Yeast Genetic Networks: Methods and Protocols

ISBN-13: 9781617790850 / Angielski / Twarda / 2011 / 358 str.

Attila Becskei

Opis

Regulation of gene expression, a major determinant of gene activity, occupies a central place in molecular biology. Yeast Genetic Networks: Methods and Protocols covers approaches to the systems biological analysis of small-scale gene networks in yeast. Divided into four convenient sections, this detailed volume discusses the methods used to analyze gene expression quantitatively, presents a collection of mathematical and computational tools to analyze stochasticity, adaptation, sensitivity in signal transmission, and oscillations in gene expression, provides instructional methods on how to utilize the tools of quantitative genetics to identify genes that regulate stochasticity and oscillations in gene expression, and concludes with a section devoted to the analysis of conserved gene expression systems and networks in different fungal species. Written in the highly successful Methods in Molecular Biology series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.Authoritative and accessible, Yeast Genetic Networks: Methods and Protocols serves as an ideal and valuable resource for both novices and experienced researchers.

Spis treści

Part I Experimental Analysis of Signalling in Gene Regulatory Networks

 

1. Global Estimation of mRNA Stability in Yeast

            Julia Marín-Navarro, Alexandra Jauhiainen, Joaquín Moreno, Paula Alepuz, José E. Pérez-Ortín, and Per Sunnerhagen

 

2. Genomic-wide Methods to Evaluate Transcription Rates in Yeast

            José García-Martínez, Vicent Pelechano, and José E. Pérez-Ortín

 

3. Construction of Cis-regulatory Input Functions of Yeast Promoters

            Prasuna Ratna and Attila Becskei

 

4. Luminescence as a Continuous Real-Time Reporter of Promoter Activity in Yeast Undergoing Respiratory Oscillations or Cell Division Rhythms

            J. Brian Robertson and Carl Hirschie Johnson

 

5. Linearizer Gene Circuits with Negative Feedback Regulation

            Dmitry Nevozhay, Rhys M. Adams, and Gábor Balázsi

 

6. Measuring In vivo Signaling Kinetics in a Mitogen-activated Kinase Pathway using Dynamic Input Stimulation

            Megan N. McClean, Pascal Hersen, and Sharad Ramanathan

 

Part II Mathematical Modelling of Network Behavior

 

7. Stochastic Analysis of Gene Expression

            Xiu-Deng Zheng and Yi Tao

 

8. Studying Adaptation and Homeostatic Behaviors of Kinetic Networks by using MATLAB

            Tormod Drengstig, Thomas Kjosmoen, and Peter Ruoff

 

9. Biochemical Systems Analysis of Signaling Pathways to Understand Fungal Pathogenicity

            Jacqueline Garcia, Kellie J. Sims, John H. Schwacke, and Maurizio Del Poeta

 

10. Clustering Change Patterns Using Fourier Transformation with Time-course Gene Expression Data

            Jaehee Kim

 

Part III Analysis of Network Behaviour by Quantitative Genetics

 

11. Finding Modulators of Stochasticity Levels by Quantitative Genetics

            Steffen Fehrmann and Gaël Yvert

 

12. Functional Mapping of Expression Quantitative Trait Loci That Regulate Oscillatory Gene Expression

            Arthur Berg, Ning Li, Chunfa Tong, Zhong Wang, Scott A. Berceli, and Rongling Wu

 

Part IV Examination of Network Behaviour in Related Yeast Species

 

13. Evolutionary Aspects of a Genetic Network: Studying the Lactose/Galactose Regulon of Kluyveromyces lactis

            Alexander Anders and Karin D. Breunig

 

14. Analysis of Subtelomeric Silencing in Candida glabrata

            Alejandro Juárez-Reyes, Alejandro De Las Peñas, and Irene Castaño

 

15. Morphological and Molecular Genetic Analysis of Epigenetic Switching of the Human Fungal Pathogen Candida albicans

            Denes Hnisz, Michael Tscherner, and Karl Kuchler

 

16. Quantitation of Cellular Components in Cryptococcus neoformans for System Biology Analysis

            Arpita Singh, Asfia Qureshi, and Maurizio Del Poeta