Genomics And Evolution Of Microbial Eukaryotes

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Genomics and Evolution of Microbial Eukaryotes

Laura A Katz,Debashish Bhattacharya
Genomics and Evolution of Microbial Eukaryotes Book PDF

Author : Laura A Katz,Debashish Bhattacharya
Publisher : OUP Oxford
Page : 256 pages
File Size : 48,6 Mb
Release : 2006-09-07
Category : Science
ISBN : 9780191513855

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Genomics and Evolution of Microbial Eukaryotes by Laura A Katz,Debashish Bhattacharya Pdf

Genomics and Evolution of Eukaryotic Microbes synthesizes the rapidly emerging fields of eukaryotic diversity and genome evolution. Eukaryotes (cells with nuclei) evolved as microbes and have existed on Earth for approximately two billion years. The tremendous diversity of eukaryotic microbes (protists) is often overlooked by those who study the macroscopic eukaryotic lineages: plants, animals, and fungi. Yet, eukaryotic microbes are of critical importance to ecosystems, human health, and our desire to understand biodiversity on Earth. By bringing together groundbreaking data from genome studies of diverse eukaryotic microbes, this book elucidates the many novelties among eukaryotic genomes and provides a single resource for otherwise widely dispersed information. Eukaryotic microorganisms impact both our health and our environment. These organisms include some of the deadliest known pathogens such as Plasmodium falciparum, a causative agent of malaria, and Entamoeba histolytica an agent of dysentery. Eukaryotic microbes also play a significant role in environments through their involvement in global biogeochemical cycles. Such roles are perhaps best exemplified by the coccolithophores, including the species Emiliania huxleyi, which can create 'blooms' in the oceans that are visible from outer space (i.e. as large as the state of Alaska). Despite the great importance and breadth of eukaryotic microbes (the vast majority of major ukaryotic lineages are microbial, with plants, animals and fungi representing just three of an estimated 60-200 major lineages), our understanding of their diversity and phylogeny is only now rapidly expanding, in part bolstered by genomic studies. This book presents analyses and interpretations from experts in the field. Recent advances, particularly in DNA sequencing technologies, have made eukaryotic microbes more accessible to genome analyses. Unravelling the wealth of information on eukaryotic genomes will invariably revolutionize our understanding of eukaryotes, including their physiology, systematics, and ecology.

Genomics and Evolution of Microbial Eukaryotes

Laura Katz Olson
Genomics and Evolution of Microbial Eukaryotes Book PDF

Author : Laura Katz Olson
Publisher : Oxford University Press on Demand
Page : 256 pages
File Size : 49,5 Mb
Release : 2006-09-07
Category : Science
ISBN : 9780198569749

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Genomics and Evolution of Microbial Eukaryotes by Laura Katz Olson Pdf

This book represents a unique combination of recently-emerged information on eukaryotic microbes, evolution and genomics. Eukaryotes, cells with nuclei, evolved as microbes and have existed on Earth for approximately 2 billion years. Although currently relatively understudied, eukaryotic microorganisms are of critical importance to ecosystems (through their involvement in global biogeochemical cycles), human health (they include some of the deadliest pathogens), and our desire tounderstand global biodiversity. Recent advances, particularly in DNA sequencing technologies, are making eukaryotic microbes more accessible through genome analyses. Insights from these studies are challenging previously held theories of genome evolution, based on studies of a limited number of plants,animals and fungi.

Molecular Mechanisms of Microbial Evolution

Pabulo H. Rampelotto
Molecular Mechanisms of Microbial Evolution Book PDF

Author : Pabulo H. Rampelotto
Publisher : Springer
Page : 448 pages
File Size : 45,9 Mb
Release : 2018-10-12
Category : Science
ISBN : 9783319690780

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Molecular Mechanisms of Microbial Evolution by Pabulo H. Rampelotto Pdf

