Recombinant viruses provide an efficient mechanism for the transfer and expression of DNA in eukaryotic cells. First, the transfer of DNA by viral infection-utilizing specific cell surface receptors and cellular intern- ization mechanisms-occurs much more readily than DNA transfer via uptake induced by such physical methods as calcium phosphate coprecipitation or electroporation. Second, the novel strategies employed by the virus to express its own genes can then be "hijacked" in the recombinant virus to express the researcher's gene of interest The purpose of Practical Molecular Virology isthus to compile a coll- tion of readily repeatable gene transfer and expression methods from wo- ers expert in the use of a variety of recombinant viral vectors . These include those designed for the production of recombinant antigens, such as pol- virus and yeast Ty-VLPs; those giving very high levels of recombinant protein expression, for example, baculovirus, vaccinia virus, and SV40; and finally viral vectors used for efficient, stable gene transfer to eu otic cells, such as retroviruses and herpesviruses . The first chapter describes the viral life cycle for each virus, and explains how this can be adapted to allow construction of recombinant vectors. Subsequent chapters deal with methods for producing and char- terizing recombinant viruses . I make no apology for the hyperproliferation of chapters dealing with recombinant retroviral methods and applications, since I believe this is clearly proportional to the recent expansion of interest in these techniques.

The future of agriculture greatly depends on our ability to enhance productivity without sacrificing long-term production potential. The application of microorganisms, such as the diverse bacterial species of plant growth promoting rhizobacteria (PGPR), represents an ecologically and economically sustainable strategy. The use of these bio-resources for the enhancement of crop productivity is gaining importance worldwide. Bacteria in Agrobiology: Crop Productivity focus on the role of beneficial bacteria in crop growth, increased nutrient uptake and mobilization, and defense against phytopathogens. Diverse group of agricultural crops and medicinal plants are described as well as PGPR-mediated bioremediation leading to food security.

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 Biology (TM) 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.

This Volume presents key microscopy and imaging methods for revealing the structure and ultrastructure of environmental and experimental samples, of microbial communities and cultures, and of individual cells. Method adaptations that specifically address problems concerning the hydrophobic components of samples are highlighted and discussed. The methods described range from electron microscopy and light and fluorescence microscopy, to confocal laser-scanning microscopy, and include experimental set-ups for the analysis of interfacial processes like microbial growth and activities at hydrocarbon:water interfaces, biofilms and microbe:mineral interfaces. Three forms of fluorescence in situ hybridization - CARD-FISH, MAR-FISH and Two-pass TSA-FISH - are described for the ecophysiological analysis of functionally active microbes in samples. The methods presented will enable readers to obtain an ultrastructural picture of, and identify the key functional microbes in, samples under investigation. This in turn will constitute a key framework for the interpretation of information from other experimental approaches, such as physicochemical analyses and genomic investigations. 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.

When one picks up a multiauthored book in a series like this, one wonders what will be distinctive about its contents. one wonders about the "Concept of Symbiosis. " does it have the same meaning for all authors and all potential readers? one is further tempted to question the concept of stress. What is the meaning of the c- cept of stress? Some change in the biotic or abiotic aspects of the environment or habitat of the symbiotic partners? many might support the more general def- tion of symbiosis credited to de bary (1879), that symbiosis is the living together of separately named organisms. Something like Smith's (1992) more restricted PoLLnPia (P ermanent or Long-Lived intimate associations between diffe- ent organisms, usually of different sizes, in which the larger organism, the host, exploits the capabilities of one or more smaller organisms) seems to be a better ft for a book centered on the effects of stress on symbiosis. PoLLnPia implies an integrated holobiont system that has adapted itself to living successfully in a particular environment that could be construed as harsh for nonsymbiotic s- tems. often, when queried for examples, one thinks of lichens, of corals living in oligotrophic tropical waters, of Pompeii worms living in association with che- lithotrophic bacteria, and of all sorts of herbivorous animals living in associations with microorganisms. Presumably, the hosts could not survive, or thrive, in their habitats without their smaller partners doing their trophic work for their holo- otic systems.

