Bifidobacteria are Gram-positive anaerobic bacteria, found naturally in the gut of humans and other mammals. They are widely used as probiotic organisms in a vast array of formulations for the prevention, alleviation, and treatment of many intestinal disorders. However, bifidobacteria are fastidious microorganisms and are difficult to study in the laboratory, so until recently, understanding of their genetics lagged behind that of other high GC content Gram-positive bacteria. The application of modern whole genome approaches to bifidobacteria research has changed all of this, permitting the accumulation of an impressive amount of data, something that could not have been foreseen a few years ago. This book brings together the expertise and enthusiasm of the leading bifidobacteria researchers from around the world to provide a state-of-the art overview of the molecular biology and genomics of this exciting and important microbial genus. Topics include: ecology, genomics, comparative geno

Mechanisms of DNA Recombination and Genome Rearrangements: Methods to Study Homologous Recombination, Volume 600, the latest release in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. Homologous genetic recombination remains the most enigmatic process in DNA metabolism. The molecular machines of recombination preserve the integrity of the genetic material in all organisms and generate genetic diversity in evolution. The same molecular machines that support genetic integrity by orchestrating accurate repair of the most deleterious DNA lesions, however, also promote survival of cancerous cells and emergence of radiation and chemotherapy resistance. This two-volume set offers a comprehensive set of cutting edge methods to study various aspects of homologous recombination and cellular processes that utilize the enzymatic machinery of recombination The chapters are written by the leading researches and cover a broad range of topics from the basic molecular mechanisms of recombinational proteins and enzymes to emerging cellular techniques and drug discovery efforts.

Methods in Enzymology, Volume 599 is the second of two volumes focused on Fe-S cluster enzymes. Topics of interest in this new release include steps towards understanding mitochondrial Fe/S cluster biogenesis, iron sulfur clusters in zinc finger proteins, electrochemistry of Iron-sulfur enzymes, NRVS for Fe in biology and its experiment and basic interpretation, methods for studying iron regulatory protein 1, an important protein in human iron metabolism, the characterization of glutaredoxin Fe-S cluster binding interactions using circular dichroism spectroscopy, fluorescent reporters to track Fe-S cluster assembly and transfer reactions, methods for studying the Fe-S cluster containing base excision repair glycosylase MUTYH, and more.

Chemical Glycobiology, Part B, Volume 598, the latest release in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume is the second release on chemical glycobiology.

A Structure-Function Toolbox for Membrane Transporter and Channels, Volume 594, a new release in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. New chapters in the updated serial include Cryo-EM on membrane proteins embedded in nanodics, Solid-Supported membrane-based electrophysiology on membrane transporters and channels, Saposin-lipoprotein scaffolds for structure determination of membrane transporters and channels, Single-molecule FRET on transporters, Dynamics of channels and transporters investigated by NMR, Structure-function studies on channels and transporters, and a section on MemStar, a new GFP-based expression and purification system for transporters and channels.

Overflow Metabolism: From Yeast to Marathon Runners provides an overview of overflow metabolism, reviewing the major phenomenological aspects as observed in different organisms, followed by a critical analysis of proposed theories to explain overflow metabolism. In our ideal view of metabolism, we think of catabolism and anabolism. In catabolism nutrients break down to carbon dioxide and water to generate biochemical energy. In anabolism nutrients break down to generate building blocks for cell biosynthesis. Yet, when cells are pushed to high metabolic rates they exhibit incomplete catabolism of nutrients, with a lower energy yield and excretion of metabolic byproducts. This phenomenon, characterized by the excretion of metabolic byproducts that could otherwise be used for catabolism or anabolism, is generally known as overflow metabolism. Overflow metabolism is a ubiquitous phenotype that has been conserved during evolution. Examples are the acetate switch in the bacterium E. coli, Crabtree effect in unicellular eukaryote yeasts, the lactate switch in sports medicine, and the Warburg effect in cancer. Several theories have been proposed to explain this seemingly wasteful phenotype. Yet, there is no consensus about what determines overflow metabolism and whether it offers any selective advantage.

G Protein Coupled Receptors, Second Edition, Volume 143, a new volume in the Methods in Cell Biology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. It contains a wide array of topics about the G protein coupled receptors, as well as updates of chapters from the first edition.

