This Volume describes methods for cultivating hydrocarbon-producing and -consuming microbes, covering compounds in a range of states - gaseous (e.g. methane), liquid (e.g. alkanes of intermediate molecular weight) and solid (e.g. many PAHs and asphaltene). It also examines the cultivation of aerobic and anaerobic hydrocarbon degraders using a range of electron acceptors (e.g. oxygen, nitrate, sulphate, metals, (per)chlorate), and a separate chapter is devoted to explaining the cultivation of methanogens. Special attention is given to: high-throughput cultivation, growing microbes as biofilms, and cultivating fastidious microbes, as well as the preservation of microbial pure cultures and consortia. Accordingly, this Volume will be of value to anyone embarking on the selective enrichment and cultivation of novel microorganisms. 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.

Microorganisms are the most diverse group of organisms and play important and distinctive roles in their ecosystems. They interact with their peers and other organisms (e.g., plants, animals) to form a complicated food web, significantly impacting ecosystem functions and services. However, understanding the diversity, composition, structure, function, activity and dynamics of microbial communities remains challenging. Over the past decade, microarray-based technologies have been developed to address such challenges. Written by expert authors this book is focused on current microarray technologies and their applications in environmental microbiology. In the first chapter microarray technologies and applications are briefly introduced and in following chapters microarray probe design, development and evaluation, and data analysis are described in detail. In later chapters, more attention is paid to phylogenetic arrays (e.g., PhyloChip) and functional gene arrays (e.g., GeoChip). These generic tools for analyzing microbial communities from disparate environments, ecosystems, and habitats including soil, water, sediment, animals and humans, are described in detail with examples of specific applications. Also included are microarrays for analyzing microbial communities from specific environments, such as soil, bioleaching ecosystems, and human microbiomes, and microarrays for detecting specific microorganisms (e.g., pathogens) in the environment. The authors also discuss the advantages and limitations of microarray technologies compared to high throughput sequencing technologies. This book is a valuable and useful source of information about microarrays for microbial community analysis and is recommended for anyone working on microbial communities, biofilms or environmental microbiology.

This detailed volume provides a toolbox for designing constructs, tackling expression and solubility issues, handling membrane proteins and protein complexes, and exploring innovative engineering of E. coli. The topics are largely grouped under four parts: high-throughput cloning, expression screening, and optimization of expression conditions, protein production and solubility enhancement, case studies to produce challenging proteins and specific protein families, as well as applications of E. coli expression. Written for the highly successful Methods in Molecular Biology series, 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, Heterologous Gene Expression in E. coli: Methods and Protocols serves molecular biologists, biochemists and structural biologists, those in the beginning of their research careers to those in their prime, to give both an historical and modern overview of the methods available to express their genes of interest in this exceptional organism.

This volume focuses on antibiotics research, a field of topical significance for human health due to the worrying increase of nosocomial infections caused by multi-resistant bacteria. It covers several basic aspects, such as the evolution of antibiotic resistance and the influence of antibiotics on the gut microbiota, and addresses the search for novel pathogenicity blockers as well as historical aspects of antibiotics. Further topics include applied aspects, such as drug discovery based on biodiversity and genome mining, optimization of lead structures by medicinal chemistry, total synthesis and drug delivery technologies. Moreover, the development of vaccines as a valid alternative therapeutic approach is outlined, while the importance of epidemiological studies on important bacterial pathogens, the problems arising from the excessive use of antibiotics in animal breeding, and the development of innovative technologies for diagnosing the "bad bugs" are discussed in detail. Accordingly, the book will appeal to researchers and clinicians alike.

Michael Lebuhn, Stefan Weiss, Bernhard Munk, Georg M. Guebitz Microbiology and Molecular Biology Tools for Biogas Process Analysis, Diagnosis and Control Veronika Dollhofer, Sabine Marie Podmirseg, Tony Martin Callaghan, Gareth Wyn Griffith & Katerina Fliegerova Anaerobic Fungi and their Potential for Biogas Production Bianca Froeschle, Monika Heiermann, Michael Lebuhn, Ute Messelhausser, Matthias Ploechl Hygiene and Sanitation in Biogas Plants Charles-David Dube and Serge R. Guiot Direct Interspecies Electron Transfer in Anaerobic Digestion: A Review Simon K.-M. R. Rittmann A Critical Assessment of Microbiological Biogas to Biomethane Upgrading Systems Manfred Lubken, Pascal Kosse, Konrad Koch, Tito Gehring, Marc Wichern Influent Fractionation for Modeling Continuous Anaerobic Digestion Processes Fermoso, F. G, van Hullebusch, E. D, Guibaud, G, Collins, G, Svensson, B. H, Carliell-Marquet, C, Vink, J.P.M, Esposito, G, Frunzo, L Fate of Trace Metals in Anaerobic Digestion

