The human pathogens Neisseria meningitidis and Neisseria gonorrhoeae are exquisitely adapted to life within the human mucosa, their only natural niche. N. meningitidis is the causative agent of rapidly transmissible meningitis and septic shock. Vaccines developed to control this pathogen can be rendered ineffective by the pathogen's ability to undergo antigenic variation. In contrast, there are no current vaccination prospects for N. gonorrhoeae, the causative agent of sexually transmitted gonorrhoea. Historically, infections caused by N. gonorrhoeae were treated with antibiotics. However, the recent advent of new strains with resistance to all known antibiotics is causing such treatment regimes to fail, necessitating the need for new and more effective control strategies. In this book, leading Neisseria authorities review the most important research on pathogenic Neisseria to provide a timely overview of the field. The topics covered include: the link between pathogenesis and important metabolic pathways * vaccine development * antibiotic resistance * transcriptomics of regulatory networks * regulatory small RNAs * interactions with neutrophils * advances in humanized mouse models. An essential guide for research scientists, advanced students, clinicians, and other professionals working with Neisseria, the book is a recommended text for all microbiology libraries.

Brucella is a genus of Gram-negative, facultative, intracellular bacteria that are highly pathogenic for a variety of mammals, including humans. Recently the WHO cited brucellosis to be the world's most widespread zoonosis. An important feature of the pathogenicity of these organisms is their ability to survive and replicate within the host macrophages. However the mechanism for this is unclear. In addition, none of the classical bacterial virulence factors found in other bacterial pathogens have been found in the genomes of the forty Brucella species and biovars analysed to date. Nevertheless the application of systems biology approaches in recent years has transformed research, permitting fascinating new insights into Brucella molecular biology and genomics. Written by highly acclaimed Brucella scientists, this book comprehensively reviews the most important advances in the field. Opening chapters focus on genetic diversity within Brucella, covering both classical and new species. Pa

This book provides an up-to-date review and analysis of the carrot's nuclear and organellar genome structure and evolution. In addition, it highlights applications of carrot genomic information to elucidate the carrot's natural and agricultural history, reproductive biology, and the genetic basis of traits important in agriculture and human health. The carrot genome was sequenced in 2016, and its relatively small diploid genome, combined with the fact that it is the most complete root crop genome released to date and the first-ever Euasterid II genome to be sequenced, mean the carrot has an important role in the study of plant development and evolution. In addition, the carrot is among the top ten vegetables grown worldwide, and the abundant orange provitamin A carotenoids that account for its familiar orange color make it the richest crop source of vitamin A in the US diet, and in much of the world. This book includes the latest genetic maps, genetic tools and resources, and covers advances in genetic engineering that are relevant for plant breeders and biologists alike.

Population genomics has revolutionized various disciplines of biology including population, evolutionary, ecological and conservation genetics, plant and animal breeding, human health, medicine and pharmacology by allowing to address novel and long-standing questions with unprecedented power and accuracy. It employs large-scale or genome-wide genetic information and bioinformatics to address various fundamental and applied aspects in biology and related disciplines, and provides a comprehensive genome-wide perspective and new insights that were not possible before. These advances have become possible due to the development of new and low-cost sequencing and genotyping technologies and novel statistical approaches and software, bioinformatics tools, and models. Population genomics is tremendously advancing our understanding the roles of evolutionary processes, such as mutation, genetic drift, gene flow, and natural selection, in shaping up genetic variation at individual loci and across the genome and populations; improving the assessment of population genetic parameters or processes such as adaptive evolution, effective population size, gene flow, admixture, inbreeding and outbreeding depression, demography, and biogeography; resolving evolutionary histories and phylogenetic relationships of extant, ancient and extinct species; understanding the genomic basis of fitness, adaptation, speciation, complex ecological and economically important traits, and disease and insect resistance; facilitating forensics, genetic medicine and pharmacology; delineating conservation genetic units; and understanding the genetic effects of resource management practices, and assisting conservation and sustainable management of genetic resources. This Population Genomics book discusses the concepts, approaches, applications and promises of population genomics in addressing most of the above fundamental and applied crucial aspects in a variety of organisms from microorganisms to humans. The book provides insights into a range of emerging population genomics topics including population epigenomics, landscape genomics, seascape genomics, paleogenomics, ecological and evolutionary genomics, biogeography, demography, speciation, admixture, colonization and invasion, genomic selection, and plant and animal domestication. This book fills a vacuum in the field and is expected to become a primary reference in Population Genomics world-wide.

