The contemporary crisis of emerging disease has been a century and a half in the making. Human, veterinary, and crop health practitioners convinced themselves that disease could be controlled by medicating the sick, vaccinating those at risk, and eradicating the parts of the biosphere responsible for disease transmission. Evolutionary biologists assured themselves that coevolution between pathogens and hosts provided a firewall against disease emergence in new hosts. Most climate scientists made no connection between climate changes and disease. None of these traditional perspectives anticipated the onslaught of emerging infectious diseases confronting humanity today. As this book reveals, a new understanding of the evolution of pathogen-host systems, called the Stockholm Paradigm, explains what is happening. The planet is a minefield of pathogens with preexisting capacities to infect susceptible but unexposed hosts, needing only the opportunity for contact. Climate change has always been the major catalyst for such new opportunities, because it disrupts local ecosystem structure and allows pathogens and hosts to move. Once pathogens expand to new hosts, novel variants may emerge, each with new infection capacities. Mathematical models and real-world examples uniformly support these ideas. Emerging disease is thus one of the greatest climate change-related threats confronting humanity. While time is short, the danger is great, and we are largely unprepared, The Stockholm Paradigm offers hope for managing the crisis. By using the DAMA (document, assess, monitor, act) protocol, we can "anticipate to mitigate" emerging disease, buying time and saving money while we search for more effective ways to cope with this challenge.

This Volume presents a comprehensive series of generic protocols for the genetic and genomic analysis of prokaryotic isolates. Genetic methods for functional analyses employ the latest cloning vectors, gene fusion methods and transposon mutagenesis systems, as well as systems for introducing protease-cleavage sequences into permissive sites in proteins under investigation. Genomic methods described include protocols for transcriptomics, shotgun proteomics, interactomics, metabolic profiling, and lipidomics. Bioinformatic tools for genome annotation, transcriptome display and the integration of transcriptomic data into genome-scale metabolic reconstructions are described. Protocols for 13C-based metabolic flux determinations and analysis of the hierarchical and metabolic regulation of fluxes through pathways are included. The Volume thus enables investigators to functionally analyse an isolate over the entire cellular range spanning the gene, the genome, the transcript repertoire, the proteome, the interactome, the metabolic network with its nodes and their regulatory hierarchies, and the metabolic fluxes and their physiological controls. Hydrocarbon and Lipid Microbiology Protocols There 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.

Presents an integrated view of the expression of bacterial genetic information, genome architecture and function, and bacterial physiology and pathogenesis This book blends information from the very latest research on bacterial chromosome and nucleoid architecture, whole-genome analysis, cell signaling, and gene expression control with well-known gene regulation paradigms from model organisms (including pathogens) to give readers a picture of how information flows from the environment to the gene, modulating its expression and influencing the competitive fitness of the microbe. Structure and Function of the Bacterial Genome explores the governance of the expression of the genes that make a bacterium what it is, and updates the basics of gene expression control with information about transcription promoter structure and function, the role of DNA as a regulatory factor (in addition to its role as a carrier of genetic information), small RNAs, RNAs that sense chemical signals, ribosomes and translation, posttranslational modification of proteins, and protein secretion. It looks at the forces driving the conservation and the evolution of the dynamic genome and offers chapters that cover DNA replication, DNA repair, plasmid biology, recombination, transposition, the roles of repetitive DNA sequences, horizontal gene transfer, the defense of the genome by CRISPR-Cas, restriction enzymes, Argonaute proteins and BREX systems. The book finishes with a chapter that gives an integrated overview of genome structure and function. Blends knowledge of gene regulatory mechanisms with a consideration of nucleoid structure and dynamics Offers a 'DNA-centric' approach to considering transcription control Views horizontal gene transfer from a gene regulation perspective Assesses the opportunities and limitations of designing synthetic microbes or rewiring existing ones Structure and Function of the Bacterial Genome is an ideal book for graduate and undergraduate students studying microbial cell biology, bacterial pathogenesis, gene regulation, and molecular microbiology. It will also appeal to principal investigators conducting research on these and related topics and researchers in synthetic biology and other arms of biotechnology.

