumption
Using a Chemostat
858
3.
Long-Period Cycles
861
4.
Short-Period Cycles
862
5.
Significance of Ultradian Cycles
863
Acknowledgments
865
References
865
Author Index
867
Subject Index
879
|
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| author_GND | (DE-588)141186623 (DE-588)1236875230 (DE-588)1236857755 |
| building | Verbundindex |
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| edition | 2. ed. |
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| genre | (DE-588)4143413-4 Aufsatzsammlung gnd-content |
| genre_facet | Aufsatzsammlung |
| id | DE-604.BV036433824 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T22:39:19Z |
| institution | BVB |
| isbn | 9780123751720 0123751721 9780123751713 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-020306354 |
| oclc_num | 699817556 |
| open_access_boolean | |
| owner | DE-703 DE-355 DE-BY-UBR DE-19 DE-BY-UBM DE-91G DE-BY-TUM DE-12 DE-20 DE-523 |
| owner_facet | DE-703 DE-355 DE-BY-UBR DE-19 DE-BY-UBM DE-91G DE-BY-TUM DE-12 DE-20 DE-523 |
| physical | LII, 892 S. Ill., graph. Darst. |
| publishDate | 2010 |
| publishDateSearch | 2010 |
| publishDateSort | 2010 |
| publisher | Elsevier, Acad. Press |
| record_format | marc |
| series | Methods in enzymology |
| series2 | Methods in enzymology |
| spelling | Guide to yeast genetics functional genomics, proteomics, and other systems analysis ed. by Jonathan Weissman ... 2. ed. Amsterdam [u.a.] Elsevier, Acad. Press 2010 LII, 892 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in enzymology 470 1. Aufl. u.d.T.: Guide to yeast genetics and molecular biology, bezw.: Guide to yeast genetics and molecular and cell biology Genetik (DE-588)4071711-2 gnd rswk-swf Methode (DE-588)4038971-6 gnd rswk-swf Hefeartige Pilze (DE-588)4230509-3 gnd rswk-swf Saccharomycetaceae (DE-588)4131614-9 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Hefeartige Pilze (DE-588)4230509-3 s Genetik (DE-588)4071711-2 s Methode (DE-588)4038971-6 s DE-604 Saccharomycetaceae (DE-588)4131614-9 s b DE-604 Weissman, Jonathan Sonstige (DE-588)141186623 oth Guthrie, Christine 19XX- Sonstige (DE-588)1236875230 oth Fink, Gerald R. 1940- Sonstige (DE-588)1236857755 oth Methods in enzymology 470 (DE-604)BV000000938 470 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020306354&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Guide to yeast genetics functional genomics, proteomics, and other systems analysis Methods in enzymology Genetik (DE-588)4071711-2 gnd Methode (DE-588)4038971-6 gnd Hefeartige Pilze (DE-588)4230509-3 gnd Saccharomycetaceae (DE-588)4131614-9 gnd |
| subject_GND | (DE-588)4071711-2 (DE-588)4038971-6 (DE-588)4230509-3 (DE-588)4131614-9 (DE-588)4143413-4 |
| title | Guide to yeast genetics functional genomics, proteomics, and other systems analysis |
| title_auth | Guide to yeast genetics functional genomics, proteomics, and other systems analysis |
| title_exact_search | Guide to yeast genetics functional genomics, proteomics, and other systems analysis |
| title_full | Guide to yeast genetics functional genomics, proteomics, and other systems analysis ed. by Jonathan Weissman ... |
| title_fullStr | Guide to yeast genetics functional genomics, proteomics, and other systems analysis ed. by Jonathan Weissman ... |
| title_full_unstemmed | Guide to yeast genetics functional genomics, proteomics, and other systems analysis ed. by Jonathan Weissman ... |
| title_short | Guide to yeast genetics |
| title_sort | guide to yeast genetics functional genomics proteomics and other systems analysis |
| title_sub | functional genomics, proteomics, and other systems analysis |
| topic | Genetik (DE-588)4071711-2 gnd Methode (DE-588)4038971-6 gnd Hefeartige Pilze (DE-588)4230509-3 gnd Saccharomycetaceae (DE-588)4131614-9 gnd |
| topic_facet | Genetik Methode Hefeartige Pilze Saccharomycetaceae Aufsatzsammlung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020306354&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV000000938 |
| work_keys_str_mv | AT weissmanjonathan guidetoyeastgeneticsfunctionalgenomicsproteomicsandothersystemsanalysis AT guthriechristine guidetoyeastgeneticsfunctionalgenomicsproteomicsandothersystemsanalysis AT finkgeraldr guidetoyeastgeneticsfunctionalgenomicsproteomicsandothersystemsanalysis |