A proper understanding of the diversity, systematics, and nomenclature of microbes is increasingly important in many branches of biological science. The molecular approach to phylogenetic analysis - pioneered by Carl Woese in the 1970s and leading to the three-domain model (Archaea, Bacteria, Eucarya) - has revolutionized our thinking about evolution in the microbial world. The technological innovation of modern molecular biology and the rapid advancement in computational science have led to a flood of nucleic acid sequence information, bioinformatic tools, and phylogenetic inference methods. Phylogenetic analysis has long played a central role in microbiology and the emerging fields of comparative genomics and phylogenomics require substantial knowledge and understanding of phylogenetic analysis and computational methods. In this book, leading scientists from around the world explore current concepts in molecular phylogeny and their application with respect to microorganisms. The authors describe the different approaches applied today to elucidate the molecular phylogeny of prokaryotes (and eukaryotic protists) and review current phylogenetic methods, techniques, and software tools. Topics covered include: a historical overview, computational tools, multilocus sequence analysis, 16S rRNA phylogenetic trees, rooting of the universal tree of life, applications of conserved indels, lateral gene transfer, endosymbiosis, and the evolution of plastids.

DNA Repair Enzymes, Part A, Volume 591 is the latest volume in the Methods in Enzymology series and the first part of a thematic that focuses on DNA repair enzymes. Topics in this new release include chapters on the Optimization of Native and Formaldehyde iPOND Techniques for Use in Suspension Cells, the Proteomic Analyses of the Eukaryotic Replication Machinery, DNA Fiber Analysis: Mind the Gap!, Comet-FISH for Ultrasensitive Strand-Specific Detection of DNA Damage in Single Cells, Examining DNA Double-Strand Break Repair in a Cell Cycle-Dependent Manner, Base Excision Repair Variants in Cancer, and Fluorescence-Based Reporters for Detection of Mutagenesis in E. coli.

Living organisms exhibit specific responses when confronted with sudden changes in their environmental conditions. The ability of the cells to acclimate to their new environment is the integral driving force for adaptive modification of the cells. Such adaptation involves a number of cellular and biochemical alteration including metabolic homeostasis and reprogramming of gene expression. Changes in metabolic pathways are generally short-lived and reversible, while the consequences of gene expression are a long-term process and may lead to permanent alternation in the pattern of adaptive responses.
The heart possesses remarkable ability to adapt itself against any stressful situation by increasing resistance to the adverse consequences. Stress composes the foundation of many degenerative heart diseases including atherosclerosis, spasm, thrombosis, cardiomyopathy, and congestive heart failure. Based on the concept that excessive stress may play a crucial role in the pathogenesis of ischemic heart disease, attempts were made to design methods for preventing of myocardial injury. Creation of stress reactions by repeated ischemia and reperfusion or subjecting the hearts to heat or oxidative stress enables them to meet the future stress challenge. Repeated stress exposures adapt the heart to withstand more severe stress reactions probably by upregulating the cellular defense and direct accumulation of intracellular mediators, which presumably constitute the material basis of increased adaptation to stress. Thus, the powerful cardioprotective effect of adaptation is likely to originate at the cellular and molecular levels that compose fundamental processes in the prophylaxis of such diseases.
Volume six of the Advances in Organ Biology series contains state-of-the-art reviews on myocardial preservation and cellular adaptation from the leading authorities in this subject.

Advances in Microbial Physiology, Volume 70 continues the long tradition of topical, important, cutting-edge reviews in microbiology with this new volume covering a variety of topics, including Bacterial Hemoprotein Sensors of NO: H-NOX and NosP, Manganese in Marine Microbiology, Nutritional Immunity and Fungal Pathogenesis: The Struggle for Micronutrients at the Host-Pathogen Interface, Metal-Based Combinations that Target Protein Synthesis by Fungi, Transition Metal Homeostasis in Streptococcus Pyogenes and Streptococcus Pneumoniae, Copper and Antibiotics: Discovery, Modes of Action, and Opportunities for Medicinal Applications, Metal Resistance and Its Association with Antibiotic Resistance, and The Role of Intermetal Competition and Mis-Metalation in Metal Toxicity.

