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Bacterial Cellular Metabolic Systems

Bacterial Cellular Metabolic Systems
  • Author : K. Shimizu
  • Publisher :Unknown
  • Release Date :2013-03-26
  • Total pages :496
  • ISBN : 9781908818201
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Summary : The metabolic regulation of a cell system is of critical importance in systems biology, and a robust model of these mechanisms is essential in predicting the effects on the metabolism of both the culture environment and the knockout of specific genes. Bacterial cellular metabolic systems focuses on this highly topical subject in relation to culture environment and provides a detailed analysis from gene level to metabolic level regulation, as well as offering a discussion of the most recent modelling approaches. The book begins with an introduction to metabolic mechanisms and to the metabolic regulation of a cell, before moving on to discussing the action of global regulators in response to a specific culture environment. The second half of the book examines conventional flux balance analysis and its applications, 13C-metabolic flux analysis, and the effect of a specific gene knockout on the metabolism. Comprehensive account of metabolic regulation via global regulators in response to changes in the culture environment Basic formulation of 13C-metabolic flux analysis based on 13C-labelling experiments Systems biology approach for the modelling and computer simulation of the main metabolic pathways of a cell system

Bacterial Metabolism

Bacterial Metabolism
  • Author : H. W. Doelle
  • Publisher :Unknown
  • Release Date :2014-06-28
  • Total pages :752
  • ISBN : 9781483272375
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Summary : Bacterial Metabolism, Second Edition describes microbial systematics and microbial chemistry and focuses on catabolic events. This book deals with the progress made in bacterial metabolism that includes data on regulatory mechanisms; comparison of bacterial growth kinetics with enzyme kinetics; aerobic amino acid catabolism; and the glucose transport mechanism. This text also emphasizes the development of photosynthetic phosphorylation in the different bacterial families. This book explains anaerobic respiration and carbohydrate metabolism—glucose, fructose, lactose, mannose, allose, and sorbitol. This text then describes aerobic respiration including the "Nitroso" and "Nitro" groups of genera, and the Knallgas bacteria, which use the reaction between molecular hydrogen and molecular oxygen as their source of energy. This book also explains the microbial transformation of iron as caused by either specific organisms (e.g. Ferrobacillus ferrooxidans) or nonspecific organisms. This selection also explains the process of fermentation by Enterobacteriaceae, lactic acid bacteria, and proteolytic clostridia. This text can be valuable for microchemists, microbiologists, students, and academicians whose disciplines are in biological chemistry and cellular biology.

Bacterial Metabolism

Bacterial Metabolism
  • Author : Gerhard Gottschalk
  • Publisher :Unknown
  • Release Date :2012-12-06
  • Total pages :359
  • ISBN : 9781461210726
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Summary : This concise yet comprehensive text surveys the field of bacterial metabolism in terms useful to students and researchers. Emphasis is on those metabolic reactions occurring only in bacteria. Thus, the book describes in detail the energy metabolism of the various groups of bacteria. In addition, it examines pathways used by bacteria for the degradation of organic compounds, the synthesis of cellular constituents, the regulation of bacterial metabolism and the fixation of molecular nitrogen.

Engineering Microbial Metabolism For Chemical Synthesis: Reviews And Perspectives