One of the most profound paradigms that have transformed our understanding about life over the last decades was the acknowledgement that microorganisms play a central role in shaping the past and present environments on Earth and the nature of all life forms. Each organism is the product of its history and all extant life traces back to common ancestors, which were microorganisms. Nowadays, microorganisms represent the vast majority of biodiversity on Earth and have survived nearly 4 billion years of evolutionary change. Microbial evolution occurred and continues to take place in a great variety of environmental conditions. However, we still know little about the processes of evolution as applied to microorganisms and microbial populations. In addition, the molecular mechanisms by which microorganisms communicate/interact with each other and with multicellular organisms remains poorly understood. Such patterns of microbe-host interaction are essential to understand the evolution of microbial symbiosis and pathogenesis.Recent advances in DNA sequencing, high-throughput technologies, and genetic manipulation systems have enabled studies that directly characterize the molecular and genomic bases of evolution, producing data that are making us change our view of the microbial world. The notion that mutations in the coding regions of genomes are, in combination with selective forces, the main contributors to biodiversity needs to be re-examined as evidence accumulates, indicating that many non-coding regions that contain regulatory signals show a high rate of variation even among closely related organisms. Comparative analyses of an increasing number of closely related microbial genomes have yielded exciting insight into the sources of microbial genome variability with respect to gene content, gene order and evolution of genes with unknown functions. Furthermore, laboratory studies (i.e. experimental microbial evolution) are providing fundamental biological insight through direct observation of the evolution process. They not only enable testing evolutionary theory and principles, but also have applications to metabolic engineering and human health. Overall, these studies ranging from viruses to Bacteria to microbial Eukaryotes are illuminating the mechanisms of evolution at a resolution that Darwin, Delbruck and Dobzhansky could barely have imagined. Consequently, it is timely to review and highlight the progress so far as well as discuss what remains unknown and requires future research. This book explores the current state of knowledge on the molecular mechanisms of microbial evolution with a collection of papers written by authors who are leading experts in the field.

Organelles, Genomes and Eukaryote Phylogeny

Robert P Hirt,David S. Horner
Organelles Genomes and Eukaryote Phylogeny Book PDF

Author : Robert P Hirt,David S. Horner
Publisher : CRC Press
Page : 462 pages
File Size : 51,5 Mb
Release : 2004-06-28
Category : Science
ISBN : 9780203508930

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Organelles, Genomes and Eukaryote Phylogeny by Robert P Hirt,David S. Horner Pdf

The recent revolution in molecular biology has spread through every field of biology including systematics and evolution. Researchers can now analyze the genomes of different species relatively quickly, and this is generating a great deal of data and theories about relationships between taxa as well as how they originated and diversified. Org

Molecular Mechanisms of Microbial Evolution

Pabulo H. Rampelotto
Molecular Mechanisms of Microbial Evolution Book PDF

Author : Pabulo H. Rampelotto
Publisher : Unknown
Page : 128 pages
File Size : 52,6 Mb
Release : 2018
Category : SCIENCE
ISBN : 3319690795

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Molecular Mechanisms of Microbial Evolution by Pabulo H. Rampelotto Pdf

One of the most profound paradigms that have transformed our understanding about life over the last decades was the acknowledgement that microorganisms play a central role in shaping the past and present environments on Earth and the nature of all life forms. Each organism is the product of its history and all extant life traces back to common ancestors, which were microorganisms. Nowadays, microorganisms represent the vast majority of biodiversity on Earth and have survived nearly 4 billion years of evolutionary change. Microbial evolution occurred and continues to take place in a great variety of environmental conditions. However, we still know little about the processes of evolution as applied to microorganisms and microbial populations. In addition, the molecular mechanisms by which microorganisms communicate/interact with each other and with multicellular organisms remains poorly understood. Such patterns of microbe-host interaction are essential to understand the evolution of microbial symbiosis and pathogenesis. Recent advances in DNA sequencing, high-throughput technologies, and genetic manipulation systems have enabled studies that directly characterize the molecular and genomic bases of evolution, producing data that are making us change our view of the microbial world. The notion that mutations in the coding regions of genomes are, in combination with selective forces, the main contributors to biodiversity needs to be re-examined as evidence accumulates, indicating that many non-coding regions that contain regulatory signals show a high rate of variation even among closely related organisms. Comparative analyses of an increasing number of closely related microbial genomes have yielded exciting insight into the sources of microbial genome variability with respect to gene content, gene order and evolution of genes with unknown functions. Furthermore, laboratory studies (i.e. experimental microbial evolution) are providing fundamental biological insight through direct observation of the evolution process. They not only enable testing evolutionary theory and principles, but also have applications to metabolic engineering and human health. Overall, these studies ranging from viruses to Bacteria to microbial Eukaryotes are illuminating the mechanisms of evolution at a resolution that Darwin, Delbruck and Dobzhansky could barely have imagined. Consequently, it is timely to review and highlight the progress so far as well as discuss what remains unknown and requires future research. This book explores the current state of knowledge on the molecular mechanisms of microbial evolution with a collection of papers written by authors who are leading experts in the field.

