This collection of diverse articles by the pioneers of modern genomics takes stock of the current state of the field and elucidates the contribution that sequencing genomes has made to our understanding of microbial metabolism and evolution. Through twenty-eight thought-provoking chapters, the authors describe some of the most common computational methods and their applications to studying pathogenic microorganisms, show how genomics can be used to reconstruct the history and dynamism of the microbial world, and discuss issues as diverse as reconstruction of metabolic pathways, cell cycle processes, microbial evolution, metagenomics, and vaccine development. Additional chapters deal with microarrays and expression analysis and the role of genomic in drug discovery.

During the past twenty years, multitudes of exciting discoveries in the field of anaerobic bacteria have been made. BIOCHEMISTRY AND PHYSIOLOGY OF ANAEROBIC BACTERIA explores the full range of these microorganisms. Many anaerobes have been found to have the uniquely fascinating quality of being able to survive, indeed even thrive, in extreme environments. Anaerobic bacteria often do not require oxygen, can survive extremes in temperature, and can withstand the presence of toxins and heavy metals. In addition, these organisms have very different metabolic processes than "conventional" microorganisms. The wide diversity of metabolism in anaerobes is only part of the story. They have distinct energies, cytochromes, electron transport proteins, hydrogenases and dohydrogenases. Their molecular biology, physiology, and ability to use many types of electron receptors (CO2, sulfur, nitrogen and metal oxides) are also extraordinary. With practical applications ranging from wastewater treatment to food storage issues, clinical diagnosis and treatment of a wide range of medical conditions to decontamination of heavy metal exposures BIOCHEMISTRY AND PHYSIOLOGY OF ANAEROBIC BACTERIA will prove indispensable to researchers and students alike.

Beginning with an introduction to relevant genetic techniques, chapters cover all major groups of LAB, including the Bifidobacteria; plasmid biology, gene transfer, phage, and sugar metabolism; gene expression of various LAB; applications for genetically engineered LAB, including the emerging field of medical applications; and the legal and consumer issues that arise from such applications. This resource will set the benchmark for the state of knowledge of LAB genetics and should be of value to food scientists and other researchers working with LAB in its present and future capacities. Professionals using lactic acid bacteria (LAB) for research and/or as working organisms, whether in food and dairy fermentations or in the exciting new field of clinical delivery agents, will find this book invaluable. In addition, professors teaching under- and post-graduates in microbiology, and postgraduate research students will also find this an essential reference work.

Macrolide Antibiotics: Chemistry, Biochemistry, and Practice, Second Edition explores the discovery of new macrolide antibiotics, their function, and their clinical use in diseases such as cancer, AIDS, cystic fibrosis and pneumonia. This book discusses the creation of synthetic macrolides and the mechanisms of antibiotic activity. The uses for antimicrobial macrolides in clinical practice are also covered. This book is designed to appeal to both the basic and applied research communities interested in microbiology, bacteriology, and antibiotic/antifungal research and treament.

The bacterium Escherichia coli – E. coli for short – has long been the organism of choice for unraveling biochemical pathways, deciphering the genetic code, learning how DNA is replicated and read, and even for manufacturing proteins of commercial interest. For some thirty years, it also has been a model for studying the molecular biology of behavior. E. coli swims in a purposeful manner, propelled by long thin helical filaments, each driven at its base by a reversible rotary engine. As a microscopic organism immersed in an aqueous environment, it has mastered physical constraints utterly different from any that we know, devising sensors, comparators, and motors on the nanometer scale. This cross-disciplinary monograph describes these feats in a manner accessible to scientists, engineers, and others not trained in microbiology who would like to learn more about living machines. It treats the history of the subject, the physiology, physics, biochemistry and genetics, largely from first principles. It is all about a small but remarkably sophisticated friend who lives in your gut. Topics discussed include: How does E. coli move about? How do cells decide whether life is getting better or worse? What is the machinery that makes this behavior possible? How is the construction of this machinery programmed? How does this machinery work? What remains to be discovered?

