Host and Microbe Adaptations in the Evolution of Immunity

Host and Microbe Adaptations in the Evolution of Immunity PDF

Author: Larry J. Dishaw

Publisher: Frontiers Media SA

Published: 2019-12-31

Total Pages: 254

ISBN-13: 2889630226

DOWNLOAD EBOOK →

The evolution of metazoans has been accompanied by new interfaces with the microbial environment that include biological barriers and surveillance by specialized cell types. Increasingly complex organisms require increased capacities to confront pathogens, achieved by co-evolution of recognition mechanisms and regulatory pathways. Two distinct but interactive forms of immunity have evolved. Innate immunity, shared by all metazoans, is traditionally viewed as simple and non-specific. Adaptive immunity possesses the capacity to anticipate new infectious challenges and recall previous exposures; the most well-understood example of such a system, exhibited by lymphocytes of vertebrates, is based on somatic gene alterations that generate extraordinary specificity in discrimination of molecular structures. Our understanding of immune phylogeny over the past decades has tried to reconcile immunity from a vertebrate standpoint. While informative, such approaches cannot completely address the complex nature of selective pressures brought to bear by the complex microbiota (including pathogens) that co-exist with all metazoans. In recent years, comparative studies (and new technologies) have broadened our concepts of immunity from a systems-wide perspective. Unexpected findings, e.g., genetic expansions of innate receptors, high levels of polymorphism, RNA-based forms of generating diversity, adaptive evolution and functional divergence of gene families and the recognition of novel mediators of adaptive immunity, prompt us to reconsider the very nature of immunity. Even fundamental paradigms as to how the jawed vertebrate adaptive immune system should be structured for “optimal” recognition potential have been disrupted more than once (e.g., the discovery of the multicluster organization and germline joining of immunoglobulin genes in sharks, gene conversion as a mechanism of somatic diversification, absence of IgM or MHC II in certain teleost fishes). Mechanistically, concepts of innate immune memory, often referred to as “trained memory,” have been realized further, with the development of new discoveries in studies of epigenetic regulation of somatic lineages. Immune systems innovate and adapt in a taxon-specific manner, driven by the complexity of interactions with microbial symbionts (commensals, mutualists and pathogens). Immune systems are shaped by selective forces that reflect consequences of dynamic interactions with microbial environments as well as a capacity for rapid change that can be facilitated by genomic instabilities. We have learned that characterizing receptors and receptor interactions is not necessarily the most significant component in understanding the evolution of immunity. Rather, such a subject needs to be understood from a more global perspective and will necessitate re-consideration of the physical barriers that afford protection and the developmental processes that create them. By far, the most significant paradigm shifts in our understanding of immunity and the infection process has been that microbes no longer are considered to be an automatic cause or consequence of illness, but rather integral components of normal physiology and homeostasis. Immune phylogeny has been shaped not only by an arms race with pathogens but also perhaps by mutualistic interactions with resident microbes. This Research Topic updates and extends the previous eBook on Changing Views of the Evolution of Immunity and contains peer-reviewed submissions of original research, reviews and opinions.

Janeway's Immunobiology

Janeway's Immunobiology PDF

Author: Kenneth Murphy

Publisher: Garland Science

Published: 2010-06-22

Total Pages:

ISBN-13: 9780815344575

DOWNLOAD EBOOK →

The Janeway's Immunobiology CD-ROM, Immunobiology Interactive, is included with each book, and can be purchased separately. It contains animations and videos with voiceover narration, as well as the figures from the text for presentation purposes.

Microbial Evolution and Co-Adaptation

Microbial Evolution and Co-Adaptation PDF

Author: Institute of Medicine

Publisher: National Academies Press

Published: 2009-05-10

Total Pages: 330

ISBN-13: 0309131219

DOWNLOAD EBOOK →

Dr. Joshua Lederberg - scientist, Nobel laureate, visionary thinker, and friend of the Forum on Microbial Threats - died on February 2, 2008. It was in his honor that the Institute of Medicine's Forum on Microbial Threats convened a public workshop on May 20-21, 2008, to examine Dr. Lederberg's scientific and policy contributions to the marketplace of ideas in the life sciences, medicine, and public policy. The resulting workshop summary, Microbial Evolution and Co-Adaptation, demonstrates the extent to which conceptual and technological developments have, within a few short years, advanced our collective understanding of the microbiome, microbial genetics, microbial communities, and microbe-host-environment interactions.

