Studies in Viral Ecology, Volume 1 E-Book

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 825

Veröffentlichungsjahr: 2011

Beschreibung

This book explains the ecology of viruses by examining their interactive dynamics with their hosting species (in this volume, in microbes and plants), including the types of transmission cycles that viruses have evolved encompassing principal and alternate hosts, vehicles, and vectoring species. Examining virology from an organismal biology approach and focusing on the concept that viral infections represent areas of overlap in the ecologies of the involved species, Viral Ecology is essential for students and professionals who either may be non-virologists or virologists whose previous familiarity has been very specialized.

Leseprobe

Contents

Cover

Volume 1

Copyright

Dedication

Preface

Contributors

Attribution Credits for Cover and Spine Artwork

Section I: An Introduction to the Structure and Behavior of Viruses

Chapter 1: Defining the Ecology of Viruses

1.1 Introduction

1.2 Surviving the Game: The Virus and it's Host

1.3 Steppin' Out and Taking The A Train: Reaching Out and Touching Someone by Vector or Vehicle

1.4 Why Things Are the Way They Are

1.5 Summary (Can There be Conclusions?)

Acknowledgement

References

Chapter 2: An Introduction to Viral Taxonomy with Emphasis on Microbial and Botanical Hosts and the Proposal of Akamara, a Potential Domain for the Genomic Acellular Agents

2.1 Introduction

2.2 The Existing Viral Families

2.3 The Proposed Domain Akamara

2.4 Conclusions

References

Chapter 3: Virus Morphology, Replication, and Assembly

3.1 Introduction

3.2 Chemical Composition

3.3 Morphology

3.4 Viral Replication Cycle

3.5 Assembly and Morphogenesis of Virus Particles

6 Conclusions

Acknowledgments

Abbreviations and Definitions

References

Chapter 4: The (Co)Evolutionary Ecology of Viruses

4.1 Vir-olution: Setting the Scene

4.2 The Obsession with Death: Mortality from a Viral Perspective

4.3 A Marriage Made in Hell

4.4 The Numbers Game

4.5 Fight to Death: Genes Are the Weapons

4.6 The Silence of the Viruses

4.7 Giving up the Viral Ghost

4.8 The Makings of Virus–Host Compatibility

4.9 Throwing Light on Virus–Host Evolution

4.10 Sometimes it Takes More than the Odd Gene

References

Section II: Viruses of Other Microorganisms

Chapter 5: Bacteriophage and Viral Ecology as Seen Through the Lens of Nucleic Acid Sequence Data