International Review of Cell and Molecular Biology, Volume 332 reviews current advances in cell and molecular biology. This latest release covers Metabolic alterations at the crossroad between aging and oncogenesis, Molecular and cellular mechanisms of auto-immunity, Old and novel functions of caspase-2, Organelle crosstalk in oncogenic metabolic reprogramming, a Molecular Biology Digest of Cellular Mitophagy, the Regulation of cell calcium and role of plasma membrane calcium ATPases, and Mechanisms of cortical differentiation. The IRCMB series has a worldwide readership, maintaining a high standard by publishing invited articles on important and timely topics that are authored by prominent cell and molecular biologists. Users will find that the articles published in IRCMB have a high impact and average cited half-life of nine years. This great resource ranks high amongst scientific journals dealing with cell biology.

Biology and Engineering of Stem Cell Niches covers a wide spectrum of research and current knowledge on embryonic and adult stem cell niches, focusing on the understanding of stem cell niche molecules and signaling mechanisms, including cell-cell/cell-matrix interactions. The book comprehensively reviews factors regulating stem cell behavior and the corresponding approaches for understanding the subsequent effect of providing the proper matrix molecules, mechanical cues, and/or chemical cues. It encompasses a variety of tools and techniques for developing biomaterials-based methods to model synthetic stem cell niches in vivo, or to enhance and direct stem cell fate in vitro. A final section of the book discusses stem cell niche bioengineering strategies and current advances in each tissue type.

DNA Structure and Function, a timely and comprehensive resource, is intended for any student or scientist interested in DNA structure and its biological implications. The book provides a simple yet comprehensive introduction to nearly all aspects of DNA structure. It also explains current ideas on the biological significance of classic and alternative DNA conformations. Suitable for graduate courses on DNA structure and nucleic acids, the text is also excellent supplemental reading for courses in general biochemistry, molecular biology, and genetics.
Special Features
* Explains basic DNA Structure and function clearly and simply
* Contains up-to-date coverage of cruciforms, Z-DNA, triplex DNA, and other DNA conformations
* Discusses DNA-protein interactions, chromosomal organization, and biological implications of structure
* Highlights key experiments and ideas within boxed sections
* Illustrated with 150 diagrams and figures that convey structural and experimental concepts

Nuclear Receptors in Development and Disease, Volume 125, the latest volume in the Current Topics in Developmental Biology series, covers nuclear receptors in development and disease, and includes contributions from an international board of authors. New chapters in this release cover the Evolution of Nuclear Receptors and Ligand Signaling: Towards a Soft Key-Lock Model?, The Function and Evolution of Nuclear Receptors in Insect Embryonic Development, Nuclear Receptors in Skeletal Homeostasis, Estrogen Hormone Biology, and the Mechanisms of Glucocorticoid Action During Development. The book's chapters provide a comprehensive set of reviews that cover such topics as nuclear differentiation and remodeling, evolution of receptors, ligand signaling and neural development.

This book provides authentic and comprehensive information on the concepts, methods, functional details and applications of nano-emulsions. Following an introduction to the applications of nanotechnology in the development of foods, it elaborates on food-grade nano-emulsion and their significance, discusses various techniques and methods for producing food-grade nano-emulsion, and reviews the main ingredient and component of food-grade nano-emulsions. Further, the book includes a critical review of the engineering aspect of fabricating food-grade nano-emulsions and describe recently developed vitamin encapsulated nano-systems. In closing, it discuss the challenges and opportunities of characterizing nano-emulsified systems, the market risks and opportunities of nano-emulsified foods, and packaging techniques and safety issues - including risk identification and risk management - for nano-foods. The book offers a unique guide for scientists and researchers working in this field. It will also help researchers, policymakers, industry personnel, journalists and the general public to understand food nanotechnology in great detail.

This volume presents methods and techniques to study oogenesis in a broad range of organisms, from plants to mammals. Oogenesis: Methods and Protocols guides readers through protocols on models of developmental biology, oogenesis in plants, worms, fruit flies, mosquitos, butterflies, starfish, zebrafish, frog, chicken and mouse. 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, Oogenesis: Methods and Protocols aims to ensure successful results in the further study of this vital field.