This work introduces the concept of reformulation, a relatively new strategy to develop foods with beneficial properties. Food reformulation by definition is the act of re-designing an existing, often popular, processed food product with the primary objective of making it healthier. In recent years the concept of food reformulation has evolved significantly as additional benefits of re-designing food have become apparent. In addition to targeting specific food ingredients that are considered potentially harmful for human health, food reformulation can also be effectively used as a strategy to make foods more nutritious by introducing essential macro- /micro-nutrients or phytochemicals in the diet. Reformulating foods can also improve sustainability by introducing "waste" (and underutilized) ingredients into the food chain. In light of these developments, reformulating existing foods is now considered a realistic and attractive opportunity to provide healthy, nutritious, and sustainable food choices to the consumers and likewise improve public health. Indeed reformulation has now become essential in many cases for redressing the health properties of foods that are popularly consumed and significantly affecting public health. This edited volume covers aspects of food reformulation from various angles, exploring the role of the food industry, academia, and consumers in developing new products. Some of the major themes contributors address include methods of reformulating food products for health, improving the nutritional composition of foods, and challenges to the food industry, including regulation as well as consumer perception of new products. The book presents several case studies to clarify these objectives and illustrate the difficulties encountered in the process of developing a reformulated product. Chapters from experts in the field identify emerging and future trends in food product development, and highlight ways in which these efforts will help with increasing food security, improving nutrition and health, and promoting sustainable production. The editors have designed the book to be useful for both industry professionals and the research community. This interdisciplinary approach incorporates a wide spectrum of food sciences (including composition, engineering, and chemistry) as well as nutrition and public health. Food and nutrition professionals, policy makers, health care and social scientists, and graduate students will also find the information relevant.

Structure-Function Relationships of Human Pathogenic Viruses provides information on the mechanisms by which viruses enter the cell, replicate, package their DNA into capsids and mature into new virions. The relation between structural features and the pathogenicity and oncogenicity of some of the most relevant human viral pathogens are demonstrated and the acquisition of defense mechanisms through virus-host interactions are presented. In contrast to textbooks, this volume combines timely research data to provide a holistic view of viral pathogenesis.

Furthermore Structure-Function Relationships of Human Pathogenic Viruses illustrates in a single volume the fundamental processes involved in viral life cycles using up-to-date information from research laboratories around the world. Knowledge of these processes is crucial to develop rationales for the design of future drugs. The timeliness of the data and the comprehensive yet concise approach this book takes in order to present the world of viral pathogens should make it a frontrunner in higher education and R&D.

Composting is increasingly used as a recycling technology for organic wastes. Knowledge on the composition and activities of compost microbial communities has so far been based on traditional methods. New molecular and physiological tools now offer new insights into the "black box" of decaying material. An unforeseen diversity of microorganisms are involved in composting, opening up an enormous potential for future process and product improvements. In this book, the views of scientists, engineers and end-users on compost production, process optimisation, standardisation and product application are presented.

Since the initial establishment of Robert Koch's postulates in the nineteenth century, microbial protein toxins have been recognized as a major factor of bacterial and fungal virulence. An increasing number of proteins produced and secreted by various bacteria, yeasts and plants are extremely toxic and most of them developed remarkably "intelligent" strategies to enter, to penetrate and to finally kill a eukaryotic target cell by modifying or blocking essential cellular components.

This book describes the strategies employed by protein toxins to render their pro- and eukaryotic producers a selective growth advantage over competitors. In providing an up-to-date overview on the mode of protein toxin actions, it accommodates biomedically and biologically relevant toxin model systems. As a result, it significantly broadens our perspective on biochemical architecture and molecular ploy behind the lethal principles of pro- and eukaryotic toxins.

