November 30, 2020

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Carbohydrate-Active Enzymes

Carbohydrate-Active Enzymes
Author : K.-H. Park
Publisher : Elsevier
Release Date : 2008-09-23
Category : Technology & Engineering
Total pages :312
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Recent advances in biochemistry and biotechnology have enabled significant progress in basic research on carbohydrate-active enzymes and advances in their effective application. The mechanism of catalytic reaction of carbohydrate-active enzymes is not fully understood, though, as they often show unusual substrate specificity and modes of action. This comprehensive collection summarises some of the most important research in the field of carbohydrate-active enzymes, focusing on the enzymatic reaction mechanism, structure-function relationship and role in the living organism The book is based on papers presented in the 2008 Agricultural Biotechnology Symposium Carbohydrate-active enzymes: structure, function and applications held on September 26th-27th 2008 in Seoul National University, Korea. This symposium was organized by the Center for Agricultural Biomaterials, Seoul National University, Korea, which has organized symposia on agricultural biotechnology annually since 1990. Many important results on new types of carbohydrate-active enzymes and their applications have been reported at these meetings. Papers in Part one of this collection focus on structure-function relationships of carbohydrate-active enzymes. Papers in Part two discuss functions and applications of carbohydrate-active enzymes, such as enzymes for grain processing and glycosidases and their mutants as useful tools for glycoside synthesis. With its distinguished editor and international team of contributors, Carbohydrate-active enzymes: structure, function and applications is an essential reference for research scientists, post-graduate students and those in the food industry with an interest in enzymes. Summarises some of the most important research in the field of carbohydrate-active enzymes Covers topics ranging from enzyme classification and structural elucidation to applications of enzymes in food processing and other industries

Enzymatic Technologies for Marine Polysaccharides

Enzymatic Technologies for Marine Polysaccharides
Author : Antonio Trincone
Publisher : CRC Press
Release Date : 2019-04-08
Category : Medical
Total pages :527
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The bioactivity potential of marine polysaccharides has long been considered an underexploited aspect. These molecules found in seaweed, microalgae, bacteria, and animal fish (shellfish, mollusks, etc.) and the derived oligosaccharides need to be explored thoroughly with an interdisciplinary approach. They are an extraordinary source of chemical diversity, and the literature highlights many applicative fields, including the food industry, cosmetics, biomedicine, agriculture, environmental protection, wastewater management, etc. More recently, a new challenge has emerged: the exploitation of marine biomass as the source of sustainable energy to participate in the future replacement of fossil resources. Enzymatic Technologies for Marine Polysaccharides provides insight into the recent research developments of marine polysaccharides and their current and potential applications. The first section of the book explores the diversity of marine polysaccharides from various angles, including a description of the chemical complexity and current applications and new perspectives in food, pharmaceutical, cosmetics, and biomaterials offered by recent research. Efficient valorization of the marine polysaccharide biomass requires a rigorous analysis of the polysaccharides structure and their biological properties. The second section of the book concerns the development of extraction techniques and the improvement of the methods aimed at the characterization of their structure and function. Finally, the third and last section of the book articulates the enzymatic technologies from the discovery of novel enzymes to their production pipelines related to the fields of biorefinery, food, pharmaceutics, and other fine chemicals. Presents the latest research in marine oligosaccharides and polysaccharides Written by world-class researchers in marine enzyme technology Discusses the latest developments in extraction methods Presents a detailed overview of enzymatic routes for modification, production, and synthesis of marine oligosaccharides Contains extensive references at the end of each chapter to enhance further study

Strategies for the Discovery of Carbohydrate-active Enzymes from Environmental Bacteria

Strategies for the Discovery of Carbohydrate-active Enzymes from Environmental Bacteria
Author : Anonim
Publisher : Unknown
Release Date : 2013
Category :
Total pages :82
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Carbohydrate-Active Enzymes

Carbohydrate-Active Enzymes
Author : Stefano Benini
Publisher : MDPI
Release Date : 2020-06-18
Category : Science
Total pages :408
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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.

