This second edition provides updated and expanded chapters covering a broad sampling of useful and current methods in the rapidly developing and expanding field of bioinformatics. Bioinformatics, Volume II: Structure, Function, and Applications, Second Edition is comprised of three sections: Structure, Function, Pathways and Networks; Applications; and Computational Methods. The first section examines methodologies for understanding biological molecules as systems of interacting elements. The Applications section covers numerous applications of bioinformatics, focusing on analysis of genome-wide association data, computational diagnostic, and drug discovery. The final section describes four broadly applicable computational methods that are important to this field. These are: modeling and inference, clustering, parameterized algorithmics, and visualization. As a volume in the highly successful Methods in Molecular Biology series, chapters feature the kind of detail and expert implementation advice to ensure positive results. Comprehensive and practical, Bioinformatics, Volume II: Structure, Function, and Applications is an essential resource for graduate students, early career researchers, and others who are in the process of integrating new bioinformatics methods into their research.

Protein Folding Protocols presents protocols for studying and characterizing protein folding from the unfolded to the folded state. Covering experiment and theory, bioinformatics approaches, and state-of-the-art simulation protocols for better sampling of the conformational space, this volume describes a broad range of techniques to study, predict, and analyze the protein folding process.
Protein Folding Protocols also provides sample approaches toward the prediction of protein structure starting from the amino acid sequence, in the absence of overall homologous sequences. These approaches have tremendous implications, ranging from drug design, functional assignment, comprehension of the nature of regulation, understanding molecular machines, viral entry into cells, and putting together cellular pathways and their dynamics.

Glycoconjugates such as glycoproteins and glycolipids play important roles in cell-cell interaction events, including development, differentiation, m- phogenesis, fertilization, inflammation, and metastasis. A number of reports have documented the association of unique oligosaccharide sequences to p- tein targeting and folding, and in mechanisms of infection, inflammation, and immunity. For glycoproteins, these glycan appendages are the result of extensive co- or post-translational modifications of the nascent proteins in the endoplasmic reticulum and in the Golgi apparatus. Although nucleic acids and proteins are copied from a template in a repeated series of identical steps using the same enzymes, complex carbohydrates are formed by the sequential actions of cellular glycosyltransferases that specifically recognize unique s- strates. The molecular biology of these transferases and other carbohydra- modifying enzymes is providing important insights on oligosaccharide recognition events. While it is acknowledged that the definition of the protein complement of cells and tissues (the so-called proteome) remains an enormous task in this postgenomic era, the characterization of all glycans produced by individual organisms (referred to as the glycome) presents an equally imp- tant challenge. This task is further complicated by the fact that oligosacc- rides cannot presently be cloned. These complex carbohydrates exist in a staggering diversity of structures, linkages, and branching, thus providing an exquisite molecular repertoire for cellular interactions.

This volume provides practical guidance on a variety of techniques and steps to ensure successful variant calling. Chapters detail methods for variant calling from single-nucleotide variants to structural variants, variant calling in specialized data types such as RNA-seq and UMI-tagged sequencing, alignment-free genotyping and SNP calling, variant detection in single-cell DNA sequencing data, variant annotation, and preanalytical quality control to ensure successful variant calling. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists step-by-step protocol to execute the algorithms, describes the input and output data, and includes tips on troubleshooting and known pitfalls. Authoritative and cutting-edge, Variant Calling: Methods and Protocols aims to be a foundation for future studies and to be a source of inspiration for new investigations in the field.

During the 45 years of communist regimes in Hungary, Poland and Slovakia, agriculture was centrally directed without regard of quality factors and market needs, and was heavily subsidized. Democratization of the countries and adoption of market driven economies, including agriculture, created conditions that require new thinking and approaches to find market areas that will fill the needs of each country, and provide produce that is not redundant for the Common Market. The aim of this book is to facilitate solving common agricultural problems using the tools of biotechnology. The book addresses five themes: Plant Transformations, Plant Genomics, Breeding Plants for Resistance and Legal Aspects of Biotechnology, including risk assessment. Some specific topics dealt with are: The way from fundamental research to start-up company, Crop improvement by transgenic technology; Strategies for improving resistance; Current procedures for applying risk assessment in genetically modified crops; Questions arising from the implementation of the Hungarian gene technology law; Public perception and legislation of Biotechnology in Poland.

The contributors present a coherent set of case studies of practices, technologies and strategies aimed at the isolation, investigation, manipulation, production, and uses of molecules including vitamins, hormones, blood products, antibiotics, and vaccines. These case studies examine how processes of molecularization were set in motion in the inter-war period, how they were used as a resource in the biomedical 'mobilization' of World War II, and how new alliances and strategies created as part of the war effort played a central role in the reorganisation of biomedicine in the post-war period.

