Modeling and Simulation of Enzyme Controlled Metabolic Networks Using Optimization Based Methods PDF Download

Author: Henning Lindhorst
Publisher:
ISBN:
Category :
Languages : en
Pages :

View

Book Description

Author: Costas D. Maranas
Publisher: John Wiley & Sons
ISBN: 1119028493
Category : Science
Languages : en
Pages : 278

View

Book Description
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

Author: Peter Mulquiney
Publisher: CRC Press
ISBN: 0203503937
Category : Mathematics
Languages : en
Pages : 327

View

Book Description
With the advent of sophisticated general programming environments like Mathematica, the task of developing new models of metabolism and visualizing their responses has become accessible to students of biochemistry and the life sciences in general. Modelling Metabolism with Mathematica presents the approaches, methods, tools, and algorithms for mode

Author: Daniel Machado
Publisher: Frontiers Media SA
ISBN: 2889197549
Category : Biology (General)
Languages : en
Pages : 117

View

Book Description
Mathematical and computational models play an essential role in understanding the cellular metabolism. They are used as platforms to integrate current knowledge on a biological system and to systematically test and predict the effect of manipulations to such systems. The recent advances in genome sequencing techniques have facilitated the reconstruction of genome-scale metabolic networks for a wide variety of organisms from microbes to human cells. These models have been successfully used in multiple biotechnological applications. Despite these advancements, modeling cellular metabolism still presents many challenges. The aim of this Research Topic is not only to expose and consolidate the state-of-the-art in metabolic modeling approaches, but also to push this frontier beyond the current edge through the introduction of innovative solutions. The articles presented in this e-book address some of the main challenges in the field, including the integration of different modeling formalisms, the integration of heterogeneous data sources into metabolic models, explicit representation of other biological processes during phenotype simulation, and standardization efforts in the representation of metabolic models and simulation results.

Author: Alberto Jesus Martin
Publisher: Frontiers Media SA
ISBN: 2832507123
Category : Science
Languages : en
Pages : 333

View

Book Description

Author: David Christopher Flowers
Publisher:
ISBN:
Category :
Languages : en
Pages : 105

View

Book Description
Recently, ensemble modeling was applied to metabolic networks for the sake of predicting the effects of genetic manipulations on the observed phenotype of the system. The ensemble of models is generated from experimental wild-type flux data and screened using phenotypic data from gene overexpression and knockout experiments, leaving predictive models. The need for data from multiple genetic perturbation experiments is an inherent limitation to this approach. In this investigation, ensemble modeling is used alongside elementary mode analysis to attempt to predict those enzymatic perturbations that are most likely to result in an increase in a target yield and a target flux when only the wild-type flux distribution is known. Elementary mode analysis indicates the maximum theoretical yield and its associated steady-state flux distribution(s), and the minimal cut set knockouts are determined that eliminate all but the highest-yield elementary modes. These knockouts and other perturbations are simulated using all of the ensemble models, and the distributions of predicted fluxes and yields over the models are compared to elucidate which reactions and metabolites most likely limit the target yield and flux. Additionally, a systematic method is developed to simultaneously identify multiple reactions that are responsible for bottlenecks after the minimal cut set knockouts are performed. These methods are applied to a metabolic network that models 3-deoxy-D-arabinoheptulosonate-7-phosphate (DAHP) production in E. coli. Results show that pyruvate accumulation due to glucose uptake and erythrose-4-phosphate (E4P) shortages resulting from the slow reaction rate of transketolase (Tkt) limit DAHP production. These results are consistent with published data, indicating that a detailed understanding of metabolic networks can be obtained with minimal experimental data. Additionally, the systematic method identifies four enzymes (Tkt, Tal, Pps, and AroG) that, when overexpressed experimentally, increase yield to nearly the maximum theoretical limit. Systematic analysis of a toy network also correctly identifies the post-MCS overexpression that results in the largest increases in yield and absolute fluxes. These results indicates that wild-type steady-state flux data can be used to accurately identify enzyme perturbation targets for increasing yield and target flux values.

Author:
Publisher: Elsevier
ISBN: 0128163968
Category : Science
Languages : en
Pages : 2444

View

Book Description
Comprehensive Foodomics, Three Volume Set offers a definitive collection of over 150 articles that provide researchers with innovative answers to crucial questions relating to food quality, safety and its vital and complex links to our health. Topics covered include transcriptomics, proteomics, metabolomics, genomics, green foodomics, epigenetics and noncoding RNA, food safety, food bioactivity and health, food quality and traceability, data treatment and systems biology. Logically structured into 10 focused sections, each article is authored by world leading scientists who cover the whole breadth of Omics and related technologies, including the latest advances and applications. By bringing all this information together in an easily navigable reference, food scientists and nutritionists in both academia and industry will find it the perfect, modern day compendium for frequent reference. List of sections and Section Editors: Genomics - Olivia McAuliffe, Dept of Food Biosciences, Moorepark, Fermoy, Co. Cork, Ireland Epigenetics & Noncoding RNA - Juan Cui, Department of Computer Science & Engineering, University of Nebraska-Lincoln, Lincoln, NE Transcriptomics - Robert Henry, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Australia Proteomics - Jens Brockmeyer, Institute of Biochemistry and Technical Biochemistry, University Stuttgart, Germany Metabolomics - Philippe Schmitt-Kopplin, Research Unit Analytical BioGeoChemistry, Neuherberg, Germany Omics data treatment, System Biology and Foodomics - Carlos Leon Canseco, Visiting Professor, Biomedical Engineering, Universidad Carlos III de Madrid Green Foodomics - Elena Ibanez, Foodomics Lab, CIAL, CSIC, Madrid, Spain Food safety and Foodomics - Djuro Josic, Professor Medicine (Research) Warren Alpert Medical School, Brown University, Providence, RI, USA & Sandra Kraljevic Pavelic, University of Rijeka, Department of Biotechnology, Rijeka, Croatia Food Quality, Traceability and Foodomics - Daniel Cozzolino, Centre for Nutrition and Food Sciences, The University of Queensland, Queensland, Australia Food Bioactivity, Health and Foodomics - Miguel Herrero, Department of Bioactivity and Food Analysis, Foodomics Lab, CIAL, CSIC, Madrid, Spain Brings all relevant foodomics information together in one place, offering readers a ‘one-stop,’ comprehensive resource for access to a wealth of information Includes articles written by academics and practitioners from various fields and regions Provides an ideal resource for students, researchers and professionals who need to find relevant information quickly and easily Includes content from high quality authors from across the globe

Author: Irwin H. Segel
Publisher:
ISBN: 9788126548156
Category : Enzyme kinetics
Languages : en
Pages : 957

View

Book Description

Author: Marco Fondi
Publisher: Humana Press
ISBN: 9781493985111
Category :
Languages : en
Pages : 410

View

Book Description
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.

Author: Reinhart Heinrich
Publisher: Springer Science & Business Media
ISBN: 1461311616
Category : Science
Languages : en
Pages : 387

View

Book Description
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.