This book presents comprehensive reviews on the principles, design and applications of nanomaterials in the food and agriculture sectors. This book is the fifth of several volumes on Nanoscience in Food and Agriculture, published in the series Sustainable Agriculture Reviews.

This book addresses the diversity of tropical microorganisms and its applications in agriculture, renewable energy production and environmental protection. It covers several tropical habitats such as rain forests, mangroves, sea and river waters and describes how microorganisms isolated from these regions can be used to control insects and plant diseases, to improve sugar cane and biofuels production among other applications. The book also aims to bring researchers' attention to the potential of tropical microorganisms for biotechnological purposes, an area that is still far from being well explored.

This edited volume focuses on the characterization, reclamation, bioremediation, and phytoremediation of salt affected soils and waterlogged sodic soils. Innovative technologies in managing marginal salt affected lands merit immediate attention in the light of climate change and its impact on crop productivity and environment. The decision-making process related to reclamation and management of vast areas of salt affected soils encompasses consideration of economic viability, environmental sustainability, and social acceptability of different approaches. The chapters in this book highlight the significant environmental and social impacts of different ameliorative techniques used to manage salt affected soils. Readers will discover new knowledge on the distribution, reactions, changes in bio-chemical properties and microbial ecology of salt affected soils through case studies exploring Indian soils. The contributions presented by experts shed new light on techniques such as the restoration of degraded lands by growing halophyte plant species, diversification of crops and introduction of microbes for remediation of salt infested soils, and the use of fluorescent pseudomonads for enhancing crop yields.

The chapters in this topical volume of Advances in Microbiology, Infectious Diseases and Public Health present exciting, insightful observations on emerging viral infections like influenza, Middle East respiratory syndrome, or mosquito-transmitted diseases, as well as the potential of social media in preventing and fighting infectious diseases. This rapidly developing field of study, which involves interdisciplinary and challenging research conducted in both industrialized and limited-resource countries, can yield vital information for the life and social sciences, for public health, and for healthcare in general. The aim of this volume is to contribute to the development of knowledge on emerging infections in the endless struggle between viruses and man. The chapters selected are not intended as a systematic collection of all emerging infections, but instead highlight recent discoveries and provide insights on today's hot topics. The book offers a valuable resource for all scientists working in the field of emerging viral infections and possible vaccines, as well as for laboratory and medical staff whose work involves preventing, controlling and combatting infectious diseases.

This book summarizes what is currently known about gravity sensing and response mechanisms in microorganisms, fungi, lower and higher plants; starting from the historical eye-opening experiments from the 19th century up to today's extremely rapid advancing cellular, molecular and biotechnological research. All forms of life are constantly exposed to gravity and it can be assumed that almost all organisms have developed sensors and respond in one way or the other to the unidirectional acceleration force,this books shows us some of these different ways. The book is written for plant biologists and microbiologists as well as scientists interested in space and gravitational biology.

This book discusses the use of microorganisms for improving nutrient quality and producing healthier foods. Conventional roles of microbes in food preservation and in producing more readily digestible nutrients via natural fermentation processes are also examined. Individual chapters explore topics such as bio-preservation, incorporation of lactic acid bacteria, traditional fermented Mongolian foods, fermented fish products of Sudan, probiotics in China, fermented soymilk, food colorants, and the effect of food on gut microbiota. Readers will gain insights into current trends and future prospects of functional foods and nutraceuticals. This volume will be of particular interest to scientists working in the fields of food sciences, microbiology, agriculture and public health.

This book gives an overview on techniques and future perspectives of various aspects of waste biomass management. It also presents the economic and environmental evaluation, and also the monetary value-benefits and sustainability of the different processes. Recycling processes of lignocellulosic biomass from palm oil mill waste are covered, as well as from sugar industry waste and agriculture waste. It also includes thermal and non-thermal technologies for resource recovery from waste biomass. Challenges in the reuse and recycling of waste biomass are discussed, i.e., the hygienic safety in biomass management and bioremediation technologies for conversion into valuable products. The book is aiming at scientists, researchers and students alike, who are working in the research areas pertaining to waste management