Carbohydrate Bioengineering

Carbohydrate Bioengineering
Author : S.B. Petersen,B. Svensson,S. Pedersen
Publisher : Elsevier
Release Date : 1995-12-08
Category : Science
Total pages :368
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The Carbohydrate Bioengineering Meeting held in Elsinore, Denmark, April 23-26, 1995, gathered 230 scientists, mostly from Europe, with interest in carbohydrate analysis and structure; carbohydrates in medicine and glycopathology; structure, function, application, and protein engineering of carbohydrate active enzymes; oligo- and polysaccharides of industrial interest; and production of carbohydrate containing new materials. The first chapters address glycoconjugates as modulatory and recognition molecules, structure determination using NMR and mass spectrometry, and microdialysis-chip enzyme-based sensors. Active site mutations coupled with crystal structures and synthetic substrate analogue interactions as well as new three-dimensional structures and binding domains for biotechnological applications are included in the chapters. Carbohydrate active enzymes turned out to be a predominant topic. The rapid development in glycobiology and glycotechnology has resulted in an enormous increase in our knowledge on the structure conversion, and application of carbohydrates in industry and medicine.

Genome-wide Analysis of Carbohydrate Active Enzyme Diversity and Expression in Eucalyptus Grandis

Genome-wide Analysis of Carbohydrate Active Enzyme Diversity and Expression in Eucalyptus Grandis
Author : Desré Pinard
Publisher : Unknown
Release Date : 2013
Category : Carbohydrates
Total pages :218
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The woody biomass derived from tree species forms a vital part of the world’s economy, and a thorough understanding of the processes of carbon sequestration and carbohydrate metabolism in trees is paramount in ensuring efficient and sustainable use of this biomass. To date, there is still much to be learnt about wood formation and polysaccharide deposition in plant cell walls. The enzymes responsible for the synthesis, degradation, and modification of polysaccharides and glycosidic bonds are known as Carbohydrate Active enZymes (CAZymes) are organized into functional classes and families based on amino acid sequence. CAZymes in plant genomes can be analyzed using the functional protein domains that form the proteins in order to better understand the functional potential of the carbohydrate metabolism strategy employed by plants. The glycosyltransferase (GT) class of CAZyme domains is responsible for the synthesis of glycosidic bonds, and the glycosylhydrolases (GH), polysaccharide lyase (PL), and carbohydrate esterase (CE) CAZyme domain classes degrade and modify these bonds. The final class of CAZyme domains is the non-enzymatic carbohydrate binding modules (CBMs), which act to increase the activity of the enzymatic CAZyme domain classes via specific binding to polysaccharides, disruption of the cell wall polysaccharide matrix, and proximity effects when appended to enzymatic CAZyme domains in complex CAZyme domain containing proteins. In this project, we used comparative genomics and transcriptomics of CAZyme domains to analyze the functional building blocks of plant carbohydrate metabolism to gain insight into the process of wood formation, with a specific focus on the biomass feedstock crop, Eucalyptus grandis. The aim of this project was to compare the CAZyme domain frequency, diversity and complexity across plant genomes representative of the major land plant lineages and green algae species to identify any delineating factors that contribute to wood formation in tree species. In addition, we analyzed the expression levels of CAZyme domains in the transcriptomes of source and sink tissues in E. grandis and Populus trichocarpa to better understand the expression investment in carbohydrate metabolism in different tissues of divergent tree species. The results show conservation of a fundamental functional strategy for carbohydrate metabolism across land plant evolution. The ratio of CAZyme domain frequency is maintained in land plants, with GTs contributing ?40% of the genomic CAZyme domain content, highlighting the importance of polysaccharide synthesis in plants. The diversity of CAZyme domain families within each class cannot be used to differentiate the genomes of major land plant lineages (lycophytes and bryophytes, monocots, and dicots) from one another, however, species-specific differences in CAZyme domain family diversity are observed. The complexity of CAZyme domain containing proteins shows that CAZyme domains are not very promiscuous, repeated CAZyme domains within a protein are more common than unique combinations of CAZyme domains within a protein, which are also conserved for the most part. The analysis of CAZyme domain expression in six tissues in E. grandis showed that in the wood forming tissue, immature xylem, GT domain families responsible for cellulose and hemicellulose biosynthesis formed the majority of the transcript abundance, a pattern not seen in the other tissues analyzed. This pattern was conserved in P. trichocarpa, highlighting the conserved mechanism for wood formation between divergent tree species. The results of this study reveal the conservation of the fundamental functional machinery responsible for carbohydrate metabolism in land plants, and highlight the importance of differential regulation of this machinery to wood formation. The long-term goal of improving the production of lignocellulosic biomass from trees will be achieved by fully understanding the regulatory mechanisms controlling the concerted expression of these CAZyme domain-containing genes.