The staphylococci are important pathogenic bacteria responsible for a variety of diseases in humans and other animals. They are the most common cause of hospital-acquired infection. Antibiotic resistant strains (MRSA) have become endemic in hospitals in most countries, causing major public health issues. In addition, the incidence of new strains that cause severe community-acquired infections in healthy people is increasing and MRSA strains are emerging in agricultural and domestic animals. In the race to understand staphylococcal pathogenesis, the focus has been on genetics, as a bacterium can only do what its genes allow. The publication of the first staphylococcal whole genome sequence in 2001 paved the way for a greater understanding of the molecular basis of its virulence, evolution, epidemiology, and drug resistance. Since then, the available genomic data has mushroomed and this, coupled with the major advances in genetic know-how and the availability of better genetic tools, has

This Volume presents generic protocols for wet experimental and computer-based systems and synthetic biology approaches relevant to the field of hydrocarbon and lipid microbiology. It complements a second Volume that describes protocols for systems and synthetic biology applications. The wet experimental tools presented in this Volume include protocols for the standardisation of transcriptional measurements, application of uracil excision-based DNA editing for, inter alia, multi-gene assembly, the use of fluxomics to optimise "reducing power availability", and the incorporation of non-canonical amino acids into proteins for optimisation of activities. Phenome-ing microbes, using a combination of RNA-seq and bioinformatic algorithms, is presented, as is an illustration, using methylotrophs as an example, of how the different key omics approaches constitute a pipeline for functional analysis, acquisition of a systems overview, and metabolic optimisation. Complementary computational tools that are presented include protocols for probing the genome architecture of regulatory networks, genome-scale metabolic reconstruction, and bioinformatic approaches to guide metabolic engineering. The Volume also includes an overview of how synthetic biology approaches can be used to improve biocontainment. 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.

Representing the latest knowledge of the ecology and the physiology of cold-adapted microorganisms, plants and animals, this book explains the mechanisms of cold-adaptation on the enzymatic and molecular level, including results from the first crystal structures of enzymes of cold-adapted organisms.

I assume that you already know a good deal of microbiology. In this book, I frequently use the word "we" by which I mean "you and I." Together we are going to consider bacteriology from a broader perspective and we will think our way through the important biological problems that are frequently just skipped over in every microbiology course. My most important reason for writing this book is to make accessible the relevant thinking from fields of science other than microbiology that are important to microbiology. The book is written for people that have already have a fascination with bacteria, but can see that their background for understanding is far complete. This book consists of topics that are largely omitted from microbiology textbooks and includes some mathematics, physics, chemistry, and evolutionary biology. It contains a good deal of my own work, both experimental and theoretical, together with a lot of speculation. If ten times bigger, it would be a full text book on microbial physiology. A third of the microbial physiology is covered by the recent is no longer treated even in textbook by White (2000). Another third current specialized tests and is greatly underrepresented in text books.

This volume aims to enhance the current understanding of clinical features, treatment and pathogenic aspects in necrotizing soft tissue infections. Various representative case studies are discussed to enhance the readers' understanding of these complex diseases. Necrotizing soft tissue infections are rapidly spreading infections that may cause extensive soft tissue or limb loss, multiorgan failure and are associated with a considerable fatality rate. It is undisputed that rapid diagnosis and prompt intervention is directly related to survival. The initial presentation may be limited to unspecific symptoms such as tenderness, swelling, erythema and pain. Thus, diagnosis and management are challenging due to heterogeneity in clinical presentation, in co-morbidities, in microbiological aetiology, as well as in the pathogenic mechanisms. An international and multidisciplinary consortium, INFECT, has for the last 6 years been pursuing research aimed to advance the understanding of the clinical and pathogenic aspects of these infections. A central part has been to create a comprehensive clinical registry and associated biobank which have also formed the basis for the experimental studies. Using the INFECT patient cohort, as well as an integrated systems biology approach in patients and clinically relevant experimental models, an advanced insight of diagnostic features, causative microbial agents, treatment strategies, and pathogenic mechanisms (host and bacterial disease traits and their underlying interaction network) has been obtained.

