Download or read book On the Systems Characterization of Metabolic Networks written by Neema Jamshidi and published by . This book was released on 2009 with total page 233 pages. Available in PDF, EPUB and Kindle. Book excerpt: Significant progress has been made in the development of genome-scale models of metabolism in the past 15 years. The majority of the efforts have focused on the analysis of the right null space. While the steady state solution space is very important since homeostatic mechanisms are continuously trying to push the system back to a steady state, there are three other subspaces which also have significance. This dissertation approaches metabolic networks with the goal of investigating all four fundamental subspaces of linear systems, particularly the row and column spaces, which determine the dynamic capabilities of networks. First, the key matrices are defined and their general properties and characteristics are identified. The subspaces are analyzed for a simple metabolic network. Next the right null space is explored in a targeted manner using real networks, the cardiomyocyte mitochondria and a genome-scale model of Mycobacterium tuberculosis, focusing on perfectly correlated reaction sets and the biologically interesting implications they may hold. This is followed by the development of analytical methods to define the time scale hierarchy in the column space of the human red cell, human folate metabolism, and yeast glycolysis. These studies are further pursued by investigating various decompositions of the stoichiometric and gradient matrices that are determined by the underlying physico-chemical characteristics. These investigations lead to the identification of key properties of metabolic networks, such as the duality between fluxes and concentrations in dynamic networks. Having established how to decompose these networks, a middle-out integration approach is described for building or reconstructing kinetic networks using '-omic' data streams that are increasingly available. This approach is applied to construct a dynamic model of human red cell metabolism with and without mechanistic integration of allosteric regulatory functions of enzymes, dynamic models of E. coli, as well as a general hepatocyte mitochondria model which can be used for application of these methods, when the appropriate data becomes available. Simulations with the regulated erythrocyte model highlight the importance of active versus inactive states of enzymes and how the binding state of the enzyme exerts control of the flux through competing pathways. The subsequent chapter investigates perturbational analyses and how they can inform functional states and identify pathophysiological conditions. This dissertation culminates in a description of a conceptually new approach to modeling, 'delta' networks, that relaxes data requirements and is focused on identifying the functional differences between different data sets in an effort to understand as much of the four subspaces as possible, not just the right null space. The studies carried out in this dissertation also further support the use of models as data interrogation tools; for data integration, analysis, as well as for the evaluation of data consistency. The developments and advancements made herein take steps towards achieving genome-scale dynamic regulated networks of metabolism, which can in principle be applied to any biological network.
Download or read book On Systems Biology and the Pathway Analysis of Metabolic Networks written by Christophe Heinz Schilling and published by . This book was released on 2000 with total page 674 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Computational Systems Biology written by Hong-Wu Ma and published by Elsevier Inc. Chapters. This book was released on 2013-11-26 with total page 35 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding the complex interactions among cellular components (genes, proteins and metabolites) at a network level is a key issue in systems biology. In this chapter, we give an overview of metabolic network reconstruction from genome information and its structural analysis. First, two approaches for genome scale metabolic network reconstruction: high throughput reconstruction and high quality reconstruction, are discussed. Then the various means for mathematical representation of metabolic networks are explained, with particular emphasis on the problem arising from currency metabolites. Several topological features of metabolic network such as the power law connection degree distribution and the “bow-tie” global connectivity structure are explained in detail. In the last section, we discuss the different types of methods for network decomposition which can be used to identify somehow structurally and functionally independent modules in a complex network. This allows us to understand the functional organization of metabolic network from a modular perspective.
Download or read book Correlation based network analysis of cancer metabolism written by Emily G. Armitage and published by Springer. This book was released on 2014-05-12 with total page 67 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the rise of systems biology as an approach in biochemistry research, using high throughput techniques such as mass spectrometry to generate metabolic profiles of cancer metabolism is becoming increasingly popular. There are examples of cancer metabolic profiling studies in the academic literature; however they are often only in journals specific to the metabolomics community. This book will be particularly useful for post-graduate students and post-doctoral researchers using this pioneering technique of network-based correlation analysis. The approach can be adapted to the analysis of any large scale metabolic profiling experiment to answer a range of biological questions in a range of species or for a range of diseases.
Download or read book Metabolic Engineering written by Jens Nielsen and published by Springer. This book was released on 2003-07-03 with total page 193 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Systemic Analysis of the Stoichiometric Matrix and Kinetic Characterization of Metabolic Networks written by Iman Famili and published by . This book was released on 2004 with total page 336 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Pathway Analysis and Optimization in Metabolic Engineering written by Néstor V. Torres and published by Cambridge University Press. This book was released on 2002-12-19 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt: Facility in the targeted manipulation of the genetic and metabolic composition of organisms, combined with unprecedented computational power, is forging a niche for a new subspecialty of biotechnology called metabolic engineering. First published in 2002, this book introduces researchers and advanced students in biology and engineering to methods of optimizing biochemical systems of biotechnological relevance. It examines the development of strategies for manipulating metabolic pathways, demonstrates the need for effective systems models, and discusses their design and analysis, while placing special emphasis on optimization. The authors propose power-law models and methods of biochemical systems theory toward these ends. All concepts are derived from first principles, and the text is richly illustrated with numerous graphs and examples throughout. Special features include: nontechnical and technical introductions to models of biochemical systems; a review of basic methods of model design and analysis; concepts of optimization; and detailed case studies.
