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A Practical Guide to Using Glycomics Databases by Kiyoko F. Aoki-Kinoshita Pdf
This book provides glycoscientists with a handbook of useful databases that can be applied to glycoscience research. Although many databases are now publicly available, one of the hurdles for their users is the learning curve required to effectively utilize those databases. Therefore, this book not only describes the existing databases, but also provides tips on how to obtain the target data. That is, because many databases provide a variety of data that could be obtained from different perspectives, each chapter provides users with potential biological questions that can be answered by a particular database and step-by-step instructions, with figures, on how to obtain that data. Troubleshooting tips are also provided to aid users encountering problems that can be predicted when using these databases. Moreover, contact information for each database is provided in case unexpected issues arise.
The Art of Carbohydrate Analysis by Gerrit J. Gerwig Pdf
The growing importance of glycobiology and carbohydrate chemistry in modern biotechnology and the pharmaceutical industry makes accurate carbohydrate analysis indispensable. This book provides the principles and protocols of various fundamental carbohydrate analysis methods. Choice of method is entirely dependent upon the type of material being investigated (biological samples, food products, etc.), and the level of structural detail required, i.e. sugar content, compositional analysis, linkages between the sugar components, or the total chemical structure of a given molecule. Full structural characterization of carbohydrate chains requires significant time, resources, and skill in several methods of analysis; no single technique can address all glycan analysis needs. This book summarizes several existing analytical techniques (both chemical and physical) in an introductory volume designed for the non-expert researcher or novice scientist. While background in carbohydrate chemistry is assumed, all information necessary to understanding the described techniques is addressed in the text.
Glycome Informatics by Kiyoko F. Aoki-Kinoshita Pdf
A Focused, State-of-the-Art Overview of This Evolving Field Presents Various Techniques for Glycoinformatics The development and use of informatics tools and databases for glycobiology and glycomics research have increased considerably in recent years. In addition to accumulating well-structured glyco-related data, researchers have now developed semi-automated methods for the annotation of mass spectral data and algorithms for capturing patterns in glycan structure data. These techniques have enabled researchers to gain a better understanding of how these complex structures affect protein function and other biological processes, including cancer. One of the few up-to-date books available in this important area, Glycome Informatics: Methods and Applications covers all known informatics methods pertaining to the study of glycans. It discusses the current status of carbohydrate databases, the latest analytical techniques, and the informatics needed for rapid progress in glycomics research. Providing an overall understanding of glycobiology, this self-contained guide focuses on the development of glycome informatics methods and current problems faced by researchers. It explains how to implement informatics methods in glycobiology. The author includes the required background material on glycobiology as well as the mathematical concepts needed to understand advanced mining and algorithmic techniques. She also suggests project themes for readers looking to begin research in the field.
Computational Methods for Predicting Post-Translational Modification Sites by Dukka B. KC Pdf
This volume describes computational approaches to predict multitudes of PTM sites. Chapters describe in depth approaches on algorithms, state-of-the-art Deep Learning based approaches, hand-crafted features, physico-chemical based features, issues related to obtaining negative training, sequence-based features, and structure-based features. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Authoritative and cutting-edge, Computational Methods for Predicting Post-Translational Modification Sites aims to be a useful guide for researchers who are interested in the field of PTM site prediction.
Dioxygen-dependent Heme Enzymes by Masao Ikeda-Saito,Emma Raven Pdf
Aerobic organisms have evolved to utilise the intrinsic oxidising power of oxygen from the atmosphere. This so-called 'activation' of oxygen is often catalysed by a heme-containing enzyme. This book highlights the many and varied catalytic activities of O2-dependent heme–iron enzymes, including monoxygenases and cytochrome P450, dioxygenases, oxidases and model heme systems. Dioxygen-dependent Heme Enzymes will be a useful resource for postgraduate students and researchers in biochemistry and metallobiology working in, or moving into, research areas involving heme proteins.
Carbohydrate-active enzymes are responsible for both biosynthesis and the breakdown of carbohydrates and glycoconjugates. They are involved in many metabolic pathways; in the biosynthesis and degradation of various biomolecules, such as bacterial exopolysaccharides, starch, cellulose and lignin; and in the glycosylation of proteins and lipids. Carbohydrate-active enzymes are classified into glycoside hydrolases, glycosyltransferases, polysaccharide lyases, carbohydrate esterases, and enzymes with auxiliary activities (CAZy database, www.cazy.org). Glycosyltransferases synthesize a huge variety of complex carbohydrates with different degrees of polymerization, moieties and branching. On the other hand, complex carbohydrate breakdown is carried out by glycoside hydrolases, polysaccharide lyases and carbohydrate esterases. Their interesting reactions have attracted the attention of researchers across scientific fields, ranging from basic research to biotechnology. Interest in carbohydrate-active enzymes is due not only to their ability to build and degrade biopolymers—which is highly relevant in biotechnology—but also because they are involved in bacterial biofilm formation, and in glycosylation of proteins and lipids, with important health implications. This book gathers new research results and reviews to broaden our understanding of carbohydrate-active enzymes, their mutants and their reaction products at the molecular level.