Parasitic diseases remain a major health problem throughout the world, for both humans and animals. For many of us, our technologically advanced lifestyle has decreased the prevalence and transmission of parasitic diseases, but for the majority of the world's population, they are ever present in homes, domestic animals, food, or the environment. The study of parasites and parasitic disease has a long and distinguished history. In some cases, it has been driven by the great importance of the presence of the parasite to the community, for example, those that affect our livestock. In other cases, it is clear that applied research has suffered for lack of funding because the parasite affects people with few resources, such as the rural poor in resource-poor countries. These instances include the so-called "neglected diseases," as defined by the World Health Organization (WHO). Parasites have complicated life cycles, and a thorough understanding of the unique characteristics of a particular parasite species is vital in attempts to avoid, prevent, or cure infection or to alleviate symptoms. Of course, the biological characteristics that each parasite has developed to aid survival and transmission, to avoid destruction by the immune system, and to adapt to a changing environment are of lasting fascination to basic biologists as well. The elegance of these biological systems has ensured that the study of protozoan and metazoan parasites also remains an active field of research in countries where the diseases are not a threat to the population.

With the predicted increase of the human population and the subsequent need for larger food supplies, root health in crop plants could play a major role in providing sustainable highly productive crops that can cope with global climate changes. While the essentiality of roots and their relation to plant performance is broadly recognized, less is known about their role in plant growth and development. Root Genomics examines how various new genomic technologies are rapidly being applied to the study of roots, including high-throughput sequencing and genotyping, TILLING, transcription factor analysis, comparative genomics, gene discovery and transcriptional profiling, post-transcriptional events regulating microRNAs, proteome profiling and the use of molecular markers such as SSRs, DArTs, and SNPs for QTL analyses and the identification of superior genes/alleles. The book also covers topics such as the molecular breeding of crops in problematic soils and the responses of roots to a variety of stresses.

It has been clear for a long time that after transplantation of a lymphoid organ, hematopoietic stem cells can regenerate the compartments of the organ, provided that the rest of its architecture - the strome, the epithelia and the vessels - is intact. Ahead lies the even greater challenge to assemble also these other architectural elements of a lymphoid organ by transplanting stem cells. The workshop on lymphoid organogenesis was convened to review current knowledge of and experimental skills involved in this grand project to build a lymphoid organ from its individual cellular components.

The aim of this first book is to introduce the readers of the series to why Cuatro Cienegas Basin (CCB) is so unique, starting with the reason why astrobiologists became interested in this oasis in the first place; namely, the high diversity and abundance of stromatolites and microbial mats in continental waters to be found in the desert oasis. As NASA has long since discovered, the basin may offer the best analog of early Earth. In essence, CCB is a time machine that can take us far back and forth in time. In the respective chapters, the contributing authors explain the extraordinary microbial diversity of Cuatro Cienegas Basin from various perspectives. In order to do so, they explain their journey as well as the different tools used to unravel the basin's mysteries, such as: Why are there so many species in a place without food? How has life there survived the enormity of tectonic shifts through the ages, maintaining its ancient marine heritage?

The technique of in situ hybridization is now vital to molecular biologists and their understanding of the pathophysiology of cellular functions. This practical guide covers all aspects of in situ hybridization, describing: practical procedures and protocols; the scientific background; areas of application; and the limitations of the technology. This edition has been completely rewritten to take into acocunt the many advances in the seven years since its initial publication.

In this comprehensive reference, leading researchers examine the biology, molecular biology, and diseases of the Bunyaviridae, and provide up-to-date information on the genetic characterization and variations of this virus group. The chapters deal with the molecular biology of five genera: Bunyavirus, Hantavirus, Nairovirus, Phlebovirus, and Tospovirus. The chapters examine Bunyaviridae assembly and intracelluar protein transport as well as Bunyaviridae genetics. The contributors discuss the Bunyaviridae diseases, including the hantavirus pulmonary syndrome.