Birds catch the public imagination like no other group of animals; in addition, birders are perhaps the largest non-professional naturalist community. Genomics and associated bioinformatics have revolutionised daily life in just a few decades. At the same time, this development has facilitated the application of genomics technology to ecological and evolutionary studies, including biodiversity and conservation at all levels. This book reveals how the exciting toolbox of genomics offers new opportunities in all areas of avian biology. It presents contributions from prominent experts at the intersection of avian biology and genomics, and offers an ideal introduction to the world of genomics for students, biologists and bird enthusiasts alike. The book begins with a historical perspective on how genomic technology was adopted by bird ecology and evolution research groups. This led, as the book explains, to a revised understanding of avian evolution, with exciting consequences for biodiversity research as a whole. Lastly, these impacts are illustrated using seminal examples and the latest discoveries from avian biology laboratories around the world.

This volume focuses on mono-ADP-ribosylation and enzymes that use NAD+ including Sirtuins, PARPs, and bacterial and eukaryotic ADP-ribosyltransferases. The chapters in this book are organized into eight parts, and offer detailed descriptions of key protocols used to study topics such as in vitro techniques for ADP-ribosylation substrate identification; biochemical and biophysical assays of PAR-WWE domain interactions; monitoring expression and enzyme activity of ecto-ARTCs; HPLC-based enzymes assays for Sirtuins; and identifying target RNAs of PARPs. 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 thorough, ADP-ribosylation and NAD+ Utilizing Enzymes: Methods and Protocols is a valuable resource for anyone interested in this developing and expanding field.

This book examines the application of soybean genome sequences to comparative, structural, and functional genomics. Since the availability of the soybean genome sequence has revolutionized molecular research on this important crop species, the book also describes how the genome sequence has shaped research on transposon biology and applications for gene identification, tilling and positional gene cloning. Further, the book shows how the genome sequence influences research in the areas of genetic mapping, marker development, and genome-wide association mapping for identifying important trait genes and soybean breeding. In closing, the economic and botanical aspects of the soybean are also addressed.

This book includes papers presented at the 2017 Joint meeting of Fodder Crops and Amenity Grasses Section and Protein Crops Working Group of EUCARPIA-Oil and Protein Crops Section. The theme of the meeting "Breeding Grasses and Protein Crops in the Era of Genomics" has been divided into six parts: (1) Utilisation of genetic resources and pre-breeding, (2) Genetic improvement of quality and agronomic traits, (3) Breeding for enhanced stress tolerance (4) Implementation of phenomics and biometrics, (5) Development of genomic tools and bioinformatics and (6) Reports of Parallel Sessions.

Every time a cell divides, a copy of its genomic DNA has to be faithfully copied to generate new genomic DNA for the daughter cells. The process of DNA replication needs to be precisely regulated to ensure that replication of the genome is complete and accurate, but that re-replication does not occur. Errors in DNA replication can lead to genome instability and cancer. The process of replication initiation is of paramount importance, because once the cell is committed to replicate DNA, it must finish this process. A great deal of progress has been made in understanding how DNA replication is initiated in eukaryotic cells in the past ten years, but this is the first one-source book on these findings. The Initiation of DNA Replication in Eukaryotes will focus on how DNA replication is initiated in eukaryotic cells. While the concept of replication initiation is simple, its elaborate regulation and integration with other cell processes results in a high level of complexity. This book will cover how the position of replication initiation is chosen, how replication initiation is integrated with the phases of the cell cycle, and how it is regulated in the case of damage to DNA. It is the cellular protein machinery that enables replication initiation to be activated and regulated. We now have an in-depth understanding of how cellular proteins work together to start DNA replication, and this new resource will reveal a mechanistic description of DNA replication initiation as well.

This volume presents protocols for Brachypodium genomics in numerous areas ranging from marker development, trait evolution, functional genomics, metabolomics, transcriptomics, genomics, and tilling. This book also explores techniques to study the widening genetic base of Brachypodium that will help researchers better understand the model plant using NGS technologies. 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, Brachypodium Genomics: Methods and Protocols is a valuable resource for bench-oriented molecular biologists and computational biologists working towards further evolving this field.

This book provides an overview of the latest advancements in the field of alien introgression in wheat. The discovery and wide application of molecular genetic techniques including molecular markers, in situ hybridization, and genomics has led to a surge in interspecific and intergeneric hybridization in recent decades. The work begins with the taxonomy of cereals, especially of those species which are potential gene sources for wheat improvement. The text then goes on to cover the origin of wheat, breeding in connection with alien introgressions, and the problems of producing intergeneric hybrids and backcross derivatives. These problems can include crossability, sterility, and unequal chromosome transmission. The work then covers alien introgressions according to the related species used, as well as new results in the field of genomics of wild wheat relatives and introgressions.

Updated and revised, this thorough volume covers a range of methods focusing on systems, including mammalian, yeast, bacterial and archaeal. This second edition of DNA Replication: Methods and Protocols describes approaches to analyze whole genomes to single molecules, as well as both in vivo and in vitro experiments. 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. Authoritative and cutting-edge, DNA Replication: Methods and Protocols, Second Edition provides a collections of methods intended for newcomers to this research field and for established laboratories.