Bioinformatics for Glycobiology and Glycomics

Bioinformatics for Glycobiology and Glycomics
Author : Claus-Wilhelm von der Lieth,Thomas Luetteke,Martin Frank
Publisher : John Wiley & Sons
Release Date : 2009-10-01
Category : Medical
Total pages :494
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This book is the first to be dedicated to the bioinformatics of carbohydrates and glycoproteins. It provides an introduction to this emerging field of science both for the experimentalist working in glycobiology and glycomics, and also for the computer scientist looking for background information for the development of highly sophisticated algorithmic approaches. The book provides an overview of the state-of-the-art in the field, with reviews on databases, and the tools in use for analysis, interpretation, and prediction of the structures of complex carbohydrates, and demonstrates the value of bioinformatics for glycobiology. The availability of comprehensive databases and corresponding bioinformatics tools, to access and analyse the large amounts of experimental data relating to the structure of carbohydrates, will be a prerequisite for the success of the large-scale glycomics projects that aim to decipher new, so far unknown, biological functions of glycans. Efficient bioinformatics descriptions and tools can considerably enhance the efficiency of glycomics research, in terms of data quality, analysis and experimental costs. For a complete understanding of the molecular processes in which carbohydrates are involved, such as protein–carbohydrate interactions and the impact of glycosylation on protein function, knowledge of the 3D structure of the carbohydrate, the protein–carbohydrate complex, or the glycoprotein is often indispensable. This book provides a thorough introduction into methods used for conformational analysis of carbohydrates. Key features: Describes bioinformatic approaches to handle carbohydrate-active enzymes and glycosylation. Provides an overview on bioinformatics tools that facilitate analysis of carbohydrate structures. Gives introduction into molecular modelling of carbohydrate 3D structure and carbohydrates contained in the Protein Databank. Assumes only a basic knowledge of biology and bioinformatics.

Carbohydrates: The Essential Molecules of Life

Carbohydrates: The Essential Molecules of Life
Author : Robert V. Stick,Spencer Williams
Publisher : Elsevier
Release Date : 2010-08-06
Category : Science
Total pages :496
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This book provides the "nuts and bolts" background for a successful study of carbohydrates - the essential molecules that not only give you energy, but are an integral part of many biological processes. A question often asked is 'Why do carbohydrate chemistry?' The answer is simple: It is fundamental to a study of biology. Carbohydrates are the building blocks of life and enable biological processes to take place. Therefore the book will provide a taste for the subject of glycobiology. Covering the basics of carbohydrates and then the chemistry and reactions of carbohydrates this book will enable a chemist to gain essential knowledge that will enable them to move smoothly into the worlds of biochemistry, molecular biology and cell biology. * includes perspective from new co-author Spencer Williams, who enhances coverage of the connection between carbohydrates and life * describes the basic chemistry and biology of carbohydrates * reviews the concepts, synthesis, reactions, and biology of carbohydrates

Chitin and Chitosan: Properties and Applications

Chitin and Chitosan: Properties and Applications
Author : Lambertus A. M. van den Broek,Carmen G. Boeriu,Christian V. Stevens
Publisher : John Wiley & Sons
Release Date : 2020-01-28
Category : Science
Total pages :536
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Offers a comprehensive guide to the isolation, properties and applications of chitin and chitosan Chitin and Chitosan: Properties and Applications presents a comprehensive review of the isolation, properties and applications of chitin and chitosan. These promising biomaterials have the potential to be broadly applied and there is a growing market for these biopolymers in areas such as medical and pharmaceutical, packaging, agricultural, textile, cosmetics, nanoparticles and more. The authors – noted experts in the field – explore the isolation, characterization and the physical and chemical properties of chitin and chitosan. They also examine their properties such as hydrogels, immunomodulation and biotechnology, antimicrobial activity and chemical enzymatic modifications. The book offers an analysis of the myriad medical and pharmaceutical applications as well as a review of applications in other areas. In addition, the authors discuss regulations, markets and perspectives for the use of chitin and chitosan. This important book: Offers a thorough review of the isolation, properties and applications of chitin and chitosan. Contains information on the wide-ranging applications and growing market demand for chitin and chitosan Includes a discussion of current regulations and the outlook for the future Written for Researchers in academia and industry who are working in the fields of chitin and chitosan, Chitin and Chitosan: Properties and Applications offers a review of these promising biomaterials that have great potential due to their material properties and biological functionalities.