Enzymes in Food Biotechnology by Mohammed Kuddus Pdf
Enzymes in Food Biotechnology: Production, Applications, and Future Prospects presents a comprehensive review of enzyme research and the potential impact of enzymes on the food sector. This valuable reference brings together novel sources and technologies regarding enzymes in food production, food processing, food preservation, food engineering and food biotechnology that are useful for researchers, professionals and students. Discussions include the process of immobilization, thermal and operational stability, increased product specificity and specific activity, enzyme engineering, implementation of high-throughput techniques, screening to relatively unexplored environments, and the development of more efficient enzymes. Explores recent scientific research to innovate novel, global ideas for new foods and enzyme engineering Provides fundamental and advanced information on enzyme research for use in food biotechnology, including microbial, plant and animal enzymes Includes recent cutting-edge research on the pharmaceutical uses of enzymes in the food industry
Industrial Applications of Glycoside Hydrolases by Smriti Shrivastava Pdf
This book gathers selected studies on the industrial applications of glycoside hydrolases (GHs), presenting an updated classification of these enzymes, and discussing their structure, mechanisms, and various approaches to improve their catalytic efficiency. Further, it explains the various industrial applications of glycoside hydrolases in food, effluent treatment, biofuel production, and the paper and pulp industries. Lastly, the book provides a comparative analysis of glycoside hydrolases and discusses the role of metagenomics in the discovery of industrially important enzymes. As such it is a thought-provoking, instructive and informative resource for biochemists, enzymologists, molecular biologists and bioprocess technologists.
Transcriptome Profiling by Mohammad Ajmal Ali,Joongku Lee Pdf
Transcriptome Profiling: Progress and Prospects assists readers in assessing and interpreting a large number of genes, up to and including an entire genome. It provides key insights into the latest tools and techniques used in transcriptomics and its relevant topics which can reveal a global snapshot of the complete RNA component of a cell at a given time. This snapshot, in turn, enables the distinction between different cell types, different disease states, and different time points during development. Transcriptome analysis has been a key area of biological inquiry for decades. The next-generation sequencing technologies have revolutionized transcriptomics by providing opportunities for multidimensional examinations of cellular transcriptomes in which high-throughput expression data are obtained at a single-base resolution. Transcriptome analysis has evolved from the detection of single RNA molecules to large-scale gene expression profiling and genome annotation initiatives. Written by a team of global experts, key topics in Transcriptome Profiling include transcriptome characterization, expression analysis of transcripts, transcriptome and gene regulation, transcriptome profiling and human health, medicinal plants transcriptomics, transcriptomics and genetic engineering, transcriptomics in agriculture, and phylotranscriptomics. Presents recent development in the tools and techniques in transcriptomic characterization Integrates expression analysis of transcripts and gene regulation Includes the application of transcriptomics in human health, genetic engineering and agriculture
A Guided Tour of Artificial Intelligence Research by Pierre Marquis,Odile Papini,Henri Prade Pdf
The purpose of this book is to provide an overview of AI research, ranging from basic work to interfaces and applications, with as much emphasis on results as on current issues. It is aimed at an audience of master students and Ph.D. students, and can be of interest as well for researchers and engineers who want to know more about AI. The book is split into three volumes: - the first volume brings together twenty-three chapters dealing with the foundations of knowledge representation and the formalization of reasoning and learning (Volume 1. Knowledge representation, reasoning and learning) - the second volume offers a view of AI, in fourteen chapters, from the side of the algorithms (Volume 2. AI Algorithms) - the third volume, composed of sixteen chapters, describes the main interfaces and applications of AI (Volume 3. Interfaces and applications of AI). This third volume is dedicated to the interfaces of AI with various fields, with which strong links exist either at the methodological or at the applicative levels. The foreword of this volume reminds us that AI was born for a large part from cybernetics. Chapters are devoted to disciplines that are historically sisters of AI: natural language processing, pattern recognition and computer vision, and robotics. Also close and complementary to AI due to their direct links with information are databases, the semantic web, information retrieval and human-computer interaction. All these disciplines are privileged places for applications of AI methods. This is also the case for bioinformatics, biological modeling and computational neurosciences. The developments of AI have also led to a dialogue with theoretical computer science in particular regarding computability and complexity. Besides, AI research and findings have renewed philosophical and epistemological questions, while their cognitive validity raises questions to psychology. The volume also discusses some of the interactions between science and artistic creation in literature and in music. Lastly, an epilogue concludes the three volumes of this Guided Tour of AI Research by providing an overview of what has been achieved by AI, emphasizing AI as a science, and not just as an innovative technology, and trying to dispel some misunderstandings.