Adaptations to a Microbial World

Adaptations to a Microbial World PDF

Author: Angela Michelle Early

Publisher:

Published: 2014

Total Pages: 322

ISBN-13:

DOWNLOAD EBOOK →

Organisms are in constant contact with both harmful and benign microbes. Evolutionary approaches can enrich our understanding of these interactions and provide insight into their dynamics through time and across space. Here, I present an evolutionary study of the fruit fly Drosophila melanogaster to investigate the multiple ways microbes and parasites have shaped the evolution of this model host. Chapter 1 explores D. melanogaster's interactions with its gut bacteria. Using 37 inbred fly lines, I found that fly genotypes differ in their amount of gut bacteria. Gut microbiome size correlated with other phenotypes assayed in these lines, suggesting that commensal bacterial load may influence aspects of fly fitness-from nutrient allocation to mating behavior. While the fly only transiently interacts with these gut microbes, it maintains a lifelong relationship with the endosymbiont Wolbachia pipientis. In Chapter 2, I present a phylogenetic analysis of 65 globally distributed Wolbachia and mitochondrial genomes. Wolbachia infections showed strong geographic structuring and no evidence of horizontal transmission or recombination. Demonstrating a tight evolutionary relationship between host and bacteria, I determined that all extant Wolbachia infections in D. melanogaster are monophyletic, coalescing to a single infected individual approximately 2200 years ago. Chapter 3 more broadly considers all classes of parasites, pathogens, and commensals. Leveraging our extensive knowledge of D. melanogaster gene function, I infer global variation in pathogen-induced selection pressures, and find that immune processes differ in extent and route of local adaptation. Parasitoid wasps and viruses have most profoundly impacted the recent evolution of D. melanogaster immune genes, but the underlying genetic architectures of these adaptive events differ. Genes also experience intra-cellular selection pressures. In Chapter 4, I investigate how these intra-organismal forces shape immune gene adaptation by calculating metrics of network position and pleiotropy for each D. melanogaster immune gene. I found that protein-protein interactions constrain a gene's adaptive potential, but that this constraint is most apparent in processes that experience strong directional selection. Taken together, these studies provide a more complete picture of the multi-faceted nature of host-microbe interactions, and establish an expanded framework for future research in Drosophila immunity.

The Hologenome Concept: Human, Animal and Plant Microbiota

The Hologenome Concept: Human, Animal and Plant Microbiota PDF

Author: Eugene Rosenberg

Publisher: Springer Science & Business Media

Published: 2014-01-31

Total Pages: 187

ISBN-13: 3319042416

DOWNLOAD EBOOK →

Groundbreaking research over the last 10 years has given rise to the hologenome concept of evolution. This concept posits that the holobiont (host plus all of its associated microorganisms) and its hologenome (sum of the genetic information of the host and its symbiotic microorganisms), acting in concert, function as a unique biological entity and therefore as a level of selection in evolution. All animals and plants harbor abundant and diverse microbiota, including viruses. Often the amount of symbiotic microorganisms and their combined genetic information far exceed that of their host. The microbiota with its microbiome, together with the host genome, can be transmitted from one generation to the next and thus propagate the unique properties of the holobiont. The microbial symbionts and the host interact in a cooperative way that affects the health of the holobiont within its environment. Beneficial microbiota protects against pathogens, provides essential nutrients, catabolizes complex polysaccharides, renders harmful chemicals inert, and contributes to the performance of the immune system. In humans and animals, the microbiota also plays a role in behavior. The sum of these cooperative interactions characterizes the holobiont as a unique biological entity. Genetic variation in the hologenome can be brought about by changes in either the host genome or the microbial population genomes (microbiome). Evolution by cooperation can occur by amplifying existing microbes, gaining novel microbiota and by acquiring microbial and viral genes. Under environmental stress, the microbiome can change more rapidly and in response to more processes than the host organism alone and thus influences the evolution of the holobiont. Prebiotics, probiotics, synbiotics and phage therapy are discussed as applied aspects of the hologenome concept.

