Development of Metabolic Flux Analysis and Antisense RNA Technologies as Tools for the Metabolic Engineering of Clostridium Acetobutylicum ATCC 824 PDF Download
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Author: Ruchir Pradip Desai
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Next, the improved model was used to analyze fermentation data from several strains of C. acetobutylicum ATCC 824. Metabolic flux analysis revealed previously obscured roles for the acid formation pathways. The acetate formation pathway supported significant fluxes throughout the stationary phase while the butyrate formation pathway was found to uptake butyrate. Metabolic flux analysis of a butyrate kinase knockout strain revealed that the enhanced solvent production characteristic was due to early induction of butanol formation as opposed to substantially higher butanol formation fluxes. Analysis also revealed enhanced uptake of acetate and substantially reduced butyrate formation and uptake.
Author: Ruchir Pradip Desai
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
Next, the improved model was used to analyze fermentation data from several strains of C. acetobutylicum ATCC 824. Metabolic flux analysis revealed previously obscured roles for the acid formation pathways. The acetate formation pathway supported significant fluxes throughout the stationary phase while the butyrate formation pathway was found to uptake butyrate. Metabolic flux analysis of a butyrate kinase knockout strain revealed that the enhanced solvent production characteristic was due to early induction of butanol formation as opposed to substantially higher butanol formation fluxes. Analysis also revealed enhanced uptake of acetate and substantially reduced butyrate formation and uptake.
Author: Christina Smolke
Publisher: CRC Press
ISBN: 142007766X
Category : Medical
Languages : en
Pages : 570
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Book Description
This second volume of the Metabolic Pathway Engineering Handbook delves into evolutionary tools and gene expression tools for metabolic pathway engineering. It covers applications of emerging technologies including recent research genome-wide technologies, DNA and phenotypic microarrays, and proteomics tools for experimentally determining flux thro
Author: Sang Yup Lee
Publisher: John Wiley & Sons
ISBN: 352782345X
Category : Science
Languages : en
Pages : 1075
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Book Description
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.
Author:
Publisher:
ISBN:
Category : Dissertations, Academic
Languages : en
Pages : 898
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Author: Jason L. Walther
Publisher:
ISBN:
Category :
Languages : en
Pages : 260
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Book Description
Many current and future applications of biological engineering hinge on our ability to measure, understand, and manipulate metabolism. Many diseases for which we seek cures are metabolic in nature. Small-molecule biomanufacturing almost always involves metabolic engineering. Biofuels, a current topic of great interest, is essentially a metabolic problem. Even bioprocesses that involve complex products, such as enzyme or antibody manufacturing, still rely on a healthy and optimal metabolism and can benefit from a greater understanding therein. A cell's metabolic flux distribution has been proposed to be one of the most solid and meaningful indicators and descriptors of metabolism. Metabolic fluxes represent integrative information and are a function of gene expression, translation, post-translational modifications, and protein-metabolite interactions. Metabolic flux analysis (MFA) is a powerful method for determining these flux distribution through a cellular reaction network. However, MFA has experimental limitations (most notably, a requirement for isotopic steady state) that restrict the scope of biological contexts in which it can be applied. Nonstationary metabolic flux analysis (NMFA) has recently emerged as a combined computational and experimental method that improves upon MFA with the capacity to estimate fluxes even during periods of isotopic transience in metabolism, allowing flux analysis to be applied in a broader range of experimental settings. In this thesis, we have developed and applied robust and efficient NMFA tools and techniques and applied them to understand various cellular physiologies. We built a software package (MetranCL) that combines the elementary metabolite unit (EMU) framework, a new network decomposition strategy termed block decoupling, and a customized differential equation solver. MetranCL performs flux estimations as much as 5000 times faster than the previous state-of-the-art NMFA methods, opening entirely new types of biological systems to the possibility of flux analysis. We applied MetranCL to a simulated large network representing E. coli metabolism and were able to successfully estimate reaction fluxes and metabolite concentrations and their 95% confidence intervals. We investigated a number of different experimental arrangements of measurement time points, and found that in general, measurements earlier in isotopic transience were more sensitive to network parameters and yielded more precise confidence intervals. We also observed that the addition of concentration measurements significantly increased estimate quality. We next used NMFA to compute fluxes from actual experimental measurements taken from brown adipocytes. We designed an appropriate network and successfully fitted simulated measurements to actual measurements (taken at 2, 4, and 6 hours after introducing tracer). A flux distribution was obtained that indicated a high level of pyruvate cycling, a low flux through the TCA cycle, and high lactate production. We developed computational and experimental tools to assist with the design of flux analysis experiments. We built a simulator that calculates the effect of different tracers on flux estimate precision and used it to study a range of different glucose and glutamine tracers in carcinoma metabolism. Of all the stand-alone tracers we tested, we found that [1,2- 13C2]glucose estimated flux distributions with the greatest precision. We built upon this work by constructing an evolutionary algorithm to generate optimal tracer mixtures for different organisms and their respective metabolisms. We applied this algorithm to the same cancer network and found optimal tracer mixtures for the system. We ran experiments with an optimized tracer mixture and compared it to results from typical tracers and saw significant improvements in flux precision. Finally, we applied these methods and tools to evaluate and understand the flux distribution and metabolism of a lipid-overproducing strain of the yeast Yarrowia lipolytica. Since NMFA of this organism required metabolite extracts taken at very precise and proximate time points, we built a rapid sampling apparatus to draw and quench samples of Yarrowia cell culture with a one-second time step. After conducting NMFA under different environmental conditions and at different stages of growth, we found that lipid synthesis fluxes increased when aeration of the cell culture was increased, and observed several corresponding changes in the intracellular flux distribution explaining the overall change in metabolism that occurs with this shift in environmental conditions. In particular, we found that Yarrowia primarily powers lipid production by regulating flux through the pentose phosphate pathway.
