Search results for: yeast-functional-genomics

Yeast Functional Genomics and Proteomics

Author : Igor Stagljar
File Size : 24.36 MB
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Given the popularity and utility of Saccharomyces cerevisiae, yeast-based functional genomics and proteomics technologies, developed over the past decade, have contributed greatly to our understanding of bacterial, yeast, fly, worm and human gene functions. In Yeast Functional Genomics and Proteomics: Methods and Protocols, experts in the field contribute stand-alone protocols suitable for daily use in research laboratories. The volume examines methods from the most major and fundamental techniques to more cutting-edge, advanced concepts. As part of the highly successful Methods in Molecular BiologyTM series, the chapters are clearly formatted with 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 easy to use, Yeast Functional Genomics and Proteomics: Methods and Protocols is an ideal reference for both yeast researchers and those who wish to use yeast as a model system for the further study of functional genomics and proteomics.

Guide to Yeast Genetics Functional Genomics Proteomics and Other Systems Analysis

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This fully updated edition of the bestselling three-part Methods in Enzymology series, Guide to Yeast Genetics and Molecular Cell Biology is specifically designed to meet the needs of graduate students, postdoctoral students, and researchers by providing all the up-to-date methods necessary to study genes in yeast. Procedures are included that enable newcomers to set up a yeast laboratory and to master basic manipulations. This volume serves as an essential reference for any beginning or experienced researcher in the field. Provides up-to-date methods necessary to study genes in yeast. Includes proceedures that enable newcomers to set up a yeast laboratory and to master basic manipulations. This volume serves as an essential reference for any beginning or experienced researcher in the field.

Investigations in Yeast Functional Genomics and Molecular Biology

Author : Matthew Eckwahl
File Size : 75.37 MB
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This book examines conserved pathways mediating cell cycle progression and cell polarity establishment. It includes examples of yeast, regulatory circuits, and feedback regulation, with emphasis on system-wide approaches. It also covers protein interaction networks and trait locus analysis and presents methods and challenges in comparative genomics analysis and evolutionary genetics.

Machine Learning and Data Mining for Yeast Functional Genomics

Author : Amanda Clare
File Size : 38.58 MB
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Yeast Functional Genomics

Author : Frédéric Devaux
File Size : 35.13 MB
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This volume provides a collection of protocols for the study of DNA-DNA contact maps, replication profiles, transcription rates, RNA secondary structures, protein-RNA interactions, ribosome profiling and quantitative proteomes and metabolomes. Written for the Methods in Molecular Biology series, 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. Authoritative and practical, Yeast Functional Genomics: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Investigations in Yeast Functional Genomics and Molecular Biology

Author : Elijah Joshua
File Size : 62.79 MB
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This book examines conserved pathways mediating cell cycle progression and cell polarity establishment. It includes examples of yeast, regulatory circuits, and feedback regulation, with emphasis on system-wide approaches. It also covers protein interaction networks and trait locus analysis and presents methods and challenges in comparative genomics analysis and evolutionary genetics.

Functional Genetics of Industrial Yeasts

Author : Johannes H. de Winde
File Size : 68.20 MB
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In recent years, new yeast species have proven their value and novel biotechnological applications have emerged. This book compiles the multi-faceted genetic repertoire of several yeasts relevant to modern biotechnology, and describes their utilization in research and application in the light of their genetic make-up and physiological characteristics. Moreover, the book presents a thorough overview of a wide array of methodologies from classical genetics to modern genomics technologies that have been and are being used in functional analysis of yeasts.

Functional and Comparative Genomics of Saccharomyces and non Saccharomyces Yeasts Potential for Industrial and Food Biotechnology