Network-based representations have become pervasive in most fields in biology. Bacterial Molecular Networks: Methods and Protocols provides authoritative descriptions of various experimental and computational methods enabling the characterization and analysis of molecular interaction networks, with a focus on bacteria. Divided into three convenient sections, this volume provides extensive coverage of various experimental and in silico approaches aiming at the characterization of network components, addresses the presentation of computational approaches to analyze the topology of molecular networks, and further introduces a variety of methods and tools enabling scientists to generate qualitative or quantitative dynamical models of molecular processes in bacteria. Written in the highly successful Methods in Molecular Biology (TM) 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 accessible, Bacterial Molecular Networks: Methods and Protocols is intended primarily for post-graduate students and researchers working in the field of experimental and computational microbiology and provides a combination of up-to-date reviews along with detailed protocols written by the developers of bioinformatics resources, such as databases and software tools.

Vaccines represent the greatest achievements of one area of science for increasing our health and well-being. This collection of papers represents the latest advances in bacterial vaccine research. The papers presented at this symposium illustrate the increasing potential and need for continuing research into disease pathogenesis, host resistance mechanisms, and vaccine development. Further, the study of bacterial vaccines provides an important method for characterizing pathogenic mechanisms and natural and induced host resistance mechanisms.

Principles of Bacterial Pathogenesis presents a molecular perspective on a select group of bacterial pathogens by having the leaders of the field present their perspective in a clear and authoritative manner. Each chapter contains a comprehensive review devoted to a single pathogen. Several chapters include work from authors outside the pathogenesis field, providing general perspectives on the evolution, regulation, and secretion of virulence and determinants.
Key Features
* Explains the basic principles of bacterial pathogenesis
* Covers diverse aspects integrating regulation, cellular microbiology and evolution of microbial disease of humans
* Discusses current strategies for the identification of virulence determinants and the methods used by microbes to deliver virulence factors
* Presents authoritative treatises of the major disease microorganisms

The fungi have been major players in the molecular revolution that has transformed biology. Because they can be manipulated as microorganisms, yeast and Neurospora provide information that is difficult to acquire with plants and animals, and experimental findings with fungi often throw light on corresponding processes in plants and animals. The filamentous fungus Neurospora crassa has become a valuable model organism because of its favorable features for genetic analysis and because of the vast store of information that has been acquired during 75 years of research. This compendium provides researchers and students with a concise account of current knowledge about the genes and genome of Neurospora, setting the stage for research that will follow completion of the genome sequence.
This book, which is fully documented and abundantly illustrated, will be an indispensable tool in any laboratory that uses fungi for research in molecular genetics, classical genetics, developmental genetics, or cell biology.
Key Features
* Molecular, genetic, and phenotypic information for over 1000 nuclear genes
* Genetic maps.
* Linkage group assignments for 1000 loci
* 2300 references, 68 figures
* Guide to electronic and other sources of information
* Summary information on the mitochondrial genome
* cDNAs identified from different stages of life
* Classical, cytogenetic, and molecular data, anticipating completion of the genome sequence

During the past twenty years Listeria monocytogenes has emerged as one of the most intensely studied bacterial pathogens. New windows are constantly being opened into the complexity of host cell biology and the interplay of the signals connecting the various cells and organs involved in the host response. This volume includes research from studies at the molecular level on the pathogenesis of Listeria monocytogenes and the response of the host to its infections.

Research on bacterial adhesion and its significance is a major field involving many different aspects of nature and human life, such as marine science, soil and plant ecology, most importantly, the biomedical field. The adhesion ofbacteria to the food industry, and human tissue surfaces and implanted biomaterial surfaces is an important step in the patho genesis of infection. Handbook 0/ Bacterial Adhesion: Principles, Methods, and Applications is an outgrowth of the editors' own quest for information on laboratory techniques for studying bacte rial adhesion to biomaterials, bone, and other tissues and, more importantly, a response to significant needs in the research community. This book is designed to be an experimental guide for biomedical scientists, biomaterials scientists, students, laboratory technicians, or anyone who plans to conduct bacterial adhesion studies. More specifically, it is intended for all those researchers facing the chal lenge of implant infections in such devices as orthopedic prostheses, cardiovascular devices or catheters, cerebrospinal fluid shunts or extradural catheters, thoracic or abdominal catheters, portosystemic shunts or bile stents, urological catheters or stents, plastic surgical implants, oral or maxillofacial implants, contraceptive implants, or even contact lenses. It also covers research methods for the study of bacterial adhesion to tis sues such as teeth, respiratory mucosa, intestinal mucosa, and the urinary tract. In short, it constitutes a handbook for biomechanical and bioengineering researchers and students at all levels."