5.1 The Ubiquity of Viruses in the Biosphere

5.2 Possible Ecological Influences of the Phage Life Cycle

5.3 Genetic and Metagenomic Approaches to Viral Diversity

5.4 Methodology Matters: Technical Concerns for Viral Metagenomics

5.5 Bioinformatic Analysis of Viral Metagenome Sequence Libraries

5.6 The Next Frontier: Functional Viral Metagenomics

Acknowledgments

References

Chapter 6: Viruses of Cyanobacteria

6.1 Introduction

6.2 Taxonomy and Characteristics of Cyanophages

6.3 Ecology of Cyanophages

6.4 Molecular Ecology of Cyanophages

6.5 Summary

References

Chapter 7: Viruses of Eukaryotic Algae

7.1 Introduction

7.2 The Phycodnaviridae: Virus Leviathans of the Aquatic World

7.3 Chlorovirus

7.4 Coccolithovirus

7.5 Prasinovirus

7.6 Prymnesioviruses and Raphidoviruses

7.7 Future Perspectives

Further Reading

Chapter 8: Viruses of Seaweeds

8.1 Introduction

8.2 Diversity

8.3 Viral Infection Strategies

8.4 Ecology

8.5 Summary

References

Chapter 9: The Ecology and Evolution of Fungal Viruses

9.1 Introduction

9.2 Biology and Diversity of Fungal Viruses

9.3 Transmission of Fungal Viruses

9.4 Effects of Viruses on Fungal Fitness

9.5 Population Biology of Fungal Viruses

9.6 Biological Control of Fungi with Viruses

9.7 Future Directions

References

Chapter 10: Prion Ecology

10.1 Introduction

10.2 Definition of “Prion”

10.3 Prion Terminology

10.4 How to Find A Prion

10.5 Structural Basis of Yeast and Fungal Prions

10.6 Prion Variants, Phenotypes, and the Species Barrier

10.7 Prion Ecology

10.8 Conclusions

References

Section III: Viruses of Macroscopic Plants

Chapter 11: Ecology of Plant Viruses, with Special Reference to Geminiviruses

11.1 Introduction

11.2 Virus–Vector–Plant Ecosystems

11.3 Control of Virus Diseases

11.4 Role of Man and Climate Change in Virus Ecology

11.5 Emergence of New Recombinant Geminiviruses

11.6 Conclusions

References

Chapter 12: Viroids and Viroid Diseases of Plants

12.1 Introduction

12.2 Structure and Classification

12.3 Replication and Movement

12.4 Host Range, Specificity, and Defense

12.5 Pathogenesis

12.6 Interactions Between Viroids and Viruses

12.7 Transmission

12.8 Viroid Epidemiology and Control

12.9 Conclusions

Acknowledgments

References

Color Plates

Index

Copyright © 2011 by Wiley-Blackwell. All rights reserved

Published by John Wiley & Sons, Inc., Hoboken, New Jersey

Published simultaneously in Canada

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Library of Congress Cataloging-in-Publication Data:

Studies in viral ecology / edited by Christon J. Hurst.

v. cm.

Includes index.

Contents: v.1. Microbial and Botanical Host Systems (ISBN 978-0-470-62396-1)

– v.2. Animal Host Systems (ISBN 978-0-470-62429-6).

ISBN (set) 978-1-118-02458-4 (cloth)

1. Viruses–Ecology. I. Hurst, Christon J.

QR478.A1S78 2011

579.2–dc22

2010046370

oBook ISBN: 978-1-118-02566-6

ePDF ISBN: 978-1-118-02564-2

ePub ISBN: 978-1-118-02565-9

Dedication

I dedicate these two volumes to the memory of my brother in spirit, Henry Hanssen. To me, he seemed a hero and I remember him most for his unfailing ability to present a sense of humanity in times of tragedy. We first met while studying together for our doctorates in Houston, Texas.

Henry was born in Colombia near Medellín and tragically orphaned as a young child after which he was lovingly raised by an aunt in Bogotá. Henry may have gained his tremendous sense of humanity from that experience. He had no biological children of his own but helped to raise two daughters. The first of those came into his life by a twist of luck while one day Henry was walking along a street in Colombia and heard what he thought might be a cat trapped inside of a garbage bin. Henry went over to free the cat and discovered instead a crying infant child in a plastic bag, presumably discarded there by a distraught mother. Henry took the baby to the police, and when no one stepped forward as a parent Henry adopted the child and eventually even helped to pay for her college tuition. The second daughter came through Henry's marriage to the love of his life.

When there arose need for representing humanity, Henry was undaunted by circumstance. His accomplishments included establishing an infant vaccination program against poliomyelitis in Angola at the personal request of Jonas Salk. Angola was in a state of civil war at that time and no one else was willing to undertake the necessary but frightening task. Henry showed equal humanitarianism to civilians and military on both sides of that conflict. Subsequently, Henry initiated a similar poliomyelitis vaccination program during a period of civil war in Central America and for his efforts was awarded honorary citizenship by one of the countries there. He then initiated a poliomyelitis vaccination program in his native Colombia, while that country's continuing civil war was in full strength.

I was proud to address Henry by the name of “brother” and always will think of him in that way. He addressed me by that same term of affection and he is lovingly remembered by everyone whom his life touched.

Henry Hanssen Villamizar (1945–2007)

Preface

Virology is a field of study which has grown and expanded greatly since the viruses as a group first received their name in 1898. Many of the people who presently are learning virology have come to perceive these acellular biological entities as being merely trinkets of nucleic acid to be cloned, probed, and spliced. However, the viruses are much more than merely trinkets to be played with in molecular biology laboratories. The viruses are indeed highly evolved biological entities with an organismal biology that is complex and interwoven with the biology of their hosting species. Ecology is defined as the branch of science which addresses the relationships between an organism of interest and the other organisms with which it interacts, the interactions between the organism of interest and its environment, and the geographical distribution of the organism of interest.