Author : Isabel Sá-Correia
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Since 1996, when the first Saccharomyces cerevisiae genome sequence was released, a wealth of genomic data has been made available for numerous S. cerevisiae strains, its close relatives, and non-conventional yeast species isolates of diverse origins. Several annotated genomes of interspecific hybrids, both within the Saccharomyces clade and outside, are now also available. This genomic information, together with functional genomics and genome engineering tools, is providing a holistic assessment of the complex cellular responses to environmental challenges, elucidating the processes underlying evolution, speciation, hybridization, domestication, and uncovering crucial aspects of yeasts´ physiological genomics to guide their biotechnological exploitation. S. cerevisiae has been used for millennia in the production of food and beverages and research over the last century and a half has generated a great deal of knowledge of this species. Despite all this, S. cerevisiae is not the best for all uses and many non-conventional yeast species have highly desirable traits that S. cerevisiae does not have. These include tolerance to different stresses (e.g. acetic acid tolerance in Zygosaccharomyces bailii, osmotolerance in Z. rouxii, and thermotolerance in Kluyveromyces marxianus and Ogataea (Hansenula) polymorpha), the capacity of assimilation of diverse carbon sources (e.g. high native capacity to metabolyze xylose and potential for the valorization of agroforest residues by Scheffersomyces (Pichia) stipites), as well as, high protein secretion, fermentation efficiency and production of desirable flavors, capacity to favor respiration over fermentation, high lipid biosynthesis and accumulation, and efficient production of chemicals other than ethanol amongst many. Several non-Saccharomyces species have already been developed as eukaryotic hosts and cell factories. Others are highly relevant as food spoilers or for desirable flavor producers. Therefore, non-conventional yeasts are now attracting increasing attention with their diversity and complexity being tackled by basic research for biotechnological applications. The interest in the exploitation of non-conventional yeasts is very high and a number of tools, such as cloning vectors, promoters, terminators, and efficient genome editing tools, have been developed to facilitate their genetic engineering. Functional and Comparative Genomics of non-conventional yeasts is elucidating the evolution of genome functions and metabolic and ecological diversity, relating their physiology to genomic features and opening the door to the application of metabolic engineering and synthetic biology to yeasts of biotechnological potential. We are entering the era of the non-conventional yeasts, increasing the exploitation of yeast biodiversity and metabolic capabilities in science and industry. In this collection the industrial properties of S. cerevisiae, in particular uses, are explored along with its closely related species and interspecific hybrids. This is followed by comparisons between S. cerevisiae and non-conventional yeasts in specific applications and then the properties of various non-conventional yeasts and their hybrids.

Applications of Functional Genomics in Studies of Yeast Signaling Networks and Genome Structure

Author : Jun Ma
File Size : 61.80 MB
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Metabolic Footprinting

Author : Jess Allen
File Size : 28.46 MB
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Yeast Functional Genomics and Proteomics

Author : Igor Stagljar
File Size : 87.1 MB
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Given the popularity and utility of Saccharomyces cerevisiae, yeast-based functional genomics and proteomics technologies, developed over the past decade, have contributed greatly to our understanding of bacterial, yeast, fly, worm and human gene functions. In Yeast Functional Genomics and Proteomics: Methods and Protocols, experts in the field contribute stand-alone protocols suitable for daily use in research laboratories. The volume examines methods from the most major and fundamental techniques to more cutting-edge, advanced concepts. As part of the highly successful Methods in Molecular BiologyTM series, the chapters are clearly formatted with 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 easy to use, Yeast Functional Genomics and Proteomics: Methods and Protocols is an ideal reference for both yeast researchers and those who wish to use yeast as a model system for the further study of functional genomics and proteomics.

Functional Genomics of Beer related Physiological Processes in Yeast

Author : Lucie Anne Hazelwood
File Size : 63.6 MB
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Plant Functional Genomics

Author : Dario Leister
File Size : 29.28 MB
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Discover cutting-edge knowledge for engineering a more productive and environment-friendly agriculture! In Plant Functional Genomics, you’ll find a cross-section of state-of-the-art research on the biological function of plant genes and how they work together in health and disease. World-leading scientists in the field present breakthrough techniques, discuss the results of projects aimed at dissecting particular plant functions, and provide an overview on the state of functional genomics for several plant and plant-related species. With figures, tables, and illustrations, this book will help scientists, researchers, and advanced students in botany find new ways of creating novel plant forms to better serve the needs of a rapidly expanding human population. Plant Functional Genomics will increase your understanding of gene networks and systems rules, as well as gene expression during specific conditions or development or treatments. This important resource contains a wealth of data generated by various plant genome sequencing projects, including the newest results from experiments with Arabidopsis thaliana—the first plant to be completely sequenced. This book also contains innovative research on: T-DNA mutagenesis transcriptomics and metabolic profiling in plants large-scale yeast two-hybrid analyses the exceptional model system of Chlamydomonas genomics functional genomics in rice, maize, and Physcomitrella prospects for functional genomics in a new model grass chloroplast and plant mitochondrial proteomics plant transporters so much more Plant Functional Genomics will help speed up the identification and isolation of genes that might be of interest with respect to diverse biological questions. This valuable contribution to the field clarifies the challenges yet to be faced and the opportunities that could some day expand the frontiers of plant sciences.

