Mapping Genetic Interaction Networks in Yeast PDF Download
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Author: Anastasija Baryshnikova
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
Author: Anastasija Baryshnikova
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
![Large-scale Mapping of Genetic Interactions in Saccharomyces Cerevisiae [microform] PDF](https://books.google.com/books/content/images/frontcover/x8-StgAACAAJ?fife=w80-h100)
Author: Amy Hin Yan Tong
Publisher: Library and Archives Canada = Bibliothèque et Archives Canada
ISBN: 9780494028339
Category :
Languages : en
Pages : 474
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Book Description
In chapter four, I describe the application of SGA analysis to the large-scale mapping of genetic interactions. A genetic interaction network containing & sim;1000 genes and & sim;4000 interactions was mapped by crossing mutations in 132 different query genes into a set of & sim;4700 viable gene deletion mutants and scoring the double mutant progeny for fitness defects. Network connectivity is predictive of function because interactions often occur among functionally related genes. Genetic interactions are largely orthogonal (non-overlapping) with protein-protein interactions, but genes coding for proteins that occur in the same pathway or complex display similar patterns of genetic interactions. The genetic network shows dense local neighbourhoods, implying the position of a gene on a partially mapped network is predictive of interactions. Because genetic networks are likely conserved, synthetic genetic interactions may underlie the complex genetics associated with inherited phenotypes in other organisms. In chapter three, I describe the development of a new method for automated identification of genetic interactions, termed synthetic genetic array (SGA) analysis. SGA analysis allows systematic construction of double mutants and examination of their fitness on a genome-wide scale. Functional genomics approaches have provided the opportunity for systematic examination of all genes in a genome, generating functional information such as gene expression profiles, protein expression and localization profiles, protein-protein interaction networks, and systematic characterization of mutants. Budding yeast has been the organism of choice for many of these pioneering studies because of its facile genetics. Large-scale studies have made significant contributions to our understanding of complex biological systems, and this trend is continuously fueled by new development of high-throughput technologies. In this thesis, I describe a general strategy to study protein-protein interaction modules (chapter two). A protein-protein interaction network was generated by focusing on yeast SH3 domains and combining data derived from phage-display ligand consensus sequences and large-scale two-hybrid physical interactions. This study produced a network that is depleted of most false positive interactions and enriched for biologically relevant interactions.
Author: Sourav Bandyopadhyay
Publisher:
ISBN: 9781109737707
Category :
Languages : en
Pages : 316
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Book Description
The goal of understanding complex biological systems and how they are perturbed to cause disease has long been a central focus of biology. The past decade has seen the creation and maturation of a number of new technologies designed to study biological pathways on a genome-wide scale. Rather than obtaining information about the function of one gene or protein at a time, such approaches can offer insight into the activity of every gene and protein in the cell all in the context of one experiment. One fundamental mode of gathering biological insight is through identifying which proteins in the cell interact physically, such as those which form protein complexes or biochemical pathways. Techniques such as yeast-two hybrid and co-immunoprecipitation followed by mass spectrometry allow the determination of a physical interaction map which details binding interactions between proteins on a large scale. Another fundamental mode of biological discovery is through assaying genetic interactions which arise when mutations in two genes produce a phenotype that is surprising in light of each mutation's individual effects. For example a synthetic lethal genetic interaction is indicated when deletions in two genes which are not essential for viability cause lethality when deleted together. Genetic interaction maps can be determined in high-throughput via SGA (Synthetic Genetic Array) technology. In Chapter 2 we derive and analyze a large physical protein interaction map centered on a set of human protein kinases and show how biological insight can be derived from such large-scale screens. In Chapter 3, we develop methods for the comparison of such physical protein interaction maps between species in order to identify proteins whose function is conserved throughout millions of years of evolution. In Chapter 4 we develop algorithms to integrate both physical and genetic interactions together for the purpose of biological pathway discovery. Moreover, our approaches create maps of genetic interactions that provide a picture of the global organization of pathways and complexes within the cell, which we apply to create a map of functional relationships among protein complexes involved in chromosomal biology. In Chapter 6, we apply this approach in two different yeast species and discover that while physical protein interactions are largely conserved across species, many genetic interactions are rewired which gives us valuable insight into pathway architecture. Finally in Chapter 7, we focus on the discovery of genetic interactions involved in the DNA damage response by assaying how different gene mutants respond to a drug which causes DNA damage and then demonstration how this elucidates pathways involved in this process.
Author: Jason B. Wolf
Publisher: Oxford University Press, USA
ISBN: 9780195128062
Category : Science
Languages : en
Pages : 348
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Book Description
Over the last two decades, research into epistasis has seen explosive growth and has moved the focus of research in evolutionary genetics from a traditional additive approach. We now know the effects of genes are rarely independent, and to reach a fuller understanding of the process of evolution we need to look at gene interactions as well as gene-environment interactions. This book is an overview of non-additive evolutionary genetics, integrating all work to date on all levels of evolutionary investigation of the importance of epistasis in the evolutionary process in general. It includes a historical perspective on this emerging field, in-depth discussion of terminology, discussions of the effects of epistasis at several different levels of biological organization and combinations of theoretical and experimental approaches to analysis.