This volume addresses the similarities and also the differences in the genomes of soil saprophytes, symbionts, and plant pathogens by using examples of fungal species to illustrate particular principles. It analyzes how the specific interactions with the hosts and the influence of the environment may have shaped genome evolution. The relevance of fungal genetic research and biotechnological applications is shown for areas such as plant pathogenesis, biomass degradation, litter decomposition, nitrogen assimilation, antibiotic production, mycoparasitism, energy, ecology, and also for soil fungi turning to human pathogens. In addition to the model organisms Neurospora and Aspergillus, the following species are covered providing a view of pathogens and mutualists: Trichoderma, Fusarium oxysporum, Cochliobolus heterostrophus, Penicillium chrysogenum, Rhizopus oryzae, Podospora anserina, and species belonging to Agaricomycetes, Archaeorhizomycetes and Magnaporthaceae. Ecology and potential applications have guided the choice of fungal genes to be studied and it will be fascinating to follow the trends of future sequencing projects.

Streptococci are Gram-positive bacteria that cause a wide spectrum of diseases, such as pharyngitis, necrotizing fasciitis and streptococcal toxic shock syndrome, as well as rheumatic fever and rheumatic heart disease as sequelae. Antibiotics alone have not been able to control the disease and in spite of many efforts an effective vaccine is not yet available. A prerequisite for novel and successful strategies for combating these bacteria is a complete understanding of the highly complex pathogenic mechanisms involved, which are analyzed in this volume. In ten chapters, prominent authors cover various aspects including streptococcal diseases and global burden, epidemiology, adaptation and transmission, and molecular mechanisms of different diseases, as well as sequelae, vaccine development and clinical management. This book will serve as a valuable reference work for scientists, students, clinicians and public health workers and provide new approaches to meeting the challenge of streptococcal diseases.

This book explores microbial symbiosis, with a particular focus on soil microorganisms, highlighting their application in enhancing plant growth and yield. It addresses various types of bacterial and fungal microbes associated with symbiotic phenomena, including rhizobium symbiosis, arbuscular mycorrhizal symbiosis, ectomycorrhizal symbiosis, algal/lichen symbiosis, and Archeal symbiosis. Presenting strategies for employing a diverse range of bacterial and fungal symbioses in nutrient fortification, adaptation of plants in contaminated soils, and mitigating pathogenesis, it investigates ways of integrating diverse approaches to increase crop production under the current conventional agroecosystem. Providing insights into microbial symbioses and the challenges of adopting a plant-microbe synergistic approach towards plant health, this book is a valuable resource for researchers, graduate students and anyone in industry working on bio-fertilizers and their agricultural applications.

The earth s biodiversity is a degree of ecosystem health which is vital to ecology and environmental sustainability. The microbial world is the largest unexplored reservoir. The agro-ecosystem enriched with rhizosphere implicit abundant and species-rich component of microbial diversity. Its global exploration designs a worldwide framework for agricultural sustainability adjoining benefits in its conservation.

Agricultural sustainability requires a major share from ecosystem management which is better paid by microbial diversity and conservation. Diversity of bacteria influences plant productivity providing nutrient convenience from soil instead altering per se community and diversity in the rhizosphere where they may influence mechanistic competent and antagonistic micro-flora. The potential species among the diversity are therefore, essential subjective to their maintenance for use around the globe. Microbial population in agro-ecosystem is influenced by stresses, reduce functionality as a component. It is therefore, important to explore secrets of planned strategy so as to unravel the microbial diversity and conservation in agricultural development. Microorganisms are minute, pervasive in nature and alleged as disease host instead tiny recognize as employee of agro-ecosystem, indulge in agricultural development and potential contributor in world of ecological and economical wealth creation. This step pertinently would help to launch scientific motivation needed to support the refrain of microbial diversity and conservation."

Negative-strand RNA viruses, so named because of the polarity of their genomic RNA to mRNA, include important human and non-human pathogens. This volume covers major advances in reverse genetics techniques over the past decade, state-of-the-art basic science and the clinical implications of experimental findings. This should rekindle interest in negative-strand RNA viruses among readers, including those in other disciplines, leading to further progress in understanding these important viruses and in developing effective measures of control.