A Practical Guide to Using Glycomics Databases

A Practical Guide to Using Glycomics Databases
Author : Kiyoko F. Aoki-Kinoshita
Publisher : Springer
Release Date : 2016-12-06
Category : Science
Total pages :370
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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.

Encyclopedia of Metagenomics

Encyclopedia of Metagenomics
Author : Karen E. Nelson
Publisher : Springer
Release Date : 2015-02-18
Category : Science
Total pages :1528
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Metagenomics has taken off as one of the major cutting-edge fields of research. The field has broad implications for human health and disease, animal production, and environmental health. Metagenomics has opened up a wealth of data, tools, technologies and applications that allow us to access the majority of organisms that we still cannot access in pure culture (an estimated 99% of microbial life). Numerous research groups are developing tools, approaches and applications to deal with this new field, as larger data sets from environments including the human body, the oceans and soils are being generated. See for example the human microbiome initiative (HMP; http://nihroadmap.nih.gov/hmp/) which has become a world-wide effort, and the Global Ocean Sampling (GOS) surveys; http://www.jcvi.org/cms/research/projects/gos/overview/). The number of publications as measured through PubMed that are focused on metagenomics continues to increase. The field of metagenomics continues to evolve with large common datasets available to the scientific community. A concerted effort is needed to collate all this information in a centralized place. By having all the information in an Encyclopedia form, we have an opportunity to gather seminal contributions from the leaders in the field, and at the same time provide this information to a significant number of junior and senior scientists. It is anticipated that the Encyclopedia will also be used by many other groups including, clinicians, undergraduate and graduate level students, as well as ethical and legal groups associated with or interested in the issues surrounding metagenome science.

Carbohydrate Chemistry and Biochemistry

Carbohydrate Chemistry and Biochemistry
Author : Michael Sinnott
Publisher : Royal Society of Chemistry
Release Date : 2013-03-28
Category : Science
Total pages :835
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This fully updated and expanded second edition of a highly popular text book focuses on the structure and mechanism in carbohydrate chemistry and biochemistry. Carbohydrates play important roles in biological systems as energy sources, as structural materials, and as informational structures (when they are often attached to proteins or lipids). Their chemical reactivity and conformational behaviour is governed by mechanistic and stereochemical rules, which apply as much to enzymic as to non-enzymic reactivity. The same principles of reactivity and conformation govern changes brought about in the process industries, such as pulp, paper and food. Extensively referenced with citations and a detailed index, the book contains everything the reader needs to know to start a carbohydrate research project with one of the real strengths being the treatment and integration of the important physical-chemical principles and methods (though lead references only are given to the finer points of carbohydrate synthesis). The book is suitable for both researchers who are new to the subject and those more established as well as a readership from diverse backgrounds and interests, including chemists, biochemists, food scientists and technologists involved with the processing of polysaccharides in the paper, textile, cosmetics, biofuels and other industries.

Carbohydrate Bioengineering

Carbohydrate Bioengineering
Author : Tuula T Teeri,B Svensson,H J Gilbert,T Feizi
Publisher : Royal Society of Chemistry
Release Date : 2007-10-31
Category : Science
Total pages :206
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Carbohydrate bioengineering is a rapidly expanding field with many applications in medicine and industry. Presenting state-of-the-art research, Carbohydrate Bioengineering: Interdisciplinary Approaches brings together international experts on many different aspects of this burgeoning topic. Coverage includes: the engineering of glycosidases for constructive purposes; structure-function studies and protein engineering of carbohydrate-active enzymes; chemo-enzymatic carbohydrate synthesis; and trends emerging from comprehensive work on genomes and glycomes. This timely publication will be welcomed by all those needing access to the latest research in the field, including practitioners in the medicinal, chemical, food and pharmaceutical areas.

