Researchers in the field of ecological genomics aim to determine how a genome or a population of genomes interacts with its environment across ecological and evolutionary timescales. Ecological genomics is trans-disciplinary by nature. Ecologists have turned to genomics to be able to elucidate the mechanistic bases of the biodiversity their research tries to understand. Genomicists have turned to ecology in order to better explain the functional cellular and molecular variation they observed in their model organisms.

We provide an advanced-level book that covers this recent research and proposes future development for this field. A synthesis of the field of ecological genomics emerges from this volume."Ecological Genomics"covers a wide array of organisms (microbes, plants and animals) in order to be able to identify central concepts that motivate and derive from recent investigations in different branches of the tree of life.

"Ecological Genomics"covers 3 fields of research that have most benefited from the recent technological and conceptual developments in the field of ecological genomics: the study of life-history evolution and its impact of genome architectures; the study of the genomic bases of phenotypic plasticity and the study of the genomic bases of adaptation and speciation.

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Although virology and immunology are now considered separate disciplines, history shows that these areas ofinvestigation always overlapped and one cannot really exist without the other. This trend has become particularly significant and fruitful in the past few years in the area of herpesvirus research. The genomes of the most important herpesviruses have been sequenced, a significant portion of their genes have been identified, and many secrets of regulation of gene expr- sion have been unraveled. Now this progress sets the stage for a true revolution in herpesvirus research: analysis of interactions between the host and the virus. Because herpesviruses can induce, suppress, and fool the immune system, the most productive herpesvirologists are also expert immunologists, and the current results ofthis interdisciplinary effort are truly remarkable. Because herpesviruses cause many important human diseases, the devel- ment of vaccines against these agents is a very significant goal. This effort is also very challenging because of the complexity of herpesviruses and the lack of sufficient information about immune responses. The remarkable ability of herpesviruses to escape immune responses is - other feature that brings immunology and virology together. Herpesviruses - code many proteins that interact with and down-regulate some key elements of the immune system. Thisproperty of herpesviruses represents amajor challenge in developing strategies against these viruses. On the positive side, these viral proteins also provide novel tools for analyzing specific immune reactions and molecular mechanisms.

The symposium, "Microbial Diversity in Time and Space," was held in the Sanjo Conference Hall, University of Tokyo, Tokyo, Japan, October 24-26, 1994. The symposium was organized under the auspices of the Japanese Society of Microbial Ecology and co-sponsored by the International Union of Biological Sciences (IUBS), International Union of Microbiological Societies (IUMS), International Committee on Microbial Ecology (ICOME), and the Japanese Society of Ecology. The aim of the symposium was to stress the importance of the global role of microorganisms in developing and maintaining biodiversity. Twenty-four speakers from seven countries presented papers in the symposium and in the workshop, "Microbial Diversity and Cycling of Bioelements," that followed the symposium. Papers presented at the symposium are published in this proceedings. Discussions of the workshop, which were energetic and enthusiastic, are also summarized in this proceedings. The symposium provided an opportunity to address the role of microorganisms in global cycles and as the basic support ofbiodiversity on the planet. Previously unrecognized as both contributing to and sustaining biodiversity, microorganisms are now considered to be primary elements of, and a driving force in, biodiversity. Financial support was provided for the symposium by the CIBA GEIGY Foundation for the Promotion of Science, Naito Foundation, and the Uchida Foundation of the Ocean Research Institute, University of Tokyo. Support from these foundations is gratefully acknowledged. CONTENTS Microbial Biodiversity-Global Aspects ................................. 1 Rita R. Colwell 2. Importance of Community Relationships in Biodiversity ...................

