Author: Marco Fondi
Publisher: Humana Press
ISBN: 9781493985111
Category :
Languages : en
Pages : 410
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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: National Academies of Sciences, Engineering, and Medicine
Publisher: National Academies Press
ISBN: 0309458390
Category : Science
Languages : en
Pages : 133
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Book Description
The 21st century has witnessed a complete revolution in the understanding and description of bacteria in eco- systems and microbial assemblages, and how they are regulated by complex interactions among microbes, hosts, and environments. The human organism is no longer considered a monolithic assembly of tissues, but is instead a true ecosystem composed of human cells, bacteria, fungi, algae, and viruses. As such, humans are not unlike other complex ecosystems containing microbial assemblages observed in the marine and earth environments. They all share a basic functional principle: Chemical communication is the universal language that allows such groups to properly function together. These chemical networks regulate interactions like metabolic exchange, antibiosis and symbiosis, and communication. The National Academies of Sciences, Engineering, and Medicine's Chemical Sciences Roundtable organized a series of four seminars in the autumn of 2016 to explore the current advances, opportunities, and challenges toward unveiling this "chemical dark matter" and its role in the regulation and function of different ecosystems. The first three focused on specific ecosystemsâ€"earth, marine, and humanâ€"and the last on all microbiome systems. This publication summarizes the presentations and discussions from the seminars.
Author: Bernhard Palsson
Publisher: Cambridge University Press
ISBN: 1107038855
Category : Medical
Languages : en
Pages : 551
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Book Description
The first comprehensive single-authored textbook on genome-scale models and the bottom-up approach to systems biology.
Author: Daniel Craig Zielinski
Publisher:
ISBN: 9781321853209
Category :
Languages : en
Pages : 120
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Book Description
Understanding the behavior of complex biochemical networks is the primary goal of systems biology. This task is often addressed through the generation of large data sets such as measurements of biological components like mRNA transcripts, proteins, and metabolites. Although these methods have become increasingly accurate and comprehensive at measuring the state of the system, uncovering the function of the system then becomes a problem of analysis to extract an understanding of the system from the data. A key challenge in analyzing biological data sets is that determining the function of the system depends on a knowledge of the relationship between the components of the system. These relationships can be captured by grouping variables by known associations, such as pathways, or by explicitly modeling their relationships mathematically. Metabolic networks are particularly primed for both of these approaches, because metabolic pathways are well-defined by network topology and the equation governing their function, the mass balance equation, is well understood. In this thesis, the capabilities of metabolic networks to interpret biological data are advanced through the development and application of models of increasing levels of detail. First, pathways systematically derived from a global human metabolic network reconstruction are used to identify metabolic perturbations tied to drug side effects from in vitro drug-treated gene expression data. Second, steady-state flux modeling of a core human metabolic network is used to identify factors underlying two hallmarks of cancer metabolism: the Warburg effect and glutamine addiction. Finally, the concept of a metabolic network reconstruction is extended by the definition of detailed enzyme kinetic mechanisms within E. coli central metabolism, integrating multiple data sets mechanistically to calculate dynamic functional states of enzymes. This work furthers the use of metabolic networks in analyzing complex biological data sets, showcasing the utility of these networks in addressing practical questions in systems biology using methods of increasing mechanistic resolution.
Author: Isabel Sá-Correia
Publisher: Springer
ISBN: 3030130355
Category : Science
Languages : en
Pages : 242
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Book Description
This book discusses genome-based strategies to provide a holistic understanding of yeasts in Human Health and as model organisms in basic research or industrial production. Using numerous Saccharomyces cerevisiae strains and various non-conventional yeast species isolated from diverse origins, it describes essential biological processes, the biotechnological exploitation of yeast and pathogenesis control. It also demonstrates how functional and comparative genomics and the development of genome engineering tools are used in modern yeast research. The use of yeasts as experimental eukaryotic models increasingly gained prominence when several Nobel Prizes in Physiology/Medicine and Chemistry were awarded for innovative research, using yeast strains to elucidate molecular mechanisms in a wide range of human physiological processes and diseases, such as autophagy, cell cycle regulation and telomerase activity. This book offers useful insights for scientists in yeast research, clinical scientists working with yeast infectious models and for industrial researchers using applied microbiology.
Author: Nicolas Loira
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Book Description
Understanding living organisms has been a quest for a long time. Since the advancesof the last centuries, we have arrived to a point where massive quantities of data andinformation are constantly generated. Even though most of the work so far has focusedon generating a parts catalog of biological elements, only recently have we seena coordinated effort to discover the networks of relationships between those parts. Notonly are we trying to understand these networks, but also the way in which, from theirconnections, emerge biological functions.This work focuses on the modeling and exploitation of one of those networks:metabolism. A metabolic network is a net of interconnected biochemical reactionsthat occur inside, or in the proximity of, a living cell. A new method of discovery, orreconstruction, of metabolic networks is proposed in this work, with special emphasison eukaryote organisms.This new method is divided in two parts: a novel approach to reconstruct metabolicmodels, based on instantiation of elements of an existing scaffold model, and a novelmethod of assigning gene associations to reactions. This two-parts method allows reconstructionsthat are beyond the capacity of the state-of-the-art methods, enablingthe reconstruction of metabolic models of eukaryotes, and providing a detailed relationshipbetween its reactions and genes, knowledge that is crucial for biotechnologicalapplications.The reconstruction methods developed for the present work were complementedwith an iterative workflow of model edition, verification and improvement. This workflowwas implemented as a software package, called Pathtastic.As a case study of the method developed and implemented in the present work,we reconstructed the metabolic network of the oleaginous yeast Yarrowia lipolytica,known as food contaminant and used for bioremediation and as a cell factory. A draftversion of the model was generated using Pathtastic, and further improved by manualcuration, working closely with specialists in that species. Experimental data, obtainedfrom the literature, were used to assess the quality of the produced model.Both, the method of reconstruction in eukaryotes, and the reconstructed model ofY. lipolytica can be useful for their respective research communities, the former as astep towards better automatic reconstructions of metabolic networks, and the latteras a support for research, a tool in biotechnological applications and a gold standardfor future reconstructions.
Author: Institute of Medicine
Publisher: National Academies Press
ISBN: 0309219396
Category : Science
Languages : en
Pages : 570
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Book Description
Many potential applications of synthetic and systems biology are relevant to the challenges associated with the detection, surveillance, and responses to emerging and re-emerging infectious diseases. On March 14 and 15, 2011, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to explore the current state of the science of synthetic biology, including its dependency on systems biology; discussed the different approaches that scientists are taking to engineer, or reengineer, biological systems; and discussed how the tools and approaches of synthetic and systems biology were being applied to mitigate the risks associated with emerging infectious diseases. The Science and Applications of Synthetic and Systems Biology is organized into sections as a topic-by-topic distillation of the presentations and discussions that took place at the workshop. Its purpose is to present information from relevant experience, to delineate a range of pivotal issues and their respective challenges, and to offer differing perspectives on the topic as discussed and described by the workshop participants. This report also includes a collection of individually authored papers and commentary.
Author: Costas D. Maranas
Publisher: John Wiley & Sons
ISBN: 1119028493
Category : Science
Languages : en
Pages : 278
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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: J. Philip Grime
Publisher: John Wiley & Sons
ISBN: 1118223276
Category : Science
Languages : en
Pages : 362
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Book Description
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.
Author: Bernhard Ø. Palsson
Publisher: Cambridge University Press
ISBN: 1139448943
Category : Science
Languages : en
Pages : 287
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Book Description
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.
