This book provides a single-source reference on the current state of the ribosome profiling method by describing experimental protocols for the quantitative analysis of translation in a variety of model organisms. In addition, the volume presents a detailed overview of the existing software tools and includes detailed description of methods for statistical analysis, data processing, and visualization of ribosome profiling data. 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, Ribosome Profiling: Methods and Protocols aims to provide the type of standardized protocols that have previously been unavailable in an effort to bypass the major barriers to wide use of ribosome profiling-based approaches.

This book presents pioneering findings on the characterization of cellular regulation and function for three recently identified protein posttranslational modifications (PTMs): lysine malonylation (Kmal), glutarylation (Kglu) and crotonylation (Kcr). It addresses three main topics: (i) Detecting Kmal substrates using a chemical reporter, which provides important information regarding the complex cellular networks modulated by Kmal; (ii) Identifying Kglu as a new histone PTM and assessing the direct impact of histone Kglu on chromatin structure and dynamics; and (iii) Revealing Sirt3's value as a regulating enzyme for histone Kcr dynamics and gene transcription, which opens new avenues for examining the physiological significance of histone Kcr. Taken together, these studies provide information critical to understanding how these protein PTMs are associated with various human diseases, and to identifying therapeutic targets for the dysregulation of these novel protein markers in various human diseases.

This book examines detailed experimental and computational approaches for the analysis of many aspects vital to the understanding of membrane protein structure and function. Readers will receive guidance on the selection and use of methods for over-expression and purification, tools to characterize membrane proteins within different phospholipid bilayers, direction on functional studies, and approaches to determine the structures of membrane proteins. Detailed experimental steps for specific membrane proteins with critical notes allow the protocols to be modified to different systems. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of practical information and implementation advice that leads to excellent, reproducible results. Authoritative and up-to-date, Structure and Function Studies of Membrane Proteins serves as an ideal guide for biologists, biochemists, and biophysicists striving to further understand these essential proteins and their many biological roles.

This book offers comprehensive information on all aspects of ELISA, starting with the fundamentals of the immune system. It also reviews the history of analytical assays prior to the advent of ELISA (enzyme-linked immunosorbent assay) and addresses the materials of choice for the fabrication of the platforms, possible biomolecular interactions, different protocols, and evaluation parameters. The book guides readers through the respective steps of the analytical assay, while also familiarizing them with the possible sources of error in the assay. It offers detailed insights into the immobilization techniques used for protein attachment, as well as methods for evaluating the assay and calculating the key parameters, such as sensitivity, specificity, accuracy and limit of detection. In addition, the book explores the advantages and shortcomings of the conventional ELISA, as well as various approaches to improving its performance. In this regard, merging and integrating other technologies with widely known ELISAs have opened new avenues for the advancement of this immunoassay. Accordingly, the book provides cutting-edge information on integrated platforms such as ELISpot, plasmonic ELISAs, sphere-/bead-based ELISAs, paper-/fiber-based ELISAs and ELISA in micro-devices.

Aging is an inevitable part of life and is becoming a worldwide social, economic and health problem. This is mainly due to the fact that the increasing proportion of individuals in the advanced age category have a higher probability of developing age-related disorders, such as type II diabetes mellitus, cardiovascular disorders, sarcopenia, and neurodegenerative conditions. New therapeutic approaches are still needed to decrease or slow the effects of such diseases. Advances in -omic technologies, such as genomics, transcriptomics, proteomics and metabolomics, have significantly advanced our understanding of disease in multiple medical areas, as the analysis of multiple molecular networks has simultaneously provided a more integrated view of disease pathways. It is hoped that emerging hits from these analyses might be prioritized for further screening as potential novel drug targets for increasing the human healthspan in line with the lifespan. In turn, this will lead to new therapeutic strategies as well as drug development projects by the pharmaceutical industry. This book presents a series of reviews describing studies that have resulted in identification of new potential drug targets for age-related disorders. Much of this information has come from -omic comparisons of healthy and disease states or from testing the effects of new therapeutic approaches. Authored by experts from around the globe, each chapter is presented in the context of specific chronic diseases or therapeutic strategies. This book is designed for researchers in the areas of aging and chronic disease, as well as clinical scientists, physicians and stakeholders in major drug companies.