Italy, the birthplace of opera in the late sixteenth century, has in recent decades seen remarkable and vital musical growth, with composers as diverse as Luciano Berio and Nino Rota, Luigi Nono and Sylvano Bussotti, Giacomo Manzoni, Bruno Maderna and Salvatore Sciarrino. The musical theatre has figured prominently in the work of Italian composers during this period, ranging from operas conceived in a traditional mode to works of a Music Theatre variety, and in style from popular to avant-garde.
In this book Raymond Fearn surveys this Italian musico-theatrical phenomenon in the period since the Second World War, examining a wide range of works such as Nono's "Intolleranza" and "Al Gran Sole Carico d'Amore," Berio's "Passaggio" and "Un re in ascolto," Manzoni's "Atomtod" and "La Sentenza" and Castiglioni's "Oberon and The King's" "Masque," and places these developments within a cultural and theatrical context. Illustrated by numerous musical examples and producti

Human teratocarcinoma has long held a fascination to the pathologist be- cause of the diversity of the seemingly benign differentiated tissues asso- ciated with the tumor. An understanding of this diversity came with the demonstration of the pluripotent nature of the embryonal carcinoma cell, the stem cell of the tumor, in experimental animals. Single cell clones of murine embryonal carcinomas were derived and the resultant cell lines injected into immunosuppressed hosts, where the embryonal carcinoma stem cell itself gave rise to the wealth of differentiated tissues seen in teratocarcinomas. It was also shown that teratocarcinomas could be pro- duced experimentally by transplantation of staged early mouse embryo to extrauterine sites; subsequent experiments suggested that the embryonal carcinoma stem cell was, in fact, comparable to a normal cell of the em- bryonic ectoderm. Many elegant experiments have since been built on this early work; murine embryonal carcinoma cells are providing the ex- perimental material for a first biochemical evaluation of the earliest dif- ferentiation events in mammalian embryogenesis. In this volume, we relate the beginnings of experimental research on human teratoma. The human embryonal carcinoma cells have been char- acterized and established in vitro, providing an experimental model to study the unique biology of these cells. Monoclonal antibodies, estab- lished from work with these in vitro cultures, provide cell surface probes that define populations of embryonal cells and their derivatives in tumor sections.

This book facilitates both the theoretical background and applications of fuzzy, intuitionistic fuzzy and rough, fuzzy rough sets in the area of data science. This book provides various individual, soft computing, optimization and hybridization techniques of fuzzy and intuitionistic fuzzy sets with rough sets and their applications including data handling and that of type-2 fuzzy systems. Machine learning techniques are effectively implemented to solve a diversity of problems in pattern recognition, data mining and bioinformatics. To handle different nature of problems, including uncertainty, the book highlights the theory and recent developments on uncertainty, fuzzy systems, feature extraction, text categorization, multiscale modeling, soft computing, machine learning, deep learning, SMOTE, data handling, decision making, Diophantine fuzzy soft set, data envelopment analysis, centrally measures, social networks, Volterra–Fredholm integro-differential equation, Caputo fractional derivative, interval optimization, decision making, classification problems. This book is predominantly envisioned for researchers and students of data science, medical scientists and professional engineers.

This book encapsulates and occupies recent advances and state-of-the-art applications of nature-inspired computing (NIC) techniques in the field of bioinformatics and computational biology, which would aid medical sciences in various clinical applications. This edited volume covers fundamental applications, scope, and future perspectives of NIC techniques in bioinformatics including genomic profiling, gene expression data classification, DNA computation, systems and network biology, solving personalized therapy complications, antimicrobial resistance in bacterial pathogens, and computer-aided drug design, discovery, and therapeutics. It also covers the role of NIC techniques in various diseases and disorders, including cancer detection and diagnosis, breast cancer, lung disorder detection, disease biomarkers, and potential therapeutics identifications.

Contents:
1. Introduction to bioenergetics, 2. Energy requirements and energy expenditure, 3. Chemical reactions and energy transduction, 4. Redox reactions: electrons as common intermediates, 5. Redox reactions in metabolism, 6. Redox reactions in the biosphere, 7. Membrane transport: ion gradients as common intermediates, 8. Energy capture: photosynthesis, Answers to numerical problems. energy expenditure; chemical reactions and energy transduction; redox reactions - electrons as common intermediates; redox reactions in metabolism; redox reactions in the biosphere; membrane transport - ion gradients as common intermediates; energy capture - photosynthesis; answers to problems.

Concentrating on proven data and adopting a structure-function approach, this text provides grounding for an intricate understanding of the molecular biology, physiological mechanisms, and routine clinical use in disease settings of colony-stimulating factors (CSFs). This edition includes eight additional chapters, with updates of recently-discovered and established CSFs, each indexed individually.