Download or read book Metabolic Networks Elementary Flux Modes and Polyhedral Cones written by Isaac Klapper and published by SIAM. This book was released on 2021-06-15 with total page 133 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a mathematical analysis of the relationship between the cell biology idea of metabolic networks and the mathematical idea of polyhedral cones. Such cones can be used to describe the set of steady state admissible fluxes through metabolic networks, and consequently they have become important constructs in the field of microbiology. Fundamental objects called elementary flux modes (EFMs) can be described mathematically via convex cone concepts; the fundamental algorithm of this relationship is the Double Description method. While this method has an extended history in the field of computational geometry, this monograph addresses its relatively recent use in the context of cellular metabolism, providing an easy-to-read introduction to a central topic of mathematical systems biology. Metabolic Networks, Elementary Flux Modes, and Polyhedral Cones addresses important topics in the mathematical description of metabolic activity that have not previously appeared in unified form and presents a careful study of the Double Description method in the context of metabolic analysis. It makes mathematical aspects of the material readily accessible to bioengineers and system biologists, and biological aspects readily accessible to mathematicians. This book is intended for readers from both mathematical and biological backgrounds, including mathematicians, engineers, and biologists interested in cell metabolism. It will also be helpful to mathematicians interested in applying computational geometry methods in computational biology as well as for systems biologists and modelers interested in the mathematical and algorithmic foundations of metabolic pathway analysis.
Download or read book The Evolution of Metabolic Function written by Robert P. Mortlock and published by CRC Press. This book was released on 1992-05-20 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Evolution of Metabolic Function presents comprehensive discussions on a variety of topics that will interest scientists and students studying the evolution of enzyme activities, the evolution of enzymatic pathways, and the evolution and development of metabolic functions. Laboratory experiments designed to develop new enzyme activities and new metabolic pathways are discussed. The most recent techniques comparing protein and gene structures are used to analyze and discuss the evolution and development of such metabolic functions as the bacterial phosphoenolpyruvate:sugar phosphotransferase system, the mandelate pathway of microorganisms, bacterial alcohol metabolism, and certain microbial amino acid biosynthetic pathways. The book also includes some unique speculations regarding the origin of early Archaean cells and the prebiotic evolution of complex molecules.
Download or read book Metabolic Network Analysis written by T.P. Jayadev Reddy and published by Daya Books. This book was released on 2007-03-02 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metabolism Is A Set Of Chemical Reactions, Used By Living Organisms To Process Chemical Compounds In Order To Take Energy, Extract Building Blocks And Eliminate Toxic Compounds. It Comprises The Network Of Interactions That Provide Energy And Building Blocks For Cells And Organisms, A Network Sustaining The Living And Allowing It To Grow And Reproduce. Understanding The Nature And Functions Of Metabolic Networks Is Imperative To Biology, Toxicology And Medicine. With The Sequencing Of Complete Genomes, It Is Now Possible To Reconstruct The Network Of Biochemical Reactions In Many Organisms, From Bacteria To Human. This Book Examines How Biological Components Interact And Form Metabolic Networks, And How These Networks Generate Cell Functions Corresponding To Observable Phenotypes. It Describes How To Model Metabolic Networks, How To Determine Their Properties, And How To Relate These To Phenotypic Functions. It Will Be A Highly Beneficial Reference Tool For Researchers And Scholars In All Areas Of Life Sciences. Contents Chapter 1: Biology Of Cellular Networks; Chapter 2: Characteristics Of Metabolic Networks; Chapter 3: Signalling Pathways; Chapter 4: Networks In Genomics And Proteomics; Chapter 5: Modelling Of Biological Network; Chapter 6: Pathway Analysis In Metabolic Networks; Chapter 7: Topological Features Of Metabolic Networks; Chapter 8: Structure Of Expanding Metabolic Networks; Chapter 9: Modularity In Metabolic Networks; Chapter 10: Connectivity In Metabolic Networks; Chapter 11: Metabolic Network Interactions; Chapter 12: Microbial Metabolic Networks; Chapter 13: Protein Interaction Networks; Chapter 14: Implications Of Human Metabolome; Chapter 15: Metabolic Network Prediction; Chapter 16: Algebraic Comparison Of Metabolic Networks; Chapter 17: Regulation Of Metabolic Pathways.
