Yeast Systems Biology: Methods and Protocols

ISBN-13: 9781493961351 / Angielski / Miękka / 2016 / 535 str.

Juan I. Castrillo; Stephen G. Oliver

Opis

This book presents an up-to-date view of yeast as a model eukaryote for systems biology studies. It provides practical, easy to use methodologies and includes key tips and vital implementation advice from the experts.

Spis treści

Part I: Yeast Systems Biology

 

1. Yeast Systems Biology: The Challenge of Eukaryotic Complexity

            Juan I. Castrillo and Stephen G. Oliver

 

Part II: Experimental Systems Biology: High-Throughput Genome-Wide and Molecular Studies

 

2. Saccharomyces cerevisiae: Gene Annotation and Genome Variability, State-of-the-Art Through Comparative Genomics

            Ed Louis

 

3. Genome-Wide Measurement of Histone H3 Replacement Dynamics in Yeast

            Oliver J. Rando

 

4. Genome-Wide Approaches to Studying Yeast Chromatin Modifications

            Dustin E. Schones, Kairong Cui, and Suresh Cuddapah

 

5. Absolute and Relative Quantification of mRNA Expression (Transcript Analysis)

            Andrew Hayes, Bharat M. Rash, and Leo A.H. Zeef

 

6. Enrichment of Unstable Non-Coding RNAs and Their Genome-Wide Identification

            Helen Neil and Alain Jacquier

 

7. Genome-Wide Transcriptome Analysis in Yeast Using High-Density Tiling Arrays

            Lior David, Sandra Clauder-Münster, and Lars M. Steinmetz

 

8. RNA Sequencing

            Karl Waern, Ugrappa Nagalakshmi, and Michael Snyder

 

9. Polyadenylation State Microarray (PASTA) Analysis

            Traude H Beilharz and Thomas Preiss

 

10. Enabling Technologies for Yeast Proteome Analysis

            Johanna Rees and Kathryn Lilley

 

11. Protein Turnover Methods in Single-Celled Organisms: Dynamic SILAC

            Amy J. Claydon and Robert J. Beynon

 

12. Protein-Protein Interactions and Networks: Forward and Reverse Edgetics

            Benoit Charloteaux, Quan Zhong, Matija Dreze, Michael E. Cusick, David E. Hill, and Marc Vidal

 

13. Use of Proteome Arrays to Globally Identify Substrates for E3 Ubiquitin Ligases

            Avinash Persaud and Daniela Rotin

 

14. Fit for Purpose Quenching and Extraction Protocols for Metabolic Profiling of Yeast Using Chromatography-Mass Spectrometry Platforms

            Catherine L. Winder and Warwick B. Dunn

 

15. The Automated Cell: Compound and Environment Screening System (ACCESS) for Chemogenomic Screening

            Michael Proctor, Malene L. Urbanus, Eula L. Fung, Daniel F. Jaramillo, Ronald W. Davis, Corey Nislow, and Guri Giaever

 

16. Competition Experiments Coupled with High-Throughput Analyses for Functional Genomics Studies in Yeast

            Daniela Delneri

 

17. Fluorescence Fluctuation Spectroscopy and Imaging Methods for Examination of Dynamic Protein Interactions in Yeast

            Brian D. Slaughter, Jay R. Unruh, and Rong Li

 

18. Nutritional Control of Cell Growth Via TOR Signaling in Budding Yeast

            Yuehua Wei and X.F. Steven Zheng

 

Part III: Computational Systems Biology: Computational Studies and Analyses

 

19. Computational Yeast Systems Biology: A Case Study for the MAP Kinase Cascade

            Edda Klipp

 

20. Standards, Tools, and Databases for the Analysis of Yeast 'Omics Data

            Axel Kowald and Christoph Wierling

 

21. A Computational Method to Search for DNA Structural Motifs in Functional Genomic Elements

            Stephen C.J. Parker, Aaron Harlap, and Thomas D. Tullius

 

22. High Throughput Analyses and Curation of Protein Interactions in Yeast

            Shoshana J. Wodak, Jim Vlasblom, and Shuye Pu

 

23. Noise in Biological Systems: Pros, Cons, and Mechanisms of Control

            Yitzhak Pilpel

 

24. Genome-Scale Integrative Data Analysis and Modeling of Dynamic Processes in Yeast

            Jean-Marc Schwartz and Claire Gaugain

 

25. Genome-Scale Metabolic Models of Saccharomyces cerevisiae

            Intawat Nookaew, Roberto Olivares-Hernández, Sakarindr Bhumiratana, and Jens Nielsen

 

26. Representation, Simulation, and Hypothesis Generation in Graph and Logical Models of Biological Networks

            Ken Whelan, Oliver Ray, and Ross King

 

27. Use of Genome-Scale Metabolic Models in Evolutionary Systems Biology

            Balázs Papp, Balázs Szappanos, and Richard A. Notebaart

 

Part IV: Yeast Systems Biology in Practice: Saccharomyces cerevisiae as a Tool for Mammalian Studies

 

28. Saccharomyces cerevisiae Contributions Towards Understanding Mammalian Gene Function and Therapy

            Nianshu Zhang and Elizabeth Bilsland

Blurb

Systems Biology aims at deciphering the genotype-phenotype relationships at the levels of genes, transcripts (RNAs), peptides, proteins, metabolites, and environmental factors participating in complex cellular networks in order to reveal the mechanisms and principles governing the behavior of complex biological systems.  Yeast Systems Biology: Methods and Protocols presents an up-to-date view of the optimal characteristics of the yeast Saccharomyces cerevisiae as a model eukaryote, perspective on the latest experimental and computational techniques  for systems biology studies, most of which were first designed for and validated in yeast, and selected examples of yeast systems biology studies and their applications in biotechnology and medicine.  These experiments under controlled conditions can uncover the complexity and interplay of biological networks with their dynamics, basic principles of internal organization, and balanced orchestrated functions between organelles in direct interaction with the environment as well as the characterization of short and long-term effects of perturbations and dysregulation of networks that may illuminate the origin of complex human diseases.  Written for the highly successful Methods in Molecular Biology™ series, this volume contains the kind of detailed description and implementation advice that is crucial for getting optimal results.

 

Practical and cutting-edge, Yeast Systems Biology: Methods and Protocols serves researchers interested in comprehensive systems biology strategies in well-defined model systems with specific objectives as well as a better knowledge of the latest post-genomic strategies at all ‘omic levels and computational approaches towards analysis, integration, and modeling of biological systems, from single-celled organisms to higher eukaryotes.