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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.
In Plant Metabolic Flux Analysis, expert researchers in the field provide detailed experimental procedures for each step of the flux quantification workflow. Steady state and dynamic modeling are considered, as well as recent developments for the reconstruction of metabolic networks and for a predictive modeling. 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 key tips on troubleshooting and avoiding known pitfalls.
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 Flux Analysis: Methods and Protocols opens up the field of metabolic flux analysis to those who want to start a new flux analysis project but are overwhelmed by the complexity of the approach. Metabolic flux analysis emerged from the current limitation for the prediction of metabolic fluxes from a measured inventory of the cell. Divided into convenient thematic parts, topics in this essential volume include the fundamental characteristics of the underlying networks, the application of quantitative metabolite data and thermodynamic principles to constrain the solution space for flux balance analysis (FBA), the experimental toolbox to conduct different types of flux analysis experiments, the processing of data from 13C experiments and three chapters that summarize some recent key findings. Written in the 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 protocols and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Metabolic Flux Analysis: Methods and Protocols presents protocols that cover a range of relevant organisms currently used in the field, providing a solid basis to anybody interested in the field of metabolic flux analysis.
Metabolic flux analysis (MFA) is a powerful technology to characterize intracellular metabolism in living cells using isotopic tracers and mass spectrometry. Therefore, in the past two decades, MFA techniques have been developed to study biological systems. However, the applications of MFA for mammalian cells have been limited due to the complexity of cellular metabolism even though mammalian cells are key platforms for biopharmaceutical production and biomedical research. Here, we present two applications for glycolysis and gluconeogenesis systems. First, we describe the analysis of metabolic fluxes in CHO metabolism at fed-batch mode. We established two metabolic models of CHO cells for non-stationary and stationary 13C-MFA. It was found that cellular metabolism in CHO cells were significantly rewired from exponential growth to stationary phases during culture. The results provide a solid foundation for applications such as cell line development and medium optimization. Second, we describe gluconeogenesis metabolism of Fao rat hepatoma cells perturbed by transcription factors. Using multiple isotopic tracers and combined 13C-MFA, we observed the regulations of metabolic fluxes by transcriptional activators and inhibitors for gluconeogenesis metabolism. The discovery and the applied MFA techniques can allow us to evaluate the pharmaceutical drug for metabolic disease, e.g. Type II diabetes. And finally, we provide the comprehensible procedures to be considered for 13C-MFA technique: isotopic and metabolic stationarity, isotopic tracer design, key measurements, multiple isotopic tracers and model validation.
Mitochondria are sometimes called the powerhouses of eukaryotic cells, because mitochondria are the site of ATP synthesis in the cell. ATP is the universal energy currency, it provides the power that runs all other life processes. Humans need oxygen to survive because of ATP synthesis in mitochondria. The sugars from our diet are converted to carbon dioxide in mitochondria in a process that requires oxygen. Just like a fire needs oxygen to burn, our mitochondria need oxygen to make ATP. From textbooks and popular literature one can easily get the impression that all mitochondria require oxygen. But that is not the case. There are many groups of organismsm known that make ATP in mitochondria without the help of oxygen. They have preserved biochemical relicts from the early evolution of eukaryotic cells, which took place during times in Earth history when there was hardly any oxygen avaiable, certainly not enough to breathe. How the anaerobic forms of mitochondria work, in which organisms they occur, and how the eukaryotic anaerobes that possess them fit into the larger picture of rising atmospheric oxygen during Earth history are the topic of this book.
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
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.