Cyanobacteria are single-celled organisms that live in fresh, brackish, and marine water. They use sunlight to make their own food. In warm, nutrient-rich environments, microscopic cyanobacteria can grow quickly, creating blooms that spread across the water 's surface and may become visible. Because of the color, texture, and location of these blooms, the common name for cyanobacteria is blue-green algae. However, cyanobacteria are related more closely to bacteria than to algae. Cyanobacteria are found worldwide, from Brazil to China, Australia to the United States. In warmer climates, these organisms can grow year-round. Scientists have called cyanobacteria the origin of plants, and have credited cyanobacteria with providing nitrogen fertilizer for rice and beans. But blooms of cyanobacteria are not always helpful. When these blooms become harmful to the environment, animals, and humans, scientists call them cyanobacterial harmful algal blooms (CyanoHABs). Freshwater CyanoHABs can use up the oxygen and block the sunlight that other organisms need to live. They also can produce powerful toxins that affect the brain and liver of animals and humans. Because of concerns about CyanoHABs, which can grow in drinking water and recreational water, the U.S. Environmental Protection Agency (EPA) has added cyanobacteria to its Drinking Water Contaminant Candidate List. This list identifies organisms and toxins that EPA considers to be priorities for investigation. Reports of poisonings associated with CyanoHABs date back to the late 1800s. Anecdotal evidence and data from laboratory animal research suggest that cyanobacterial toxins can cause a range of adverse humanhealth effects, yet few studies have explored the links between CyanoHABs and human health. Humans can be exposed to cyanobacterial toxins by drinking water that contains the toxins, swimming in water that contains high concentrations of cyanobacterial cells, or breathing air that contains cyanobacterial cells or toxins (while watering a lawn with contaminated water, for example). Health effects associated with exposure to high concentrations of cyanobacterial toxins include: stomach and intestinal illness; trouble breathing; allergic responses; skin irritation; liver damage; and neurotoxic reactions, such as tingling fingers and toes. Scientists are exploring the human health effects associated with long-term exposure to low levels of cyanobacterial toxins. Some studies have suggested that such exposure could be associated with chronic illnesses, such as liver cancer and digestive-system cancer. This monograph contains the proceedings of the International Symposium on Cyanobacterial Harmful Algal Blooms held in Research Triangle Park, NC, September 6-10, 2005. The symposium was held to help meet the mandates of the Harmful Algal Bloom and Hypoxia Research and Control Act, as reauthorized and expanded in December 2004. The monograph will be presented to Congress by an interagency task force. The monograph includes: 1) A synopsis which proposes a National Research Plan for Cyanobacteria and their Toxins; 2) Six workgroup reports that identify and prioritize research needs; 3) Twenty-five invited speaker papers thatdescribe the state of the science; 4) Forty poster abstracts that describe novel research.

The tetracyclines have an illustrious history as therapeutic agents which dates back over half a century. Initially discovered as an antibiotic in 1947, the four ringed molecule has captured the fancy of chemists and biologists over the ensuing decades. Of further interest, as described in the chapter by George Armelagos, tetracyclines were already part of earlier cultures, 1500-1700 years ago, as revealed in traces of drug found in Sudanese Nubian mummies. The diversity of chapters which this book presents to the reader should illus trate the many disciplines which have examined and seen benefits from these fascinating natural molecules. From antibacterial to anti-inflammatory to anti autoimmunity to gene regulation, tetracyclines have been modified and redesigned for various novel properties. Some have called this molecule a biol ogist's dream because of its versatility, but others have seen it as a chemist's nightmare because of the synthetic chemistry challenges and "chameleon-like" properties (see the chapter by S. Schneider).

The use of renewable bioenergy is increasing, and so is the production of associated wastes: biomass ashes. This book presents eleven chapters on the options for recycling such biomass ashes, ranging from their use as fertilizer in agriculture and forestry to their application as a supplement for the production of cement-based materials or bricks. The book also examines the pros and cons for each of the different uses of biomass ashes.

In the post genomic era, understanding of the innate immune system is enriched by findings on the specificity of innate immune reactions as well as to novel functions that do not strictly correlate with immunological defense and surveillance, immune modulation or inflammation. This volume covers natural killer cells, mast cells, phagocytes, toll-like receptors, complement, host defense in plants and invertebrates, evasion strategies of microorganisms, pathophysiology, protein structures, design of therapeutics, and experimental approaches.

Magnetoreception or magnetotaxis in bacteria was discovered only some 30 years ago. All magnetotactic bacteria, which occur in many environments and display a remarkable diversity, synthesize magnetosomes, complex intracellular organelles that contain magnetic iron crystals.

Recent developments in the research on magnetotactic bacteria are presented in this volume. Included are reviews on the formation and organization of magnetosomes, the genes controlling magnetosome biomineralization, and new cryogenic techniques to visualize novel cytoskeleton structures. Described here are potential nanobiotechnological applications of the magnetosome crystals, which have magnetic and crystalline characteristics unmatched by their inorganic counterparts. Related topics such as the impact of biogenic magnetic crystals in geobiology and paleomagnetism also are discussed. The aim of the book is to provide a broad survey of this multidisciplinary field and to inspire future research on these fascinating organisms.

Current information in applied microbioogy is provided in this text supported by an extensive bibliography.

Cold-adapted microorganisms play a major role in nutrient turnover and primary biomass production in cold ecosystems and have important applications in biotechnology and in the study of food spoilage microorganisms. Divided into three main sections, the book covers the major aspects of biodiversity in cold ecosystems, the physiology and molecular adaptation mechanisms, and the various biomolecules related to cold adaptation.