The Social Biology of Microbial Communities

The Social Biology of Microbial Communities PDF

Author: Institute of Medicine

Publisher: National Academies Press

Published: 2013-01-10

Total Pages: 633

ISBN-13: 0309264324

DOWNLOAD EBOOK →

Beginning with the germ theory of disease in the 19th century and extending through most of the 20th century, microbes were believed to live their lives as solitary, unicellular, disease-causing organisms . This perception stemmed from the focus of most investigators on organisms that could be grown in the laboratory as cellular monocultures, often dispersed in liquid, and under ambient conditions of temperature, lighting, and humidity. Most such inquiries were designed to identify microbial pathogens by satisfying Koch's postulates.3 This pathogen-centric approach to the study of microorganisms produced a metaphorical "war" against these microbial invaders waged with antibiotic therapies, while simultaneously obscuring the dynamic relationships that exist among and between host organisms and their associated microorganisms-only a tiny fraction of which act as pathogens. Despite their obvious importance, very little is actually known about the processes and factors that influence the assembly, function, and stability of microbial communities. Gaining this knowledge will require a seismic shift away from the study of individual microbes in isolation to inquiries into the nature of diverse and often complex microbial communities, the forces that shape them, and their relationships with other communities and organisms, including their multicellular hosts. On March 6 and 7, 2012, the Institute of Medicine's (IOM's) Forum on Microbial Threats hosted a public workshop to explore the emerging science of the "social biology" of microbial communities. Workshop presentations and discussions embraced a wide spectrum of topics, experimental systems, and theoretical perspectives representative of the current, multifaceted exploration of the microbial frontier. Participants discussed ecological, evolutionary, and genetic factors contributing to the assembly, function, and stability of microbial communities; how microbial communities adapt and respond to environmental stimuli; theoretical and experimental approaches to advance this nascent field; and potential applications of knowledge gained from the study of microbial communities for the improvement of human, animal, plant, and ecosystem health and toward a deeper understanding of microbial diversity and evolution. The Social Biology of Microbial Communities: Workshop Summary further explains the happenings of the workshop.

CRISPR-Cas Systems

CRISPR-Cas Systems PDF

Author: Rodolphe Barrangou

Publisher: Springer Science & Business Media

Published: 2012-12-13

Total Pages: 300

ISBN-13: 364234657X

DOWNLOAD EBOOK →

CRISPR/Cas is a recently described defense system that protects bacteria and archaea against invasion by mobile genetic elements such as viruses and plasmids. A wide spectrum of distinct CRISPR/Cas systems has been identified in at least half of the available prokaryotic genomes. On-going structural and functional analyses have resulted in a far greater insight into the functions and possible applications of these systems, although many secrets remain to be discovered. In this book, experts summarize the state of the art in this exciting field.

Bacterial Pathogenesis

Bacterial Pathogenesis PDF

Author:

Publisher: Academic Press

Published: 1998-07-01

Total Pages: 620

ISBN-13: 9780080860565

DOWNLOAD EBOOK →

Established almost 30 years ago, Methods in Microbiology is the most prestigious series devoted to techniques and methodology in the field. Now totally revamped, revitalized, with a new format and expanded scope, Methods in Microbiology will continue to provide you with tried and tested, cutting-edge protocols to directly benefit your research. Focuses on the methods most useful for the microbiologist interested in the way in which bacteria cause disease Includes section devoted to 'Approaches to characterising pathogenic mechanisms' by Stanley Falkow Covers safety aspects, detection, identification and speciation Includes techniques for the study of host interactions and reactions in animals and plants Describes biochemical and molecular genetic approaches Essential methods for gene expression and analysis Covers strategies and problems for disease control

Ending the War Metaphor

Ending the War Metaphor PDF

Author: Institute of Medicine

Publisher: National Academies Press

Published: 2006-07-09

Total Pages: 306

ISBN-13: 0309096014

DOWNLOAD EBOOK →

Infectious diseases have existed longer than us, as long as us, or are relatively newer than us. It may be the case that a disease has existed for many, many years but has only recently begun affecting humans. At the turn of the century the number of deaths caused by infections in the United States had been falling steadily but since the '80s has seen an increase. In the past 30 years alone 37 new pathogens have been identified as human disease threats and 12% of known human pathogens have been classified as either emerging or remerging. Whatever the story, there is currently a "war" on infectious diseases. This war is simply the systematic search for the microbial "cause" of each disease, followed by the development of antimicrobial therapies. The "war" on infectious diseases, however, must be revisited in order to develop a more realistic and detailed picture of the dynamic interactions among and between host organisms and their diverse populations of microbes. Only a fraction of these microbes are pathogens. Thus, in order to explore the crafting of a new metaphor for host-microbe relationships, and to consider how such a new perspective might inform and prioritize biomedical research, the Forum on Microbial Threats of the Institute of Medicine (IOM) convened the workshop, Ending the War Metaphor: The Changing Agenda for Unraveling the Host-Microbe Relationship on March 16-17, 2005. Workshop participants examined knowledge and approaches to learning about the bacterial inhabitants of the human gut, the best known host-microbe system, as well as findings from studies of microbial communities associated with other mammals, fish, plants, soil, and insects. The perspective adopted by this workshop is one that recognizes the breadth and diversity of host-microbe relationships beyond those relative few that result in overt disease. Included in this summary are the reports and papers of individuals participating in the Forum as well as the views of the editors.