The purpose of this book is to help define and explain the ecology of viruses, i.e., to examine what life might seem like from a “virocentric” point of view, as opposed to our normal “anthropocentric” perspective. As we begin our examination of the virocentric life, it is important to realize that in nature both the viruses of macroorganisms and the viruses of microorganisms exist in cycles with their respective hosts. Under normal conditions, the impact of viruses upon their natural host populations may be barely apparent due to factors such as evolutionary coadaptation between the virus and those natural hosts. However, when viruses find access to new types of hosts and alternate transmission cycles, or when they encounter a concentrated population of susceptible genetically similar hosts such as occurs in densely populated human communities, communities of cultivated plants or animals, or algal blooms, then the impact of the virus upon its host population can appear catastrophic. The key to understanding these types of cycles lies in understanding the viruses and how their ecology relates to the ecology of their hosts, their alternate hosts, and any vectors which they utilize, as well as their relationship to the availability of suitable vehicles that can transport the different viral groups.

I hope that you will enjoy the information presented in this book set as much as I and the other authors have enjoyed presenting it to you. The written word is a marvelous thing, able to convey understanding and enthusiasm across unimaginable distances and through time.

Christon J. HurstbrCincinnati, Ohio

Contributors

Michael J. Allen, Plymouth Marine Laboratory, Plymouth, United Kingdom

Francesco Di Serio, Istituto di Virologia Vegetale (CNR), Bari, Italy

Nuria Duran-Vila, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Spain

Claude M. Fauquet, ILTAB/Danforth Plant Science Center, St. Louis, MO

Ricardo Flores, Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Valencia, Spain

Bradley I. Hillman, Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ

Christon J. Hurst, Departments of Biology and Music, Xavier University, Cincinnati, OH; Engineering Faculty, Universidad del Valle, Ciudad Universitaria Meléndez, Santiago de Cali, Valle, Colombia

William Kress, Delaware Biotechnology Institute, University of Delaware, Newark, DE

Lauren D. McDaniel, USF College of Marine Science, University of South Florida, St. Petersburg, FL

Michael G. Milgroom, Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY

Beatriz Navarro, Istituto di Virologia Vegetale (CNR), Bari, Italy

Debi P. Nayak, David Geffen School of Medicine at UCLA, Los Angeles, CA

Robert A. Owens, Beltsville Agricultural Research Center (USDA), Beltsville, MD

Basavaprabhu L. Patil, ILTAB/Danforth Plant Science Center, St. Louis, MO

Eric Sakowski, Delaware Biotechnology Institute, University of Delaware, Newark, DE

Declan C. Schroeder, Marine Biological Association of the UK, Plymouth, United Kingdom

Reed B. Wickner, Laboratory of Biochemistry and Genetics, National Institute of Diabetes, Digestive, and Kidney Disease, National Institutes of Health, Bethesda, MD