This thorough book aims to present the methods that have enabled the success of peptides and proteins in a wide variety of applications. It opens with a section on chemical tools applied to the production or engineering of peptides and proteins, and concludes with a collection of chapters on biological approaches used to engineer structure and function in peptides and proteins. As a book in the Springer Protocols Handbooks series, chapters include the kind of detailed descriptions and tips necessary for successful results in practice. Authoritative and practical, Peptide and Protein Engineering: From Concepts to Biotechnological Applications will be of great use to scientists in academia and industry seeking a better understanding of the emerging principles and methodologies in peptide and protein engineering.

This book explores the broad and diverse biological and physiological impacts of established and newly discovered cyclic di-nucleotide second messenger signaling systems, while also providing descriptions of the intriguing biochemical characteristics of multiple turnover enzymes and receptors. The respective chapters discuss the commonalities and diversity of cyclic di-GMP, cyclic di-AMP and recently discovered cyclic GMP-AMP signaling systems in manifold Gram-negative and Gram-positive bacteria. The global human pathogens Mycobacterium tuberculosis, Vibrio cholerae, Salmonella typhimurium, Escherichia coli and Streptococcus pneumoniae, the facultative human pathogen Pseudomonas aeruginosa, global plant pathogens as exemplified by Xanthomonas campestris and Burkholderia spp., and the omnipresent probiotic Lactobacilli, as well as environmentally important photoautotrophic cyanobacteria, the multicellular Myxococcus xanthus, and chemolithotrophic Acidithiobacillus are among the representatives of the microbial kingdom that are described. In turn, the various aspects of bacterial physiology affected by these signaling systems- e.g. biofilm formation and dispersal, the cell cycle, motility, virulence, production of antimicrobials, fundamental metabolism and osmohomeostasis - are discussed in detail in the context of different microorganisms. Dedicated chapters focus on the population diversity of cyclic dinucleotide signaling systems, their tendency to be horizontally transferred, the cyclic di-GMP signaling system in the social amoeba Dictyostelium, honorary cyclic (di)nucleotides, and the development of strategies for interfering with cyclic dinucleotide signaling in order to manipulate microbial behavior. Taken together, the chapters provide an authoritative source of information for a broad readership: beginners and advanced researchers from various disciplines; individuals seeking a broad overview of cyclic di-nucleotide signaling; and those who want to learn more about specific aspects. Also featuring reviews with a forward-looking perspective, the book offers a valuable source of inspiration for future research directions.

Written by a pioneer in the development of spin labeling in biophysics, this expert book covers the fundamentals of nitroxide spin labeling through cutting-edge applications in chemistry, physics, materials science, molecular biology, and biomedicine. Nitroxides have earned their place as one of the most popular organic paramagnets due to their suitability as inhibitors of oxidative processes, as a means to polarize magnetic nuclei, and, in molecular biology, as probes and labels to understand molecular structures and dynamics AS DRAGS FOR CANCER AND OTHER DISEASES. Beginning with an overview of the basic methodology and nitroxides' 145-year history, this book equips students with necessary background and techniques to undertake original research and industry work in this growing field.

This book presents a new view of the mechanism of functional expression of ATP-driven motors (proteins or protein complexes). It is substantially different from the prevailing idea that the motor converts chemical energy to mechanical work. To facilitate understanding, the differences between the new and prevailing views are explained using many illustrations. The book is of interest to those who are not convinced of the notion of chemo-mechanical coupling. The claims presented are the following: The system, which comprises not only the motor but also water, does no mechanical work during the ATP hydrolysis cycle; a protein is moved or a protein in the complex is rotated by the entropic force generated by water. The highlight of the explanation in the book is that the mechanism of unidirectional rotation of the central shaft in F1-ATPase is discussed in detail on the basis of this new view. The hydration entropy of each subunit to which a specific chemical compound (ATP, ADP and Pi, Pi, or nothing) is bound, the hydration entropy of the 3 3 complex, and the dependence of the hydration entropy of F1-ATPase on the orientation of the subunit play essential roles.