Microbial genomics challenge Darwin

Didier Raoult,Eugene V. Koonin
Microbial genomics challenge Darwin Book PDF

Author : Didier Raoult,Eugene V. Koonin
Publisher : Frontiers E-books
Page : 179 pages
File Size : 53,9 Mb
Release : 2024-06-29
Category : Electronic
ISBN : 9782889191222

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Microbial genomics challenge Darwin by Didier Raoult,Eugene V. Koonin Pdf

The 200th anniversary of Darwin’s birthday was celebrated in 2009, making the concept of Darwinism even more popular than at the time it was originally proposed, to the extent that it has acquired quasi-religious status. His theory revolves around a Tree of Life in which all living organisms are considered to have descended from a single ancestor, and each node represents a common ancestor. It comprises hierarchy and dichotomy, which are typical characteristics of the post-biblical 19th century vision. Indeed, according to post-modern philosophy (also called the French theory) the majority of theories, including scientific ones, are based only on meta-narratives expressing the influence of a culture at a given time. Buddhism or Hinduism may have generated a very different story of evolution. Our way of thinking about life, and the way we describe evolution, have changed radically in the 21st century due to the genomic revolution. Comparative genome analyses have demonstrated that gene repertoires are characterized by plasticity, and there is strong evidence that nearly all genes have been exchanged at some point. Genomic data show that the genetic information of living organisms is inherited not only vertically but also laterally. Lateral gene transfers were at first observed only in bacteria, which contain genes originating from eukaryotes, Archaea and viruses. Such transfers were subsequently identified in all living organisms; giant viruses have chimeric genomes and the human genome is a mosaic of genes with eukaryotic, bacterial, and viral origins. We cannot identify a single common ancestor for the gene repertoire of any organism. Furthermore, a very high proportion of genes have been newly created through gene fusion or degradation, and others show no homology to sequences found in other species. It is now clear that every living organism has a variety of ancestors, while exchanges between species are intense, and the creation of new genes is frequent and permanent in all living organisms. Our current genomic knowledge contradicts the tree of life theory, as established by Darwin. Recent analyses have produced bushes rather than resolved trees, with the structure of some parts remaining elusive. It becomes more and more obvious that phylogenetic relationships are better described by forests and networks and that species evolution looks more like a rhizome. The chimerism and mosaic structure of all living organisms through both non-vertical inheritance and de novo creation can only be assimilated and described by a post-Darwinist concept. In this Research Topic we wish to highlight the influence of microbiology and genomics on our understanding of the complexity of gene repertoires, and also demonstrate how current knowledge does not support Darwin’s theory. Microbiology has offered a great advance in the way we perceive life. Evidence obtained from studies on bacterial and viral evolution, lateral inheritance, phylogenetic trees and biodiversity continues to challenge what constituted, until recently, an unimpeded dogma in biology.

Microbial Evolution

Howard Ochman
Microbial Evolution Book PDF

Author : Howard Ochman
Publisher : Unknown
Page : 0 pages
File Size : 52,7 Mb
Release : 2016
Category : Science
ISBN : 1621820378

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Microbial Evolution by Howard Ochman Pdf

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.

Lateral Gene Transfer in Evolution

Uri Gophna
Lateral Gene Transfer in Evolution Book PDF

Author : Uri Gophna
Publisher : Springer Science & Business Media
Page : 290 pages
File Size : 42,6 Mb
Release : 2013-07-20
Category : Medical
ISBN : 9781461477808

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Lateral Gene Transfer in Evolution by Uri Gophna Pdf

Although the phenomenon of lateral gene transfer has been known since the 1940's, it was the genomics era that has really revealed the extent and many facets of this evolutionary/genetic phenomenon. Even in the early 2000s with but a handful of genomes available it became clear that the nature of microorganisms is full of genetic exchange between lineages that are sometimes far apart. The years following this saw an explosion of genomic data, which shook the "tree of life" and also raised doubts about the most appropriate species concepts for prokaryotes. This book attempts to represent the many-fold contributions of LGT to the evolution of micro and, to an extent, macro-organisms by focusing on the areas where the Editor felt it had the largest impact: metabolic innovations and adaptations and speciation.