Engineering Microbial Metabolism For Chemical Synthesis: Reviews And Perspectives
  • Author : Yan Yajun
  • Publisher :Unknown
  • Release Date :2017-12-26
  • Total pages :272
  • ISBN : 9781786344311
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Summary : Microbial metabolism refers to how microbes obtain energy and nutrients needed to live and reproduce. Its uses in chemical synthesis are multiple, and, when engineered, can provide reliable and reproducible reactions for application in industrial or biogeochemical processes. This book provides expert reviews and perspectives on how to engineer microbial metabolism for chemical synthesis. Major metabolic pathways or networks in microbial systems, including glycolysis, citric acid and photosynthesis, are briefly summarized. Following this, the metabolic engineering efforts of extending these pathways and networks for the biosynthesis of various chemicals are reviewed with the emphasis on the biochemical reactions and engineering strategies. The potential of these pathways for further metabolic engineering are also discussed. From graduate to professional level, cellular metabolism and metabolic engineering applications are introduced to the readers gradually and systematically, making it perfect for students, researchers and practitioners of chemistry, biochemistry and metabolic engineering. Contents: Glycolysis and Its Metabolic Engineering Applications (Jian Wang and Yajun Yan)Citric Acid Cycle and Its Metabolic Engineering Applications (Jia Wang and Xiaolin Shen)Amino Acid Biosynthesis and Its Metabolic Engineering Applications (Yi-Xin Huo)Fatty Acid Biosynthesis and Its Metabolic Engineering Applications (Yi Liu and Tiangang Liu)Photosynthesis and Its Metabolic Engineering Applications (Jason T Ku and Ethan I Lan)Pentose Phosphate Pathway and Its Metabolic Engineering Applications (Ying Wang and Chun Li)Mevalonate/2-Methylerythritol 4-Phosphate Pathways and Their Metabolic Engineering Applications (Xinxiao Sun and Qipeng Yuan)Xylose Metabolism and Its Metabolic Engineering Applications (Maria K McClintock and Kechun Zhang)Engineering Metabolism for the Synthesis of Polyhydroxyalkanoate Biopolymers (Guo-Qiang Chen and Xiao-Ran Jiang) Readership: Graduate students, researchers and practitioners of chemistry, biochemistry and metabolic engineering. Keywords: Microbial Metabolism;Chemical Synthesis;Biosynthesis;Biochemical Reactions;Photosynthesis;Metabolic Engineering;Cellular Metabolism;GlycolysisReview:0

Prokaryotic Metabolism and Physiology

Prokaryotic Metabolism and Physiology
  • Author : Byung Hong Kim,Geoffrey Michael Gadd
  • Publisher :Unknown
  • Release Date :2019-05-16
  • Total pages :510
  • ISBN : 9781107171732
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Summary : Extensive and up-to-date review of key metabolic processes in bacteria and archaea and how metabolism is regulated under various conditions.

Sequence — Evolution — Function

Sequence — Evolution — Function
  • Author : Eugene V. Koonin,Michael Galperin
  • Publisher :Unknown
  • Release Date :2013-06-29
  • Total pages :462
  • ISBN : 9781475737837
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Summary : Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.

Systems and Synthetic Metabolic Engineering

Systems and Synthetic Metabolic Engineering
  • Author : Yanfeng Liu,Guocheng Du,Long Liu
  • Publisher :Unknown
  • Release Date :2020-07-10
  • Total pages :294
  • ISBN : 9780128217528
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Summary : Systems and Synthetic Metabolic Engineering provides an overview of the development of metabolic engineering within medicine that is fueled by systems and synthetic biology. These newly developed, successful strategies of metabolic engineering guide the audience on how to propose and test proper strategies for metabolic engineering research. In addition to introductory, regulatory and challenges in the field, the book also covers dynamic control and autonomous regulation to control cell metabolism, along with computational modeling and industrial applications. The book is written by leaders in the field, making it ideal for synthetic biologists, researchers, students and anyone working in this area. Discusses the current progress of metabolic engineering, focusing on systems biology and synthetic biology Covers introductory, regulatory, strategies, production and challenges in the field Written technically for synthetic biologists, researchers, students, industrialists, policymakers and stakeholders

Bacterial Persistence

Bacterial Persistence
  • Author : Jan Michiels,Maarten Fauvart
  • Publisher :Unknown
  • Release Date :2016-08-23
  • Total pages :244
  • ISBN : 1493949047
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Summary : This volume presents a comprehensive collection of methods that have been instrumental to the current understanding of bacterial persisters. Chapters in the book cover topics ranging from general methods for measuring persister levels in Escherichia coli cultures, protocols for the determination of the persister subpopulation in Candida albicans, quantitative measurements of Type I and Type II persisters using ScanLag, to in vitro and in vivo models for the study of the intracellular activity of antibiotics. 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. Authoritative and cutting-edge, Bacterial Persistence: Methods and Protocols brings together the most respected researchers in bacterial persistence whose studies will remain vital to understanding this field for many years to come.