In this book, the major paradigm-shifting discoveries made in the past century on key cellular nanomachines are described in great detail: their complex yet precise and elegant design and function, as well as the diseases linked to their dysfunction and the therapeutic approaches to overcome them. The major focus of this book is the "porosome" nanomachine, the universal secretory portal in cells. This is an ideal book for students, researchers, and professionals in the fields of nanoscience and nanotechnology.

This book summarizes all the important aspects of CRLs (Cullin-RING E3 Ubiquitin Ligases), while providing details of mechanistic specifics that go beyond protein ubiquitination and neddylation. Ubiquitin ligases, including the CRLs, which are activated by neddylation, play an important role in diverse biological processes and are involved in various human diseases, particularly cancer. The book covers various topics, such as CRL structure, biology, genetics, its regulation by neddylation, its pivotal role in human disease, and its potential in drug discovery and targeted therapies. The book appeals to biochemists and biologists working in other fields, and, given the importance of CRLs in all aspects of cell biology and the great promise of targeting these complexes for therapy, is a valuable resource anyone interested in modern biology or medicine.

This book offers an authoritative review of biopharmaceuticals and their clinical relevance. Biopharmaceuticals have been showing high therapeutic potential by means of biological and biosimilar medicines, particularly for the treatment of cancer, chronic diseases (e.g. diabetes, Crohn's disease, psoriasis and rheumatoid arthritis), neurodegenerative disorders (e.g. multiple sclerosis), and they have also been contributing to the progress of innovative therapies such as assisted reproductive medicine. Since the eighties, several biopharmaceuticals have been approved and, due to patents expiration, many biosimilars are also marketed. In this book, readers will find the most relevant updated information about the main clinical applications of pharmaceutical biotechnology. The authors provide expert analysis about the industrial challenges of recombinant proteins and the different classes of biopharmaceuticals, including monoclonal antibodies, vaccines, growth factors and stem cells. Topics such as bioprinting technologies in tissue engineering, gene therapy and personalized medicine are also covered in this book. Professionals, students and researchers interested in this field will find this work an important account.

This book presents an exploratory analysis based on proteomic and ionomics studies comparing the blood serum of patients with bipolar disorder (BD), healthy controls, patients with schizophrenia (SCZ), and patients with other disorders (OD) in order to identify biomarkers of BD. Bipolar disorder is a psychiatric condition that affects thousands of people worldwide. The absence of biomarkers for BD has resulted in misdiagnosis and ineffective treatment in some patients, causing additional health problems and high costs for health systems. As such, this book evaluates various strategies for sample preparation for proteomic and ionomic studies in order to simplify complex serum samples and allow the quantification of chemical species (proteins and metal ions), which are potential candidates for BD biomarkers. In addition, it describes the development of a new membrane-based methodology for extracting urine proteins to be used in biomarker discovery.

This book presents a comprehensive overview of important immune molecules and their structure-function relationships. The immune system is highly complex, consisting of a network of molecules, cells, tissues and organs, and the immune reaction is involved in various physiological as well as pathological processes, including development, self-tolerance, infection, immunity, and cancer. Numerous molecules participate in immune recognition, inhibition and activation, and these important immune molecules can be roughly divided into cell surface receptors, intracellular receptors and intracellular signaling molecules. The study of how these immune molecules function at molecular level has laid the foundation for understanding the immune system. The book provides researchers and students with the latest research advances concerning the structural biology of key immune molecules/pathways, and offers immunologists essential insights into how these immune molecules function.

This book is a collection of principles and current practices in omics research, applied to skeletal muscle physiology and disorders. The various sections are categorized according to the level of biological organization, namely, genomics (DNA), transcriptomics (RNA), proteomics (protein), and metabolomics (metabolite). With skeletal muscle as the unifying theme, and featuring contributions from leading experts in this traditional field of research, it highlights the importance of skeletal muscle tissue in human development, health and successful ageing. It also discusses other fascinating topics like developmental biology, muscular dystrophies, exercise, insulin resistance and atrophy due to disuse, ageing or other muscle diseases, conveying the vast opportunities for generating new hypotheses as well as testing existing hypotheses by combining high-throughput techniques with proper experiment designs, bioinformatics and statistical analyses. Presenting the latest research techniques, this book is a valuable resource for the physiology community, particularly researchers and grad students who want to explore the new opportunities for omics technologies in basic physiology research.