Evolution of Microbial Life

Society for General Microbiology. Symposium,David McLean Roberts
Evolution of Microbial Life Book PDF

Author : Society for General Microbiology. Symposium,David McLean Roberts
Publisher : Cambridge University Press
Page : 318 pages
File Size : 44,9 Mb
Release : 1996-11-13
Category : Medical
ISBN : 0521564328

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Evolution of Microbial Life by Society for General Microbiology. Symposium,David McLean Roberts Pdf

This volume considers the evolution and diversification of early unicellular life.

In the Light of Evolution

National Academy of Sciences
In the Light of Evolution Book PDF

Author : National Academy of Sciences
Publisher : Sackler Colloquium
Page : 388 pages
File Size : 45,8 Mb
Release : 2007
Category : Science
ISBN : UOM:39015073872999

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In the Light of Evolution by National Academy of Sciences Pdf

The Arthur M. Sackler Colloquia of the National Academy of Sciences address scientific topics of broad and current interest, cutting across the boundaries of traditional disciplines. Each year, four or five such colloquia are scheduled, typically two days in length and international in scope. Colloquia are organized by a member of the Academy, often with the assistance of an organizing committee, and feature presentations by leading scientists in the field and discussions with a hundred or more researchers with an interest in the topic. Colloquia presentations are recorded and posted on the National Academy of Sciences Sackler colloquia website and published on CD-ROM. These Colloquia are made possible by a generous gift from Mrs. Jill Sackler, in memory of her husband, Arthur M. Sackler.

Microbial Phylogeny and Evolution

Jan Sapp
Microbial Phylogeny and Evolution Book PDF

Author : Jan Sapp
Publisher : Oxford University Press
Page : 352 pages
File Size : 40,7 Mb
Release : 2005-03-03
Category : Science
ISBN : 0198037775

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Microbial Phylogeny and Evolution by Jan Sapp Pdf

The birth of bacterial genomics since the mid-1990s brought withit several conceptual modifications and wholly new controversies. Working beyond the scope of the neo-Darwinian evolutionary synthesis, a group of leading microbial evolutionists addresses the following and related issues, often with markedly varied viewpoints: ? Did the eukaryotic nucleus, cytoskeleton and cilia also orginate from symbiosis? ? Do the current scenarios about he origin of mitochondria and plastids require revision? ? What is the extent of lateral gene transfer (between "species") among bacteria? ? Does the rDNA phylogenetic tree still stand in the age of genomics? ? Is the course of the first 3 billion years of evolution even knowable?

Prokaryotes and Evolution

Jean-Claude Bertrand,Philippe Normand,Bernard Ollivier,Télesphore Sime-Ngando
Prokaryotes and Evolution Book PDF

Author : Jean-Claude Bertrand,Philippe Normand,Bernard Ollivier,Télesphore Sime-Ngando
Publisher : Springer
Page : 396 pages
File Size : 49,9 Mb
Release : 2019-01-01
Category : Science
ISBN : 9783319997841

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Prokaryotes and Evolution by Jean-Claude Bertrand,Philippe Normand,Bernard Ollivier,Télesphore Sime-Ngando Pdf

The purpose of this book is to show the essential and indispensable role of prokaryotes in the evolution of aliving world. The evolutionary success of prokaryotes is explained together with their role in the evolution of the geosphere, the biosphere and its functioning, as well as their ability to colonize all biotopes, including the most extreme ones. We consider that all past and present living beings emerged from prokaryotes and have interacted with them. Forces and mechanisms presented in the various theories of evolution apply to prokaryotes. The major stages of their evolution and biodiversity are also described. Finally, it is emphasized that prokaryotes are living organisms that provide indisputable evidence of evolutionary processes. Many examples of ongoing evolution in prokaryotes, observable at the human scale, are provided.

