Download or read book Inferring Phylogenies written by Joseph Felsenstein and published by Sinauer Associates Incorporated. This book was released on 2004-01 with total page 664 pages. Available in PDF, EPUB and Kindle. Book excerpt: Phylogenies, or evolutionary trees, are the basic structures necessary to think about and analyze differences between species. Statistical, computational, and algorithmic work in this field has been ongoing for four decades now, and there have been great advances in understanding. Yet no book has summarized this work. Inferring Phylogenies does just that in a single, compact volume. Phylogenies are inferred with various kinds of data. This book concentrates on some of the central ones: discretely coded characters, molecular sequences, gene frequencies, and quantitative traits. Also covered are restriction sites, RAPDs, and microsatellites.
Download or read book The Pangenome written by Hervé Tettelin and published by Springer Nature. This book was released on 2020-04-30 with total page 311 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book’s respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.
Download or read book Microbial Evolution written by Howard Ochman and published by . This book was released on 2016 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book The New Science of Metagenomics written by National Research Council and published by National Academies Press. This book was released on 2007-06-24 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Bacteriophages written by David R. Harper and published by Springer Nature. This book was released on 2021-01-30 with total page 1376 pages. Available in PDF, EPUB and Kindle. Book excerpt: This first major reference work dedicated to the mannifold industrial and medical applications of bacteriophages provides both theoretical and practical insights into the emerging field of bacteriophage biotechnology. The book introduces to bacteriophage biology, ecology and history and reviews the latest technologies and tools in bacteriophage detection, strain optimization and nanotechnology. Usage of bacteriophages in food safety, agriculture, and different therapeutic areas is discussed in detail. This book serves as essential guide for researchers in applied microbiology, biotechnology and medicine coming from both academia and industry.
Download or read book New Approaches to Prokaryotic Systematics written by Michael Goodfellow and published by Academic Press. This book was released on 2014-11-25 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volume 41 of Methods in Microbiology is a methods book designed to highlight procedures that will revitalize the purposes and practices of prokaryotic systematics. This volume will notably show that genomics and computational biology are pivotal to the new direction of travel and will emphasise that new developments need to be built upon historical good practices, notably the continued use of the nomenclatural type concept and the requirement to deposit type strains in at least two service culture collections in different countries.
Download or read book Horizontal Gene Transfer written by Michael Syvanen and published by Academic Press. This book was released on 2001-12-19 with total page 475 pages. Available in PDF, EPUB and Kindle. Book excerpt: The second edition of Horizontal Gene Transfer has been organized to provide a concise and up-to-date coverage of the most important discoveries in this fascinating field. Written by the most prominent gene transfer and genome analytical scientists, this book details experimental evidence for the phenomenon of horizontal gene transfer and discusses further evidence provided by the recent completion of genomic sequences from Archea, Bacteria, and Eucarya members. The relevance of horizontal gene transfer to plant and metazoan taxonomy, GM foods, antibiotic resistance, paleontology, and phylogenetic reconstruction is also explored. Horizontal Gene Transfer is essential for microbiologists, geneticists, biochemists, evolutionary biologists, infectious disease specialists, paleontologists, ecologists, and researchers working in plant/animal systematics and agriculture with an interest in gene transfer. This includes scientific researchers from government and industry concerned with the release of genetically modified organisms. - Up-to-the-minute reviews, maps, conclusions, urls to relevant websites and colour figures - Unique chapters, for example one written by paleontologists presents data for horizontal gene transfer from fingerprints form the fossil record
Download or read book The Tangled Tree written by David Quammen and published by Simon & Schuster. This book was released on 2019-08-06 with total page 480 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this New York Times bestseller and longlist nominee for the National Book Award, “our greatest living chronicler of the natural world” (The New York Times), David Quammen explains how recent discoveries in molecular biology affect our understanding of evolution and life’s history. In the mid-1970s, scientists began using DNA sequences to reexamine the history of all life. Perhaps the most startling discovery to come out of this new field—the study of life’s diversity and relatedness at the molecular level—is horizontal gene transfer (HGT), or the movement of genes across species lines. It turns out that HGT has been widespread and important; we now know that roughly eight percent of the human genome arrived sideways by viral infection—a type of HGT. In The Tangled Tree, “the grandest tale in biology….David Quammen presents the science—and the scientists involved—with patience, candor, and flair” (Nature). We learn about the major players, such as Carl Woese, the most important little-known biologist of the twentieth century; Lynn Margulis, the notorious maverick whose wild ideas about “mosaic” creatures proved to be true; and Tsutomu Wantanabe, who discovered that the scourge of antibiotic-resistant bacteria is a direct result of horizontal gene transfer, bringing the deep study of genome histories to bear on a global crisis in public health. “David Quammen proves to be an immensely well-informed guide to a complex story” (The Wall Street Journal). In The Tangled Tree, he explains how molecular studies of evolution have brought startling recognitions about the tangled tree of life—including where we humans fit upon it. Thanks to new technologies, we now have the ability to alter even our genetic composition—through sideways insertions, as nature has long been doing. “The Tangled Tree is a source of wonder….Quammen has written a deep and daring intellectual adventure” (The Boston Globe).