Download or read book Optimization Methods in Metabolic Networks written by Costas D. Maranas and published by John Wiley & Sons. This book was released on 2016-01-05 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Download or read book Fundamentals of Systems Analysis and Modeling of Biosystems and Metabolism written by Kazuyuki Shimizu and published by Bentham Science Publishers. This book was released on 2015-06-04 with total page 343 pages. Available in PDF, EPUB and Kindle. Book excerpt: An understanding of biological systems at cellular and molecular levels helps researchers to model cellular behavior in different experimental conditions. This, in turn, can lead to insights about the influence of cell culture environment and the effect of knockout gene research when studying mutations that affect specific metabolic pathways. A systems biology approach, therefore, allows researchers to simulate experimental observations in order to predict outcomes at the cellular level. Fundamentals of Systems Analysis and Modeling of Biosystems and Metabolism presents the basic concepts required for a systems biology approach towards cellular modeling. The book is intended as a primer for systems biology and biomedical engineering graduates and researchers. The text introduces readers to concepts related to cellular metabolism and its regulation, (enzymatic regulation and transcriptional regulation) which are also incorporated into a main metabolic model of a cell. The book also has chapters dedicated to identifying and incorporating steady-state and dynamic characteristics when considering a biological model for a computer simulation. Readers will be able to (1) understand the basis of systems analysis towards creating appropriate biological models and simulations, (2) develop useful kinetic models based on cellular transport phenomena and metabolic regulation, (3) understand how to simulate a cell growth phenotype, and analyze it with experimental data.
Download or read book Metabolome Analyses written by Seetharaman Vaidyanathan and published by Springer Science & Business Media. This book was released on 2006-03-20 with total page 396 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metabolome analysis is now recognized as a crucial component of functional genomic and systems biology investigations. Innovative approaches to the study of metabolic regulation in microbial, plant and animal systems are increasingly facilitating the emergence of systems approaches in biology. This book highlights analytical and bioinformatics strategies now available for investigating metabolic networks in microbial, plant and animal systems. The contributing authors are world leaders in this field and they present an unambiguous case for pursuing metabolome analysis as a means to attain a systems level understanding of complex biological systems.
Download or read book Metabolic Engineering written by Sang Yup Lee and published by John Wiley & Sons. This book was released on 2021-06-02 with total page 1075 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Metabolomics written by Jens Nielsen and published by Springer Science & Business Media. This book was released on 2007-09-19 with total page 292 pages. Available in PDF, EPUB and Kindle. Book excerpt: Giving a fresh, substantial and in-depth overview of the topic, this book brings together the latest results in the field of metabolomics. It comprehensively presents the current state of the metabolomics field by underscoring experimental methods, analysis techniques, standardization practices, and advances in specific model systems. As a result, it helps to significantly broaden our perspective on the principles and strategies underpinning this emerging field.
Download or read book The Evolutionary Strategies that Shape Ecosystems written by J. Philip Grime and published by John Wiley & Sons. This book was released on 2012-03-26 with total page 362 pages. Available in PDF, EPUB and Kindle. Book excerpt: THE EVOLUTIONARY STRATEGIES THAT SHAPE ECOSYSTEMS In 1837 a young Charles Darwin took his notebook, wrote “I think”, and then sketched a rudimentary, stick-like tree. Each branch of Darwin’s tree of life told a story of survival and adaptation – adaptation of animals and plants not just to the environment but also to life with other living things. However, more than 150 years since Darwin published his singular idea of natural selection, the science of ecology has yet to account for how contrasting evolutionary outcomes affect the ability of organisms to coexist in communities and to regulate ecosystem functioning. In this book Philip Grime and Simon Pierce explain how evidence from across the world is revealing that, beneath the wealth of apparently limitless and bewildering variation in detailed structure and functioning, the essential biology of all organisms is subject to the same set of basic interacting constraints on life-history and physiology. The inescapable resulting predicament during the evolution of every species is that, according to habitat, each must adopt a predictable compromise with regard to how they use the resources at their disposal in order to survive. The compromise involves the investment of resources in either the effort to acquire more resources, the tolerance of factors that reduce metabolic performance, or reproduction. This three-way trade-off is the irreducible core of the universal adaptive strategy theory which Grime and Pierce use to investigate how two environmental filters selecting, respectively, for convergence and divergence in organism function determine the identity of organisms in communities, and ultimately how different evolutionary strategies affect the functioning of ecosystems. This book refl ects an historic phase in which evolutionary processes are finally moving centre stage in the effort to unify ecological theory, and animal, plant and microbial ecology have begun to find a common theoretical framework. Companion website This book has a companion website www.wiley.com/go/grime/evolutionarystrategies with Figures and Tables from the book for downloading.
Download or read book Methods in Bioengineering written by Arul Jayaraman and published by Artech House. This book was released on 2009 with total page 329 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This cutting-edge volume provides a detailed look at the two main aspects of systems biology: the design of sophisticated experimental methods and the development of complex models to analyze the data. Focusing on methods that are being used to solve current problems in biomedical science and engineering, this comprehensive, richly illustrated resource shows you how to: design of state-of-the art methods for analyzing biological systems Implement experimental approaches for investigating cellular behavior in health and disease; use algorithms and modeling techniques for quantitatively describing biomedical problems; and integrate experimental and computational approaches for a more complete view of biological systems." --Book Jacket.