Microbial Evolution under Extreme Conditions

Corien Bakermans
Microbial Evolution under Extreme Conditions Book PDF

Author : Corien Bakermans
Publisher : Walter de Gruyter GmbH & Co KG
Page : 290 pages
File Size : 45,9 Mb
Release : 2015-03-10
Category : Nature
ISBN : 9783110340716

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Microbial Evolution under Extreme Conditions by Corien Bakermans Pdf

Today's microorganisms represent the vast majority of biodiversity on Earth and have survived nearly 4 billion years of evolutionary change. However, we still know little about the processes of evolution as applied to microorganisms and microbial populations. Microbial evolution occurred and continues to take place in a vast variety of environmental conditions that range from anoxic to oxic, from hot to cold, from free-living to symbiotic, etc. Some of these physicochemical conditions are considered "extreme", particularly when inhabitants are limited to microorganisms. It is easy to imagine that microbial life in extreme environments is somehow more constrained and perhaps subjected to different evolutionary pressures. But what do we actually know about microbial evolution under extreme conditions and how can we apply that knowledge to other conditions? Appealingly, extreme environments with their relatively limited numbers of inhabitants can serve as good model systems for the study of evolutionary processes. A look at the microbial inhabitants of today's extreme environments provides a snapshot in time of evolution and adaptation to extreme conditions. These adaptations manifest at different levels from established communities and species to genome content and changes in specific genes that result in altered function or gene expression. But as a recent (2011) report from the American Academy of Microbiology observes: "A complex issue in the study of microbial evolution is unraveling the process of evolution from that of adaptation. In many cases, microbes have the capacity to adapt to various environmental changes by changing gene expression or community composition as opposed to having to evolve entirely new capabilities." We have learned much about how microbes are adapted to extreme conditions but relatively little is known about these adaptations evolved. How did the different processes of evolution such as mutation, immigration, horizontal (lateral) gene transfer, recombination, hybridization, genetic drift, fixation, positive and negative selection, and selective screens contribute to the evolution of these genes, genomes, microbial species, communities, and functions? What are typical rates of these processes? How prevalent are each of these processes under different conditions? This book explores the current state of knowledge about microbial evolution under extreme conditions and addresses the following questions: What is known about the processes of microbial evolution (mechanisms, rates, etc.) under extreme conditions? Can this knowledge be applied to other systems and what is the broader relevance? What remains unknown and requires future research? These questions will be addressed from several perspectives including different extreme environments, specific organisms, and specific evolutionary processes.

The Eukaryote Genome in Development and Evolution

John Bernard
The Eukaryote Genome in Development and Evolution Book PDF

Author : John Bernard
Publisher : Springer Science & Business Media
Page : 432 pages
File Size : 40,9 Mb
Release : 2012-12-06
Category : Science
ISBN : 9789401159913

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The Eukaryote Genome in Development and Evolution by John Bernard Pdf

'The mind unlearns with difficulty what has long been impressed upon it. ' Seneca Reductionism, is, without question, the most successful analytical approach available to the experimental scientist. With the advent of techniques for cloning and sequencing DNA, and the development of a variety of molecular probes for localizing macromolecules in cells and tissues, the biologist now has available the most powerful reductionist tools ever invented. The application of these new technologies has led to a veritable explosion of facts regarding the types and organization of nucleotide sequences present in the genomes of eukaryotes. These data offer a level of precision and predictability which is unparalleled in biology. Recombinant DNA techniques were initially developed to gather information about the structure and organization of the DNA sequences within a genome. The power and potential of these techniques, however, extend far beyond simple data collection of this kind. In an attempt to use the new technology as a basis for analyzing development and evolution, attention was first focused on the topic of gene regulation, an approach that had proven so successful in prokaryotes. It is now clear that this has not been an adequate approach. Lewin (1984) has quoted Brenner as stating 'at the beginning it was said that the answer to the understanding of development was going to come from a knowledge of the molecular mechanisms of gene control. I doubt whether anyone believes this any more.

The New Science of Metagenomics

National Research Council,Division on Earth and Life Studies,Board on Life Sciences,Committee on Metagenomics: Challenges and Functional Applications
The New Science of Metagenomics Book PDF

Author : National Research Council,Division on Earth and Life Studies,Board on Life Sciences,Committee on Metagenomics: Challenges and Functional Applications
Publisher : National Academies Press
Page : 170 pages
File Size : 46,9 Mb
Release : 2007-06-24
Category : Science
ISBN : 9780309106764

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The New Science of Metagenomics by National Research Council,Division on Earth and Life Studies,Board on Life Sciences,Committee on Metagenomics: Challenges and Functional Applications Pdf

Although we can't usually see them, microbes are essential for every part of human life-indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying-one at a time-the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.