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Synthetic Biology

Synthetic Biology Author Josefine Liljeruhm
ISBN-10 9789814579568
Release 2014-04-24
Pages 204
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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



BioBuilder

BioBuilder Author Natalie Kuldell PhD.
ISBN-10 9781491907535
Release 2015-06-22
Pages 238
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Today’s synthetic biologists are in the early stages of engineering living cells to help treat diseases, sense toxic compounds in the environment, and produce valuable drugs. With this manual, you can be part of it. Based on the BioBuilder curriculum, this valuable book provides open-access, modular, hands-on lessons in synthetic biology for secondary and post-secondary classrooms and laboratories. It also serves as an introduction to the field for science and engineering enthusiasts. Developed at MIT in collaboration with award-winning high school teachers, BioBuilder teaches the foundational ideas of the emerging synthetic biology field, as well as key aspects of biological engineering that researchers are exploring in labs throughout the world. These lessons will empower teachers and students to explore and be part of solving persistent real-world challenges. Learn the fundamentals of biodesign and DNA engineering Explore important ethical issues raised by examples of synthetic biology Investigate the BioBuilder labs that probe the design-build-test cycle Test synthetic living systems designed and built by engineers Measure several variants of an enzyme-generating genetic circuit Model "bacterial photography" that changes a strain’s light sensitivity Build living systems to produce purple or green pigment Optimize baker’s yeast to produce ?-carotene



Synthetic Biology Handbook

Synthetic Biology Handbook Author Darren N. Nesbeth
ISBN-10 9781466568488
Release 2016-04-06
Pages 318
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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.



Synthetic Biology

Synthetic Biology Author Huimin Zhao
ISBN-10 9780123978202
Release 2013-03-21
Pages 352
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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.



Forensic DNA Biology

Forensic DNA Biology Author Kelly M. Elkins
ISBN-10 9780123945853
Release 2012
Pages 198
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A collection of forensic DNA typing laboratory experiments designed for academic and training courses at the collegiate level.



Biopunk

Biopunk Author Marcus Wohlsen
ISBN-10 9781101476352
Release 2011-04-14
Pages 272
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Bill Gates recently told Wired that if he were a teenager today, he would be hacking biology. "If you want to change the world in some big way," he says, "that's where you should start-biological molecules." The most disruptive force on the planet resides in DNA. Biotech companies and academic researchers are just beginning to unlock the potential of piecing together life from scratch. Champions of synthetic biology believe that turning genetic code into Lego-like blocks to build never-before-seen organisms could solve the thorniest challenges in medicine, energy, and environmental protection. But as the hackers who cracked open the potential of the personal computer and the Internet proved, the most revolutionary discoveries often emerge from out-of-the-way places, forged by brilliant outsiders with few resources besides boundless energy and great ideas. In Biopunk, Marcus Wohlsen chronicles a growing community of DIY scientists working outside the walls of corporations and universities who are committed to democratizing DNA the way the Internet did information. The "biohacking" movement, now in its early, heady days, aims to unleash an outbreak of genetically modified innovation by making the tools and techniques of biotechnology accessible to everyone. Borrowing their idealism from the worlds of open-source software, artisinal food, Internet startups, and the Peace Corps, biopunks are devoted advocates for open-sourcing the basic code of life. They believe in the power of individuals with access to DNA to solve the world's biggest problems. You'll meet a new breed of hackers who aren't afraid to get their hands wet, from entrepreneurs who aim to bring DNA-based medical tools to the poorest of the poor to a curious tinkerer who believes a tub of yogurt and a jellyfish gene could protect the world's food supply. These biohackers include: -A duo who started a cancer drug company in their kitchen -A team who built an open-source DNA copy machine -A woman who developed a genetic test in her apartment for a deadly disease that had stricken her family Along with the potential of citizen science to bring about disruptive change, Wohlsen explores the risks of DIY bioterrorism, the possibility of genetic engineering experiments gone awry, and whether the ability to design life from scratch on a laptop might come sooner than we think.