This Volume provides protocols for the biochemical analysis of hydrocarbon- and lipid-relevant products, cell components and activities of microbes that interact with hydrophobic compounds. They include methods for the extraction, purification and characterisation of surface tension-reducing bioemulsifiers and biosurfactants that increase the surface area and hence bioavailability of hydrophobic substrates. Protocols for the isolation and biochemical analysis of lipids and polyhydroxyalkanoates, food storage products made during nutrient abundance that represent important biotechnological products, are presented. The extraction of membrane lipid rafts, sub-organelles that fulfil important functional roles for the cell membrane, and the isolation and characterisation of membrane phospholipid biomarkers, are also described. The purification and characterisation of integral membrane hydrocarbon-oxidising enzymes are addressed. Lastly, two generic methods for the genetic analysis of catabolic pathways and analysis of ligand binding are presented. Hydrocarbon and Lipid Microbiology ProtocolsThere are tens of thousands of structurally different hydrocarbons, hydrocarbon derivatives and lipids, and a wide array of these molecules are required for cells to function. The global hydrocarbon cycle, which is largely driven by microorganisms, has a major impact on our environment and climate. Microbes are responsible for cleaning up the environmental pollution caused by the exploitation of hydrocarbon reservoirs and will also be pivotal in reducing our reliance on fossil fuels by providing biofuels, plastics and industrial chemicals. Gaining an understanding of the relevant functions of the wide range of microbes that produce, consume and modify hydrocarbons and related compounds will be key to responding to these challenges. This comprehensive collection of current and emerging protocols will facilitate acquisition of this understanding and exploitation of useful activities of such microbes.

The introduction of synthetic organic chemicals into the environment during the last few decades has given rise to major concern about the ecotoxicological effects and ultimate fate of these compounds. The pollutants that are considered to be most hazardous because of their intrinsic toxicity, high exposure level, or recalcitrant behavior in the environment have been placed on blacklists and other policy priority lists. The fate of synthetic compounds that enter the environment is mainly determined by their rate of biodegradation, which therefore also has a major effect on the degree of bioaccumulation and the risk of ecotoxicological effects. The degree and rate of biodegradation is also of critical importance for the feasibility of biological techniques to clean up contaminated sites and waste streams. The biodegradation of xenobiotics has thus been the subject of numerous studies, which resulted in thousands of publications in scientific journals, books, and conference proceedings. These studies led to a deeper understanding of the diversity of biodegradation processes. As a result, it has become possible to enhance the rate of degradation of recalcitrant pollutants during biological treatment and to design completely new treatment processes. At present, much work is being done to expand the range of pollutants to which biodegradation can be applied, and to make treatment techniques less expensive and better applicable for waste streams which are difficult to handle.

Achieving environmental sustainability with rapid industrialization is currently a major global challenge. Industries are the key economic drivers, but are also the main polluters as untreated/partially treated effluents from industry are usually discharged into the aquatic environment or dumped. Industrial effluents often contain highly toxic and hazardous pollutants, which cause ecological damage and present and health hazards to living beings. As such, there is a pressing need to find ecofriendly solutions to deal with industrial waste, and to develop sustainable methods for treating/detoxifying waste before it's released into the environment. As a low cost and eco-friendly clean technology, bioremediation can offer a sustainable alternative to conventional remediation technologies for the treatment and management of industrial wastes. This book (Volume II) describes the role of biological agents in the degradation and detoxification of organic and inorganic pollutants in industrial wastes, and presents recent bioremediation approaches for waste treatment and management, such as constructed wetlands, electro- bioremediation and nano-bioremediation, as well as microbial fuel cells. It appeals to students, researchers, scientists, industry professionals and experts in the field of microbiology, biotechnology, environmental sciences, eco-toxicology, environmental remediation and waste management and other relevant areas who are interested in biodegradation and bioremediation of industrial wastes for environmental safety.

Neutrophils, the most abundant white cells in humans, serve as the primary cellular defense against infection. Neutrophil Methods and Protocols, Second Edition provides a concise set of protocols written by leading researchers in the field for assessing basic neutrophil functions, investigating specialized areas in neutrophil research, and completing step diagnostic assays of common neutrophil disorders. Topics covered include an overview of neutrophils and their role in host defense and inflammation; methods most commonly used for isolating neutrophils from humans and other animal species; procedures for subcellular fractionation of human neutrophils, analysis of in vivo transmigrated neutrophils, generation of mature neutrophils from induced pluripotent stem cells and analysis of neutrophil gene expression; methods for investigating priming, oxidant production, phagocytosis, bactericidal activity and extracellular trap formation and protocols for investigating neutrophil adhesion, chemotaxis and outside-in signaling via integrins. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Neutrophil Methods and Protocols, Second Edition is a comprehensive source for detailed explanations and applications of the most modern methodological advances in neutrophil biology. Both basic scientists and clinicians will find a collection of this caliber to be an invaluable aid in their work with neutrophils.