Functional Genomics of the Yeast Gene YDR533Cand Its Human Homolog DJ 1

Author : Jennifer Collins
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The Application of Yeast Functional Genomics to Haploinsufficiency Sporulation and Quantitative Trait Mapping

Author : Adam Michael Deutschbauer
File Size : 39.64 MB
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Functional Genomics of GABA Metabolism in Yeast Thermotolerance

Author :
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High Throughput Methods for Functional Genomics in Saccharomyces Cerevisiae

Author : Sarah Elizabeth Pierce
File Size : 39.34 MB
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The Saccharomyces cerevisiae deletion collection has revolutionized yeast genetics by allowing genome-wide deletion screens to be performed in pooled cultures. The inclusion of unique, 20-bp DNA sequences known as "tags" or "barcodes" in each strain allows all ~6000 yeast deletion mutants to be analyzed in a single culture by using a microarray to detect changes in tag abundance. Here we discuss improvements and extensions made to the pooled-yeast-deletion assay. This includes a redesign of the barcode array that is used for detecting the tags included in the deletion collection. Our analysis of this barcode array examines whether it is better to use available microarray surface area on a single feature for each probe, or to instead include multiple smaller features. It also covers aspects of data analysis such as the correction of hybridization defects and array saturation, tag-sequence repairs, and estimation of background hybridization. In addition to these microarray changes, we also examine the impact of experimental design on the quality of pooled growth data. Each step in both the experimental protocol and the data-analysis pipeline is examined for possible improvement. Finally, we discuss preliminary experiments testing the application of pooled fitness profiling to the study of epistasis. Data are shown that demonstrate the feasibility of a pooled-double-mutant fitness assay that is compatible with existing barcode array technology. This assay has the potential to become a valuable functional-genomics tool that may provide an improved understanding of pathway relationships in yeast.

Patterns and Determinants of Variation in Functional Genomics Phenotypes in the Yeast Saccharomyces Cerevisiae

Author : Daniel A. Skelly
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Phenotypic variation among individuals within populations is ubiquitous in the natural world, and a preeminent challenge in biology is understanding the contribution of genetic variation to this phenotypic variation. Despite technological advances in the development of genome-scale methods for querying molecular phenotypes, our understanding of the molecular basis of morphological and physiological variation remains rudimentary. In this dissertation, I outline computational methods I have developed and analyses I have conducted in the yeast Saccharomyces cerevisiae to make inferences about the relationship between DNA sequences and the molecular phenotypes to which they give rise. First, I describe a population genomics study of a class of genomic elements, intron splice sequences, in a diverse set of complete S. cerevisiae genomes. I obtained quantitative estimates of the strength of purifying selection acting on these sequences, and present analyses suggesting that introns in some subsets of genes are actively maintained in natural populations of S. cerevisiae. Next, I shift my focus to the genetic basis of variation in a particular molecular phenotype, gene expression. I examine genes that show allele-specific expression (ASE) due to cis-regulatory variation, and present a Bayesian statistical model for quantifying ASE measured by RNA-Seq. A novel feature of this model is the ability to detect variable ASE, where the level of ASE differs across a transcript, as can occur in the case of variations in transcript structure. Finally, I explore molecular phenotypic variation more comprehensively, presenting the results of an analysis of deeply phenotyped S. cerevisiae strains. I analyze genome sequence, gene expression, protein abundance, metabolite abundance, and cellular morphological phenotypes in this phenomics study. I identify abundant natural variation across all phenotypic classes, pinpoint loci that act in cis to affect RNA and protein levels, and provide initial clues as to the predictability of phenotypic traits that vary between individuals within a species. I conclude by discussing the need for new statistical models to make use of the rich information contained in functional genomics datasets and the necessity of considering environmental context when disentangling the functional consequences of genetic variation.

Investigations in Yeast Functional Genomics and Molecular Biology

Author : Matthew Eckwahl
File Size : 39.76 MB
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This title includes a number of Open Access chapters. This book examines conserved pathways mediating cell cycle progression and cell polarity establishment. It includes examples of yeast, regulatory circuits, and feedback regulation, with emphasis on system-wide approaches. It also covers protein interaction networks and trait locus analysis and presents methods and challenges in comparative genomics analysis and evolutionary genetics.

Establishment of a Genome wide Microscope based Functional Genomics Screen to Identify Microtubule Regulators in Fission Yeast

Author : Xenia Elisabeth Studera
File Size : 72.57 MB
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