This second edition integrates the more technical and mathematical aspects of bioinformatics with concrete examples of their application to current research problems in molecular, cellular and evolutionary biology. This broad, unified approach is made possible, in large part, by the very wide scope of Dr. Xia's own research experience. The integration of genomics, proteomics and transcriptomics into a single volume makes this book required reading for anyone entering the new and emerging fields of Systems Biology and Evolutionary Bioinformatics.

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.

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.

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.

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.

Novel molecular motifs named Immunoreceptor Tyrosine-based Inhibition Motifs (ITIMs) have recently been recognized in the intracytoplasmic domains of a still-increasing number of receptors which control cell activation and proliferation. Research on ITIM-bearing molecules has developed exponentially during the last three years, generating new concepts with important consequences in basic research and with exciting potential clinical applications. The present volume contains 15 reviews written by authors who all made significant contributions to the identification of ITIM-bearing molecules and the study of their biological properties. It constitutes the first synthesis ever published that is specifically devoted to this emerging topic.

This volume introduces the reader to the field of enzyme stabilization and the different theories of enzyme stabilization, including the use of immobilization as a stabilization technique. The first part of the book focuses on protocols for enzyme stabilization in solutions including liposome formation, micelle introduction, crosslinking, and additives. The second part of the book discusses protocols for enzyme stabilization during enzyme immobilization, including common techniques like sol-gel encapsulation, polymer encapsulation, and single enzyme nanoparticle formation. Protocols for a variety of enzymes are shown, but the enzymes are chosen as examples to show that these protocols can be used for both enzymes of biological importance, as well as enzymes of industrial importance. The final part details spectroscopic protocols, methods, and assays for studying the effectiveness of the enzyme stabilization and immobilization strategies. 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, Enzyme Stabilization and Immobilization: Methods and Protocols, Second Edition provides molecular biologists, biochemists, and biomedical and biochemical engineers with the state-of-the-art technical information required to effectively stabilize their enzyme of interest in a variety of environments (i.e., harsh temperature, pH, or solvent conditions).

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.

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.

This contributed volume presents an overview of concepts, methods, and applications used in several quantitative areas of drug research, development, and marketing. Chapters bring together the theories and applications of various disciplines, allowing readers to learn more about quantitative fields, and to better recognize the differences between them. Because it provides a thorough overview, this will serve as a self-contained resource for readers interested in the pharmaceutical industry, and the quantitative methods that serve as its foundation. Specific disciplines covered include: Biostatistics Pharmacometrics Genomics Bioinformatics Pharmacoepidemiology Commercial analytics Operational analytics Quantitative Methods in Pharmaceutical Research and Development is ideal for undergraduate students interested in learning about real-world applications of quantitative methods, and the potential career options open to them. It will also be of interest to experts working in these areas.

This textbook introduces readers to the recent advances in the emerging field of genetic design automation (GDA). Starting with an introduction and the basic concepts of molecular biology, the authors provide an overview of various genetic design automation tools. The authors then present the DVASim tool (Dynamic Virtual Analyzer and Simulator) which is used for the analysis and verification of genetic logic circuits. This includes methods and algorithms for the timing and threshold value analyses of genetic logic circuits. Next, the book presents the GeneTech tool (A technology mapping tool for genetic circuits) and the methods developed for optimization, synthesis, and technology mapping of genetic circuits. Chapters are followed by exercises which give readers hands-on practice with the tools presented. The concepts and algorithms are thoroughly described, enabling readers to improve the tools or use them as a starting point to develop new tools. Both DVASim and GeneTech are available from the developer's website, free of charge. This book is intended for a multidisciplinary audience of computer scientists, engineers and biologists. It provides enough background knowledge for computer scientists and engineers, who usually do not have any background in biology but are interested to get involved in this domain. This book not only presents an accessible basic introduction to molecular biology, it also includes software tools which allow users to perform laboratory experiments in a virtual in-silico environment. This helps newbies to get a quick start in understanding and developing genetic design automation tools. The third part of this book is particular useful for biologists who usually find it difficult to grasp programming and are reluctant to developing computer software. They are introduced to the graphical programming language, LabVIEW, from which they can start developing computer programs rapidly. Readers are further provided with small projects which will help them to start developing GDA tools.

