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 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 The Regulation of Cellular Systems written by Reinhart Heinrich and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 387 pages. Available in PDF, EPUB and Kindle. Book excerpt: There is no doubt that nowadays, biology benefits greatly from mathematics. In particular, cellular biology is, besides population dynamics, a field where tech niques of mathematical modeling are widely used. This is reflected by the large number of journal articles and congress proceedings published every year on the dynamics of complex cellular processes. This applies, among others, to metabolic control analysis, where the number of articles on theoretical fundamentals and experimental applications has increased for about 15 years. Surprisingly, mono graphs and textbooks dealing with the modeling of metabolic systems are still exceptionally rare. We think that now time is ripe to fill this gap. This monograph covers various aspects of the mathematical description of enzymatic systems, such as stoichiometric analysis, enzyme kinetics, dynamical simulation, metabolic control analysis, and evolutionary optimization. We believe that, at present, these are the main approaches by which metabolic systems can be analyzed in mathematical terms. Although stoichiometric analysis and enzyme kinetics are classical fields tracing back to the beginning of our century, there are intriguing recent developments such as detection of elementary biochemical syn thesis routes and rate laws for the situation of metabolic channeling, which we have considered worth being included. Evolutionary optimization of metabolic systems is a rather new field with promising prospects. Its goal is to elucidate the structure and functions of these systems from an evolutionary viewpoint.
Download or read book Systems Metabolic Engineering written by Christoph Wittmann and published by Springer Science & Business Media. This book was released on 2012-06-15 with total page 391 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems Metabolic Engineering is changing the way microbial cell factories are designed and optimized for industrial production. Integrating systems biology and biotechnology with new concepts from synthetic biology enables the global analysis and engineering of microorganisms and bioprocesses at super efficiency and versatility otherwise not accessible. Without doubt, systems metabolic engineering is a major driver towards bio-based production of chemicals, materials and fuels from renewables and thus one of the core technologies of global green growth. In this book, Christoph Wittmann and Sang-Yup Lee have assembled the world leaders on systems metabolic engineering and cover the full story – from genomes and networks via discovery and design to industrial implementation practises. This book is a comprehensive resource for students and researchers from academia and industry interested in systems metabolic engineering. It provides us with the fundaments to targeted engineering of microbial cells for sustainable bio-production and stimulates those who are interested to enter this exiting research field.
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 ANALYSIS OF STOICHIOMETRY IN METABOLIC NETWORKS CELL METABOLISM LINEAR OPTIMIZATION written by JOANNE MARY SAVINELL and published by . This book was released on 1991 with total page 470 pages. Available in PDF, EPUB and Kindle. Book excerpt: the metabolic capabilities of the cell, interpreting flux measurements, improving experimental design, and studying metabolic design.
Download or read book Metabolic Flux Analysis written by Jens O. Krömer and published by . This book was released on 2014 with total page 316 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This book is dedicated to Metabolic Flux Analysis in systems that can be studied under metabolic steady-state or pseudo-steady-state conditions, also called stationary approaches. Under these conditions the change of intracellular metabolite concentrations ( CMET ) as a function of the stoichiometric matrix S and the flux vector v can be approximated to zero. This approximation converts the equations system from a differential to a linear one and greatly simplifies its solution. We hope that this book will open the field of metabolic flux analysis to a wider scientific community by providing helpful tricks to those who want to start a new flux analysis project but are overwhelmed by the complexity of the approach. We tried to break it up into manageable bits of information that can be implemented step by step following the methods chapters provided. The overview chapters are there to explain the necessary basics to get started and also to review what has been achieved within a few model organisms."--Preface, page vi.
Download or read book Mechanisms of Catalysis written by and published by Academic Press. This book was released on 1991-01-28 with total page 471 pages. Available in PDF, EPUB and Kindle. Book excerpt: The remarkable expansion of information leading to a deeper understanding of enzymes on the molecular level necessitated the development of this volume which not only introduces new topics to The Enzymes series but presents new information on some covered in Volume I and II of this edition.
Download or read book A First Course in Systems Biology written by Eberhard O. Voit and published by Garland Science. This book was released on 2012-03-28 with total page 465 pages. Available in PDF, EPUB and Kindle. Book excerpt: A First Course in Systems Biology is a textbook designed for advanced undergraduate and graduate students. Its main focus is the development of computational models and their applications to diverse biological systems. Because the biological sciences have become so complex that no individual can acquire complete knowledge in any given area of specialization, the education of future systems biologists must instead develop a student's ability to retrieve, reformat, merge, and interpret complex biological information. This book provides the reader with the background and mastery of methods to execute standard systems biology tasks, understand the modern literature, and launch into specialized courses or projects that address biological questions using theoretical and computational means. The format is a combination of instructional text and references to primary literature, complemented by sets of small-scale exercises that enable hands-on experience, and larger-scale, often open-ended questions for further reflection.
