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| crispr guide rna design: CRISPR Guide RNA Design Tudor A. Fulga, David J. H. F. Knapp, Quentin R. V. Ferry, 2020-11-19 This detailed volume focuses on the CRISPR-associated guide RNA and how it can be designed, modified, and validated for a broad repertoire of purposes. Beginning with a section on computational design of target-specific guide RNAs, the book continues by covering chemical modifications to alter guide RNA stability, specificity, and efficiency, as well as to create inducible guide RNAs, append additional functional domains, and express guide RNAs in a conditional manner. It concludes with methods for measuring off-target guide RNA activity. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and essential, CRISPR Guide RNA Design: Methods and Protocols provides a comprehensive pipeline for guide RNA design and aims to be an invaluable resource in applying this powerful technology to basic research and therapeutic applications. |
| crispr guide rna design: CRISPR-Cas Systems Rodolphe Barrangou, John van der Oost, 2012-12-13 CRISPR/Cas is a recently described defense system that protects bacteria and archaea against invasion by mobile genetic elements such as viruses and plasmids. A wide spectrum of distinct CRISPR/Cas systems has been identified in at least half of the available prokaryotic genomes. On-going structural and functional analyses have resulted in a far greater insight into the functions and possible applications of these systems, although many secrets remain to be discovered. In this book, experts summarize the state of the art in this exciting field. |
| crispr guide rna design: CRISPR Gene Editing Yonglun Luo, 2019-04-23 This detailed volume guides readers through strategic planning and user-friendly guidelines in order to select the most suitable CRISPR-Cas system and target sites with high activity and specificity. Methods covering CRISPR gRNA design, CRISPR delivery, CRISPR activity quantification (indel quantification), and examples of applying CRISPR gene editing in human pluripotent stem cells, primary cells, gene therapy, and genetic screening are included. Written for the highly successful Methods in Molecular Biology series, 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 invaluable, CRISPR Gene Editing: Methods and Protocols will assist undergraduates, graduates, and researchers with detailed guidelines and methods for the vitally important CRISPR gene editing field. Chapter 3 is available open access under a CC BY 4.0 license via link.springer.com. |
| crispr guide rna design: RNA Nanotechnology Bin Wang, 2014-04-02 In the past few decades there has been incredible growth in bionano-related research, which has been accompanied by numerous publications in this field. Although various compilations address topics related to deoxyribonucleic acid (DNA) and protein, there are few books that focus on determining the structure of ribonucleic acid (RNA) and using RNA as building blocks to construct nanoarchitectures for biomedical and healthcare applications. RNA Nanotechnology is a comprehensive volume that details both the traditional approaches and the latest developments in the field of RNA-related technology. This book targets a wide audience: a broad introduction provides a solid academic background for students, researchers, and scientists who are unfamiliar with the subject, while the in-depth descriptions and discussions are useful for advanced professionals. The book opens with reviews on the basic aspects of RNA biology, computational approaches for predicting RNA structures, and traditional and emerging experimental approaches for probing RNA structures. This section is followed by explorations of the latest research and discoveries in RNA nanotechnology, including the design and construction of RNA-based nanostructures. The final segment of the book includes descriptions and discussions of the potential biological and therapeutic applications of small RNA molecules, such as small/short interfering RNAs (siRNAs), microRNAs (miRNAs), RNA aptamers, and ribozymes. |
| crispr guide rna design: RNA Tagging Manfred Heinlein, 2021-08-08 This book provides a compendium of state-of-the-art methods for the labeling, detection, and purification of RNA and RNA-protein complexes and thereby constitutes an important toolbox for researchers interested in understanding the complex roles of RNA molecules in development, signaling, and disease. Beginning with a section on in situ detection of RNA molecules using FISH techniques, the volume continues with parts exploring in vivo imaging of RNA transport and localization, imaging and analysis of RNA uptake and transport between cells, identification and analysis of RNA-binding proteins, guide RNAs in genome editing, as well as other specific analytical techniques. Written for the highly successful Methods in Molecular Biology series, 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 practical, RNA Tagging: Methods and Protocols serves as a vital reference for researchers looking to further the increasingly important research in RNA biology. |
| crispr guide rna design: CRISPR-Cas Jennifer A. Doudna, Prashant Mali, 2016 CRISPR/Cas-based techniques are revolutionizing the way geneticists and molecular biologists modify DNA sequences and modulate gene expression in cells and organisms. This laboratory manual presents step-by-step protocols for applying this cutting-edge technology to any system of interest. Contributors describe approaches for de. |
| crispr guide rna design: CRISPR-Cas Methods M. Tofazzal Islam, Kutubuddin Ali Molla, 2021-07-31 This second volume provides new and updated methods detailing advancements in CRISPR-Cas technical protocols. Chapters guide readers through protocols on prime editing, base editing, multiplex editing, editing in cell-free extract, in silico analysis of gRNA secondary structure and CRISPR-diagnosis. Authoritative and cutting-edge, CRISPR-Cas Methods, Volume 2 aims to serves as a laboratory manual providing scientists with a holistic view of CRISPR-Cas methodologies and its practical application for the editing of crop plants, cell lines, nematode and microorganism. The chapter “CRISPR/Cas9-mediated gene editing in human induced pluripotent stem cells” is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com. |
| crispr guide rna design: Genome Editing for Precision Crop Breeding Matthew R. Willmann, 2021 Part 1 of this volume reviews advances in gene editing techniques such as insertion-based genome edits, base editing, guide RNAs and CRISPR/Cas off targeting. Part 2 surveys applications of gene editing in key cereal and vegetable crops. |
| crispr guide rna design: Genome Editing and Engineering Krishnarao Appasani, 2018-08-23 A complete guide to endonuclease-based genomic engineering, from basic science to application in disease biology and clinical treatment. |