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.

This book provides a comprehensive overview of topics describing the earliest steps of fertilization, from egg activation and fertilization to the activation of the zygotic genome, in various studied vertebrate model systems. The contribution of maternal and paternal factors and their role in the early embryo as parental DNA becomes modified and embryonic genes become activated is fundamental to the initiation of embryogenesis in all animal systems. It can be argued that this is a unique developmental period, when information from the parents is compressed to direct the development of the body plan of the entire organism, a process of astounding simplicity, elegance and beauty. In addition to their fundamental scientific interest, many frontiers of biomedicine, such as reproductive biology, stem cells and reprogramming, and the understanding of intergenerational diseases, depend on advances in our knowledge of these early processes. Vertebrate Development: Maternal to Zygotic Control brings together chapters from experts in various disciplines describing the latest advances related to this important developmental transition. Each chapter is a synthesis of knowledge relevant to all vertebrates, with details on specific systems as well as comparisons between the various studied vertebrate models. The editorial expertise encompasses the fields of major vertebrate model systems (mammalian, amphibian and teleost) ensuring a balanced approach to various topics. This unique book-with its combination of in-depth and up-to-date basic research, inter-species comprehensiveness and emphasis on the very early stages of animal development-is essential for research scientists studying vertebrate development, as well as being a valuable resource for college educators teaching advanced courses in developmental biology.

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

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.

Molecular Biology of Placental Development and Disease, the latest volume in the Progress in Molecular Biology and Translational Science series, focuses on placental development and disease.

This book describes efforts to improve subject-independent automated classification techniques using a better feature extraction method and a more efficient model of classification. It evaluates three popular saliency criteria for feature selection, showing that they share common limitations, including time-consuming and subjective manual de-facto standard practice, and that existing automated efforts have been predominantly used for subject dependent setting. It then proposes a novel approach for anomaly detection, demonstrating its effectiveness and accuracy for automated classification of biomedical data, and arguing its applicability to a wider range of unsupervised machine learning applications in subject-independent settings.

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 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.

A clear introduction to the complex and fast moving field of "Human Molecular Genetics"; recommended for""students studying the subject as part of a general biology, genetics or medical degree.

New to the third edition:

• Concise up-to-day introduction to human molecular genetics
• Fully revised chapter on complex diseases including the use of population based genome-wide association studies to identify risk alleles.
• New chapter on small RNAs and their role in gene regulation and disease
• Fully revised chapter on genome sequencing and associated technologies, including how the draft human genome sequence was finished and the advent of next-generation sequencing technologies.
• Updated chapter on single gene disorders reviewing advances in our understanding of their underlying molecular pathologies.

The following online resources support the text:

• For Instructors: powerpoint slides

This book contains the proceedings of the 3rd IUPAC International Conference on Biodiversity (ICOB-3), November 3-8, 2001, Antalya, Turkey. This book discusses the value of bioresources and the need for their conservation in terms of the biomolecular chemistry of naturally occurring molecular systems. The development of pharmaceutical, agricultural and industrial products from bioresources can be used to promote incentives for conservation by providing an economic return to sustainable use of those sources. The 54 chapters inform readers on the search for insight into the species and documents how much of life remains to be scientifically identified. They also explore identification strategies and methods along with the implications for protecting biodiversity. In summary, biomolecular aspects of biodiversity and innovative utilization of bioresources are discussed from very diverse points of view ranging from their botanical, zoological, taxonomic and genomic expressions to their biomolecular, structural, mechanistic and functional aspects.

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.