Bacterial Physiology and Metabolism

Bacterial Physiology and Metabolism
  • Author : Byung Hong Kim,Geoffrey Michael Gadd
  • Publisher :Unknown
  • Release Date :2008-02-21
  • Total pages :229
  • ISBN : 113946762X
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Summary : Recent determination of genome sequences for a wide range of bacteria has made in-depth knowledge of prokaryotic metabolic function essential in order to give biochemical, physiological, and ecological meaning to the genomic information. Clearly describing the important metabolic processes that occur in prokaryotes under different conditions and in different environments, this advanced text provides an overview of the key cellular processes that determine bacterial roles in the environment, biotechnology, and human health. Prokaryotic structure is described as well as the means by which nutrients are transported into cells across membranes. Glucose metabolism through glycolysis and the TCA cycle are discussed, as well as other trophic variations found in prokaryotes, including the use of organic compounds, anaerobic fermentation, anaerobic respiratory processes, and photosynthesis. The regulation of metabolism through control of gene expression and control of the activity of enzymes is also covered, as well as survival mechanisms used under starvation conditions.

Metabolism and Bacterial Pathogenesis

Metabolism and Bacterial Pathogenesis
  • Author : Tyrrell Conway,Paul S. Cohen
  • Publisher :Unknown
  • Release Date :2020-07-24
  • Total pages :382
  • ISBN : 9781555818883
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Summary : Groundbreaking thinking on how bacterial metabolism is foundational to pathogenesis For too long, bacterial metabolism and bacterial pathogenesis have been studied as separate entities. However, the scientific community is beginning to realize that not only are bacterial nutrient acquisition and utilization essential for pathogenesis, but that interfering with the pathogen-specific metabolic pathways used during infection can regulate virulence factor expression and might lead to effective breakthroughs in a variety of treatments. Editors Paul Cohen and Tyrrell Conway, who pioneered the use of metabolic mutants in competitive colonization assays, an approach now widely used to investigate the nutrition of pathogens in vivo, are uniquely qualified to advance our knowledge of this integrative field of research. They convened a group of contributors who are breaking new ground in understanding how bacterial metabolism is foundational to pathogenesis to share their expert perspectives and outlook for the future. Beginning with overviews, Metabolism and Bacterial Pathogenesis covers a wide range of diseases and both Gram-positive and -negative bacteria that serve as model systems for in vitro and in vivo investigations intracellular, respiratory, and enteric pathogens pathogen-specific nutrient acquisition in hosts mechanisms of host-driven metabolic adaptation by pathogens metabolic regulation of virulence gene expression Useful for specialists in bacterial pathogenesis and specialists in metabolism as well as molecular biologists, physicians, veterinarians, dentists, graduate and undergraduate students, and laboratory technicians, Metabolism and Bacterial Pathogenesis is also essential reading for scientists studying the microbiome.