Plant Virology Protocols: New Approaches to Detect Viruses and Host Responses addresses recent developments in genome analyses and cytological technologies being used today to learn more about plant virology. Opening with chapters covering techniques relevant to the detection of unknown viruses and disease diagnosis, this detailed volume continues with chapters on the utilization of meta-genome sequencing and global gene expression analyses for the search and identification of viruses, as well as the elucidation of host responses to viral infection, construction methods of infectious cDNAs, and methods relevant to plant virus control. 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 practical, Plant Virology Protocols: New Approaches to Detect Viruses and Host Responses will be an invaluable guide to researchers working in the field of plant sciences.

Campylobacter jejuni (C. jejuni) is often regarded as the one of the most common causes of bacterial gastroenteritis worldwide. The goal of this volume is to highlight key protocols for working with C. jejuni. In particular, chapters aim to highlight recent developments with regards to in vivo models for C. jejuni pathogenesis, different approaches to isolate Campylobacter, and a systems biology approach for studying the effect of all potential Campylobacter gene mutants.Written in the highly successful Methods in Molecular Biologyseries 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, Campylobacter jejuni: Methods and Protocols encourages existing Campylobacter researchers to employ novel methods to further their own research and also encourages new researchers to include Campylobacter in their future research initiatives.

Cyanobacterial symbioses are no longer regarded as mere oddities but as important components of the biosphere, occurring both in terrestrial and aquatic habitats worldwide. It is becoming apparent that they can enter into symbiosis with a wider variety of organisms than hitherto known, and there are many more still to be discovered, particularly in marine environments. The chapters cover cyanobacterial symbioses with plants (algae, bryophytes, Azolla, cycads, Gunnera), cyanobacterial symbioses in marine environments, lichens, Nostoc-Geosiphon (a fungus closely related to arbuscular mycorrhiza fungi) symbiosis, and artificial associations of cyanobacteria with economically important plants. In addition, cyanobiont diversity, sensing-signalling, and evolutionary aspects of the symbiosis are dealt with. Renowned experts actively involved in research on cyanobacterial symbioses deal with ecological, physiological, biochemical, molecular, and applied aspects of all known cyanobacterial symbioses.
This volume on cyanobacteria in symbiosis complements the two earlier volumes on cyanobacteria published by Kluwer (Molecular Biology of Cyanobacteria, edited by D.A. Bryant and Ecology of Cyanobacteria, edited by B.A. Whitton and M. Potts). Together, the three volumes provide the most comprehensive treatment of cyanobacterial literature as a whole. The book will serve as a valuable reference work and text for teaching and research in the field of plant-microbe interactions and nitrogen fixation.

In a sense, propionic acid bacteria are domesticated bacteria. They might have been used for cheese making as early as 9000 years Be. In the last 40 years their pmctical uses have expanded to include vitamin B12 and propionic acid production, bread baking, starters for ensilage and some pharmaceutical prepamtions. New prospects for their future uses are also emerging, based on the useful properties recently discovered. This monograph is the result of many years of investigating propioni bacteria by the faculty, staff and postgraduate students in the Department of Microbiology at the Moscow State University, as well as a number of scientists in other countries. The encouragement and various contributions of my colleagues has made this book possible, which might as well be entitled "My life with propionic acid bacteria," since these bacteria were the subject of our investigations for more than 40 years. I hope that this book will be of interest not only to scientists of biological specialties, but also to those associated with industrial firms and medical institutions. L.l. Vorobjeva IX Acknowledgements Writing a monograph is impossible without the cooperation of many people I am very grateful to all my postgraduate students - thirty of them - who work at present not only in Russia, but also in various other countries, including Canada, Cuba, Egypt, India, Iran and Vietnam. Many thanks are due to my colleagues who shared my scientific interests and enthusiasm in experimental research. Special thanks are to N. Baranova, E. lordan, N."

"Advanced Techniques in Soil Microbiology" presents a wide range of biotechnological methods for application in soil microbiology analysis. These include all essential methods involving molecular biology, immunology, microbiology, and structural biology, such as transcriptome analysis, RNAi technology, molecular matchmaking, RAPD, T-RFLP and FT/MS.