This book will provide assistance to the broad range of readers involved in the crude oil import and production; renewable energy production; biomass analysis and bioconversion; greenhouse gas emissions; techno-economic analysis and government policies for implementing biofuels in India. This book presents important aspects on the large scale production of biofuels following a bio-refinery concept and its commercialization and sustainability issues. Hence, it is a useful resource to policy makers, policy analysts, techno-economic analysts and business managers who deal with commercialization and implementation of bio-based energy and other value-added products. The following features of this book attribute its distinctiveness: As a first uniquely focused scientific and technical literature on bioenergy production in the context of India. To its coverage of technological updates on biomass collection, storage and use, biomass processing, microbial fermentation, catalysis, regeneration, solar energy and monitoring of renewable energy and recovery process. To the technical, policy analysis, climate change, geo-political analysis of bioenergy and green transportation fuels at industrial scale.

This second edition volume expands on the previous editions with detailed protocols on (cyano) bacterial and mold fungus toxins, and a specific focus on Gram-negative endotoxins (lipopolysaccharides). The chapters in Microbial Toxins: Methods and Protocols, Second Edition present techniques that cover topics such as detection of cholera toxin by an immunochromatographic test strip; label-free immune-sensors for the fast detection of Listeria in food; endotoxin removal from Escherichia coli bacterial lysate using biphasic liquid system; and micromethods for isolation and structural characterization of lipid A, and polysaccharide regions of bacterial lipopolysaccharides. 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. Cutting-edge and practical, Microbial Toxins: Methods and Protocols, Second Edition is a valuable and useful resource for scientists who are interested in this field, and is a great tool for researchers who are looking to learn about new, particular techniques to further enhance their work.

This book focuses on the use of microorganisms in relation to agriculture, aquaculture and related fields, ranging from biofertilizers to poultry production. The latest innovations are also included to provide insights into the unlimited potentials of microorganisms in these areas.Individual chapters explore topics such as probiotics in poultry, biopurification of wastewater, converting agrowastes into value-added applications and products, rice cultivation, surfactants and bacteriocin as biopreservatives, bioplastics, crop productivity, biofloc, and the production of natural antibiotics. This volume will be of particular interest to scientists, policymakers and industrial practitioners working in the fields of agriculture, aquaculture and public health.

This book provides in-depth reviews of the effects of nanoparticles on the soil environment, their interactions with plants and also their potential applications as nanofertilizers and pesticides. It offers insights into the current trends and future prospects of nanotechnology, including the benefits and risks and the impact on agriculture and soil ecosystems. Individual chapters explore topics such as nanoparticle biosynthesis, engineered nanomaterials, the use of nanoclays for remediation of polluted sites, nanomaterials in water desalination, their effect on seed germination, plant growth, and nutrient transformations in soil, as well as the use of earthworms as bioremediating agents for nanoparticles. It is a valuable resource for researchers in academia and industry working in the field of agriculture, crop protection, plant sciences, applied microbiology, soil biology and environmental sciences.

This contributed volume provides insights into multiple applications using microbes to promote productivity in agriculture, to produce biochemicals or to respond to challenges in biomedicine. It highlights the microbial production of nanocompounds with medical functionality alongside new anti-mycobacterial strategies, and introduces plant-growth-promoting Rhizobacteria as well as the correlation between biofilm formation and crop productivity. Further, the authors illustrate the green synthesis of biochemical compounds, such as hydroxamid acid or biosurfactants, using microbial and fungal enzymes. It inspires young researchers and experienced scientists in the field of microbiology to explore the combined use of green, white and red biotechnology for industrial purposes, which will be one of the central topics for future generations.

This book describes the vast variety of xenobiotics, such as pesticides, antibiotics, antibiotic resistance genes, agrochemicals and other pollutants, their interactions with the soil environment, and the currently available strategies and techniques for soil decontamination and bioremediation. Topics covered include: transport mechanisms of pollutants along the Himalayas; use of earthworms in biomonitoring; metagenomic strategies for assessing contaminated sites; xenobiotics in the food chain; phyto-chemical remediation; biodegradation by fungi; and the use of enzymes and potential microbes in biotransformation. Accordingly, the book offers a valuable guide for scientists in the fields of environmental ecology, soil and food sciences, agriculture, and applied microbiology.