Microbial Hydrogen Metabolism

Microbial Hydrogen Metabolism
  • Author : Chris Greening,Eric Boyd
  • Publisher :Unknown
  • Release Date :2020-02-20
  • Total pages :229
  • ISBN : 9782889635405
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Summary :

Molecular Biology of the Cell

Molecular Biology of the Cell
  • Author : Bruce Alberts
  • Publisher :Unknown
  • Release Date :2004
  • Total pages :229
  • ISBN : 0815332181
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Summary :

Size Limits of Very Small Microorganisms

Size Limits of Very Small Microorganisms
  • Author : National Research Council,Division on Engineering and Physical Sciences,Space Studies Board,Commission on Physical Sciences, Mathematics, and Applications,Steering Group for the Workshop on Size Limits of Very Small Microorganisms
  • Publisher :Unknown
  • Release Date :1999-09-13
  • Total pages :164
  • ISBN : 0309172748
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Summary : How small can a free-living organism be? On the surface, this question is straightforward-in principle, the smallest cells can be identified and measured. But understanding what factors determine this lower limit, and addressing the host of other questions that follow on from this knowledge, require a fundamental understanding of the chemistry and ecology of cellular life. The recent report of evidence for life in a martian meteorite and the prospect of searching for biological signatures in intelligently chosen samples from Mars and elsewhere bring a new immediacy to such questions. How do we recognize the morphological or chemical remnants of life in rocks deposited 4 billion years ago on another planet? Are the empirical limits on cell size identified by observation on Earth applicable to life wherever it may occur, or is minimum size a function of the particular chemistry of an individual planetary surface? These questions formed the focus of a workshop on the size limits of very small organisms, organized by the Steering .Group for the Workshop on Size Limits of Very Small Microorganisms and held on October 22 and 23, 1998. Eighteen invited panelists, representing fields ranging from cell biology and molecular genetics to paleontology and mineralogy, joined with an almost equal number of other participants in a wide-ranging exploration of minimum cell size and the challenge of interpreting micro- and nano-scale features of sedimentary rocks found on Earth or elsewhere in the solar system. This document contains the proceedings of that workshop. It includes position papers presented by the individual panelists, arranged by panel, along with a summary, for each of the four sessions, of extensive roundtable discussions that involved the panelists as well as other workshop participants.

Evolution of Metabolic Pathways

Evolution of Metabolic Pathways
  • Author : R. Ibrahim,L. Varin,V. De Luca,John Romeo
  • Publisher :Unknown
  • Release Date :2000-09-15
  • Total pages :480
  • ISBN : 0080531326
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Summary : The past decade has seen major advances in the cloning of genes encoding enzymes of plant secondary metabolism. This has been further enhanced by the recent project on the sequencing of the Arabidopsis genome. These developments provide the molecular genetic basis to address the question of the Evolution of Metabolic Pathways. This volume provides in-depth reviews of our current knowledge on the evolutionary origin of plant secondary metabolites and the enzymes involved in their biosynthesis. The chapters cover five major topics: 1. Role of secondary metabolites in evolution; 2. Evolutionary origins of polyketides and terpenes; 3. Roles of oxidative reactions in the evolution of secondary metabolism; 4. Evolutionary origin of substitution reactions: acylation, glycosylation and methylation; and 5. Biochemistry and molecular biology of brassinosteroids.

Developing an Individual-based Model to Study the Bacterial Denitrification Process