The techniques and procedures have been selected with the aim of offering practical guides for immediate use in the laboratory. The systems investigated range from individual molecules and cells to entire eukaryotic organisms, with a focus on bacteria, fungi, mycorrhiza, and higher plants. This volume of state-of-the-art, practice oriented methods will be of great use both to the first-timer and to the experienced scientist.

The objectives of this Second Edition of Biotechnology: A Laboratory Course remain unchanged: to create a text that consists of a series of laboratory exercises that integrate molecular biology with protein biochemistry techniques while providing a continuum of experiments. The course begins with basic techniques and culminates in the utilization of previously acquired technical experience and experimental material. Two organisms, "Sacchaomyces cerevisiae" and "Escherichia coli," a single plasmid, and a single enzyme are the experimental material, yet the procedures and principles demonstrated are widely applicable to other systems. This text will serve as an excellent aid in the establishment or instruction of introductory courses in the biological sciences.
Key Features of this new edition:
* All exercises and appendixes have been updated
* Includes new exercises on
* Polymerase chain reaction
* Beta-Galactosidase detection in yeast colonies
* Western blotting
* New procedures introduced for
* Large-scale plasmid isolation
* Yeast transformation
* DNA quantitation
* New appendixes added, one of which provides details on accessing biological information sites on the Internet (World Wide Web)
* Use of non-radioactive materials and easy access to microbial cultures
* Laboratory exercises student tested for seven years

One hundred years ago, when Martinus W. Beijerinck in Delft and Friedrich Loeffler on Riems Island discovered a new class of infectious agents in plants and animals, a new discipline was born. This book, a compilation of papers written by well-recognized scientists, gives an impression of the early days, the pioneer period and the current state of virology. Recent developments and future perspectives of this discipline are sketched against a historic background. With contributions by A. Alcami, D. Baulcombe, F. Brown, L. W. Enquist, H. Feldmann, A. Garcia-Sastre, D. Griffiths, M. C. Horzinek, A. van Kammen, H.-D. Klenk, F. A. Murphy, T. Muster, R. O'Neill, P. Palese, C. Patience, R. Rott, H.- P. Schmiedebach, S. Schneider-Schaulies, G. L. Smith, J. A. Symons, Y. Takeuchi, V. ter Meulen, P. J. W. Venables, V. E. Volchkov, V. A. Volchkova, R. A. Weiss, W. Wittmann, H. Zheng

This book compiles the latest research in the area of Trichoderma Rhizosphere Biology. It covers topics such as microbial interaction, crosstalk between plants and microbes, interactions with abiotic and biotic factors, and advances in biocontrol agents, biofertilizers and biostimulants. The respective chapters describe innovative ways of adapting fungal communities to improve their survival in highly dynamic environments and agroecosystems. In closing, the book discusses the use of Trichoderma as a bio-growth enhancer and biostimulant for organic agriculture.

Endophytic prokaryotes can invade the tissue of the host plant without triggering defense reactions or disease symptoms. Instead, they promote the growth of the host plant due to their ability to fix atmospheric dinitrogen and/or to produce plant growth-promoting substances.

This Microbiology Monographs volume presents up-to-date findings on the interactions between plants and beneficial prokaryotes, including the use of genomics for the analysis of plant-prokaryote symbioses and their evolution. Rhizobia-legume, actinorhizal and cyanobacterial symbioses are presented.

The need for the development of techniques based on the characteristics of the viral proteins and genomic nucleic acids was realized in order to detect, identify, differentiate and quantify viruses in the infected plants/planting materials with or without symptoms of infection. Immunoassays have been successfully applied for the detection of viruses in crop and weed host plant species as well as in the vectors. Nucleic acid-based techniques have been demonstrated to be the most reliable and sensitive tests for detection, identification and differentiation of viruses and viroids present in plants and planting materials.. Inclusion of numerous protocols in appropriate chapters as appendix is a unique feature of this volume.

This book is focused on the current status of industrial pollution, its source, characteristics, and management through various advanced treatment technologies. The book covers the recycle, reuse and recovery of waste for the production of value-added products. The book explores industrial wastewater pollution and its treatment through various advanced technologies and also the source and characteristics of solid waste and its management for environmental safety. It discusses new methods and technologies to combat the waste-related pollution and focuses on the use of recycled products. This book is of value to upcoming students, researchers, scientists, industry persons and professionals in the field of environmental science and engineering, microbiology, biotechnology, toxicology, further it is useful for global and local authorities and policy makers responsible for the management of liquid and solid wastes.