Download or read book Advances in the Theory of Control Signals and Systems with Physical Modeling written by Jean Levine and published by Springer Science & Business Media. This book was released on 2010-09-30 with total page 374 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the 60's, control, signals and systems had a common linear algebraic background and, according to their evolution, their respective backgrounds have now dramatically differed. Recovering such a common background, especially in the nonlinear context, is currently a fully open question. The role played by physical models, finite or infinite dimensional, in this hypothetical convergence is extensively discussed in this book. The discussion does not only take place on a theoretical basis but also in the light of two wide classes of applications, among the most active in the current industrially oriented researches: - Electrical and Mechatronical systems; - Chemical Processes and systems appearing in Life Sciences. In this perspective, this book is a contribution to the enhancement of the dialogue between theoretical laboratories and more practically oriented ones and industries. This book is a collection of articles that have been presented by leading international experts at a series of three workshops of a Bernoulli program entitled “Advances in the Theory of Control, Signals and Systems, with Physical Modeling” hosted by the Bernoulli Centre of EPFL during the first semester of 2009. It provides researchers, engineers and graduate students with an unprecedented collection of topics and internationally acknowledged top-quality works and surveys.
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 Systems Biology written by Bernhard Palsson and published by Cambridge University Press. This book was released on 2015-01-26 with total page 551 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first comprehensive single-authored textbook on genome-scale models and the bottom-up approach to systems biology.
Download or read book White Biotechnology written by Roland Ulber and published by Springer Science & Business Media. This book was released on 2007-02-13 with total page 309 pages. Available in PDF, EPUB and Kindle. Book excerpt: With contributions by numerous experts
Download or read book The Handbook of Polyhydroxyalkanoates written by Martin Koller and published by CRC Press. This book was released on 2020-10-19 with total page 515 pages. Available in PDF, EPUB and Kindle. Book excerpt: This second volume of the "Handbook of Polyhydroxyalkanoates (PHA): Kinetics, Bioengineering and Industrial Aspects" focusses on thermodynamic and mathematical considerations of PHA biosynthesis, bioengineering aspects regarding bioreactor design and downstream processing for PHA recovery from microbial biomass. It covers microbial mixed culture processes and includes a strong industry-focused section with chapters on the economics of PHA production, industrial-scale PHA production from sucrose, next generation industrial biotechnology approaches for PHA production based on novel robust production strains, and holistic techno-economic and sustainability considerations on PHA manufacturing. Aimed at professionals and graduate students in Polymer (plastic) industry, wastewater treatment plants, food industry, biodiesel industry, this book Provides an insight into microbial thermodynamics to reveal the central domain governing in PHA formation, both aerobically and anaerobically. Includes systematic overview of mathematical modelling approaches, starting from low-structured and formal kinetic models until modern tools like metabolic models, cybernetic models and so forth Discusses challenges during scale up of PHA production processes and on development of non-sterile processes and contamination-resistant strains Presents a holistic picture of the current state of PHA research by mixed cultures Reviews the industry-related point of view about current and future trends in PHA production and processing
Download or read book Metabolic Pathway Design written by Pablo Carbonell and published by Springer Nature. This book was released on 2019-11-05 with total page 168 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook presents solid tools for in silico engineering biology, offering students a step-by-step guide to mastering the smart design of metabolic pathways. The first part explains the Design-Build-Test-Learn-cycle engineering approach to biology, discussing the basic tools to model biological and chemistry-based systems. Using these basic tools, the second part focuses on various computational protocols for metabolic pathway design, from enzyme selection to pathway discovery and enumeration. In the context of industrial biotechnology, the final part helps readers understand the challenges of scaling up and optimisation. By working with the free programming language Scientific Python, this book provides easily accessible tools for studying and learning the principles of modern in silico metabolic pathway design. Intended for advanced undergraduates and master’s students in biotechnology, biomedical engineering, bioinformatics and systems biology students, the introductory sections make it also useful for beginners wanting to learn the basics of scientific coding and find real-world, hands-on examples.
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 Systems Biology written by Bernhard Ø. Palsson and published by Cambridge University Press. This book was released on 2006-01-16 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genome sequences are now available that enable us to determine the biological components that make up a cell or an organism. The discipline of systems biology examines how these components interact and form networks, and how the networks generate whole cell functions corresponding to observable phenotypes. This textbook, devoted to systems biology, describes how to model networks, how to determine their properties, and how to relate these to phenotypic functions. The prerequisites are some knowledge of linear algebra and biochemistry. Though the links between the mathematical ideas and biological processes are made clear, the book reflects the irreversible trend of increasing mathematical content in biology education. Therefore to assist both teacher and student, in an associated website Palsson provides problem sets, projects and Powerpoint slides, and keeps the presentation in the book concrete with illustrative material and experimental results.
