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This volume highlights recent breakthroughs in the interdisciplinary areas of synthetic biology, metabolic engineering and bioprocess engineering for the production of green chemicals. It also presents practical experimental and computational tools for the design, construction and manipulation of cyanobacteria cell factories. The respective contributions cover new technologies in the field, such as novel genetic transformation techniques and bioinformatics analysis methods and address various aspects of cyanobacterial synthetic biology, offering a valuable resource for students and researchers in the fields of industry microbiology and biomedical engineering.
This volume explores the latest metabolic flux analysis (MFA) techniques that cover the analysis of cellular, organ level, and whole-body metabolism. The chapters in this book discuss topics such as deutrium tracing; isotopologue fractions using GC-TOF; non-targeted mass isotopolome analysis; large-scale profiling of cellular metabolic activities using deep 13C labeling medium; metastases in mice; SWATH; Exo-MFA; metabolic flux from time-course metabolomics; and thermodynamic approaches in flux analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Metabolic Flux Analysis in Eukaryotic Cells: Methods and Protocols is a valuable resource for both experts in MFA techniques and researchers getting involved in the role of quantitative studies to uncover the dysregulated pathways in human diseases.
Learn more about foundational and advanced topics in metabolic engineering in this comprehensive resource edited by leaders in the field Metabolic Engineering: Concepts and Applications delivers a one-stop resource for readers seeking a complete description of the concepts, models, and applications of metabolic engineering. This guide offers practical insights into the metabolic engineering of major cell lines, including E. Coli, Bacillus and Yarrowia Lipolytica, and organisms, including human, animal, and plant). The distinguished editors also offer readers resources on microbiome engineering and the use of metabolic engineering in bioremediation. Written in two parts, Metabolic Engineering begins with the essential models and strategies of the field, like Flux Balance Analysis, Quantitative Flux Analysis, and Proteome Constrained Models. It also provides an overview of topics like Pathway Design, Metabolomics, and Genome Editing of Bacteria and Eukarya. The second part contains insightful descriptions of the practical applications of metabolic engineering, including specific examples that shed light on the topics within. In addition to subjects like the metabolic engineering of animals, humans, and plants, you’ll learn more about: Metabolic engineering concepts and a historical perspective on their development The different modes of analysis, including flux balance analysis and quantitative flux analysis An illuminating and complete discussion of the thermodynamics of metabolic pathways The Genome architecture of E. coli, as well as genome editing of both bacteria and eukarya An in-depth treatment of the application of metabolic engineering techniques to organisms including corynebacterial, bacillus, and pseudomonas, and more Perfect for students of biotechnology, bioengineers, and biotechnologists, Metabolic Engineering: Concepts and Applications also has a place on the bookshelves of research institutes, biotechnological institutes and industry labs, and university libraries. It's comprehensive treatment of all relevant metabolic engineering concepts, models, and applications will be of use to practicing biotechnologists and bioengineers who wish to solidify their understanding of the field.
Metabolic engineering is a rapidly evolving field that is being applied for the optimization of many different industrial processes. In this issue of Advances in Biochemical Engineering/Biotechnology, developments in different areas of metabolic engineering are reviewed. The contributions discuss the application of metabolic engineering in the improvement of yield and productivity - illustrated by amino acid production and the production of novel compounds - in the production of polyketides and extension of the substrate range - and in the engineering of S. cerevisiae for xylose metabolism, and the improvement of a complex biotransformation process.
A thorough introduction to the basics of bioengineering, with a focus on applications in the emerging "white" biotechnology industry. As such, this latest volume in the "Advanced Biotechnology" series covers the principles for the design and analysis of industrial bioprocesses as well as the design of bioremediation systems, and several biomedical applications. No fewer than seven chapters introduce stoichiometry, kinetics, thermodynamics and the design of ideal and real bioreactors, illustrated by more than 50 practical examples. Further chapters deal with the tools that enable an understanding of the behavior of cell cultures and enzymatically catalyzed reactions, while others discuss the analysis of cultures at the level of the cell, as well as structural frameworks for the successful scale-up of bioreactions. In addition, a short survey of downstream processing options and the control of bioreactions is given. With contributions from leading experts in industry and academia, this is a comprehensive source of information peer-reviewed by experts in the field.
The first comprehensive single-authored textbook on genome-scale models and the bottom-up approach to systems biology.
This special volume "Tools and Applications of Biochemical Engineering Science" is dedicated to Professor Wolf-Dieter Deckwer on the occasion of his 60th bir- day. It was a great pleasure for me to act together with Professor Karl Schtigerl as volume editor and to present here a collection of 11 outstanding review articles written mainly by former students, associates, colleagues and friends of Wolf- Dieter Deckwer. The title of this special volume well reflects the research interests and sci- tific pursuit of Wolf-Dieter Deckwer during his more than 20 years’ work in the area of biochemical engineering, particularly during the last 15 years when he was the head of the Biochemical Engineering Division of GBF (German Nat- nal Research Center for Biotechnology). He has decisively pushed the devel- ment not only of "software tools" ranging from analytical means and mathe- tical models for monitoring and understanding cellular processes to gene expression systems for designing microorganisms, but also of "hardware tools" such as computer control systems, bioreaction and separation devices for eff- tively producing a variety of bioproducts on semi-production scale. New developments in some of these important tools in biochemical engineering are reviewed in articles included in this volume. Wolf-Dieter Deckwer was among the leading biochemical engineers who timely pointed out the necessity of applying these tools in an integrated manner for bioprocess development. By establishing "Integrated Bioprocess Development" as one of the GBF main - search topics as early as 1990 he also actively promoted this idea.
With contributions by numerous experts
The metabolic regulation of a cell system is of critical importance in systems biology, and a robust model of these mechanisms is essential in predicting the effects on the metabolism of both the culture environment and the knockout of specific genes. Bacterial cellular metabolic systems focuses on this highly topical subject in relation to culture environment and provides a detailed analysis from gene level to metabolic level regulation, as well as offering a discussion of the most recent modelling approaches. The book begins with an introduction to metabolic mechanisms and to the metabolic regulation of a cell, before moving on to discussing the action of global regulators in response to a specific culture environment. The second half of the book examines conventional flux balance analysis and its applications, 13C-metabolic flux analysis, and the effect of a specific gene knockout on the metabolism. - Comprehensive account of metabolic regulation via global regulators in response to changes in the culture environment - Basic formulation of 13C-metabolic flux analysis based on 13C-labelling experiments - Systems biology approach for the modelling and computer simulation of the main metabolic pathways of a cell system
Provides a tutorial on the computational tools that use mathematical optimization concepts and representations for the curation, analysis and redesign of metabolic networks Organizes, for the first time, the fundamentals of mathematical optimization in the context of metabolic network analysis Reviews the fundamentals of different classes of optimization problems including LP, MILP, MLP and MINLP Explains the most efficient ways of formulating a biological problem using mathematical optimization Reviews a variety of relevant problems in metabolic network curation, analysis and redesign with an emphasis on details of optimization formulations Provides a detailed treatment of bilevel optimization techniques for computational strain design and other relevant problems