Molecular Biology Techniques

Molecular Biology Techniques Author Sue Carson
ISBN-10 9780123855442
Release 2012
Pages 200
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This manual is an indispensable tool for introducing advanced undergraduates and beginning graduate students to the techniques of recombinant DNA technology, or gene cloning and expression. The techniques used in basic research and biotechnology laboratories are covered in detail. Students gain hands-on experience from start to finish in subcloning a gene into an expression vector, through purification of the recombinant protein. The third edition has been completely re-written, with new laboratory exercises and all new illustrations and text, designed for a typical 15-week semester, rather than a 4-week intensive course. The "project" approach to experiments was maintained: students still follow a cloning project through to completion, culminating in the purification of recombinant protein. It takes advantage of the enhanced green fluorescent protein - students can actually visualize positive clones following IPTG induction. Cover basic concepts and techniques used in molecular biology research labs Student-tested labs proven successful in a real classroom laboratories Exercises simulate a cloning project that would be performed in a real research lab "Project" approach to experiments gives students an overview of the entire process Prep-list appendix contains necessary recipes and catalog numbers, providing staff with detailed instructions



Regenesis

Regenesis Author George M. Church
ISBN-10 9780465038657
Release 2014-04-08
Pages 304
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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.



Synthetic Biology

Synthetic Biology Author Clyde A. Hutchinson, III
ISBN-10 1621821188
Release 2017-04-30
Pages 350
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Synthetic biology involves the rational design and construction of biological components and systemsfrom genetic elements and metabolic pathways to entirely new organisms. Progress in this field has been rapid, and it promises to significantly expand our capabilities in biotechnology, medicine, and agriculture. Written and edited by experts in the field, this collection from Cold Spring Harbor Perspectives in Biology examines the tools and techniques employed by synthetic biologists, how these may be used to develop new drugs, diagnostic approaches, food sources, and clean energy, and what the field of synthetic biology has taught us about natural living systems. The contributors discuss advances in DNA synthesis and assembly, genome editing (e.g., CRISPR/Cas9), and artificial genetic systems. Progress in designing complex genetic switches and circuits, expanding the genetic code, modifying cellular organization, producing proteins using cell-free systems, and developing biodesign automation tools is also covered. The authors also explore ways to produce new organisms and products that have particular attributesfor example, microbial "molecular factories," synthetic organs and tissues, and plants with novel traits. This volume is an essential resource for molecular, cell, and systems biologists who seek to engineer living systems for human benefit.



Chemistry

Chemistry Author John Kenkel
ISBN-10 1420032992
Release 2000-06-23
Pages 225
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Have you ever had a discussion with an industrial chemist about the job? Have you ever shadowed a chemist or chemical technician in an industrial or government laboratory for a day? If you have done these things, you were likely surprised at how foreign the language seemed or startled at how unfamiliar the surroundings were. Was there any talk of the quantum mechanical model of the atom? No. Was there any activity relating to Molecular Orbital Theory of bonding? No. Was the lab a large room with six 12-foot lab benches capable of accommodating up to two dozen chemists? No, not usually. Unless you took an "industry based" chemistry course, you probably came away from this experience with the thought "Why don't textbooks and lab manuals do a better job of communicating what real-world chemists do?" Chemistry: An Industry-Based Laboratory Manual does just that. It covers laboratory safety, record-keeping, control charts, certified reference materials, and much more. "Who uses this stuff anyway?" you may ask. Chemistry: An Industry-Based Laboratory Manual supplies the answer. It features applications of basic chemistry concepts to the real-world work of chemistry professionals. It brings real-world examples to laboratory experiences and covers voluntary industry standards for laboratory workers in the chemical process industries. It places a strong emphasis on the real work of chemistry professionals.



Synthetic Biology A Primer

Synthetic Biology     A Primer Author
ISBN-10 9781783268818
Release 2015-08-24
Pages 196
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Synthetic Biology — A Primer (Revised Edition) presents an updated overview of the field of synthetic biology and the foundational concepts on which it is built. This revised edition includes new literature references, working and updated URL links, plus some new figures and text where progress in the field has been made. The book introduces readers to fundamental concepts in molecular biology and engineering and then explores the two major themes for synthetic biology, namely 'bottom-up' and 'top-down' engineering approaches. 'Top-down' engineering uses a conceptual framework of systematic design and engineering principles focused around the Design-Build-Test cycle and mathematical modelling. The 'bottom-up' approach involves the design and building of synthetic protocells using basic chemical and biochemical building blocks from scratch exploring the fundamental basis of living systems. Examples of cutting-edge applications designed using synthetic biology principles are presented, including: the production of novel, microbial synthesis of pharmaceuticals and fine chemicalsthe design and implementation of biosensors to detect infections and environmental waste. The book also describes the Internationally Genetically Engineered Machine (iGEM) competition, which brings together students and young researchers from around the world to carry out summer projects in synthetic biology. Finally, the primer includes a chapter on the ethical, legal and societal issues surrounding synthetic biology, illustrating the integration of social sciences into synthetic biology research. Final year undergraduates, postgraduates and established researchers interested in learning about the interdisciplinary field of synthetic biology will benefit from this up-to-date primer on synthetic biology. Contents:List of ContributorsPrefaceIntroduction to BiologyBasic Concepts in Engineering BiologyFoundational TechnologiesMinimal Cells and Synthetic LifeParts, Devices and SystemsModelling Synthetic Biology SystemsApplications of Designed Biological SystemsiGEMThe Societal Impact of Synthetic BiologyAppendices:Proforma of Common Laboratory TechniquesGlossaryIndex Readership: Students, professionals, researchers in biotechnology and bioengineering. Keywords:Synthetic Biology;Engineering Principles;Biosociety;Biological Engineering;BiotechnologyKey Features:The book is written in a way that is accessible to students and researchers from different disciplinesThe authors are part of the internationally recognised Centre for Synthetic Biology and Innovation and are among the leaders in this field



