Download or read book Dynamic Analysis and Design of Metabolic Networks written by Shyamsundhar Srinivasan and published by . This book was released on 2019 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mathematical models of biological networks play an important role in metabolic engineering through their ability to provide a complete systems level understanding of the numerous interactions that govern metabolism, and consequently cellular function. Models of metabolism are extensively used to design these networks to achieve various engineering and pharmacological objectives. Constraint-based models of metabolism assume that metabolism operates under a pseudo steady state and represent them only in terms of their reaction stoichiometry and fluxes. The numerous regulatory interactions that constitute metabolism are not considered, and the dynamics of the networks cannot be deciphered using constraint-based models. In contrast, kinetic models can represent all of the interactions in the metabolic network, and also facilitate studying the dynamic characteristics of metabolism. Nonetheless, computational limitations encountered during various stages of kinetic model development and use limit their widespread adoption for model-based prediction and design. This thesis aims to address some of these limitations using the metabolism of Escherichia coli as an example. First, we demonstrate the use of kinetic models to characterize the steady state behaviour of a bistable metabolic network with a positive feedback loop, and to design this bistable network to produce at the highest possible steady state. Next, we explore the use of metabolic network topology and structure to assess the ability of the network to exhibit more than one steady state. We also show how this assessment can be used to design networks with either monostable or multistable topologies. Finally, we develop two scalable frameworks to assess the structural identifiability and estimability of parameters in a kinetic model of a metabolic network, based on steady state data. The application of these frameworks to determine the quality and quantity of experiments necessary to generate the steady state data required for estimating all model parameters is also shown. The methods developed and demonstrated in this thesis aim to improve the adoption of kinetic models to design metabolic networks exhibiting bistability. They also provide alternative avenues for parameter estimation in kinetic models using steady state data, while reducing the quantity of time course data needed for kinetic model parameter estimation.
Download or read book Plant Metabolic Networks written by Jörg Schwender and published by Springer Science & Business Media. This book was released on 2009-06-12 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plants are the basis for human nutrition and of increasing interest for the chemical industry as a source of chemical feed stocks. Fuels derived from plant biomass will increasingly replace fossil fuels in the future. In order to increase crop productivity, design new plant products, and create new energy crops, there is need for methods of qualitative and quantitative analysis of metabolism which are able to guide the rational re-design of metabolic networks. In this book, recent advances in qualitative and quantitative analysis of metabolism are summarized to give an overview of the current state of knowledge. Principles of the analysis of network structure, flux analysis, and kinetic modeling are described. Analytical methods necessary to produce the data needed for metabolic flux analysis and for kinetic modeling are described. The analysis of larger metabolic networks is only possible by using computer assistance. Therefore each chapter of the book shall also describe software available for this purpose.
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 Dynamic Models of Metabolic Networks and Analysis of Cell free Protein Synthesis written by Michael Vilkhovoy and published by . This book was released on 2019 with total page 253 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metabolism is the central process through which cells manage their resources to survive, adapt and meet energetic demands. To implement these diverse functions, cells have complex and highly interconnected networks of chemical reactions between genes, RNA, proteins and metabolites. Systems modeling and metabolic engineering arose from the desire to harness the power of metabolism to produce products that benefit society. A primary challenge is the development of metabolic mathematical models that are able to describe the effect genetic perturbations have on cellular behavior. In this study, we first review metabolic modeling methods and go on to develop computational tools for the analysis and engineering of microbial systems with a focus on cell-free protein synthesis (CFPS). Cell-free protein expression has become a widely used research tool in systems and synthetic biology, and a promising technology for biomanufacturing of proteins. Cell-free systems offer many advantages for the study, manipulation and modeling of metabolism compared to in vivo processes. Central amongst these is direct access to metabolites and the biosynthetic machinery without the interference of a cell wall or the complications associated with cell growth. However, if CFPS is to become a mainstream technology for applications such as point of care manufacturing, we must understand the performance limits and costs of these systems. Cell-free protein synthesis relies on transcription and translation machinery to produce a protein of interest. To fuel this process requires biochemical enzymes and reactions that are involved in complex metabolic pathways. Toward this, we developed dynamic mathematical models that describe CFPS metabolism and provide insights into improving these systems. We began with a sequence specific constraint based model that coupled transcription/translation processes and the regulation of gene expression with the availability of metabolic resources. Then, we developed a robust comprehensive analysis to quantify absolute levels of metabolites in CFPS using isotopically labeled standards. We expanded our modeling framework by integrating absolute metabolite measurements along with kinetic parameters, enzyme levels, and enzyme activity assays. The framework predicted the overall production of mRNA and protein along with changes in metabolic behavior with two different oxidative phosphorylation inhibitors. Taken together, we provided a comprehensive mathematical framework of CFPS metabolism that could be used to identify strategies for the improvement of CFPS productivity, yield and efficiency.