Health Information Science by Siuly Siuly,Zhisheng Huang,Uwe Aickelin,Rui Zhou,Hua Wang,Yanchun Zhang,Stanislav Klimenko Pdf
This book constitutes the refereed proceedings of the 6th International Conference on Health Information Science, HIS 2017, held in Moscow, Russia, in October 2017. The 11 full papers and 7 short papers presented were carefully reviewed and selected from 44 submissions. The papers feature multidisciplinary research results in health information science and systems that support health information management and health service delivery. They relate to all aspects of the conference scope, such as medical/health/biomedicine information resources such as patient medical records, devices and equipments, software and tools to capture, store, retrieve, process, analyze, and optimize the use of information in the health domain; data management, data mining, and knowledge discovery, management of publichealth, examination of standards, privacy and security issues; computer visualization and artificial intelligence for computer aided diagnosis; development of new architectures and applications for health information systems.
Handbook of Glycomics by Richard D. Cummings,J. Michael Pierce Pdf
The Handbook of Glycomics provides the first comprehensive overview of the emerging field of glycomics, defined as the study of all complex carbohydrates in an organism or cell ("the glycome"). Beginning with analytic approaches and bioinformatics, this work provides a detailed discussion of relevant databases, data integration, and analysis. It then moves on to a discussion of specific model organism and pathogen glycomes followed by therapeutic approaches to human disorders of glycosylization. Structure and function of glycomes are included along with state-of-the-art technologies and systems approaches to the analysis of glycans. Synthesizes contributions from experts in biology, chemistry, bioinformatics, biotechnology, and medicine Highlights chapters devoted to chemical synthesis, cancer glycomics and immune cell glycomics Includes discussions of proteomics, mass spectrometry, NMR, array technology, and transcriptomics analytic approaches
Glycoside Hydrolases by Arun Goyal,Kedar Sharma Pdf
Glycoside Hydrolases provides a detailed overview of the biochemical, biophysical, and protein engineering properties of glycoside hydrolases, a class of enzymes in growing use across various applications. Here, more than a dozen global experts discuss the structural and catalytic mechanisms of specific glycoside hydrolases, followed by their implications in biotechnological applications of different industrial sectors such as the food and feed industry, paper and pulp industry, the bioenergy sector and the pharmaceutical industry. Authors consider how the application of glycoside hydrolases may boost industrial production of valued products, and the broader environmental and sustainability goals of converting agrowaste into valued products. This book helps researchers and students across industry and academia gain deep knowledge of glycoside hydrolases, to advance new experimental research and applications from biofuel to drug discovery. Details glycoside hydrolase classification, enzyme assays for biochemical characterization, and biophysical methods for structure determination and catalytic mechanisms Discusses the use of glycoside hydrolases across various applications from biofuels to drug development, enzyme technology, and fermented food production Features chapter contributions from international leaders in the field
Essentials of Glycobiology by Ajit Varki,Maarten J. Chrispeels Pdf
Sugar chains (glycans) are often attached to proteins and lipids and have multiple roles in the organization and function of all organisms. "Essentials of Glycobiology" describes their biogenesis and function and offers a useful gateway to the understanding of glycans.
This volume provides a comprehensive understanding of the enigmatic identity of the glycome, a complex but important area of research that has been largely ignored due to its complexity. The authors thoroughly deal with almost all aspects of the glycome, i.e., elucidation of the glycan identity enigma and its role in regulation of the cellular process, and in disease etiology. The book bridges the knowledge gap in understanding the glycome, from being a cell signature to its applications in disease etiology. In addition, it details many of the major insights regarding the possible role of the glycome in various diseases as a therapeutic marker. The book systematically covers the major aspects of the glycome, including the significance of substituting the diverse monosaccharide units to glycoproteins, the role of glycans in disease pathologies, and the challenges and advances in glycobiology. The authors stress the significance and huge encoding power of carbohydrates as well as provide helpful insights in framing the bigger picture. The Glycome: Understanding the Diversity and Complexity of Glycobiology details state-of-the-art developments and emerging challenges of glycome biology, which are going to be key areas of future research, not only in the glycobiology field but also in pharmaceutics.