Choice Recommended Title, August 2019 Read an exclusive interview with Professor Vera Kolb here. Astrobiology is the study of the origin, evolution, distribution, and future of life on Earth. This exciting and significant field of research also investigates the potential existence and search for extra-terrestrial life in the Solar System and beyond. This is the first handbook in this burgeoning and interdisciplinary field. Edited by Vera Kolb, a highly respected astrobiologist, this comprehensive resource captures the history and current state of the field. Rich in information and easy to use, it assumes basic knowledge and provides answers to questions from practitioners and specialists in the field, as well as providing key references for further study. Features: Fills an important gap in the market, providing a comprehensive overview of the field Edited by an authority in the subject, with chapters written by experts in the many diverse areas that comprise astrobiology Contains in-depth and broad coverage of an exciting field that will only grow in importance in the decades ahead

Due to the vital biological importance of RNA and proteins functioning together within a cell, a protocol volume describing experimental procedures to study their interactions should find a home in many laboratories. RNA-Protein Interaction Protocols, Second Edition updates, complements, and expands upon the popular first edition by providing a collection of cutting-edge techniques developed or refined in the past few years along with tried-and-true methods. The expert contributors explore the isolation and characterization of RNA-protein complexes, the analysis and measurement of RNA-protein interaction, and related novel techniques and strategies. Written in the highly successful Methods in Molecular Biologya"[ series format, the chapters include brief introductions to the material, lists of necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and a Notes section which highlights tips on troubleshooting and avoiding known pitfalls.

Comprehensive and up-to-date, RNA-Protein Interaction Protocols, Second Edition is an ideal guide for researchers continuing the study of this all-important biological partnership.

This book provides an overview of the history of integrative bioinformatics and the actual situation and the relevant tools. Subjects cover the essential topics, basic introductions, and latest developments; biological data integration and manipulation; modeling and simulation of networks; as well as a number of applications of integrative bioinformatics. It aims to provide basic introduction of biological information systems and guidance for the computational analysis of systems biology. This book covers a range of issues and methods that unveil a multitude of omics data integration and relevance that integrative bioinformatics has today. It contains a unique compilation of invited and selected articles from the Journal of Integrative Bioinformatics (JIB) and annual meetings of the International Symposium on Integrative Bioinformatics.

A comprehensive collection of optimized methods for dissecting the mechanisms that control epidermal growth factors (EGF) and their regulators in both normal and pathological states. These readily reproducible techniques range from the study of purified EGF receptor to complex signaling and processing networks in intact cells, including a chapter on the clinical and pharmacological considerations of their use in cancer therapy. The protocols follow the successful Methods in Molecular Biology (TM) series format, each offering step-by-step laboratory instructions, an introduction outlining the principles behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.

This volume provides updated, in-depth material on the application of intelligent optimization in biology and medicine. The aim of the book is to present solutions to the challenges and problems facing biology and medicine applications. This Volume comprises of 13 chapters, including an overview chapter, providing an up-to-date and state-of-the research on the application of intelligent optimization for bioinformatics applications, DNA based Steganography, a modified Particle Swarm Optimization Algorithm for Solving Capacitated Maximal Covering Location Problem in Healthcare Systems, Optimization Methods for Medical Image Super Resolution Reconstruction and breast cancer classification. Moreover, some chapters that describe several bio-inspired approaches in MEDLINE Text Mining, DNA-Binding Proteins and Classes, Optimized Tumor Breast Cancer Classification using Combining Random Subspace and Static Classifiers Selection Paradigms, and Dental Image Registration. The book will be a useful compendium for a broad range of readers-from students of undergraduate to postgraduate levels and also for researchers, professionals, etc.-who wish to enrich their knowledge on Intelligent Optimization in Biology and Medicine and applications with one single book.

This book highlights the recent advances in the field of microbial engineering and its application in human healthcare. It underscores the systemic and synthetic biology approaches for engineering microbes and discusses novel treatments for inflammatory bowel diseases based on engineered probiotics. The book also reviews the different options and methods for engineering microbes, ranging from recombinant DNA technology to designing microbes for targeting specific sites and delivering therapeutics. Further, it discusses genetically engineered microorganisms for smart diagnostics and describes current approaches in microbial gene editing using CRISPR-Cas9-based tools. Lastly, it summarizes the potential applications of human microbiome engineering in improving human health and explores potential strategies for scaling-up the production of engineered microbial strains for commercial purposes, as well as the challenges. Given its scope, this book is a valuable resource for students, researchers, academics and entrepreneurs interested in understanding microbial engineering for the production of commercial products.