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 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.
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 Bioinformatics written by Dev Bukhsh Singh and published by Academic Press. This book was released on 2021-10-21 with total page 512 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioinformatics: Methods and Applications provides a thorough and detailed description of principles, methods, and applications of bioinformatics in different areas of life sciences. It presents a compendium of many important topics of current advanced research and basic principles/approaches easily applicable to diverse research settings. The content encompasses topics such as biological databases, sequence analysis, genome assembly, RNA sequence data analysis, drug design, and structural and functional analysis of proteins. In addition, it discusses computational approaches for vaccine design, systems biology and big data analysis, and machine learning in bioinformatics.It is a valuable source for bioinformaticians, computer biologists, and members of biomedical field who needs to learn bioinformatics approaches to apply to their research and lab activities. - Covers basic and more advanced developments of bioinformatics with a diverse and interdisciplinary approach to fulfill the needs of readers from different backgrounds - Explains in a practical way how to decode complex biological problems using computational approaches and resources - Brings case studies, real-world examples and several protocols to guide the readers with a problem-solving approach
Download or read book Biosystems Engineering I written by Christoph Wittmann and published by Springer Science & Business Media. This book was released on 2010-09-03 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt: -Integration of Systems Biology with Bioprocess Engineering: L-Threonine Production by Systems Metabolic Engineering of Escherichia Coli, By Sang Yup Lee and Jin Hwan Park; -Analysis and Engineering of Metabolic Pathway Fluxes in Corynebacterium glutamicum, By Christoph Wittmann; -Systems Biology of Industrial Microorganisms, Marta Papini, Margarita Salazar, and Jens Nielsen; -De Novo Metabolic Engineering and the Promise of Synthetic DNA, By Daniel Klein-Marcuschamer, Vikramaditya G. Yadav, Adel Ghaderi, and Gregory N. Stephanopoulos; -Systems Biology of Recombinant Protein Production in Bacillus megaterium, Rebekka Biedendieck, Boyke Bunk, Tobias Fürich, Ezequiel Franco-Lara, Martina Jahn, and Dieter Jahn; -Extending Synthetic Routes for Oligosaccharides by Enzyme, Substrate and Reaction Engineering; By Jürgen Seibel, Hans-Joachim Jördening, and Klaus Buchholz; -Regeneration of Nicotinamide Coenzymes: Principles and Applications for the Synthesis of Chiral Compounds; By Andrea Weckbecker, Harald Gröger, and Werner Hummel;
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 2016-02-23 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 Metabolic Network Based Analyses of Omics Data written by A. Ercument Cicek and published by . This book was released on 2013 with total page 178 pages. Available in PDF, EPUB and Kindle. Book excerpt: Omics studies have shed light to human metabolism for decades, with the advancement of high throughput screening technologies. Each domain provides traces of information that may lead to solving mechanisms of complex diseases. However the number of candidate hypotheses is usually exponential with respect to the number of variables. Thus, there is a need for algorithms that explore the search space efficiently while reasoning in a biologically sound way. Biological networks have been used as a roadmap to investigate the interplays between the variables. As they provide apriori knowledge on the biological problem at hand, they enable algorithms to prune the search space and consider only related variables together. In this thesis, we describe algorithms and systems that use metabolic networks in order to analyze omics data. First, we address the problem of predicting changes in the metabolite levels based on a condition, such as a genetic perturbation. We propose ADEMA, An Algorithm to Determine Expected Metabolite Level Changes Using Mutual Information. ADEMA detects related metabolites in the metabolic network, and then using mutual information, it calculates the expected metabolite level changes based on the given condition. Next, we briefly describe SMDA Algorithm (Steady-state Metabolic Network Dynamics Analysis Algorithm). The