Developing an Individual-based Model to Study the Bacterial Denitrification Process
  • Author : Pablo Alejandro Araujo Granda
  • Publisher :Unknown
  • Release Date :2017
  • Total pages :108
  • ISBN : OCLC:1120512359
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Summary : It is crucial to study the denitrification process driven by bacteria as it is one of the most important environmental processes for several reasons: i) it has an application in the removal of nitrogen (N) from high-N waste materials ii), it is one of the mechanisms to N-fertilizer¿s loss, iii) it contributes to the emissions of gasses with large global warming potential, and iv) it is the mechanism by which the global nitrogen cycle is balanced. Many models have been developed in the framework of continuous models to deal with the complexity of the denitrification process in order to become predictive models, but some of the assumptions contained in them are not realistic enough in those contexts, and also they have their own constraints and limitations. On the other hand, the researchers have paid more attention to the role of microbial activity with the advance of experimental techniques. Discrete models, such as individual-based models (IBMs), can be developed and applied to microbial systems due to the fact that they allow representation of some intracellular characteristics regarding the complexity of the micro-organisms, which constitutes a key advantage of this modelling approach in the study of the different biotechnological processes. The IBM is able to incorporate and accommodate the behaviour of denitrifying bacteria, and investigate their metabolism from different and attractive perspectives. A key factor in modelling the microbial activity is the methodology followed to represent metabolic pathways. A cellular metabolic model could be based on a non-equilibrium thermodynamic approach such as the Thermodynamic Electron Equivalents Model (TEEM), which is developed for biomass yield prediction using the associated standard Gibbs free energies and the bioenergetics growth efficiency between cell anabolism and catabolism. The main objective of this doctoral thesis is to develop an IBM to study denitrification processes driven by denitrifying bacteria, using TEEM to write microbial metabolic reactions (10Rs) which represent the metabolic pathways as the center of the individual sub-model. Two new computational models of the INDISIM family, INDISIM-Paracoccus and INDISIM-Denitrification have been designed, implemented on the NetLogo platform, parameterized and calibrated with experimental data to analyze the system dynamics in a bioreactor in batch and continuous culture with denitrifying bacteria growing in it. The bioreactor conditions can be aerobic and/or anaerobic, and the growing media is liquid medium with an electron donor, C-source, N-source, and oxygen and all N-oxides as electron acceptors. An open access and open source tool has been developed to write 10Rs based on TEEM. It is called MbT-tool which stands for Metabolism-based on Thermodynamics. Using MbT-Tool three sets of 10Rs have been written, which are the centre of the individual sub-model for INDISIM-Paracoccus and INDISIM-denitrification, representing reactions involved in: i) cellular maintenance, ii) individual mass synthesis, and iii) individual mass degradation to reduce cytotoxic products. The simulation results obtained with INDISIM-Paracoccus and INDISIM-Denitrification have been compared with experimental data published by Felgate et al. (2012) regarding the growth of Paracoccus denitrificans and Achromobacter xylosoxidans in a bioreactor. According to the statistical analysis of the simulations results, for both denitrifying bacteria tested, the IBMs developed show better adjustments in the assays with electron donor limited than in the assays with electron acceptor limited.

Systems Metabolic Engineering

Systems Metabolic Engineering
  • Author : Christoph Wittmann,Sang Yup Lee
  • Publisher :Unknown
  • Release Date :2012-06-15
  • Total pages :388
  • ISBN : 9789400745346
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Summary : 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.

Microbiology

Microbiology
  • Author : Nina Parker,OpenStax,Mark Schneegurt,AnhHue Thi Tu,Brian M. Forster,Philip Lister
  • Publisher :Unknown
  • Release Date :2016-05-30
  • Total pages :1301
  • ISBN : 1938168143
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Summary : "Microbiology covers the scope and sequence requirements for a single-semester microbiology course for non-majors. The book presents the core concepts of microbiology with a focus on applications for careers in allied health. The pedagogical features of the text make the material interesting and accessible while maintaining the career-application focus and scientific rigor inherent in the subject matter. Microbiology's art program enhances students' understanding of concepts through clear and effective illustrations, diagrams, and photographs. Microbiology is produced through a collaborative publishing agreement between OpenStax and the American Society for Microbiology Press. The book aligns with the curriculum guidelines of the American Society for Microbiology."--BC Campus website.

Bacterial Signal Transduction: Networks and Drug Targets

Bacterial Signal Transduction: Networks and Drug Targets
  • Author : Ryutaro Utsumi
  • Publisher :Unknown
  • Release Date :2008-12-05
  • Total pages :242
  • ISBN : 0387788859
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Summary : This fascinating book encourages many microbiologists and students to enter the new world of signal transduction in microbiology. Over the past decade, a vast amount of exciting new information on the signal transduction pathway in bacteria has been unearthed.