This third edition details new and updated methods and protocols on important databases and data mining tools. Chapters guides readers through archives of macromolecular sequences and three-dimensional structures, databases of protein-protein interactions, methods for prediction conformational disorder, mutant thermodynamic stability, aggregation, and drug response. Quality of structural data and their release, soft mechanics applications in biology, and protein flexibility are considered, too, together with pan-genome analyses, rational drug combination screening and Omics Deep Mining. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials, includes step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Data Mining Techniques for the Life Sciences, Third Edition aims to be a practical guide to researches to help further their study in this field.

The Immunological Synapse, Part A, Volume 173 in the Methods in Cell Biology series provides state-of-the-art methods for the study of the immunological synapse. Sections cover Imaging polarized granule release at the cytotoxic T cell immunological synapse using TIRF microscopy: control by polarity regulators, Analysis of centrosomal area actin reorganization and centrosome polarization upon lymphocyte activation at the immunological synapse, P815-based redirected degranulation assay to study human NK cell effector functions, Cytotoxic and Chemotactic Dynamics of Natural Killer Cells Quantified by Live-cell Imaging, Quantification of interaction frequency between antigen-presenting cells and T cells by conjugation assay, and more. Other chapters focus on the Study of the Effects of NK-Tumor Cell Interaction by Proteomic Analysis and Imaging, Quantification of lymphocytic choriomeningitis virus specific T cells and LCMV viral titers, Quantification of lymphocytic choriomeningitis virus specific T cells and LCMV viral titers, An in vitro model to monitor natural killer cell effector functions against primary breast cancer, and Standardized Protocol for the Evaluation of Chimeric Antigen Receptor (CAR)-modified Cell Immunological Synapse Quality using the Glass-supported Planar L.

This volume is the first to combine latest information on viral, microbial and cellular proteolytic enzymes as potential targets for human therapeutics. Proteases control a large array of physiological reactions, and are involved in a variety of pathological processes for which effective medications are currently needed and/or being sought after. Although protease inhibitors have been investigated for many years, few have been employed therapeutically. Recent break- through by HIV protease inhibitors as therapeutic drugs has re-encouraged the search for inhibitors of other proteolytic enzymes. Klaus von der Helm, who described the first viral protease has brought leading experts together to discuss not only the success and problems of clinical use and continuing prospects, but to review further potential drug targets. This volume provides detailed information and evaluations of key viral, bacterial, fungal, and cellular proteases as potential future drug candidates.

This book presents detailed methods on a variety of aspects of Salmonella research, focusing on those which provide landmarks for future discovery. It is the first comprehensive volume of methods and protocols for studying Salmonella and will be indispensable to researchers engaged in the study of Salmonella, and enterobacteria in general. Each chapter provides a short overview of the topic, followed by detailed explanations of techniques.

Over the past decade, neuroproteomics has shed light on the molecular features of schizophrenia by depicting biological processes involved with its establishment, maintenance and treatment. These studies have also pointed to potential biomarkers applicable to diagnosis and medication monitoring. Edited by a leader in the field of neuroproteomics with contributions from subject experts, this new volume will address recent findings and compile evidence from difference perspectives-such as human samples, animal models, pluripotent stem cell-derived in vitro pre-clinical models-and provide findings to inform the development of innovative future treatment strategies. This volume will be useful for a broad audience of researchers and professionals, including biologists, neurologists, psychiatrists, analytical chemists, and pharmacists, among others.

This book provides an interdisciplinary look at emerging trends in signal processing and biomedicine found at the intersection of healthcare, engineering, and computer science. Bringing together expanded versions of selected papers presented at the 2020 IEEE Signal Processing in Medicine and Biology Symposium (IEEE SPMB), it examines the vital role signal processing plays in enabling a new generation of technology based on big data and looks at applications ranging from medical electronics to data mining of electronic medical records. Topics covered include analysis of medical images, machine learning, biomedical nanosensors, wireless technologies, and instrumentation and electrical stimulation. Biomedical Sensing and Analysis: Signal Processing in Medicine and Biology presents tutorials and examples of successful applications, and will appeal to a wide range of professionals, researchers, and students interested in applications of signal processing, medicine, and biology. Presents an interdisciplinary look at research trends in signal processing and biomedicine; Promotes collaboration between healthcare practitioners and signal processing researchers; Includes tutorials and examples of successful applications.

This book is the first comprehensive compilation describing the importance of sandalwood in national and international markets, genetic resources, molecular markers, whole genome sequencing, and pathway genes involved in oil biosynthesis, aroma and fragrance. Application of various "omics" approaches in delineating genome architecture and annotation of genes is highlighted. This book comprises 10 chapters covered over 200 pages authored by the researchers involved in sandalwood genomics. The sandalwood, Santalum album is known for its unique fragrance and finest wood available for carving. Also, sandalwood is intertwined with Indian culture and it is the second most valuable and expensive tree in the world.