The type I interferon (IFN) signaling pathway is well recognized as a pathway activated by viral infections. It is activated by a variety of microbial pattern recognition receptors including the Toll-like receptors, NOD-like receptors and several cytosolic receptors. Activation of the type I IFN pathway leads to the production of both antiviral factors and products that influence immune cell function. More recently it has been shown that bacteria are also capable of activating this pathway. Bacterial Activation of Type I Interferons reviews both the current understanding of how different bacterial species are able to activate this pathway as well as the influence type I IFNs have on the outcome to infection. Several different bacterial species are covered, spanning Gram positive and Gram negative, intracellular, extracellular, and different host infection sites. An introduction to the pathogenesis of each organism is provided, and the signaling molecules involved in the activation of the type I IFN pathway and the role it plays in animal infection models are also covered.

The genus Borrelia, in the spirochete phylum, is not closely related to any other bacteria and has a highly unusual genome composed of a linear chromosome and multiple circular and linear plasmids that appear to be in a constant state of rearrangement, recombination, and deletion. The determination of the genome sequence of Borrelia strains has facilitated tremendous advances in understanding this genus at the molecular and cellular level, as well as the pathogenesis of Lyme disease and relapsing fever. In recent years, there has been an explosion of new insights into the molecular biology, genetics, physiology, and ecology of Borrelia and its tick/vertebrate life cycle. This research is of particular importance as the incidence of Lyme borreliosis continues to increase. Written by renowned scientists who have made seminal contributions to the field, this book is a comprehensive guide to the pathogenic Borrelia, providing researchers, advanced students, clinicians, and other professionals with an encyclopedic overview of the molecular biology of this important genus and the pathogenesis of diseases. Leading authorities have made contributions on topics such as Borrelia genomics, DNA replication, gene regulation, transcriptomics, proteomics, metabolism and physiology, cellular structure, motility and chemotaxis, genetic manipulation, evolutionary genetics, ecology, tick interactions, Lyme disease and relapsing fever pathogenesis, animal models, host response, detection, and vaccines. The volume is essential for anyone involved in Borrelia research and is strongly recommended for microbiologists, immunologists, and physicians involved in spirochete research, Lyme borreliosis, or relapsing fever. The book is a recommended reference volume for all microbiology libraries.

This volume will be of interest to epidemiologists, food microbiologists, and anyone working on comparing bacterial isolates. Pulse Field Gel Electrophoresis: Methods and Protocols guides readers through methods and protocols that will advance the harmonisation of PFGE methodologies and facilitate inter-laboratory comparisons of PFGE profiles from pathogenic and non-pathogenic bacteria. As a volume in the highly successful Methods in Molecular Biology series, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. Concise and easy-to-use, Pulse Field Gel Electrophoresis: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Microorganisms play an important role in the maintenance of the ecosystem structure and function. Bacteria constitute the major part of the microorganisms and possess tremendous potential in many important applications from environmental clean up to the drug discovery. Much advancement has been taken place in the field of research on bacterial systems. This book summarizes the experimental setups required for applied microbiological studies. Important background information, representative results, step by step protocol in this book will be of great use to the students, early career researchers as well as the academicians. The book describes many experiments covering the basic microbiological experiments to the applications of microbial systems for advanced research. Researchers in any field who utilize bacterial systems will find this book very useful. In addition to microbiology and bacteriology, this book will also find useful in molecular biology, genetics, and pathology and the volume should prove to be a valuable laboratory resource in clinical and environmental microbiology, microbial genetics and agricultural research. Unique features * Easy to follow by the users as the experiments have been written in simple language and step-wise manner. * Role of each reagents to be used in each experiment have been described which will help the beginners to understand quickly and design their own experiment. * Each experiment has been equipped with the coloured illustrations for proper understanding of the concept. * Trouble-shootings at the end of each experiment will be helpful in overcoming the problems faced by the users. * Flow-chart of each experiment will quickly guide the users in performing the experiments.