This book describes how epigenetic context, in a large sense, affects gene expression and the development of an organism, using the asymptotic limit theorems of information theory to construct statistical models useful in data analysis. The approach allows deep understanding of how embedding context affects development. We find that epigenetic information sources act as tunable catalysts, directing ontogeny into characteristic pathways, a perspective having important implications for epigenetic epidemiology. In sum, environmental stressors can induce a broad spectrum of developmental dysfunctions, and the book explores a number of pandemic chronic diseases, using U.S. data at different scales and levels of organization. In particular, we find the legacy of slavery has been grossly compounded by accelerating industrial decline and urban decay. Individual chapters are dedicated to obesity and its sequelae, coronary heart disease, cancer, mental disorders, autoimmune dysfunction, Alzheimer's disease, and other conditions. Developmental disorders are driven by environmental factors channeled by historical trajectory and are unlikely to respond to medical interventions at the population level in the face of persistent individual and community stress. Drugs powerful enough to affect deleterious epigenetic programming will likely have side effects leading to shortened lifespan. Addressing chronic conditions and developmental disorders requires significant large-scale changes in public policy and resource allocation.

This volume provides an overview of RNA bioinformatics methodologies, including basic strategies to predict secondary and tertiary structures, and novel algorithms based on massive RNA sequencing. Interest in RNA bioinformatics has rapidly increased thanks to the recent high-throughput sequencing technologies allowing scientists to investigate complete transcriptomes at single nucleotide resolution. Adopting advanced computational technics, scientists are now able to conduct more in-depth studies and present them to you in this book. Written in the highly successful Methods of Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and equipment, step-by-step, readily reproducible bioinformatics protocols, and key tips to avoid known pitfalls. Authoritative and practical, RNA Bioinformatics seeks to aid scientists in the further study of bioinformatics and computational biology of RNA.

In the past half century, filamentous fungi have grown in commercial importance not only in the food industry but also as sources of pharmaceutical agents for the treatment of infectious and metabolic diseases and of specialty proteins and enzymes used to process foods, fortify detergents, and perform biotransformations. The commercial impact of molds is also measured on a negative scale since some of these organisms are significant as pathogens of crop plants, agents of food spoilage, and sources of toxic and carcinogenic compounds. Recent advances in the molecular genetics of filamentous fungi are finding increased application in the pharmaceutical, agricultural, and enzyme industries, and this trend promises to continue as the genomics of fungi is explored and new techniques to speed genetic manipulation become available.

This volume focuses on the filamentous fungi and highlights the advances of the past decade, both in methodology and in the understanding of genomic organization and regulation of gene and pathway expression.

This volume presents a list of cutting-edge protocols for the study of CRISPR-Cas defense systems and their applications at the genomic, genetic, biochemical and structural levels. CRISPR: Methods and Protocols guides readers through techniques that have been developed specifically for the analysis of CRISPR-Cas and techniques adapted from standard protocols of DNA, RNA and protein biology. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, CRISPR: Methods and Protocols provides a broad list of tools and techniques to study the interdisciplinary aspects of the prokaryotic CRISPR-Cas defense systems.

This authoritative text/reference presents a review of the history, current status, and potential future directions of computational biology in molecular evolution. Gathering together the unique insights of an international selection of prestigious researchers, this must-read volume examines the latest developments in the field, the challenges that remain, and the new avenues emerging from the growing influx of sequence data. These viewpoints build upon the pioneering work of David Sankoff, one of the founding fathers of computational biology, and mark the 50th anniversary of his first scientific article. The broad spectrum of rich contributions in this essential collection will appeal to all computer scientists, mathematicians and biologists involved in comparative genomics, phylogenetics and related areas.

This volume expands on statistical analysis of genomic data by discussing cross-cutting groundwork material, public data repositories, common applications, and representative tools for operating on genomic data. Statistical Genomics: Methods and Protocols is divided into four sections. The first section discusses overview material and resources that can be applied across topics mentioned throughout the book. The second section covers prominent public repositories for genomic data. The third section presents several different biological applications of statistical genomics, and the fourth section highlights software tools that can be used to facilitate ad-hoc analysis and data integration. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible analysis protocols, and tips on troubleshooting and avoiding known pitfalls. Through and practical, Statistical Genomics: Methods and Protocols, explores a range of both applications and tools and is ideal for anyone interested in the statistical analysis of genomic data.