This volume discusses various methods and protocols used for the experimentation of a wide range of bacterial species, such as Streptococcus pyogenes, Staphylococcus aureus, Streptococcus pneumonia, Listeria monocytogenes, and Mycobacterium marinum. Bacterial Pathogens: Methods and Protocols is divided into 6 parts: Part 1 describes different approaches to identifying and characterizing bacterial effector molecules; Part 2 deals with structural biology of bacterial pathogenesis and how to overcome folding and stability problems with recombinantly expressed proteins; Part 3 details methodology that identifies bacteria in complex communities and how genomes of bacterial pathogens have evolved; Part 4 reflects on the rapid development of advanced imaging techniques that address questions about molecular properties of individual live bacteria, ultrastructure of surfaces, and subcellular localization of bacterial proteins; Part 5 describes methods from in vitro and in vivo modeling of bacterial infections; and Part 6 explores how bacterial pathogens are the true experts of the immune system. 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. Cutting-edge and comprehensive, Bacterial Pathogens: Methods and Protocols is a valuable resource for anyone who is interested in this fascinating and evolving field.

This Volume describes methods for investigating microbes in their natural environment and how to obtain representative samples and preserve them for subsequent analyses. Chapters are arranged according to the environments under investigation, which include: oil reservoirs, fracking fluids, aquifers, coal beds, oil sands and their tailing ponds, lakes, rivers, leaves, polar seas and ice, the sea-surface microlayer, mud flats, microbialites, and deep-sea fauna. A variety of downstream analytical procedures are described, including: nucleic-acid extraction and preparation for high-throughput sequencing, fluorescence in-situ hybridisation, and cultivation of aerobic and anaerobic hydrocarbon-degrading microbes. Though most chapters focus on hydrocarbon-rich environments, many of the approaches used are generic, and as such will be of value to researchers embarking on studies of microbes and their processes in the field. Hydrocarbon and Lipid Microbiology Protocols There 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.

This book is the third volume on Nanoscience in Food and Agriculture, published in the Sustainable Agriculture Reviews series. In this book we present ten chapters describing the synthesis and application of nanomaterials for health, food, agriculture and bioremediation.Nanomaterials with unique properties are now being used to improve food and agricultural production. Research on nanomaterials is indeed revealing new applications that were once thought to be imaginary. Specifically, applications lead to higher crop productivity with nanofertilisers, better packaging, longer food shelf life and better sensing of aromas and contaminants. These applications are needed in particular in poor countries where food is scarce and the water quality bad. Nanotechnology also addresses the age old issue of water polluted by industrial, urban and agricultural pollutants. For instance, research produces nanomaterials that clean water more efficiently than classical methods, thus yielding water for drinking and irrigation. However, some nano materials have been found to be toxic. Therefore, nanomaterials should be engineered to be safe for the environment.

This Volume presents applications of hydrocarbon microbiology in the context of environmental pollutant degradation, covering pollutants such as petroleum and related wastes (i.e. oil sludge), biofuels, lipid-rich wastes, chlorinated solvents and BTEX, in several environments (marine, soil, groundwater). The approaches presented range from laboratory experiments and treatment in reactors to field applications. Two chapters highlight innovative approaches to address relevant questions in pollutant degradation, such as low environmental concentrations of pollutants, and the biodegradation of complex pollutant mixtures using biofilms. Rather than presenting the applications in the form of protocols, some of the chapters in this Volume include detailed practical information on the opportunities offered by and limitations of the different approaches, providing valuable information for researchers planning to perform bioremediation experiments. Hydrocarbon and Lipid Microbiology Protocols There 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.