Designing Human Practices

Designing Human Practices Author Paul Rabinow
ISBN-10 9780226703152
Release 2012-05-21
Pages 200
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In 2006 anthropologists Paul Rabinow and Gaymon Bennett set out to rethink the role that human sciences play in biological research, creating the Human Practices division of the Synthetic Biology Engineering Research Center—a facility established to create design standards for the engineering of new enzymes, genetic circuits, cells, and other biological entities—to formulate a new approach to the ethical, security, and philosophical considerations of controversial biological work. They sought not simply to act as watchdogs but to integrate the biosciences with their own discipline in a more fundamentally interdependent way, inventing a new, dynamic, and experimental anthropology that they could bring to bear on the center’s biological research. Designing Human Practices is a detailed account of this anthropological experiment and, ultimately, its rejection. It provides new insights into the possibilities and limitations of collaboration, and diagnoses the micro-politics which effectively constrained the potential for mutual scientific flourishing. Synthesizing multiple disciplines, including biology, genetics, anthropology, and philosophy, alongside a thorough examination of funding entities such as the National Science Foundation, Designing Human Practices pushes the social study of science into new and provocative territory, utilizing a real-world experience as a springboard for timely reflections on how the human and life sciences can and should transform each other.



Illustrated Guide to Home Forensic Science Experiments

Illustrated Guide to Home Forensic Science Experiments Author Robert Bruce Thompson
ISBN-10 9781449334475
Release 2012-08-07
Pages 448
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Have you ever wondered whether the forensic science you’ve seen on TV is anything like the real thing? There’s no better way to find out than to roll up your sleeves and do it yourself. This full-color book offers advice for setting up an inexpensive home lab, and includes more than 50 hands-on lab sessions that deal with forensic science experiments in biology, chemistry, and physics. You’ll learn the practical skills and fundamental knowledge needed to pursue forensics as a lifelong hobby—or even a career. The forensic science procedures in this book are not merely educational, they’re the real deal. Each chapter includes one or more lab sessions devoted to a particular topic. You’ll find a complete list of equipment and chemicals you need for each session. Analyze soil, hair, and fibers Match glass and plastic specimens Develop latent fingerprints and reveal blood traces Conduct drug and toxicology tests Analyze gunshot and explosives residues Detect forgeries and fakes Analyze impressions, such as tool marks and footprints Match pollen and diatom samples Extract, isolate, and visualize DNA samples Through their company, The Home Scientist, LLC (thehomescientist.com/forensics), the authors also offer inexpensive custom kits that provide specialized equipment and supplies you’ll need to complete the experiments. Add a microscope and some common household items and you’re good to go.