This volume brings together a set of reviews that provide a summary of our current knowledge of the proteolytic machinery and of the pathways of protein breakdown of prokaryotic and eukaryotic cells. Intracellular protein degradation is much more than just a mechanism for the removal of incorrectly folded or damaged proteins. Since many short-lived proteins have important regulatory functions, proteolysis makes a significant contribution to many cellular processes including cell cycle regulation and transciptional control. In addition, limited proteolytic cleavage can provide a rapid and efficient mechanism of enzyme activation or inactivation in eukaryotic cells.
In the first chapter, Maurizi provides an introduction to intracellular protein degradation, describes the structure and functions of bacterial ATP-dependent proteases, and explores the relationship between chaperone functions and protein degradation. Many of the principles also apply to eukaryotic cells, although the proteases involved are often not the same. Interestingly, homologues of one of the bacterial proteases, Ion protease, have been found in mitochondria in yeast and mammals, and homologues of proteasomes, which are found in all eukaryotic cells (see below), have been discovered in some eubacteria.
Studies of proteolysis in yeast have contributed greatly to the elucidation of both lysosomal (vacuolar) and nonlysosomal proteolytic pathways in eukaryotic cells. Thumm and Wolf (chapter 2) describe studies that have elucidated the functions of proteasomes in nonlysosomal proteolysis and the contributions of lysosomal proteases to intracellular protein breakdown. Proteins can be selected for degradation by a variety of differen mechanisms. The ubiquitin system is one complex and highly regulated mechanism by which eukaryotic proteins are targetted for degradation by proteosomes. In chapter 3, Wilkinson reviews the components and functions of the ubiquitin system and considers some of the known substrates for this pathway which include cell cycle and transcriptional regulators.
The structure and functions of proteosomes and their regulatory components are described in the two subsequent chapters by Tanaka and Tanahashi and by Dubiel and Rechsteiner. Proteasomes were the first known example of threonine proteases. They are multisubunit complexes that, in addition to being responsible for the turnover of most short-lived nuclear and cytoplasmic protein, are also involved in antigen processing for presentation by the MHC class I pathway. Recent studies reviewed by McCracken and colleagues (chapter 6) lead to the exciting conclusion that some ER-associated proteins are degraded by cytosolic proteasomes.
Lysosomes are responsible for the degradation of long-lived proteins and for the enhanced protein degradation observed under starvation conditions. In chapter 7 Knecht and colleagues review the lysosomal proteases and describe studies of the roles of lysosomes and the mechanisms for protein uptake into lysosomes. Methods of measuring the relative contribution of different proteolytic systems (e.g., ubiquitin-proteasome pathway, calcium-dependent proteases, lysosomes) to muscle protein degradation, and the conclusions from such studies, are reviewed by Attai and Taillinder in the following chapter.
Finally, proteases play an important role in signaling apoptosis by catalyzing the limited cleavage of enzymes. Mason and Beyette review the role of the major players, caspases, which are both activated by and catalyze limite proteolysis, and also consider the involvement of other protoelytic enzymes in this pathway leading cell death.

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.

This book features research contributions from The Abel Symposium on Statistical Analysis for High Dimensional Data, held in Nyvagar, Lofoten, Norway, in May 2014. The focus of the symposium was on statistical and machine learning methodologies specifically developed for inference in "big data" situations, with particular reference to genomic applications. The contributors, who are among the most prominent researchers on the theory of statistics for high dimensional inference, present new theories and methods, as well as challenging applications and computational solutions. Specific themes include, among others, variable selection and screening, penalised regression, sparsity, thresholding, low dimensional structures, computational challenges, non-convex situations, learning graphical models, sparse covariance and precision matrices, semi- and non-parametric formulations, multiple testing, classification, factor models, clustering, and preselection. Highlighting cutting-edge research and casting light on future research directions, the contributions will benefit graduate students and researchers in computational biology, statistics and the machine learning community.

This book presents the theoretical foundations of Systems Biology, as well as its application in studies on human hosts, pathogens and associated diseases. This book presents several chapters written by renowned experts in the field. Some topics discussed in depth in this book include: computational modeling of multiresistant bacteria, systems biology of cancer, systems immunology, networks in systems biology.

This book contains some selected papers from the International Conference on Extreme Learning Machine 2015, which was held in Hangzhou, China, December 15-17, 2015. This conference brought together researchers and engineers to share and exchange R&D experience on both theoretical studies and practical applications of the Extreme Learning Machine (ELM) technique and brain learning. This book covers theories, algorithms ad applications of ELM. It gives readers a glance of the most recent advances of ELM.