Over the years of cancer investigation a lot of discoveries in this field were made, and many associations between various biological carcinogens and cancer were revealed. Some of them are credibly determined, thus these infectious agents (human papilloma virus, hepatitis B virus, hepatitis C virus, Epstein-Barr virus, human herpes virus 8, human T-cell lymphotropic virus 1, human immunodeficiency virus, Merkel cell polyomavirus, Helicobacter pylori, Opisthorchis viverrini, Clonorchis sinensis, Schistosoma haematobium) are recognized as carcinogens and probable carcinogens by International Agency for Research on Cancer (IARC). The problem is of large importance, since share of infectious agents-related cancer cases is steadily increasing, reaching 25% according to certain estimates. It is worth noting that many of cancer cases are caused by infectious agents other than -conventional ones- like HPV, EBV, HBV, HCV, H.pylori etc. In recent years, a number of significant breakthroughs in the field were performed, such as the discovery of the microbiota role in cancer causation."

Plasmids are fascinating entities which can replicate autonomously in bacterial, archaeal, and eukaryotic cells. They profit from the cellular environment of the host but can also carry a rich diversity of genes which can be beneficial for the host. Plasmids confer the ability to degrade organic compounds and to fix nitrogen. In addition, plasmids carry antibiotic resistance genes and their spread in pathogenic bacteria is of great medical importance. Plasmids are used in molecular studies of various organisms with ramifications in synthetic biology, medicine, ecology, and evolution, as well as basic research in molecular and structural biology. Written by acknowledged experts in the field, this volume provides an up-to-date treatment of the structure, function, and application of plasmids, with a particular emphasis on current and future trends. The book is aimed primarily at research scientists, graduate students, and professional scientists, but will also be of great interest to all

The book contains recent developments and contemporary research in mathematical analysis and in its application to problems arising from the biological and physical sciences. The book is of interest to readers who wish to learn of new research in such topics as linear and nonlinear analysis, mathematical biology and ecology, dynamical systems, graph theory, variational analysis and inequalities, functional analysis, differential and difference equations, partial differential equations, approximation theory, and chaos. All papers were prepared by participants at the International Conference on Recent Advances in Mathematical Biology, Analysis and Applications (ICMBAA-2015) held during 4-6 June 2015 in Aligarh, India. A focal theme of the conference was the application of mathematics to the biological sciences and on current research in areas of theoretical mathematical analysis that can be used as sophisticated tools for the study of scientific problems. The conference provided researchers, academicians and engineers with a platform that encouraged them to exchange their innovative ideas in mathematical analysis and its applications as well as to form interdisciplinary collaborations. The content of the book is divided into three parts: Part I contains contributions from participants whose topics are related to nonlinear dynamics and its applications in biological sciences. Part II has contributions which concern topics on nonlinear analysis and its applications to a variety of problems in science, engineering and industry. Part III consists of contributions dealing with some problems in applied analysis.

Strategies of Bacterial Interaction with Eukaryotic Cells *Tobias A. Oelschlaeger and Jorg Hacker 1. BENEFICIAL BACTERIAL-HOST INTERACTIONS Already during birth and soon thereafter mammals are colonized by bacte- ria belonging to the resident microbial flora. Cutaneous and mucosal sur- faces and the gastrointestinal tract are the areas which become colonized. These indigenous or autochthonous bacteria have a variety of beneficial effects on their hosts. They play a protective role by bacterial antagonism in fighting infections (Hoszowski and Truszczynski, 1997; Hentges, 1979). Pro- duction of vitamin K is another essential contribution of the resident microbial flora to the health of the host (Hill, 1997). Even more important, studies with germ-free animals demonstrated the involvement of the microbial flora on the development of the immune system. Such animals have underdeveloped and relatively undifferentiated lymphoid tissues and low concentrations of serum immune globulins ( Cebra et at., 1998). They TOBIAS A. OELSCHLAEGER and JORG HACKER Institut filr Molekulare lnfektionsbiologie, Universitiit Wiirzburg, 97070 Wiirzburg, Germany. *Corresponding author; Phone: (0)931-312150; FAX: (0)931-312578; E-mail: [email protected] xxix Tobias A. Oelschlaeger and Jorg Hacker also show defects in specific immune responsiveness and in nonspecific resistance induced by endotoxin, which may account for their lowered resis- tance. A more typical example of symbiotic interaction of bacteria with a host are bacteria like Ruminococcus in the gut of ruminants, essential for degradation of cellulose (Hobson, 1988). The closest benefical bacterial-host interactions are those of intracellular symbiotic bacteria and their host cells.