William H. Wilson, Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, ME

K. Eric Wommack, Delaware Biotechnology Institute, University of Delaware, Newark, DE

Attribution Credits for Cover and Spine Artwork

Cover credits

“Montage showing botanical and microbial hosts”, montage image used with permission of the artist, Christon J. Hurst. Those images incorporated into this montage were: Chestnut Tree - File:Châtaigner (Castanea sativa) JPG01.jpg (author: Jean-Pol Grandmont; document made public with permission of the author; also Creative Commons Attribution-Share Alike 2.5 Generic license); Coastal Redwoods in Muir Woods - File:Trees and sunshine.JPG (author: Wikipedia user name Richs5812; public domain image); Aspen Overview -File:AspenOverview0172.JPG (author: Mark Muir; Forest Service, U.S. Department of Agriculture, public domain image); Fungus (microscope image) Morchella elata (morel) - File:Morelasci.jpg (author: Peter G. Werner; Creative Commons Attribution 3.0 Unported license); Fungus on tree trunk - File:Stumpfungus.jpg (author: Wikipedia user name Ecornerdropshop; public domain image); Lichen on Wall - File:N2 Lichen.jpg (author: Wikipedia user name Roantrum; Creative Commons Attribution 2.0 Generic license); Phage on bacteria - File:Phage.jpg (author: Graham Colm; public domain image); Algal Bloom killed by virus ? True color satellite image of a milky E. huxleyi bloom in the English Channel south of Plymouth, U.K. on the 30 July 1999 (source: Remote Sensing Group, Plymouth Marine Laboratory, provided by Michael J. Allen of the Plymouth Marine Laboratory); Brown Giant Kelp 3600ppx ?File:BrownGiantKelp3600ppx.jpg (author: Wikipedia user name Fastily; Creative Commons Attribution-Share Alike 3.0 Unported license); Taiwan 2009 Giant Stone Steps Algae - File:Taiwan 2009 East Coast ShihTiPing Giant Stone Steps Algae FRD 6581.jpg (author: Fred Hsu; Creative Commons Attribution-Share Alike 3.0 Unported license); Volvox tertius darkfield Matt Herron - (Author: Matthew D. Herron; image supplied by and used with author?s permission); Bluegreen algae - File:Bluegreen algae.jpg (author unknown; NOAA, U.S. Government, public domain image); Kelp Forest - File:Kelp forest.jpg (author: Kip Evans; NOAA, U.S. Government, public domain image); and Seaweed on submerged rocks - File:2006 seaweed.JPG (author: Wikipedia user name Sigurdas, actual name Romuald Bokej of Stockholm, Sweden; Creative Commons Attribution 2.0 Generic license).

Spine credits

“Montage showing animal, botanical and microbial hosts”, montage image used with permission of the artist, Christon J. Hurst. Those images incorporated into this montage were: Calliope Hummingbird - File:Calliope-nest.jpg (author: Wolfgang Wander; Creative Commons Attribution-Share Alike 3.0 Unported license); Cassava - File:Casava.jpg (author: Bob Walker; Creative Commons Attribution-ShareAlike 2.5 License); Tiger Salamander (Ambystoma tigrinum) - File:Salamandra Tigre.png (author: Carla Isabel Ribeiro; Creative Commons Attribution-Share Alike 3.0 Unported license); Volvox tertius (author: Matthew D. Herron; image supplied by and used with author?s permission); Volvox aureus (author: Matthew D. Herron; image supplied by and used with author?s permission); Molluscs (mostly bivalves) harvested from contaminated water in Zulia, Venezuela (author: Christon J. Hurst; image provided for use in this montage); and giant clam - File:Tridacna crocea.jpg (author: Nick Hobgood; Creative Commons Attribution-Share Alike 3.0 Unported license).

Section I

An Introduction to the Structure and Behavior of Viruses

Chapter 1

Defining the Ecology of Viruses1

Christon J. Hurst1,2

1Departments of Biology and Music, Xavier University, Cincinnati, OH

2Engineering Faculty, Universidad del Valle, Ciudad Universitaria Meléndez, Santiago de Cali, Valle, Colombia

1.1 Introduction

The goal of virology is to understand the viruses and their behavior. Virology is an interesting subject and even has contributed to the concepts of what we consider to represent dieties and art. Sekhmet, an ancient Egyptian goddess, was for a time considered to be the source of both causation and cure for many of the diseases that we now know to be caused by viruses (Figure 1.1). Influenza, a viral-induced disease of vertebrates, was once assumed to be caused by the influence of the stars, and that is represented by the origin of it's name which is derived from Italian. The following was a rhyme which children in the United Sates sang while skipping rope during the influenza pandemic of 1918–1919:

I had a little bird

It's name was Enza

I opened a window

And in-flew-Enza.

(Source: The flu of 1918, by Eileen A Lynch, The Pennsylvania Gazette November/December 1998 (http://www.upenn.edu/gazette/1198/lynch.html).

Figure 1.1 Image of Sekhmet, “Bust Fragment from a colossal statue of Sekhmet”, Cincinnati Art Museum, John J. Emery Fund, Accession #1945.65 Cincinnati, Ohio. Originally the warrior goddess of Upper Egypt, Sekhmet was for a time believed to be the bringer of disease. She would inflict pestilence if not properly appeased, and if appeased could cure such illness.

