Genetic Determinants Of Phenotypic Evolution In Saccharomyces Yeast PDF Download
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Author | : Jeremy Roop Roop |
Publisher | : |
Total Pages | : 120 |
Release | : 2016 |
Genre | : |
ISBN | : |
Download Genetic Determinants of Phenotypic Evolution in Saccharomyces Yeast Book in PDF, ePub and Kindle
Years of trait mapping studies have uncovered the genetic determinants underlying phenotypic evolution over both short and long timescales in a variety of organisms. A more general understanding of the mechanisms through which evolution produces phenotypic novelty, however, still remains out of reach. Many outstanding questions remain, among them how coding sequence divergence and gene expression divergence respectively contribute to trait evolution, as well as what role rare and large effect genetic variants play in the genetic networks underlying evolving phenotypes. Using Saccharomyces yeast as a genetically tractable model system in which to probe these questions, we identify and dissect several examples of trait divergence within and between yeast species. We first investigate an instance of intraspecific variation among yeasts isolated from a single population, finding that large effect rare variants at hypermutable loci are drivers of many common morphological and growth phenotypes. Next, in a comparison of both recently-diverged and long-diverged species, we investigate the role that gene expression variation plays in phenotypic evolution. We find evidence in multiple gene networks for complex and coherent regulatory evolution, and in one instance we succeed in identifying the loci that effect this change, as well as several phenotypic novelties they produce. Collectively, these investigations will contribute to the growing body of literature that describe the genetic mechanisms that underlie phenotypic change and seek, eventually, to achieve a greater understanding of basic evolutionary principles.
Author | : Hana Lee |
Publisher | : |
Total Pages | : 102 |
Release | : 2012 |
Genre | : |
ISBN | : |
Download Investigating Genetic Determinants of Phenotypic Variation in Natural Isolates of Saccharomyces Cerevisiae Book in PDF, ePub and Kindle
The causal link between genotype and phenotype is one of the fundamental principles of modern biology; yet there remain significant challenges to successfully identifying and validating the effect of a specific genetic variant on an organism. Much of the tremendous diversity observed in nature, even among individuals of the same species, remains unexplained. Here, we used the model eukaryote, Saccharomyces cerevisiae, to investigate naturally occurring variation and employ a candidate gene approach, through a combination of genome sequence analysis and mining functional gene annotations, to identify genetic determinants of the phenotypes observed. First, we took a look at morphological variation, a major source of biological diversity, in an environmental isolate of S. cerevisiae and found that its allele of CDC28 underlies multiple phenotypes: linearly arranged spores after meiosis, elongated cell shape during mitosis, and branching filaments during filamentous growth. Second, we studied a wild yeast population, using a comparative transcriptomics approach, which revealed divergence in iron metabolism that exhibited itself as slow growth in a high iron environment. We again identified two of the genetic determinants, YAP5 and CCC1, both essential for resistance to iron toxicity, that contribute to the phenotype and show evidence that genes involved in iron homeostasis have undergone non-neutral evolution. Our work illustrates the viability of using genomic data to successfully predict the genes responsible for phenotypes of interest as well as the power of yeast a model system for investigating natural variation.
Author | : Daniel A. Skelly |
Publisher | : |
Total Pages | : 188 |
Release | : 2012 |
Genre | : |
ISBN | : |
Download Patterns and Determinants of Variation in Functional Genomics Phenotypes in the Yeast Saccharomyces Cerevisiae Book in PDF, ePub and Kindle
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.
Author | : Howard Ochman |
Publisher | : |
Total Pages | : 0 |
Release | : 2016 |
Genre | : Science |
ISBN | : 9781621820376 |
Download Microbial Evolution Book in PDF, ePub and Kindle
Bacteria have been the dominant forms of life on Earth for the past 3.5 billion years. They rapidly evolve, constantly changing their genetic architecture through horizontal DNA transfer and other mechanisms. Consequently, it can be difficult to define individual species and determine how they are related. Written and edited by experts in the field, this collection from Cold Spring Harbor Perspectives in Biology examines how bacteria and other microbes evolve, focusing on insights from genomics-based studies. Contributors discuss the origins of new microbial populations, the evolutionary and ecological mechanisms that keep species separate once they have diverged, and the challenges of constructing phylogenetic trees that accurately reflect their relationships. They describe the organization of microbial genomes, the various mutations that occur, including the birth of new genes de novo and by duplication, and how natural selection acts on those changes. The role of horizontal gene transfer as a strong driver of microbial evolution is emphasized throughout. The authors also explore the geologic evidence for early microbial evolution and describe the use of microbial evolution experiments to examine phenomena like natural selection. This volume will thus be essential reading for all microbial ecologists, population geneticists, and evolutionary biologists.
