Yeast Genetic Networks: Methods and Protocols (Methods in Molecular Biology)

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(TM) 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. Part I Experimental Analysis of Signalling in Gene Regulatory Networks   1. Global Estimation of mRNA Stability in Yeast             Julia Marn-Navarro, Alexandra Jauhiainen, Joaqun Moreno, Paula Alepuz, Jos E. Prez-Ortn, and Per Sunnerhagen   2. Genomic-wide Methods to Evaluate Transcription Rates in Yeast             Jos Garca-Martnez, Vicent Pelechano, and Jos E. Prez-Ortn   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 Gbor Balzsi   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 Gal 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 Jurez-Reyes, Alejandro De Las Peas, and Irene Castao   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