This book demonstrates the potential of urine as a biomarker resource for early disease detection, covering the related theory, strategies, tools and findings. Biomarkers are measurable changes associated with diseases. Blood, as a critical part of its internal environment, is closely monitored and controlled by the body to maintain homeostasis, especially in the early stages of diseases. In contrast, urine, as a form of waste excreted by the body, collects a variety of substance changes. Accordingly, urine can offer an ideal resource for early biomarker discovery. In addition, urine is more stable than blood in vitro, and is easy to store and analyze. The book discusses exciting preliminary applications of urine biomarkers for diseases affecting major biological systems. Its main goal is to make scientists, clinicians and medical companies aware of this important, exciting, undeveloped, and profitable field.

Using both epidemiological and model organism approaches, we have gained new insights into the physiological and molecular aspects of aging, which has led to significant advancements in potential anti-aging strategies. Reviews on Biomarker Studies in Aging and Anti-Aging Research presents a series of reviews in various aspects of aging and age-related disease research along with several methods which have shown progress as potential anti-aging approaches. The book is aimed at researchers in the areas of aging and chronic disease, as well as to clinical scientists, physicians and major drug companies. It provides important information on disease mechanisms, and each chapter is presented in the context of the aging process, specific chronic diseases or different therapeutic areas.

This volume highlights recent progress on the fundamental chemistry and mechanistic understanding of metallocofactors, with an emphasis on the major development in these areas from the perspective of bioinorganic chemistry. Metallocofactors are essential for all forms of life and include a variety of metals, such as iron, molybdenum, vanadium, and nickel. Structurally fascinating metallocofactors featuring these metals are present in many bacteria and mediate remarkable metabolic redox chemistry with small molecule substrates, including N2, CO, H2, and CO2. Current interest in understanding how these metallocofactors function at the atomic level is enormous, especially in the context of sustainably feeding and fueling our planet; if we can understand how these cofactors work, then there is the possibility to design synthetic catalysts that function similarly.

This highly readable textbook serves as a concise and engaging primer to the emerging field of antibody engineering and its various applications. It introduces readers to the basic science and molecular structure of antibodies, and explores how to characterize and engineer them. Readers will find an overview of the latest methods in antibody identification, improvement and biochemical engineering. Furthermore, alternative antibody formats and bispecific antibodies are discussed. The book's content is based on lectures for the specializations "Protein Engineering" and "Medical Biotechnology" within the Master's curriculum in "Biotechnology." The lectures have been held at the University of Natural Resources and Life Sciences, Vienna, in cooperation with the Medical University of Vienna, since 2012 and are continuously adapted to reflect the latest developments in the field. The book addresses Master- and PhD students in biotechnology, molecular biology and immunology, and all those who are interested in antibody engineering.

This book discusses the decoding of the lytic mechanism of an -helical pore-forming toxin, YaxAB, composed of two different subunits. Pore-forming toxins (PFTs) are among the most common bacterial toxins. They are produced by a variety of pathogens, which infect a wide range of organisms including plants, insects and humans. Yet the maturation of these particles and the structural changes required for pore formation are still poorly understood for many PFT families. Using a diverse panel of biochemical and structural techniques, including X-ray crystallography and cryo-electron microscopy, Dr. Brauning and colleagues have succeeded in identifying the mechanistic contributions of the two toxin components and elucidating the lytic state of the pore complex. The results of this thesis on the YaxAB system are applicable to orthologues from agriculturally relevant insect pathogens, and offer valuable structural and mechanistic insights to inform future bioengineering efforts.