Synthetic Biology

Synthetic Biology Author Gigi Gronvall
ISBN-10 1539336832
Release 2016-10-08
Pages 198
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Synthetic biology aims to make biology easier to engineer and to program. Thanks to advances in computing power, the ability to make long tracts of DNA, new tools like CRISPR that can be used to edit genomes, and the enthusiasm of young scientists and even amateurs who want to enter the field, synthetic biology is poised to change the future of medicine, agriculture, and manufacturing. Yet, while this new field promises vast opportunities and benefits, there are also risks. There are biosecurity risks that these technologies will be deliberately used for harm; safety risks to people and the environment; ethical and social considerations for how to apply these technologies; and there are risks to the competitiveness of nations that do not invest in these technologies that are likely to spur economic growth. This volume is dedicated to a discussion of what can be done to minimize risks and maximize the benefits of synthetic biology. Praise for Synthetic Biology: Safety, Security, and Promise "There can be no doubt that advances in the life sciences, including new insights and tools provided by synthetic biology, place us in a position to create exciting and novel products and approaches for patients in need. Gigi Gronvall describes that promise but also lays forth critical policy concerns that need to be addressed so that we don't risk safety, security, or the competitiveness of US science." - Margaret Hamburg, MD, Former FDA Commissioner and Foreign Secretary, National Academy of Medicine "Synthetic biology gives us tools that can help tackle global problems that affect humanity-but for that to happen, the risks of bioterror or bio-error need to be dealt with and managed, as well. Gronvall clearly describes the policy challenges that must be addressed and concludes with steps to enhance US leadership and competitiveness in the global bio-economy." - J. Craig Venter, PhD, founder, chairman, and CEO of the J. Craig Venter Institute and co-founder, executive chairman and co-chief scientist of Synthetic Genomics, Inc. "For those of us working in the lab, it is important to embrace conversations with those who aren't - including strategies for biological security, to create new synthetic biology products - with respect for facts about GMO risk/benefit balances, creating a culture of safe lab practices and norms worldwide. Gigi Gronvall dissects such issues at stake in synthetic biology and presents a pragmatic and scientifically responsive path forward for anyone in a position to influence, regulate, decide upon, or benefit from the science to follow." - George Church, PhD, Professor of Genetics Harvard Medical School and Director of PersonalGenomes.org "Synthetic biology presents some of the greatest challenges and opportunities of the 21st Century. Gigi Gronvall navigates a path to follow, to make sure risks are addressed and opportunities are not squandered. It should be read by all concerned about national security." - The Honorable Andrew Weber, head of global partnerships for Metabiota and former Assistant Secretary of Defense for Nuclear, Chemical, and Biological Defense Programs



The Condensed Protocols from Molecular Cloning a Laboratory Manual

The Condensed Protocols from Molecular Cloning   a Laboratory Manual Author Joseph Sambrook
ISBN-10 9780879697716
Release 2006
Pages 800
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The Condensed Protocols From Molecular Cloning: A Laboratory Manualis a single–volume adaptation of the three–volume third edition of Molecular Cloning: A Laboratory Manual.This condensed book contains only the step–by–step portions of the protocols, accompanied by selected appendices from the world's best–selling manual of molecular biology techniques. Each protocol is cross–referenced to the appropriate pages in the original manual. This affordable companion volume, designed for bench use, offers individual investigators the opportunity to have their own personal collection of short protocols from the essential Molecular Cloning.



Synthetic Biology

Synthetic Biology Author Christopher Voigt
ISBN-10 9780123851208
Release 2011
Pages 500
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Synthetic biology encompasses a variety of different approaches, methodologies and disciplines, and many different definitions exist. This Volume of Methods in Enzymology has been split into 2 Parts and covers topics such as Measuring and Engineering Central Dogma Processes, Mathematical and Computational Methods and Next-Generation DNA Assembly and Manipulation. Encompasses a variety of different approaches, methodologies and disciplines Split into 2 parts and covers topics such as measuring and engineering central dogma processes, mathematical and computational methods and next-generation DNA assembly and manipulation



CRISPR Cas

CRISPR Cas Author University Jennifer Doudna
ISBN-10 1621821307
Release 2016-03-23
Pages 192
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The development of CRISPR-Cas technology is revolutionizing biology. Based on machinery bacteria use to target foreign nucleic acids, these powerful techniques allow investigators to edit nucleic acids and modulate gene expression more rapidly and accurately than ever before. Featuring contributions from leading figures in the CRISPR-Cas field, this laboratory manual presents a state-of-the-art guide to the technology. It includes step-by-step protocols for applying CRISPR-Cas-based techniques in various systems, including yeast, zebrafish, Drosophila, mice, and cultured cells (e.g., human pluripotent stem cells). The contributors cover web-based tools and approaches for designing guide RNAs that precisely target genes of interest, methods for preparing and delivering CRISPR-Cas reagents into cells, and ways to screen for cells that harbor the desired genetic changes. Strategies for optimizing CRISPR-Cas in each system--especially for minimizing off-target effects--are also provided. Authors also describe other applications of the CRISPR-Cas system, including its use for regulating genome activation and repression, and discuss the development of next-generation CRISPR-Cas tools. The book is thus an essential laboratory resource for all cell, molecular, and developmental biologists, as well as biochemists, geneticists, and all who seek to expand their biotechnology toolkits.