Metabolic Engineering

Metabolic Engineering
  • Author : Sang Yup Lee,E. Terry Papoutsakis
  • Publisher :Unknown
  • Release Date :2020-11-26
  • Total pages :450
  • ISBN : 9781000105551
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Summary : This unique reference/text presents the basic theory and practical applications of metabolic engineering (ME). It offers systematic analysis of complex metabolic pathways and ways of employing recombinant DNA techniques to alter cell behavior, metabolic patterns, and product formation. Treating ME as a distinct subfield of genetic engineering, the book demonstrates new means of enabling cells to produce valuable proteins, polypeptides, and primary and secondary metabolites. Written by more than 35 leading international experts in the field, this book discusses metabolic engineering in plant and mammalian cells, bacteria, and yeasts and assesses metabolic engineering applications in agriculture, pharmaceuticals, and environmental systems. It illuminates the potential of the "cell factory" model for production of chemicals and therapeutics and examines methods for developing new antiviral and antibacterial molecules and effective gene and somatic-cell therapies. Metabolic Engineering also addresses the use of metabolic flux analysis, metabolic control analysis, and online metabolic flux analysis.

Physiology of the Bacterial Cell

Physiology of the Bacterial Cell
  • Author : Frederick Carl Neidhardt,Neidhardt, Frederick Carl Neidhardt,John L. Ingraham,Moselio Schaechter
  • Publisher :Unknown
  • Release Date :1990
  • Total pages :506
  • ISBN : UOM:39015032694443
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Summary : Textbook for upper-division and graduate students in the biological and biochemical sciences introduces the properties of bacteria that have led to their success as colonizers of this planet. The major theme is the analysis of the molecular devices that have led to the ability of bacteria to grow rapidly in a variety of environments, to adapt quickly to changes in their surroundings, to withstand starvation and exposure to toxic agents, and to compete successfully with other organisms. Annotation copyrighted by Book News, Inc., Portland, OR

Bridging the Genomic Gaps

Bridging the Genomic Gaps
  • Author : Anonim
  • Publisher :Unknown
  • Release Date :2018
  • Total pages :113
  • ISBN : OCLC:1035382445
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Summary : The advent of next-generation DNA sequencing and the acceleration of computational resources have significantly impacted the speed at which genetic information from microbes and the environments they occupy is obtained and processed. However, these tools have also revealed the limitation of our knowledge base. Sequencing depth and volume are uncovering gene products with little-to-no shared sequence similarity to current collections and databases, thus impeding the ability of homology-based approaches to characterize all sequenced genetic material and downstream analyses describing metabolic capabilities and functional diversity. In silico genome-scale metabolic models are increasingly supplementing genomic and metagenomic studies. These metabolic models enable exploration of the metabolism of an organism within a systems biology perspective. As a reconstruction of the complex metabolic network, models contain information on the genes, enzymes, biochemical reactions, and metabolites of an organism. Metabolic models are typically used with constraint-based linear programming methods to predict cellular phenotypic properties in various growth conditions. Furthermore, metabolic models are reconciled with experimentation to improve the model’s predictive accuracy and to increase our knowledge base of the organism, providing opportunities to use quantitative methods to analyze the bacterial cell. This thesis project aims to exploit genome-scale metabolic models to extend the traditional bioinformatics workflow to provide more accurate descriptions of bacteria, to quantitatively characterize the metabolic landscape of bacteria, and to produce a development environment where systems biology questions are explored and tested. With PMAnalyzer and PyFBA, these computational tools provide the infrastructure to facilitate the aims of this project. PMAnalyzer quickly and automatically calculates bacterial growth properties (e.g, growth rate and yield) from temporal absorbance data measuring cellular accumulation. PyFBA supplies a programmatic environment to explore and use genome-scale metabolic models built from genomic annotations. The use of phenotypic observations and metabolic predictions will provide a new context to discuss genomic-based studies. This project involves studies describing taxonomically-diverse bacteria isolated from the Southern California kelp forest environment.