Author | : Ivan Emmanuel Wallin |
Publisher | : Рипол Классик |
Total Pages | : 208 |
Release | : 1927 |
Genre | : History |
ISBN | : |
Download Symbionticism and the Origin of Species Book in PDF, ePub and Kindle
Author | : Ruth Ashbee |
Publisher | : Springer Science & Business Media |
Total Pages | : 367 |
Release | : 2009-10-27 |
Genre | : Science |
ISBN | : 3642031501 |
Download Pathogenic Yeasts Book in PDF, ePub and Kindle
Mycological studies of yeasts are entering a new phase, with the sequencing of multiple fungal genomes informing our understanding of their ability to cause disease and interact with the host. At the same time, the ongoing use of traditional methods in many clinical mycology laboratories continues to provide information for the diagnosis and treatment of patients. This volume reviews various aspects of pathogenic yeasts and what is known about their molecular and cellular biology and virulence, in addition to looking at clinical and laboratory findings. As each chapter is written by a leading expert in the field, this book summarizes in one volume much of the latest research on several pathogenic yeasts, including Candida, Cryptococcus, Malassezia and yeasts of emerging importance. The importance of laboratory diagnosis, antifungal susceptibility testing, antifungal resistance and yeast diseases in animals are reviewed.
Author | : National Research Council |
Publisher | : National Academies Press |
Total Pages | : 348 |
Release | : 2000-12-21 |
Genre | : Nature |
ISBN | : 0309070864 |
Download Scientific Frontiers in Developmental Toxicology and Risk Assessment Book in PDF, ePub and Kindle
Scientific Frontiers in Developmental Toxicology and Risk Assessment reviews advances made during the last 10-15 years in fields such as developmental biology, molecular biology, and genetics. It describes a novel approach for how these advances might be used in combination with existing methodologies to further the understanding of mechanisms of developmental toxicity, to improve the assessment of chemicals for their ability to cause developmental toxicity, and to improve risk assessment for developmental defects. For example, based on the recent advances, even the smallest, simplest laboratory animals such as the fruit fly, roundworm, and zebrafish might be able to serve as developmental toxicological models for human biological systems. Use of such organisms might allow for rapid and inexpensive testing of large numbers of chemicals for their potential to cause developmental toxicity; presently, there are little or no developmental toxicity data available for the majority of natural and manufactured chemicals in use. This new approach to developmental toxicology and risk assessment will require simultaneous research on several fronts by experts from multiple scientific disciplines, including developmental toxicologists, developmental biologists, geneticists, epidemiologists, and biostatisticians.
Author | : |
Publisher | : Elsevier |
Total Pages | : 482 |
Release | : 2012-12-02 |
Genre | : Nature |
ISBN | : 0323140068 |
Download Molecular Biology of the Fission Yeast Book in PDF, ePub and Kindle
This highly researched yeast, which represents a system used by cell biologists, geneticists and molecular biologists, has been given only minimal coverage in the literature. Its properties make it an excellent organism for DNA and related biotechnology reseach. This book, which is the first attempt to collate existing information in one source, will be an invaluable aid to those initiating projects with this organism.
Author | : Susumu Ohno |
Publisher | : Springer Science & Business Media |
Total Pages | : 171 |
Release | : 2013-12-11 |
Genre | : Medical |
ISBN | : 364286659X |
Download Evolution by Gene Duplication Book in PDF, ePub and Kindle
It is said that "necessity is the mother of invention". To be sure, wheels and pulleys were invented out of necessity by the tenacious minds of upright citi zens. Looking at the history of mankind, however, one has to add that "Ieisure is the mother of cultural improvement". Man's creative genius flourished only when his mind, freed from the worry of daily toils, was permitted to entertain apparently useless thoughts. In the same manner, one might say with regard to evolution that "natural selection mere(y tnodifted, while redundanry created". Natural selection has been extremely effective in policing alleHe mutations which arise in already existing gene loci. Because of natural selection, organisms have been able to adapt to changing environments, and by adaptive radiation many new species were created from a common ancestral form. Y et, being an effective policeman, natural selection is extremely conservative by nature. Had evolution been entirely dependent upon natural selection, from a bacterium only numerous forms of bacteria would have emerged. The creation of metazoans, vertebrates and finally mammals from unicellular organisms would have been quite impos sible, for such big leaps in evolution required the creation of new gene loci with previously nonexistent functions. Only the cistron which became redun dant was able to escape from the relentless pressure of natural selection, and by escaping, it accumulated formerly forbidden mutations to emerge as a new gene locus.
Author | : Xinghua Mindy Shi |
Publisher | : Humana |
Total Pages | : 252 |
Release | : 2021-01-02 |
Genre | : Science |
ISBN | : 9781071600283 |
Download eQTL Analysis Book in PDF, ePub and Kindle
This volume details state-of-art eQTL analysis, where interdisciplinary researchers are provided both theoretical and practical guidance to eQTL analysis and interpretation. Chapters guide readers through methods and tools for eQTL and QTL analysis and the usage of such analysis in various scenarios. 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. Authoritative and cutting-edge, eQTL Analysis: Methods and Protocols to ensure successful results in the further study of this vital field.