Author: Jens O. Krömer
Publisher: Humana
ISBN: 9781493941599
Category : Science
Languages : en
Pages : 0
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Book Description
Metabolic Flux Analysis: Methods and Protocols opens up the field of metabolic flux analysis to those who want to start a new flux analysis project but are overwhelmed by the complexity of the approach. Metabolic flux analysis emerged from the current limitation for the prediction of metabolic fluxes from a measured inventory of the cell. Divided into convenient thematic parts, topics in this essential volume include the fundamental characteristics of the underlying networks, the application of quantitative metabolite data and thermodynamic principles to constrain the solution space for flux balance analysis (FBA), the experimental toolbox to conduct different types of flux analysis experiments, the processing of data from 13C experiments and three chapters that summarize some recent key findings. Written in the 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 protocols and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Metabolic Flux Analysis: Methods and Protocols presents protocols that cover a range of relevant organisms currently used in the field, providing a solid basis to anybody interested in the field of metabolic flux analysis.
Author: Christoph Wittmann
Publisher: Springer Science & Business Media
ISBN: 9400745346
Category : Medical
Languages : en
Pages : 391
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Book Description
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.
Author: Christina Smolke
Publisher: CRC Press
ISBN: 9780849339233
Category : Science
Languages : en
Pages : 1259
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Book Description
Christina Smolke, who recently developed a novel way to churn out large quantities of drugs from genetically modified brewer’s yeast, is regarded as one of the most brilliant minds in biomedical engineering. In this handbook, she brings together pioneering scientists from dozens of disciplines to provide a complete record of accomplishment in metabolic pathway engineering. With a wealth of cutting edge research and analysis, this work also serves as an invaluable resource for those seeking to add their own contributions. Organized by topic, this 3000 page reference is available as two volumes that can be purchased individually or as a set. Fundamentals The first volume provides an overview of metabolic pathway engineering with a look towards the future. It discusses cellular metabolism, including transport processes inside the cell and energy generating reactions, as well as rare metabolic conversions. This volume also explores balances and reaction models, the regulation of metabolic pathways, and genome scale and multiscale modeling tools. It also covers developing appropriate hosts for metabolic engineering including the use of Escherichia coli, yeast, Bacillus subtilis, Streptomyces, filamentous fungi, annd mammalian cells using cell culture. Tool and Applications The second volume delves into evolutionary tools, including those associated with gene expression for metabolic pathway engineering. It covers applications of emerging technologies, including research on genome-wide technologies, DNA and phenotypic microarrays, and proteomics tools for experimentally determining flux through pathways. It also evaluates emerging applications for producing fine chemicals, drugs, and alternative fuels.
Author: Christoph Wittmann
Publisher: John Wiley & Sons
ISBN: 352734179X
Category : Science
Languages : en
Pages : 789
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Book Description
The latest volume in the Advanced Biotechnology series provides an overview of the main production hosts and platform organisms used today as well as promising future cell factories in a two volume book. Alongside describing tools for genetic and metabolic engineering for strain improvement, the authors also impart topical information on computational tools, safety aspects and industrial-scale production. Following an introduction to general concepts, historical developments and future technologies, the text goes on to cover multi-purpose bacterial cell factories, including those organisms that exploit anaerobic biosynthetic power. Further chapters deal with microbes used for the production of high-value natural compounds and those obtained from alternative raw material sources, concluding with eukaryotic workhorses.
Author: Peter Duerre
Publisher: CRC Press
ISBN: 113550198X
Category : Medical
Languages : en
Pages : 1451
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Book Description
Clostridia is one of the largest bacterial genera with an enormous potential for biotechnical and medical applications. Despite growing scientific, medical, and industrial interest, information on basic methods, biochemical fundamentals, clinical practice, industrial applications, and novel developments remains scattered in a variety of research ar