Download or read book Mobile DNA III written by Michael Chandler and published by John Wiley & Sons. This book was released on 2020-07-24 with total page 1321 pages. Available in PDF, EPUB and Kindle. Book excerpt: An exploration of the raw power of genetic material to refashion itself to any purpose... Virtually all organisms contain multiple mobile DNAs that can move from place to place, and in some organisms, mobile DNA elements make up a significant portion of the genome. Mobile DNA III provides a comprehensive review of recent research, including findings suggesting the important role that mobile elements play in genome evolution and stability. Editor-in-Chief Nancy L. Craig assembled a team of multidisciplinary experts to develop this cutting-edge resource that covers the specific molecular mechanisms involved in recombination, including a detailed structural analysis of the enzymes responsible presents a detailed account of the many different recombination systems that can rearrange genomes examines the tremendous impact of mobile DNA in virtually all organisms Mobile DNA III is valuable as an in-depth supplemental reading for upper level life sciences students and as a reference for investigators exploring new biological systems. Biomedical researchers will find documentation of recent advances in understanding immune-antigen conflict between host and pathogen. It introduces biotechnicians to amazing tools for in vivo control of designer DNAs. It allows specialists to pick and choose advanced reviews of specific elements and to be drawn in by unexpected parallels and contrasts among the elements in diverse organisms. Mobile DNA III provides the most lucid reviews of these complex topics available anywhere.
Download or read book Structure and Function of the Bacterial Genome written by Charles J. Dorman and published by John Wiley & Sons. This book was released on 2020-04-28 with total page 437 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents an integrated view of the expression of bacterial genetic information, genome architecture and function, and bacterial physiology and pathogenesis This book blends information from the very latest research on bacterial chromosome and nucleoid architecture, whole-genome analysis, cell signaling, and gene expression control with well-known gene regulation paradigms from model organisms (including pathogens) to give readers a picture of how information flows from the environment to the gene, modulating its expression and influencing the competitive fitness of the microbe. Structure and Function of the Bacterial Genome explores the governance of the expression of the genes that make a bacterium what it is, and updates the basics of gene expression control with information about transcription promoter structure and function, the role of DNA as a regulatory factor (in addition to its role as a carrier of genetic information), small RNAs, RNAs that sense chemical signals, ribosomes and translation, posttranslational modification of proteins, and protein secretion. It looks at the forces driving the conservation and the evolution of the dynamic genome and offers chapters that cover DNA replication, DNA repair, plasmid biology, recombination, transposition, the roles of repetitive DNA sequences, horizontal gene transfer, the defense of the genome by CRISPR-Cas, restriction enzymes, Argonaute proteins and BREX systems. The book finishes with a chapter that gives an integrated overview of genome structure and function. Blends knowledge of gene regulatory mechanisms with a consideration of nucleoid structure and dynamics Offers a 'DNA-centric' approach to considering transcription control Views horizontal gene transfer from a gene regulation perspective Assesses the opportunities and limitations of designing synthetic microbes or rewiring existing ones Structure and Function of the Bacterial Genome is an ideal book for graduate and undergraduate students studying microbial cell biology, bacterial pathogenesis, gene regulation, and molecular microbiology. It will also appeal to principal investigators conducting research on these and related topics and researchers in synthetic biology and other arms of biotechnology.
Download or read book Computational Methods for Understanding Bacterial and Archaeal Genomes written by Ying Xu and published by World Scientific. This book was released on 2008 with total page 494 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over 500 prokaryotic genomes have been sequenced to date, and thousands more have been planned for the next few years. While these genomic sequence data provide unprecedented opportunities for biologists to study the world of prokaryotes, they also raise extremely challenging issues such as how to decode the rich information encoded in these genomes. This comprehensive volume includes a collection of cohesively written chapters on prokaryotic genomes, their organization and evolution, the information they encode, and the computational approaches needed to derive such information. A comparative view of bacterial and archaeal genomes, and how information is encoded differently in them, is also presented. Combining theoretical discussions and computational techniques, the book serves as a valuable introductory textbook for graduate-level microbial genomics and informatics courses.
Download or read book The Society of Genes written by Itai Yanai and published by Harvard University Press. This book was released on 2016-01-11 with total page 295 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nearly four decades ago Richard Dawkins published The Selfish Gene, famously reducing humans to “survival machines” whose sole purpose was to preserve “the selfish molecules known as genes.” How these selfish genes work together to construct the organism, however, remained a mystery. Standing atop a wealth of new research, The Society of Genes now provides a vision of how genes cooperate and compete in the struggle for life. Pioneers in the nascent field of systems biology, Itai Yanai and Martin Lercher present a compelling new framework to understand how the human genome evolved and why understanding the interactions among our genes shifts the basic paradigm of modern biology. Contrary to what Dawkins’s popular metaphor seems to imply, the genome is not made of individual genes that focus solely on their own survival. Instead, our genomes comprise a society of genes which, like human societies, is composed of members that form alliances and rivalries. In language accessible to lay readers, The Society of Genes uncovers genetic strategies of cooperation and competition at biological scales ranging from individual cells to entire species. It captures the way the genome works in cancer cells and Neanderthals, in sexual reproduction and the origin of life, always underscoring one critical point: that only by putting the interactions among genes at center stage can we appreciate the logic of life.