Advances in the Regulation and Production of Fungal Enzymes by Transcriptomics, Proteomics and Recombinant Strains Design

Advances in the Regulation and Production of Fungal Enzymes by Transcriptomics, Proteomics and Recombinant Strains Design
Author : André Damasio,Gustavo H. Goldman,Roberto N. Silva,Fernando Segato
Publisher : Frontiers Media SA
Release Date : 2019-10-04
Category :
Total pages :129
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Several efforts have been made in developing strategies to supply the enzyme market, as well as in reducing its costs. It includes the selection of an appropriate enzyme source and the optimization of enzyme properties and secretion. Carbohydrate-Active Enzymes (CAZymes) are industrially relevant biocatalysts that are capable of degrading plant cell wall biomass. The most important secreted enzymes related to plant cell wall decomposition are cellulases, hemicellulases, and auxiliary enzymes. These enzymes have been applied in the hydrolysis of plant biomass for the production of second-generation (2G) ethanol and several other high added value products. One of the bottlenecks for 2G ethanol production is the cost of enzymes applied on plant biomass hydrolysis. The improvement of proteins production by fungi applying system biology and genetic engineering is an interesting and promising strategy to reduce the enzymes cost and make the 2G ethanol production viable. Fungi play an important role in plant biomass degradation and biotechnology by producing and secreting high yields of enzymes. In spite of the fact that filamentous fungi present several advantages compared to other microorganisms due to the high level of proteins production, heterologous protein production is far from optimal levels and still needs to be improved. Currently, heterologous production of certain proteins is generally considerably lower than the levels obtained to homologous production. Many strategies have been studied in order to improve heterologous production of proteins by filamentous fungi, including the deletion of genes that encode for proteases, the deletion of lectin-like ER-Golgi cargo receptors and the co-expression of specific chaperones. It has been shown that the main bottleneck in the production of heterologous proteins is not caused by the low expression of the target gene. An experimental evidence suggests that most target proteins produced in filamentous fungi are lost or stuck in the secretory pathway due to errors in processing, modification or misfolding that result in their elimination by endoplasmic reticulum (ER) quality control. Misfolded proteins alter homeostasis and proper ER functioning resulting in a state known as ER stress. ER stress activates a conserved signaling pathway called unfolded protein response (UPR) and ER-associated protein degradation (ERAD), which upregulates genes responsible for restoring protein folding homeostasis in the cell and degrades misfolded protein in the cytosol by the ubiquitin-proteasome system. The genetic manipulation of individual genes and changes in the genome seems not to be the best alternative to overcome the main bottlenecks in heterologous protein secretion. However, the understanding of complex interactions of important proteins and genes, as well as how they are regulated is more promising.

Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches

Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches
Author : Gaurav Sablok,Sunil Kumar,Saneyoshi Ueno,Jimmy Kuo,Claudio Varotto
Publisher : Springer
Release Date : 2015-07-16
Category : Science
Total pages :241
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Provides a global view of the recent advances in the biological sciences and the adaption of the pathogen to the host plants revealed using NGS. Molecular Omic’s is now a major driving force to learn the adaption genetics and a great challenge to the scientific community, which can be resolved through the application of the NGS technologies. The availability of complete genome sequences, the respective model species for dicot and monocot plant groups, presents a global opportunity to delineate the identification, function and the expression of the genes, to develop new tools for the identification of the new genes and pathway identification. Genome-wide research tools, resources and approaches such as data mining for structural similarities, gene expression profiling at the DNA and RNA level with rapid increase in available genome sequencing efforts, expressed sequence tags (ESTs), RNA-seq, gene expression profiling, induced deletion mutants and insertional mutants, and gene expression knock-down (gene silencing) studies with RNAi and microRNAs have become integral parts of plant molecular omic’s. Molecular diversity and mutational approaches present the first line of approach to unravel the genetic and molecular basis for several traits, QTL related to disease resistance, which includes host approaches to combat the pathogens and to understand the adaptation of the pathogen to the plant host. Using NGS technologies, understanding of adaptation genetics towards stress tolerance has been correlated to the epigenetics. Naturally occurring allelic variations, genome shuffling and variations induced by chemical or radiation mutagenesis are also being used in functional genomics to elucidate the pathway for the pathogen and stress tolerance and is widely illustrated in demonstrating the identification of the genes responsible for tolerance in plants, bacterial and fungal species.