This volume provides broad coverage of computational and mathematical techniques and concepts related to the field of comparative genomics. The topics covered in the chapters range from those concerned with general techniques and concepts that apply to all organisms to others that are more specialized, covering specific biological systems such as viruses, Drosophila, and Homo sapiens. Written in the highly successful Methods in Molecular Biology series format, by authors who are active researchers in the field, many chapters include step-by-step procedures, which illustrate practical applications of the techniques described. Cutting-edge and thorough, Comparative Genomics: Methods and Protocols should be useful to students and researchers in the continually growing and exciting field of comparative genomics.

The application of modern genomic approaches to research on halophilic Archaea and Bacteria and their viruses in recent years has yielded fascinating insights into the adaptations and evolution of these unique organisms. This book highlights current genetics and genomics research to provide a timely overview.

Current knowledge of the mechanisms that regulate DNA repair has grown significantly over the past years with technology advances such as RNA interference, advanced proteomics and microscopy as well as high throughput screens. The third edition of DNA Repair Protocols covers various aspects of the eukaryotic response to genomic insult including recent advanced protocols as well as standard techniques used in the field of DNA repair. Both mammalian and non-mammalian model organisms are covered in the book, and many of the techniques can be applied with only minor modifications to other systems than the one described. Written in the highly successful Methods in Molecular Biology? series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, DNA Repair Protocols, Third Edition provides expert guidance for DNA repair, recombination, and replication.

Innate DNA and RNA Recognition: Method and Protocols presents validated experimental strategies to dissect nucleic acid sensing in-vitro and in-vivo sources. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Innate DNA and RNA Recognition: Method and Protocols provides a resource for immunologists, molecular biologists, virologists, microbiologists, and researchers studying how the innate immune system handles nucleic acids from endogenous or foreign sources.

Metagenomics has taken off as one of the major cutting-edge fields of research. The field has broad implications for human health and disease, animal production and environmental health. Metagenomics has opened up a wealth of data, tools, technologies and applications that allow us to access the majority of organisms that we still cannot access in pure culture (an estimated 99% of microbial life). Numerous research groups are developing tools, approaches and applications to deal with this new field, as larger data sets from environments including the human body, the oceans and soils are being generated. See for example the human microbiome initiative (HMP) which has become a world-wide effort and the Global Ocean Sampling (GOS) surveys. The number of publications as measured through PubMed that are focused on metagenomics continues to increase. The field of metagenomics continues to evolve with large common datasets available to the scientific community. A concerted effort is needed to collate all this information in a centralized place. By having all the information in an Encyclopedia form, we have an opportunity to gather seminal contributions from the leaders in the field, and at the same time provide this information to a significant number of junior and senior scientists. It is anticipated that the Encyclopedia will also be used by many other groups including, clinicians, undergraduate and graduate level students, as well as ethical and legal groups associated with or interested in the issues surrounding metagenome science.

Metagenomics has taken off as one of the major cutting-edge fields of research. The field has broad implications for human health and disease, animal production and environmental health. Metagenomics has opened up a wealth of data, tools, technologies and applications that allow us to access the majority of organisms that we still cannot access in pure culture (an estimated 99% of microbial life). Numerous research groups are developing tools, approaches and applications to deal with this new field, as larger data sets from environments including the human body, the oceans and soils are being generated. See for example the human microbiome initiative (HMP) which has become a world-wide effort and the Global Ocean Sampling (GOS) surveys. The number of publications as measured through PubMed that are focused on metagenomics continues to increase. The field of metagenomics continues to evolve with large common datasets available to the scientific community. A concerted effort is needed to collate all this information in a centralized place. By having all the information in an Encyclopedia form, we have an opportunity to receive seminal contributions from the leaders in the field and at the same time provide this information to a significant number of junior and senior scientists, via colleges, libraries, and just through online access. This format also allows scientists in the developing world to have continued access to this growing field. It is anticipated that the Encyclopedia will also be used by many other groups including, clinicians, undergraduate and graduate level students, as well as ethical and legal groups associated with or interested in the issues surrounding metagenome science.

This book describes how genomics has revolutionized our scientific understanding of agriculturally important plant-associated bacteria. Each chapter focuses on the genomics of particular bacteria: the first described plant pathogen, "Erwinia amylovora"; phytoplasmas lacking cell walls; fastidious, phloem-restricted liberibacters; "Pseudomonas syringae," which is a genetically tractable model system; "Xanthomonas citri," which causes a disease that can devastate citrus crops and "Pseudomonas fluorescens," which can protect plants from diseases.

Topics considered in this volume include the importance of horizontal gene transfer in originating new bacterial strains and species and advances in transcriptomics that allow us to describe the complex regulatory networks critical to plant-microbe interactions. The availability of the "Xanthomonas oryzae" genome has led to new technologies in genome editing, which will revolutionize approaches to genetic engineering, even in eukaryotes. The contributions show how genomics has greatly accelerated progress toward understanding the biology of these bacteria and how that understanding can be translated into novel crop protection methods.