This volume focuses on mitochondrial RNA metabolism, emphasizing recent discoveries and technological advances in this fast moving area that increase our understanding of mitochondrial gene function. Topics addressed include the interplay of mitochondria with the nucleus and cytosol, structure-function connections, and relevance to human disease. Mitochondria are the powerhouses of the cell, and a great deal is known about mitochondrial energy metabolism. Less well known is the plethora of amazing mechanisms that have evolved to control expression of mitochondrial genomes. Several RNA processes and machineries in protozoa, plants, flies and humans are discussed, including: transcription and RNA polymerase mechanism; tRNA processing of 5' and 3' ends; mRNA maturation by nucleotide insertion/deletion editing and by RNA splicing; mRNA stability; and RNA import. Specialized factors and ribonucleoproteins (RNPs) examined include pentatricopeptide repeat (PPR) proteins, RNase P, polymerases, helicases, nucleases, editing and repair enzymes. Remarkable features of these processes and factors are either not found outside mitochondria, differ substantially among eukaryotic lineages, or are unique in biology.

This book presents the latest results related to photocatalytic inactivation/killing of microorganisms, which is a promising alternative disinfection method that produces less or even no disinfection byproduct. The book is divided into 13 chapters, which introduce readers to the latest developments in the photocatalytic disinfection of microorganisms, examine essential photocatalytic (PC) and photoelectrocatalytic (PEC) disinfection studies, and forecast and make recommendations for the further development of PC and PEC disinfection. Bringing together contributions by various leading research groups worldwide, it offers a valuable resource for researchers and the industry alike, as well as the general public. Taicheng An, PhD, is Chair Professor and Director at the Institute of Environmental Health and Pollution Control, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, China. Huijun Zhao, PhD, is Chair Professor and Director at the Centre for Clean Environment and Energy & Griffith School of Environment, Griffith University, Australia. Po Keung Wong, PhD, is a Professor at the School of Life Sciences, the Chinese University of Hong Kong, Hong Kong SAR, China.

This Volume describes methods for simulating natural environments by using reproducible and controllable meso- and microcosm experiments to analyse hydrocarbon-degrading microorganisms and to test hypotheses. It presents important aspects of the preparation of experimental set-ups, hydrocarbon application and sampling, and features protocols for experiments with different types of samples, such as biofilms, aquatic systems (e.g. groundwater, streams), and sediments, including oscillating oxic-anoxic mesocosms, as well as for in-situ experimentation in subtidal and deep sediments. Two chapters are dedicated to cultivation under high-pressure conditions, and several chapters include protocols for processing samples for downstream chemical, microbial or activity analyses. Several of the approaches presented are generic and will benefit anyone embarking on designing meso- and microcosm experiments. < Hydrocarbon and Lipid Microbiology Protocols There 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.

Novel Food Fermentation Technologies provides a comprehensive overview of innovations in food fermentation technologies and their application. Current novel technologies for microbial culture production and preservation are covered in detail, as are fermentation techniques for the production of bioactives from various food matrices, including food processing by-products and waste. Readers are provided with a close look at thermal and non-thermal technologies applicable to fermented food products. The text covers immobilization, microencapsulation technologies and novel preservation techniques for cultures in fermentation. In-depth studies of high pressure processing, pulsed electric field, power ultrasound and gamma irradiation in fermentation are provided in addition to novel thermal and non-thermal technologies and process analytical techniques. A wide variety of fermented products are covered, including meat, marine-based, grain-based, dairy and vegetable-based products. Current technologies for extraction of bioactives are examined, as are current innovations in fermented food packaging. Readers are presented with current and future challenges in food fermentation as well. As a comprehensive reference for food fermentation, this work provides up-to-date insights into emerging fermentation technologies which facilitate the processing of wholesome and safe food products.

This volume discusses various basic and advanced methods and protocols that have been proven to be successful among certain bacterial species, or a family of species, in type III secretion systems (T3S system). The chapters in this book cover topics such as: site-directed mutagenesis and its application in studying the interactions of T3S components; use of transcriptional control to increase expression and secretion of heterologous proteins in T3S systems; fractionation techniques to examine effector translocation; detecting immune responses to T3S systems; mouse immunization with purified needle proteins from T3S systems and the characterization of the immune responses to these proteins; and detection of protein interactions in T3S systems using yeast 2-hybrid analysis. 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. Practical and comprehensive, Type 3 Secretion Systems: Methods and Protocols is a valuable resource for anyone interested in learning about the fascinating and ever-changing T3S systems.