This Volume presents methods for quantifying microbial populations and characterising microbial communities by extracting and analysing biomarkers such as RNA, DNA and lipids. The chapters cover a wide range of topics, including: cell separation from oil-rich environments, enumeration of hydrocarbon degraders and sulphate reducers using most-probable-number techniques, and quantification by means of real-time PCR. A variety of molecular methods are described for microbial community profiling, such as phospholipid fatty acid analysis, DGGE, T-RFLP and SSCP. One chapter examines high-throughput sequencing, and provides important information on the associated procedures required for thorough data analysis. A further chapter is devoted to the characterisation of protistan communities, while the closing chapter describes multiplex fluorescent antibody microarrays for detecting microbial biomarkers. 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 new edition provides a comprehensive look at the molecular genetics and biochemical basis of fungal biology, covering important model organisms such as Aspergilli while also integrating advances made with zygomycetes and basidiomycetes. This book groups a total of 15 chapters authored by expert scholars in their respective fields into four sections. Five chapters cover various aspects of gene expression regulation. These range from regulation in organismal interactions between parasitic fungi and their host plant, heavy metal stress and global control of natural product genes to conidiation and regulation through RNA interference. Two chapters are dedicated to signal transduction, highlighting MAP-kinase-dependent signaling and heterotrimeric G-proteins. Fungal carbohydrates are the subject of the third section, which addresses both polymeric cell wall carbohydrates and trehalose as an important, low molecular weight carbohydrate. The fourth section emphasizes the metabolism of major elements (carbon, nitrogen, sulfur) and critical cellular pathways for primary and secondary products.

Since its discovery in 1998, RNA interference (RNAi) has heralded the advent of novel tools for biological research and drug discovery. This exciting new technology is emerging as a powerful modality for battling some of the most notoriously challenging viral clinical targets, such as the hepatitis C virus (HCV) and the human immunodeficiency virus (HIV). However, several critical issues associated with this novel technology must be resolved before it can progress to testing in human clinical trials, and these have been the target of intensive research in recent years. In this book, expert RNAi specialists from around the world have teamed up to produce a timely and thought-provoking review of the area. The two central themes are: 1) the latest findings on RNAi-virus interactions and 2) progress in the development of RNAi-based antiviral therapeutics. A number of chapters explain general concepts concerned with the role of RNAi in natural antiviral defense mechanisms. Other chapters discuss how to improve the efficacy and safety of RNAi-based antiviral drugs, as well as describe how this technology is being developed as a new therapeutic tool for fighting specific viruses, including HIV, HCV, and respiratory viruses. The book also outlines potential new avenues for research. RNA Interference and Viruses is essential reading for researchers involved in RNAi or antiviral research and is a recommended text for all virology laboratories.

This volume presents a comprehensive perspective of the biopesticides Bacillus thuringiensis and Lysinibacillus sphaericus, from their basic biology to agriculture, forestry and public-health applications. It covers their ecology, virulence factors, and genetic characterization. The topics related to agriculture and forestry include mode of action, receptors of insect pests, and heterologous expression of toxins in insect cells and plants. Public-health researchers will find information on vector control programs with an emphasis on the Neotropical region. The book also discusses new products and the global market.

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.

Baculovirus Expression Systems and Biopesticides Edited by Michael L. Shuler, H. Alan Wood, Robert R. Granados, and Daniel A. Hammer Baculovirus Expression Systems and Biopesticides provides an integrated perspective on the use of the continually evolving baculovirus-insect cell system in the production of recombinant proteins and genetically engineered pesticides. Divided into three main sections--Developing Effective Virus-Insect Culture Systems, Bioreactor Design and Scale-Up Issues, and Commercial Application of Insect Cell Culture--the book, written by highly regarded editors in the field, describes:
* The molecular biology and genetics of baculoviruses
* The use of baculoviruses as expression systems
* Principles and methods for small- and large-scale insect cultures
* The use of wild type and genetically engineered baculoviruses as viral pesticides
The breadth of coverage in Baculovirus Expression Systems and Biopesticides will meet the needs of molecular biologists, chemical engineers, biotechnologists, virologists, and entomologists.

