Synthetic Biology

Author: Huimin Zhao
Publisher: Academic Press
ISBN: 0123978203
Format: PDF, Mobi
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Synthetic Biology provides a framework to examine key enabling components in the emerging area of synthetic biology. Chapters contributed by leaders in the field address tools and methodologies developed for engineering biological systems at many levels, including molecular, pathway, network, whole cell, and multi-cell levels. The book highlights exciting practical applications of synthetic biology such as microbial production of biofuels and drugs, artificial cells, synthetic viruses, and artificial photosynthesis. The roles of computers and computational design are discussed, as well as future prospects in the field, including cell-free synthetic biology and engineering synthetic ecosystems. Synthetic biology is the design and construction of new biological entities, such as enzymes, genetic circuits, and cells, or the redesign of existing biological systems. It builds on the advances in molecular, cell, and systems biology and seeks to transform biology in the same way that synthesis transformed chemistry and integrated circuit design transformed computing. The element that distinguishes synthetic biology from traditional molecular and cellular biology is the focus on the design and construction of core components that can be modeled, understood, and tuned to meet specific performance criteria and the assembly of these smaller parts and devices into larger integrated systems that solve specific biotechnology problems. Includes contributions from leaders in the field presents examples of ambitious synthetic biology efforts including creation of artificial cells from scratch, cell-free synthesis of chemicals, fuels, and proteins, engineering of artificial photosynthesis for biofuels production, and creation of unnatural living organisms Describes the latest state-of-the-art tools developed for low-cost synthesis of ever-increasing sizes of DNA and efficient modification of proteins, pathways, and genomes Highlights key technologies for analyzing biological systems at the genomic, proteomic, and metabolomic levels which are especially valuable in pathway, whole cell, and multi-cell applications Details mathematical modeling tools and computational tools which can dramatically increase the speed of the design process as well as reduce the cost of development.

Synthetic Biology Handbook

Author: Darren N. Nesbeth
Publisher: CRC Press
ISBN: 1466568488
Format: PDF, Docs
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The Synthetic Biology Handbook explains the major goals of the field of synthetic biology and presents the technical details of the latest advances made in achieving those goals. Offering a comprehensive overview of the current areas of focus in synthetic biology, this handbook: Explores the standardisation of classic molecular bioscience approaches Addresses the societal context and potential impacts of synthetic biology Discusses the use of legacy systems as tools for new product development Examines the design and construction of de novo cells and genetic codes Describes computational methods for designing genes and gene networks Thus, the Synthetic Biology Handbook provides an accurate sense of the scope of synthetic biology today. The handbook also affords readers with an opportunity to scrutinize the underlying science and decide for themselves what aspects of synthetic biology are most valuable to their research and practice.

Regenesis

Author: George M. Church
Publisher: Basic Books
ISBN: 0465038654
Format: PDF, ePub, Docs
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“Bold and provocative… Regenesis tells of recent advances that may soon yield endless supplies of renewable energy, increased longevity and the return of long-extinct species.”—New Scientist In Regenesis, Harvard biologist George Church and science writer Ed Regis explore the possibilities—and perils—of the emerging field of synthetic biology. Synthetic biology, in which living organisms are selectively altered by modifying substantial portions of their genomes, allows for the creation of entirely new species of organisms. These technologies—far from the out-of-control nightmare depicted in science fiction—have the power to improve human and animal health, increase our intelligence, enhance our memory, and even extend our life span. A breathtaking look at the potential of this world-changing technology, Regenesis is nothing less than a guide to the future of life.

Game Theoretical Models in Biology

Author: Mark Broom
Publisher: CRC Press
ISBN: 1439853215
Format: PDF, ePub
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Covering the major topics of evolutionary game theory, Game-Theoretical Models in Biology presents both abstract and practical mathematical models of real biological situations. It discusses the static aspects of game theory in a mathematically rigorous way that is appealing to mathematicians. In addition, the authors explore many applications of game theory to biology, making the text useful to biologists as well. The book describes a wide range of topics in evolutionary games, including matrix games, replicator dynamics, the hawk-dove game, and the prisoner’s dilemma. It covers the evolutionarily stable strategy, a key concept in biological games, and offers in-depth details of the mathematical models. Most chapters illustrate how to use MATLAB® to solve various games. Important biological phenomena, such as the sex ratio of so many species being close to a half, the evolution of cooperative behavior, and the existence of adornments (for example, the peacock’s tail), have been explained using ideas underpinned by game theoretical modeling. Suitable for readers studying and working at the interface of mathematics and the life sciences, this book shows how evolutionary game theory is used in the modeling of these diverse biological phenomena.

Fundamentals of Systems Biology

Author: Markus W. Covert
Publisher: CRC Press
ISBN: 1498728472
Format: PDF, ePub
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For decades biology has focused on decoding cellular processes one gene at a time, but many of the most pressing biological questions, as well as diseases such as cancer and heart disease, are related to complex systems involving the interaction of hundreds, or even thousands, of gene products and other factors. How do we begin to understand this complexity? Fundamentals of Systems Biology: From Synthetic Circuits to Whole-cell Models introduces students to methods they can use to tackle complex systems head-on, carefully walking them through studies that comprise the foundation and frontier of systems biology. The first section of the book focuses on bringing students quickly up to speed with a variety of modeling methods in the context of a synthetic biological circuit. This innovative approach builds intuition about the strengths and weaknesses of each method and becomes critical in the book’s second half, where much more complicated network models are addressed—including transcriptional, signaling, metabolic, and even integrated multi-network models. The approach makes the work much more accessible to novices (undergraduates, medical students, and biologists new to mathematical modeling) while still having much to offer experienced modelers--whether their interests are microbes, organs, whole organisms, diseases, synthetic biology, or just about any field that investigates living systems.