algorithm starts by classifying each measurement as low, normal or high based on the concentrations published in the literature. However, usually there is no consensus on what is normal and what is not, which leads algorithm to end up with an empty result set. We propose semi-automated approaches to locate and fix misclassifications due to such discrepancies. Then, we describe MIRA, Mutual Information-based Reporter Algorithm. MIRA{8217}s goal is to find the metabolites around which transcriptional regulation is centered, based on the transcriptome and the metabolic network of the organism. MIRA is an improvement over the current z-score based reporter algorithm, as it considers expressions of multiple genes at a time. Finally, we describe ReconModels.org, which is an online database of published genome-scale reconstructed metabolic networks of the organisms with browsing, querying, visualizing, edit and comparing metabolic networks.
Download or read book Metabolic Network Reconstruction and Modeling written by Marco Fondi and published by Humana Press. This book was released on 2018-08-30 with total page 410 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume looks at the latest methodologies used to study cellular metabolism with in silico approaches. The chapters in this book are divided into 3 parts: part I discusses tools and methods used for metabolic reconstructions and basic constraint-based metabolic modeling (CBMM); Part II explores protocols for the generation of experimental data for metabolic reconstruction and modeling, including transcriptomics, proteomics, and mutant generations; and Part III cover advanced techniques for quantitative modeling of cellular metabolism, including dynamic Flux Balance Analysis and multi-objective optimization. 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 thorough, Metabolic Network Reconstruction and Modeling: Methods and Protocols is a valuable resource for qualified investigators studying cellular metabolism, and novice researchers who want to start working with CBMM.
Download or read book Microbial Growth Dynamics written by Robert K. Poole and published by . This book was released on 1990 with total page 192 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume records a conference on microbial growth and population dynamics held in honour of the retirement of Professor S. John Pirt. After a general overview, it discusses mycelial growth, kinetics of secondary metabolite production and many other views.
Download or read book Advances in Oscillating Reactions written by Zeljko Dimitrije Cupic and published by Frontiers Media SA. This book was released on 2021-06-29 with total page 133 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Systems Modeling Approaches and Applications Volume II written by Alberto Jesus Martin and published by Frontiers Media SA. This book was released on 2022-11-25 with total page 333 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book A First Course in Systems Biology written by Eberhard Voit and published by Garland Science. This book was released on 2017-09-05 with total page 480 pages. Available in PDF, EPUB and Kindle. Book excerpt: A First Course in Systems Biology is an introduction for advanced undergraduate and graduate students to the growing field of systems biology. Its main focus is the development of computational models and their applications to diverse biological systems. The book begins with the fundamentals of modeling, then reviews features of the molecular inventories that bring biological systems to life and discusses case studies that represent some of the frontiers in systems biology and synthetic biology. In this way, it provides the reader with a comprehensive background and access to methods for executing standard systems biology tasks, understanding the modern literature, and launching into specialized courses or projects that address biological questions using theoretical and computational means. New topics in this edition include: default modules for model design, limit cycles and chaos, parameter estimation in Excel, model representations of gene regulation through transcription factors, derivation of the Michaelis-Menten rate law from the original conceptual model, different types of inhibition, hysteresis, a model of differentiation, system adaptation to persistent signals, nonlinear nullclines, PBPK models, and elementary modes. 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 large-scale, often open-ended questions for further reflection.