Retroviruses comprise a diverse family of enveloped RNA viruses, remarkable for their use of reverse transcription of viral RNA into linear double stranded DNA during replication and the subsequent integration of this DNA into the genome of the host cell. Members of this family include important pathogens such as HIV-1, feline leukemia, and several cancer-causing viruses. However, interest in these viruses extends beyond their disease-causing capabilities. For example, research in this area led to the discovery of oncogenes, a major advance in the field of cancer genetics. Studies of retroviruses have contributed greatly to our understanding of mechanisms that regulate eukaryotic gene expression. In addition, retroviruses are proving to be valuable research tools in molecular biology and have been used successfully in gene therapy (e.g. to treat X-linked severe combined immunodeficiency). Written by the top retroviral specialists, this book reviews the genomics, molecular biology, and pathogenesis of these important viruses, comprehensively covering all the recent advances. Topics include: host and retroelement interactions * endogenous retroviruses * retroviral proteins and genomes * viral entry and uncoating * reverse transcription and integration * transcription * splicing and RNA transport * pathogenesis of oncoviral infections * pathogenesis of immunodeficiency virus infections * retroviral restriction factors, molecular vaccines, and correlates of protection * gammaretroviral and lentiviral vectors * non-primate mammalian and fish retroviruses * simian exogenous retroviruses * and HTLV and HIV. It is essential reading for every retrovirologist and it is a recommended text for all virology and molecular biology laboratories.

This Microbiology Monographs volume covers the current and most recent advances in genomics and genetics, biochemistry, physiology, and molecular biology of C. reinhardtii. Expert international scientists contribute with reviews on the genome, post-genomic techniques, the genetic toolbox development as well as new insights in regulation of photosynthesis and acclimation strategies towards environmental stresses and other structural and genetic aspects, including applicable aspects in biotechnology and biomedicine. Powerful new strategies in functional genomic and genetics combined with biochemical and physiological analyses revealed new insights into Chlamydomonas biology.

Yeast Protocols, Third Edition presents up-to-date advances in research using yeasts as models. Chapters cover topics such as basic protocols in yeast culture and genomic manipulation, protocols that study certain organelles such as mitochondria and peroxisomes and their functions in autophagy and assays commonly used in yeast-based studies that can be adapted to other organisms. As the first sequenced living organism, budding yeast S. cerevisiae and other model yeasts have helped greatly in life science research. The easy switch between the haploid and diploid state makes yeast a paradigm of genetic manipulation. 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, Yeast Protocols, Third Edition seeks to serve both professionals and novices with newly-developed protocols to study this essential model organism.

Bringing together key research on bisphenol A (BPA) removal to allow students, and designers and operators of treatment plants to gain knowledge and insight into operating practices, this book presents developments in the technology of wastewater treatment for the removal of micropollutants, using BPA as an example. The difficulties in removing BPA from wastewater in traditional wastewater treatment plants are addressed along with a detailed analysis on integrated technologies for BPA removal; wastewater microorganisms that biodegrade BPA, and physical and chemical methods to support the biodegradation of BPA and its removal from wastewater. Readers are able to gain a general understanding of up-to-date techniques for removing BPA from wastewater, and are able to use the book as a reference for specific questions that they have.

This book sheds new light on how microbes can be used as effective and sustainable resources to produce green energy in the form of biogas, algal diesel, ethanol, hydrogen and direct electricity. It discusses topics such as microbial energy conversion technologies, including ethanol production by microbial catalytic reaction, biomethanization, biodiesel from microalgae, microbial fuel cells, and the microbiological production of hydrogen. The book will inspire scientists to find new approaches to meet local energy demands with the help of sustainable microbial resources available in and around a given location.

This book reviews efforts to produce chemicals and fuels from forest and plant products, agricultural residues and more. Algae can potentially capture solar energy and atmospheric CO2; the book details needed research and legislative initiatives.

Metagenomics is a rapidly growing field of research that has had a dramatic effect on the way we view and study the microbial world. By permitting the direct investigation of bacteria, viruses, and fungi, irrespective of their culturability and taxonomic identities, metagenomics has changed microbiological theory and methods and has also challenged the classical concept of species. This new field of biology has proven to be rich and comprehensive and is making important contributions in many areas including ecology, biodiversity, bioremediation, bioprospection of natural products, and medicine. This book addresses, in a coherent manner, the diverse and multiple aspects of metagenomics and the multiplicity of its potential applications. Renowned authors from around the world have contributed chapters covering the new theoretical insights, the more recent applications, and the dynamically developing methods of data acquisition and analysis. Topics include: conceptual frameworks * tools and methods * integration of complementary approaches * horizontal gene transfer * analysis of complex microbial communities * public data resources * plant-microbe interactions * bioremediation * industrial bioproducts * archaeal metagenomics * bioprospecting novel genes * the human microbiome * and philosophical themes in metagenomics. The book is essential reading for all researchers currently performing metagenomics studies and it is highly recommended for all students and scientists wishing to increase their understanding of this field.