Synthetic Biology

Author: Josefine Liljeruhm
Publisher: World Scientific
ISBN: 9814579564
Format: PDF, ePub, Mobi
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Synthetic Biology: A Lab Manual is the first manual for laboratory work in the new and rapidly expanding field of synthetic biology. Aimed at non-specialists, it details protocols central to synthetic biology in both education and research. In addition, it provides all the information that teachers and students from high schools and tertiary institutions need for a colorful lab course in bacterial synthetic biology using chromoproteins and designer antisense RNAs. As a bonus, practical material is provided for students of the annual international Genetically Engineered Machine (iGEM) competition. The manual is based upon a highly successful course at Sweden's Uppsala University and is coauthored by one of the pioneers of synthetic biology and two bioengineering postgraduate students. An inspiring foreword is written by another pioneer in the field, Harvard's George Church: “Synthetic biology is to early recombinant DNA as a genome is to a gene. Is there anything that SynBio will not impact? There was no doubt that the field of SynBio needed ‘A Lab Manual’ such as the one that you now hold in your hands.” Read about the interview with the authors! Contents:Introduction:What is Synthetic Biology, Exactly?The iGEM OutbreakA Synthetic Biology Lab ManualGenes, Chromoproteins and Antisense RNAs:E. coli DNA: Chromosomes, Plasmids and Copy NumberCoupling of Transcription and Translation in BacteriaPromoter and Terminator for TranscriptionRibosome Binding Site (RBS)Codon BiasChromoproteinsSmall Regulatory RNAs (sRNAs)Lab Rooms and Equipment:The Physical Lab SpacesEquipmentSafety is Priority #1:FiresChemicalsBiological Safety and DisposalDangerous EquipmentLab Course Projects:Time and ResourcesProject Overview and Learning ObjectivesThe Lab NotebookLab Section 1. Preparation of Chemical Solutions and Agar PlatesLab Section 2. Coloring Bacteria by Adding a Promoter to a Chromoprotein GeneLab Section 3: Rational Engineering of Chromoprotein Expression LevelLab Section 4. Other ExperimentsThe “Dreaded” ExamProtocols:IntroductionProtocol 1. Preparation of Solutions and Agar PlatesProtocol 2. Overnight Cultures with Antibiotics, and Glycerol StocksProtocol 3. BioBrick™ 3A Assembly and Gel AnalysisProtocol 4. Agarose Gel ElectrophoresisProtocol 5. Preparation of Competent E. coli Cells Using CaCl2Protocol 6. Transformation of CaCl2-Competent E. coli CellsProtocol 7. Bacterial Re-Streaking TechniquesProtocol 8. Lysis of E. coli Cells with LysozymeProtocol 9. Polymerase Chain Reaction (PCR)Protocol 10. Inverse PCR MutagenesisProtocol 11. Colony PCRProtocol 12. Gibson AssemblyAdvanced Methods:Flow Cytometry and Cell SortingRecombination in Plasmids and the ChromosomeElectrocompetent CellsThe International Genetically Engineered Machine (iGEM) Competition:How to Start an iGEM TeamUppsala iGEM 2011 — Show Color with ColorUppsala iGEM 2012 — Resistance is FutileUppsala iGEM 2013 — Lactonutritious — It's DeliciousAppendices Readership: Students and researchers in biotechnology, cell/molecular biology and genetics. Keywords:Synthetic Biology;Genetic Engineering;DNA Cloning;Polymerase Chain Reaction;Molecular Biology;Laboratory;Biobrick;Chromoprotein;Manual;CourseReviews: It provides an introductory workflow for common techniques and would be of definite use to educators wanting to bring synthetic biology into the classroom or for motivated undergraduate students with the desire to start thir own iGEM team.” Synthetic Biology See Full Review

Synthetic Aesthetics

Author: Alexandra Daisy Ginsberg
Publisher: MIT Press
ISBN: 026201999X
Format: PDF, ePub
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As synthetic biology transforms living matter into a medium for making, what is the role of design and its associated values?

Synthetic

Author: Sophia Roosth
Publisher: University of Chicago Press
ISBN: 022644046X
Format: PDF, ePub, Docs
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In the final years of the twentieth century, emigres from mechanical and electrical engineering and computer science resolved that if the aim of biology was to understand life, then making life would yield better theories than experimentation. Sophia Roosth, a cultural anthropologist, takes us into the world of these self-named synthetic biologists who, she shows, advocate not experiment but manufacture, not reduction but construction, not analysis but synthesis. Roosth reveals how synthetic biologists make new living things in order to understand better how life works. What we see through her careful questioning is that the biological features, theories, and limits they fasten upon are determined circularly by their own experimental tactics. This is a story of broad interest, because the active, interested making of the synthetic biologists is endemic to the sciences of our time."

An Introduction to Systems Biology

Author: Uri Alon
Publisher: CRC Press
ISBN: 1584886420
Format: PDF, ePub, Mobi
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Thorough and accessible, this book presents the design principles of biological systems, and highlights the recurring circuit elements that make up biological networks. It provides a simple mathematical framework which can be used to understand and even design biological circuits. The textavoids specialist terms, focusing instead on several well-studied biological systems that concisely demonstrate key principles. An Introduction to Systems Biology: Design Principles of Biological Circuits builds a solid foundation for the intuitive understanding of general principles. It encourages the reader to ask why a system is designed in a particular way and then proceeds to answer with simplified models.