During the last decade a wealth of new data has arisen from the use of new fluorescent labelling techniques and the sequencing of whole microbial genomes. One important conclusion from these data is that bacterial cells are much more structured than previously thought. The wall and the outer membrane contain topological domains, some proteins localize or move in specific patterns inside the cells, and some genes appear clustered in the chromosome and form conserved evolutionary units. Many of these structures are related to the cell cycle and to the process of cell morphogenesis, two processes that are themselves related to each other. From these observations the dcw gene cluster appears as a phylogenetic trait that is mainly conserved in bacilli. Molecules in Time and Space reviews the data on the formation of subcellular patterns or structures in bacteria, presents observations and hypotheses on the establishment and the maintenance of cell shape, and on the organization of genetic information in the chromosome.

This book provides a comprehensive and detailed source of information on the genetic and regulatory aspects of biological nitrogen fixation in free-living (non-symbiotic) prokaryotes. Biological nitrogen fixation is represented in a diverse range of microorganisms, among which Klebsiella pneumoniae serves as a paradigm for the genetic analysis of diazotrophy, which is the ability to grow with N2 as sole nitrogen source. The volume uses two major complementary approaches to the subject matter. The initial chapters use an organismic-based approach by concentrating on the well-characterized diazotrophic proteobacteria, cyanobacteria, Gram-positive clostridia, and Archea. The later chapters use a comparative process-based approach and serve as overviews dealing with different regulatory aspects, electron transport to nitrogenase, and molybdenum metabolism, across the range of organisms. Whenever appropriate, historical aspects and agricultural and ecological impacts have been taken into consideration. Each chapter contains an extensive list of references. This book is the self-contained second volume of a comprehensive seven-volume series. No other available work provides the up-to-date and in-depth coverage of this series and this volume. This book is intended to serve as an indispensable reference work for all scientists working in this and closely related fields, to assist students to enter this challenging area of research, and to provide science administrators easy access to vital relevant information.

The functional analysis of plant-microbe interactions has re-emerged in the past 10 years due to spectacular advances in integrative study models. This book summarizes basic and technical information related to the plant growth promoting rhizobacteria (PGPR) belonging to the genus Azospirillum, considered to be one of the most representative PGPR last 40 years. We include exhaustive information about the general microbiology of genus Azospirillum, their identification strategies; the evaluation of plant growth promoting mechanisms, inoculants technology and agronomic use of these bacteria and some special references to the genetic technology and use.

Toxins are virulence determinants that play an important role in microbial pathogenicity and/or evasion of the host immune response. This makes them ideal targets for the development of novel antimicrobial strategies. The potential applications of toxin research extend beyond simple combating microbial pathogens and include use as novel anti-cancer drugs and other front-line medicines and as tools in neurobiology. This book serves as an update on the most important recent advances in the genetics, cellular biology and practical applications of the most important bacterial toxins.

The future of agriculture strongly depends on our ability to enhance productivity without sacrificing long-term production potential. An ecologically and economically sustainable strategy is the application of microorganisms, such as the diverse bacterial species of plant growth promoting bacteria (PGPB). The use of these bio-resources for the enhancement of crop productivity is gaining worldwide importance.

"Bacteria in Agrobiology: Crop Ecosystems" describes the beneficial role of plant growth promoting bacteria with special emphasis on oil yielding crops, cereals, fruits and vegetables. Chapters present studies on various aspects of bacteria-plant interactions, soil-borne and seed-borne diseases associated with food crops such as rice, sesame, peanuts, and horticultural crops. Further reviews describe technologies to produce inoculants, the biocontrol of post harvest pathogens as a suitable alternative to agrochemicals, and the restoration of degraded soils.

In this timely book, leading international Pasteurellaceae scientists critically review the most important current research providing an up-to-date review of the molecular biology, genomics and virulence of these fascinating organisms. Topics covered include taxonomy and biodiversity, phylogeny, comparative genomics, competence, DNA uptake and transformation, proteomics and protein secretion, RTX toxins, lipopolysaccharides, biofilms, quorum sensing, antimicrobial resistance, diagnosis, and OMP and iron uptake. Each chapter is independent and can be read in isolation and as a whole the book provides an important resource summarising our current knowledge of Pasteurellaceae genomics and molecular biology. Essential reading for everyone working on Pasteurellaceae and related organisms.

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.

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.

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."

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.