Download or read book Horizontal Gene Transfer written by Maria Boekels Gogarten and published by Humana Press. This book was released on 2009-03-11 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Horizontal gene transfer (HGT) events encompass processes as varied as the exchange of genetic material between microbes coexisting in the same environment, between symbiotic bacteria and their eukaryotic hosts, and the evolution of organelles by symbiosis, in which whole genomes are acquired. In Horizontal Gene Transfer: Genomes in Flux, expert researchers contribute an overview of HGT concepts as well as specific case histories that highlight the most current progress to inspire future work. Divided into three sections, the volume begins with an overview of terminology, concepts and the implications of HGT on current evolutionary thought and philosophy, and continues with methods involving computer and bioinformatics analyses of genomic data as well as molecular biology techniques for identifying, quantifying, and differentiating instances of HGT. A section of case studies follows, which provides detailed accounts of how HGT has shaped evolution across the diversity of organisms and organismal lineages. As a volume of the highly successful Methods in Molecular BiologyTM series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results. Cutting-edge and thoroughly detailed, Horizontal Gene Transfer: Genomes in Flux examines how HGT has contributed to genome evolution and how understanding HGT impacts our ability to accurately reconstruct and comprehend the web-like evolutionary history in order to aid scientists in furthering their own research.
Download or read book Antibiotic Drug Resistance written by José-Luis Capelo-Martínez and published by John Wiley & Sons. This book was released on 2019-09-24 with total page 730 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a thorough and authoritative overview of the multifaceted field of antibiotic science – offering guidance to translate research into tools for prevention, diagnosis, and treatment of infectious diseases. Provides readers with knowledge about the broad field of drug resistance Offers guidance to translate research into tools for prevention, diagnosis, and treatment of infectious diseases Links strategies to analyze microbes to the development of new drugs, socioeconomic impacts to therapeutic strategies, and public policies to antibiotic-resistance-prevention strategies
Download or read book Prokaryotic Genomics written by Michel Blot and published by Birkhäuser. This book was released on 2013-12-01 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt: Prokaryotic Genomics provides molecular microbiologists in particular and researchers working with bacteria in general with the most important established recipes needed for their work. The volume covers both revisited classical methods and new tools for global analysis such as genomics or proteomics. It is written for those in need of a bench manual to complete their experiments and for those wanting to understand the modern tools used in microbiology.
Download or read book Fighting Campylobacter Infections written by Steffen Backert and published by Springer Nature. This book was released on 2021-02-23 with total page 334 pages. Available in PDF, EPUB and Kindle. Book excerpt: This edited volume explores Campylobacter species, which are some of the most important foodborne pathogens. Above all, contaminated poultry meat can cause human gastroenteritis in both developed and developing countries. The respective contributions reveal how these infections can also increase the risk of generalized paralytic diseases such as Guillain-Barré syndrome, Miller-Fisher syndrome, and Chinese paralytic syndrome. Due to their influence on the nervous system, circulatory system, and various organs, Campylobacter infections represent a serious public health concern. Campylobacter can be effectively combated by addressing the hygienic conditions in both food production and human lifestyles. Accordingly, the authors put forward a One Health perspective, which provides readers with essential insights into the basic biology of Campylobacter, as well as practical guidance on aspects ranging from food production to the clinical treatment of infections. Chapters 'Population Biology and Comparative Genomics of Campylobacter Species' and 'Natural Competence and Horizontal Gene Transfer in Campylobacter' are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
Download or read book Microbial Megaplasmids written by Edward Schwartz and published by Springer Science & Business Media. This book was released on 2009-01-29 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: Megaplasmids are extrachromosomal genetic elements in the size range of 100 kb and larger. They are found in physiologically and phylogenetically diverse groups of bacteria and archaea. By definition, megaplasmids are not essential for the viability of their hosts under all growth conditions, but paradoxically many megaplasmids carry the genetic information for the defining and characteristic traits of the organism in which they reside. Microbial Megaplasmids reviews our knowledge of the extensively studied representatives, such as the catabolic plasmids of the pseudomonads, the rhizobial Sym plasmids, the Ti plasmids of the genus Agrobacterium and the giant enterobacterial virulence plasmids. It also presents snapshots of more recently discovered megaplasmids. The contribution of megaplasmids to the biology of their hosts is described, highlighting the interactions between megaplasmid and chromosomal genes.