This edited volume summarizes the recent advancements made in plant science including molecular biology and genome editing , particularly in the development of novel pathways tolerant to climate change-induced stresses such as drought, extreme temperatures, cold, salinity, flooding, etc. These stresses are liable for decrease in yields in many crop plants at global level. Till date conventional plant breeding approaches have resulted in significant improvement of crop plants for producing higher yields during adverse climatic conditions. However, the pace of improvement through conventional plant breeding needs to be accelerated in keeping with the growing demand of food and increasing human populationl, particularly in developing world. This book serves as a comprehensive reference material for researchers, teachers, and students involved in climate change-related abiotic stress tolerance studies in plants.

Metal toxicity and deficiency are both common abiotic problems faced by plants. While metal contamination around the world is a critical issue, the bioavailability of some essential metals like zinc (Zn) and selenium (Se) can be seriously low in other locations. The list of metals spread in high concentrations in soil, water and air includes several toxic as well as essential elements, such as arsenic (As), cadmium (Cd), chromium (Cr), aluminum (Al), and selenium (Se). The problems for some metals are geographically confined, while for others, they are widespread. For instance, arsenic is an important toxic metalloid whose contamination in Southeast Asia and other parts of world is well documented. Its threats to human health via food consumption have generated immense interest in understanding plants' responses to arsenic stress. Metals constitute crucial components of key enzymes and proteins in plants. They are important for the proper growth and development of plants. In turn, plants serve as sources of essential elements for humans and animals. Studies of their physiological effects on plants metabolism have led to the identification of crucial genes and proteins controlling metal uptake and transport, as well as the sensing and signaling of metal stresses. Plant-Metal Interactions sheds light on the latest development and research in analytical biology with respect to plant physiology. More importantly, it showcases the positive and negative impacts of metals on crop plants growth and productivity.

This textbook introduces readers in an accessible and engaging way to the nuts and bolts of protein expression and engineering. Various case studies illustrate each step from the early sequence searches in online databases over plasmid design and molecular cloning techniques to protein purification and characterization. Furthermore, readers are provided with practical tips to successfully pursue a career as a protein engineer. With protein engineering being a fundamental technique in almost all molecular biology labs, the book targets advanced undergraduates and graduate students working in molecular biology, biotechnology and related scientific fields.

The book recognizes that throughout the scientific, medical, and economic communities, new tests incorporating biomarkers are needed to improve the diagnosis of patients suffering from metabolic disorders. The early identification of those at risk of developing obesity will help to place these individuals on the best treatment course as early as possible for improved treatment outcomes. This will also help to cut costs incurred by the healthcare services. For all of this to occur, new research efforts are needed to identify novel biomarkers that can be used to predict the disease in the presymptomatic stage, for disease monitoring and for prediction of treatment response. It is also possible that new drug targets can be identified using these approaches which, in turn, can lead to the development of new treatment approaches. This volume also includes a series of reviews on biomarker discovery and usage in the study of diseases marked by perturbations in metabolism. It will describe the pros and cons of the various approaches and cover the successes and failures in this important research field.

In this book, renowned scientists describe how cholesterol interacts with various proteins. Recent progress made in the high-resolution visualization of cholesterol-protein interactions using crystallography and cryogenic electron microscopy has substantially advanced the knowledge of critical features. These features enable specific recognition of the cholesterol molecule by proteins, a process that was built on earlier studies using binding assays, computational modeling and site-directed mutagenesis. Direct Mechanisms in Cholesterol Modulation of Protein Function offers comprehensive insights into the current understanding of cholesterol-driven modulation of protein function via direct sensing. Its nine chapters are organized into two distinct parts. In the first part, the chapters introduce the reader to the general characteristics of cholesterol binding sites in proteins. This part starts with a tour into common cholesterol recognition motifs, followed by an overview of the major classes of steroid-binding proteins. It then continues with two chapters that present a comprehensive analysis of molecular and structural characteristics of cholesterol binding sites in transmembrane and soluble protein domains. In the second part of the book, examples of cholesterol binding sites and consequences of specific cholesterol recognition for protein function are presented for G protein-coupled receptors, ion channels and cholesterol-transporting proteins. The book is valuable for undergraduate and graduate students in biochemistry and nutrition, as well as basic science and medical researchers with a keen interest in the biophysical properties of cholesterol and physiological consequences of cholesterol presence in biological systems.