And a bit more recently an interesting poem was written about viruses (Source: Michael Newman, 1984):

“The Virus”

Observe this virus: think how small

Its arsenal, and yet how loud its call;

It took my cell, now takes your cell,

And when it leaves will take our genes as well.

Genes that are master keys to growth

That turn it on, or turn it off, or both;

  Should it return to me or you

  It will own the skeleton keys to do

  A number on our tumblers; stage a coup.

But would you kill the us in it,

The sequence that it carries, bit by bit?

The virus was the first to live,

Or lean in that direction; now we give

Attention to its way with locks,

And how its tickings influence our clocks;

  Its gears fit in our clockworking,

  Its habits of expression have a ring

  That makes our carburetors start to ping.

This happens when cells start to choke

As red cells must in monoxic smoke,

When membranes get the guest list wrong

And single-file becomes a teeming throng,

And growth exists for its own sake;

Then soon enough the healthy genes must break;

  If we permit this with our cells,

  With molecules abet the clanging bells;

  Lend our particular tone to our death knells.

The purpose of this book is to define the ecology of viruses and, in so doing, try to approach the question of what life is like from a “virocentric” (as opposed to our normal anthropocentric) point of view. Ecology is defined as the branch of science which addresses the relationships between an organism of interest and the other organisms with which it interacts, the interactions between the organism of interest and its environment, and the geographic distribution of the organism of interest. The objective of this chapter is to introduce the main concepts of viral ecology. The remaining chapters of this book set, Studies in Viral Ecology volumes 1 and 2, will then address those concepts in greater detail and illustrate the way in which those concepts apply to various host systems.

1.1.1 What is a Virus?

Viruses are biological entities which possess a genome composed of either ribonucleic acid (RNA) or deoxyribonucleic acid (DNA). Viruses are infectious agents which do not possess a cellular structure of their own, and hence are “acellular infectious agents”. Furthermore, the viruses are obligate intracellular parasites, meaning that they live (if that can be said of viruses) and replicate within living host cells at the expense of those host cells. Viruses accomplish their replication by usurping control of the host cell's biomolecular machinery. Those which are termed “classical viruses” will form a physical structure termed a “virion” that consists of their RNA or DNA genome surrounded by a layer of proteins (termed “capsid proteins”) which form a shell or “capsid” that protects the genomic material. Together, this capsid structure and its enclosed genomic material are often referred to as being a “nucleocapsid”. The genetic coding for the capsid proteins generally is carried by the viral genome. Most of the presently known virus types code for their own capsid proteins. However, there are some viruses which are termed as being “satellite viruses”. The satellite viruses encapsidate with proteins that are coded for by the genome of another virus which coinfects (simultaneously infects) that same host cell. That virus which loans its help by giving its capsid proteins to the satellite virus is termed as being a “helper virus”. The capsid or nucleocapsid is, in the case of some groups of viruses, surrounded in turn by one or more concentric lipid bilayer membranes which are obtained from the host cell. There exist many other types of acellular infectious agents which have commonalities with the classical viruses in terms of their ecology. Two of these other types of acellular infectious agents, the viroids and prions, are included in this book set and are addressed within their own respective chapters (Volume 1, chapters 10 and 12). Viroids are biological entities akin to the classical viruses and likewise can replicate only within host cells. The viroids possess RNA genomes but lack capsid proteins. The agents which we refer to as prions were once considered to be nonclassical viruses. However, we now know that the prions appear to be aberrant cellular protein products which, at least in the case of those afflicting mammals, have acquired the potential to be environmentally transmitted. The natural environmental acquisition of a prion infection occurs when a susceptible host mammal ingests the bodily material of an infected host mammal. The reproduction of prions is not a replication, but rather seems to result from a conversion of a normal host protein into an abnormal form (Volume 1, chapter 10). The Acidianus two-tailed virus, currently the sole member of the viral family Bicaudaviridae, undergoes a morphological maturation following its release from host cells and this is unique among all of the biological entities now considered to be viruses suggesting that this species may represent the initial discovery of an entirely new category of biological entities.