Author: Alan R. Templeton
Publisher: John Wiley & Sons
ISBN: 0470047216
Category : Science
Languages : en
Pages : 720
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Book Description
The advances made possible by the development of molecular techniques have in recent years revolutionized quantitative genetics and its relevance for population genetics. Population Genetics and Microevolutionary Theory takes a modern approach to population genetics, incorporating modern molecular biology, species-level evolutionary biology, and a thorough acknowledgment of quantitative genetics as the theoretical basis for population genetics. Logically organized into three main sections on population structure and history, genotype-phenotype interactions, and selection/adaptation Extensive use of real examples to illustrate concepts Written in a clear and accessible manner and devoid of complex mathematical equations Includes the author's introduction to background material as well as a conclusion for a handy overview of the field and its modern applications Each chapter ends with a set of review questions and answers Offers helpful general references and Internet links
Author: Michael Breitenbach
Publisher: Springer Nature
ISBN: 3030777383
Category : Science
Languages : en
Pages : 249
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Book Description
The word stress is everywhere and highly overused. Everyone is stressed, it seems, all the time. Looking into the meaning of stress in the natural science and the humanities, this book explores cellular stress as cause of and in correlation with what humans experience as stress. When do we psychologically feel stress and when do we show physiological evidence of stress in our brain? Stress is a deviation from what feels normal and healthy. It can be created by social or economic factors and become chronic, which has substantial impacts on the individual and society as a whole. Focusing on poverty as one chronic inducer of stress, this book explores how the lack of pressure-free time, the hardships and unpredictability of everyday life and a general lack of protection lead to destructive toxic stress. This pressure affects cognitive and social functioning, brain development during childhood and may also result in premature aging. How can the sciences inform our understanding of and our response to stress? What can be done about toxic stress both on a personal level and in terms of structures and policies? The book is written for anyone interested in stress, its causes and consequences, and its relationship to poverty.
Author: Jeffrey S. Smith
Publisher: Humana
ISBN: 9781493951826
Category : Science
Languages : en
Pages : 0
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Book Description
Yeast Genetics: Methods and Protocols is a collection of methods to best study and manipulate Saccharomyces cerevisiae, a truly genetic powerhouse. The simple nature of a single cell eukaryotic organism, the relative ease of manipulating its genome and the ability to interchangeably exist in both haploid and diploid states have always made it an attractive model organism. Genes can be deleted, mutated, engineered and tagged at will. Saccharomyces cerevisiae has played a major role in the elucidation of multiple conserved cellular processes including MAP kinase signaling, splicing, transcription and many others. Written in the 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 protocols and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Yeast Genetics: Methods and Protocols will provide a balanced blend of classic and more modern genetic methods relevant to a wide range of research areas and should be widely used as a reference in yeast labs.
Author: Florian Markowetz
Publisher: Cambridge University Press
ISBN: 131638098X
Category : Science
Languages : en
Pages : 287
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Book Description
Whereas genetic studies have traditionally focused on explaining heritance of single traits and their phenotypes, recent technological advances have made it possible to comprehensively dissect the genetic architecture of complex traits and quantify how genes interact to shape phenotypes. This exciting new area has been termed systems genetics and is born out of a synthesis of multiple fields, integrating a range of approaches and exploiting our increased ability to obtain quantitative and detailed measurements on a broad spectrum of phenotypes. Gathering the contributions of leading scientists, both computational and experimental, this book shows how experimental perturbations can help us to understand the link between genotype and phenotype. A snapshot of current research activity and state-of-the-art approaches to systems genetics are provided, including work from model organisms such as Saccharomyces cerevisiae and Drosophila melanogaster, as well as from human studies.
Author: Paul L. Bartel
Publisher: Oxford University Press, USA
ISBN: 9780195109382
Category : Carrier proteins
Languages : en
Pages : 362
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Book Description
This volume, part of the Advances in Molecular Biology series, presents work by pioneers in the field and is the first publication devoted solely to the yeast two-hybrid system. It includes detailed protocols, practical advice on troubleshooting, and suggestions for future development. In addition, it illustrates how to construct an activation domain hybrid library, how to identify mutations that disrupt an interaction, and how to use the system in mammalian cells. Many of the contributors have developed new applications and variations of the technique.
Author: G. N. Cohen
Publisher: Springer
ISBN: 9401789088
Category : Science
Languages : en
Pages : 618
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Book Description
Microbial physiology, biochemistry and genetics allowed the formulation of concepts that turned out to be important in the study of higher organisms. In the first section, the principles of bacterial growth are given, as well as the description of the different layers that enclose the bacterial cytoplasm, and their role in obtaining nutrients from the outside media through different permeability mechanism described in detail. A chapter is devoted to allostery and is indispensable for the comprehension of many regulatory mechanisms described throughout the book. Another section analyses the mechanisms by which cells obtain the energy necessary for their growth, glycolysis, the pentose phosphate pathway, the tricarboxylic and the anaplerotic cycles. Two chapters are devoted to classes of microorganisms rarely dealt with in textbooks, namely the Archaea, mainly the methanogenic bacteria, and the methylotrophs. Eight chapters describe the principles of the regulations at the transcriptional level, with the necessary knowledge of the machineries of transcription and translation. The next fifteen chapters deal with the biosynthesis of the cell building blocks, amino acids, purine and pyrimidine nucleotides and deoxynucleotides, water-soluble vitamins and coenzymes, isoprene and tetrapyrrole derivatives and vitamin B12. The two last chapters are devoted to the study of protein-DNA interactions and to the evolution of biosynthetic pathways. The considerable advances made in the last thirty years in the field by the introduction of gene cloning and sequencing and by the exponential development of physical methods such as X-ray crystallography or nuclear magnetic resonance have helped presenting metabolism under a multidisciplinary attractive angle.
