Yeast Systems Biology: Methods and Protocols

ISBN-13: 9781493997350 / Angielski / Twarda / 2019 / 447 str.

Stephen G. Oliver; Juan Castrillo

Spis treści

Dedication…

Preface…

Table of Contents…

Contributing Authors…

Part I Yeast Systems Biology

1. Yeast Systems Biology: The Continuing Challenge of Eukaryotic Complexity

Stephen G. Oliver

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

2. Capture of Ribonucleotides in Yeast Genomic DNA using Ribose-Seq

Sathya Balachander, Taehwan Yang, Gary Newnam, Waleed M. M. El-Sayed, Kyung Duk Koh, and Francesca Storici

3. Method for Multiplexed Integration of Synergistic Alleles and Metabolic Pathways in Yeasts via CRISPR-Cas9

Jessica M. Walter, Max G. Schubert, Stephanie H. Kung, Kristy Hawkins, Darren M. Platt, Aaron D. Hernday, Tina Mahatdejkul-Meadows, Wayne Szeto, Sunil S. Chandran, Jack D. Newman, and Andrew A. Horwitz

4. Ultra-High-Density Screens for Genome-Wide Yeast EMAPs in a Single Plate

Katherine Licon, John Paul Shen, Brenton P. Munson, Manuel Michaca, Cole Fassino, Luke Fassino, Jason F. Kreisberg, and Trey Ideker

5. Epi-ID: Systematic and Direct Screening for Chromatin Regulators in Yeast by Barcode ChIP-Seq

Deepani W. Poramba-Liyanage, Tessy Korthout, and Fred van Leeuwen

6. Transcript Profiling Analysis through Paired-End Ditag (PET) Approach Coupled with Deep Sequencing Revealing Transcriptome Complexity in Yeast

Yani Kang, Hong Sain Ooi, and Xiaodong Zhao

7. RNA Sequencing Best Practices: Experimental Protocol and Data Analysis

Andy Hesketh

 

8.    Advanced Methods for the Analysis of Altered Pre-mRNA Splicing in Yeast     and Disease

Huw B. Thomas and Raymond T. O’Keefe

9. PAT-Seq: A Method for Simultaneous Quantitation of Gene Expression, Poly(A)-Site Selection and Poly(A) Length-Distribution in Yeast Transcriptomes

Angavai Swaminathan, Paul F. Harrison, Thomas Preiss, and Traude H. Beilharz

10. Mapping the Saccharomyces cerevisiae Spatial Proteome with High Resolution using hyperLOPIT

Daniel J. H. Nightingale, Stephen G. Oliver, and Kathryn S. Lilley

11. Data-Independent Acquisition for Yeast Glycoproteomics

Lucía F. Zacchi and, Benjamin L. Schulz

12. Protein-Protein Interaction Profiling in Candida albicans Revealed by Biochemical Purification-Mass Spectrometry (BP/MS)

Reza Pourhaghighi, Teresa R. O'Meara, Leah E. Cowen, and Andrew Emili

13. Probing the RNA-Binding Proteome from Yeast to Man: Major Advances and Challenges

Benedikt M. Beckmann and SanderGranneman

14. Metabolomic Analysis of Yeast and Human Cells: Latest Advances and Challenges

Romanas Chaleckis , Kazuto Ohashi, Isabel Meister, Shama Naz, and Craig E. Wheelock

15. Measuring the Activity of Plasma Membrane and Vacuolar Transporters in Yeast

Melody Cools, Maria Rompf, Andreas Mayer, and Bruno André

16. Self-Establishing Communities: A Yeast Model to Study the Physiological Impact of Metabolic Cooperation in Eukaryotic Cells

Kate Campbell, Clara Correia-Melo, and Markus Ralser

 

Part III Computational System Biology: Data Management and Modeling the Cell

17. Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices

Natalie J. Stanford, Martin Scharm, Paul D. Dobson, Martin Golebiewski, Mike Hucka, Varun B. Kothamachu, David Nickerson, Stuart Owen, Jürgen Pahle, Ulrike Wittig, Dagmar Waltemath, Carole Goble, Pedro Mendes, and Jacky Snoep

18. Rational Design and Methods of Analysis for the Study of Short- and Long-Term Dynamic Responses of Eukaryotic Systems

Duygu Dikicioglu

19. Genome-Scale Metabolic Modeling from Yeast to Human Cell Models of Complex Diseases: Latest Advances and Challenges

Yu Chen, Gang Li, and Jens Nielsen

20. Next-Generation Genome-Scale Models Incorporating Multilevel ‘omics Data:  From Yeast to Human

Tunahan Çakır, Emel Kökrek, Gülben Avşar, Ecehan Abdik, and Pınar Pir

21. Advanced Modeling of Cellular Proliferation: Towards a Multi-Scale Framework Coupling Cell Cycle to Metabolism by Integrating Logical and Constraint-Based Models

Lucas van der Zee and Matteo Barberis

Part IV Using Yeast to Model Human Diseases

22. Yeast Genome Screening and Methods for the Discovery of Metabolism    Pathways Involved in a Phenotypic Response to Anti-Cancer Agents 

Magdalena Cal, Irwin Matyjaszczyk, and Stanisław Ułaszewski 

23. Advanced Yeast Models of Familial Alzheimer Disease Expressing FAD-Linked Presenilin to Screen Mutations and g-Secretase Modulators

Eugene Futai

24. From Yeast-to-Humans: Leveraging New Approaches in Yeast to Accelerate Discovery of Therapeutic Targets for Synucleinopathies

Jeff S. Piotrowski and Daniel F. Tardiff

Blurb

This second edition volume expands on the previous edition with a look at the latest advances in techniques to study yeast and its core set of interactions, modules, architectures, and network dynamics that are common in all eukaryotes. The chapters in this book are organized into Four Parts: Part One provides readers with an update on the development of novel experimental and computational approaches to yeast systems biology; Part Two explores high-throughput methods used to study yeast epigenome, transcriptome, proteome, and metabolome; Part Three talks about computational systems biology, and focuses on data management, dynamic modeling, constraint-based models of metabolic networks, and multi-level ‘omics data; while Part Four looks at experimental platforms that utilize yeast to model systemic human diseases such as Alzheimer’s and Parkinson’s diseases. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics; lists of the necessary materials and reagents; step-by-step, readily reproducible laboratory protocols; and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and comprehensive, Yeast System Biology: Methods and Protocols, Second Edition is a valuable tool for graduate students, post-doctoral researchers, and experts who are interested in learning about the latest developments in the study of yeast.