| crispr guide rna design: Computational Methods in Synthetic Biology Mario Andrea Marchisio, 2021-11-27 This second edition book provides complete coverage of the computational approaches currently used in Synthetic Biology. New chapters detail computational methods and algorithms for the design of bio-components, insight on CAD programs, analysis techniques, and distributed systems. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, application details for both the expert and non-expert reader, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Computational Methods in Synthetic Biology, Second Edition aims to feature a broad overview of the research areas that can be met in the area of in silico Synthetic Biology. |
| crispr guide rna design: Human Genome Editing National Academies of Sciences, Engineering, and Medicine, National Academy of Medicine, National Academy of Sciences, Committee on Human Gene Editing: Scientific, Medical, and Ethical Considerations, 2017-08-13 Genome editing is a powerful new tool for making precise alterations to an organism's genetic material. Recent scientific advances have made genome editing more efficient, precise, and flexible than ever before. These advances have spurred an explosion of interest from around the globe in the possible ways in which genome editing can improve human health. The speed at which these technologies are being developed and applied has led many policymakers and stakeholders to express concern about whether appropriate systems are in place to govern these technologies and how and when the public should be engaged in these decisions. Human Genome Editing considers important questions about the human application of genome editing including: balancing potential benefits with unintended risks, governing the use of genome editing, incorporating societal values into clinical applications and policy decisions, and respecting the inevitable differences across nations and cultures that will shape how and whether to use these new technologies. This report proposes criteria for heritable germline editing, provides conclusions on the crucial need for public education and engagement, and presents 7 general principles for the governance of human genome editing. |
| crispr guide rna design: Oligonucleotide Synthesis Piet Herdewijn, 2008-02-04 A collection of powerful new techniques for oligonucleotide synthesis and for the use of modified oligonucleotides in biotechnology. Among the protocol highlights are a novel two-step process that yields a high purity, less costly, DNA, the synthesis of phosphorothioates using new sulfur transfer agents, the synthesis of LNA, peptide conjugation methods to improve cellular delivery and cell-specific targeting, and triple helix formation. The applications include using molecular beacons to monitor the PCR amplification process, nuclease footprinting to study the sequence-selective binding of small molecules of DNA, nucleic acid libraries, and the use of small interference RNA (siRNA) as an inhibitor of gene expression. |
| crispr guide rna design: CRISPR-Cas Enzymes , 2019-01-25 CRISPR-Cas Enzymes, Volume 616, the latest release in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. Topics covered in this release include CRISPR bioinformatics, A method for one-step assembly of Class 2 CRISPR arrays, Biochemical reconstitution and structural analysis of ribonucleoprotein complexes in Type I-E CRISPR-Cas systems, Mechanistic dissection of the CRISPR interference pathway in Type I-E CRISPR-Cas system, Site-specific fluorescent labeling of individual proteins within CRISPR complexes, Fluorescence-based methods for measuring target interference by CRISPR-Cas systems, Native State Structural Characterization of CRISRP Associated Complexes using Mass Spectrometry, and more. - Provides the authority and expertise of leading contributors from an international board of authors - Presents the latest release in the Methods in Enzymology series - Updated release includes the latest information on the CRISPR-Cas Enzymes |
| crispr guide rna design: Yarrowia Lipolytica Ian Wheeldon, Mark Blenner, 2021 This volume provides a collection of protocols for the most common experimental methods used for engineering Yarrowia lipolytica. Chapters detail the basic theories underlying the methods described in each chapter. 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, Yarrowia lipolytica: Methods and Protocols aims to provide experimentalists with a full account of the practical steps necessary for carrying out each protocol successfully. |
| crispr guide rna design: Genome Editing in Neurosciences Rudolf Jaenisch, Feng Zhang, Fred Gage, 2020-10-08 Innovations in molecular biology are allowing neuroscientists to study the brain with unprecedented resolution, from the level of single molecules to integrated gene circuits. Chief among these innovations is the CRISPR-Cas genome editing technology, which has the precision and scalability to tackle the complexity of the brain. This Colloque Médecine et Recherche has brought together experts from around the world that are applying genome editing to address important challenges in neuroscience, including basic biology in model organisms that has the power to reveal systems-level insight into how the nervous system develops and functions as well as research focused on understanding and treating human neurological disorders. This work was published by Saint Philip Street Press pursuant to a Creative Commons license permitting commercial use. All rights not granted by the work's license are retained by the author or authors. |
| crispr guide rna design: Gene Editing in Plants , 2017-07-14 Gene Editing in Plants, Volume 149 aims to provide the reader with an up-to-date survey of cutting-edge research with gene editing tools and an overview of the implications of this research on the nutritional quality of fruits, vegetables and grains. New chapters in the updated volume include topics relating to Genome Engineering and Agriculture: Opportunities and Challenges, the Use of CRISPR/Cas9 for Crop Improvement in Maize and Soybean, the Use of Zinc-Finger Nucleases for Crop Improvement, Gene Editing in Polyploid Crops: Wheat, Camelina, Canola, Potato, Cotton, Peanut, Sugar Cane, and Citrus, and Gene Editing With TALEN and CRISPR/Cas in Rice. This ongoing serial contain contributions from leading scientists and researchers in the field of gene editing in plants who describe the results of their own research in this rapidly expanding area of science. - Shows the importance of revolutionary gene editing technology on plant biology research and its application to agricultural production - Provides insight into what may lie ahead in this rapidly expanding area of plant research and development - Contains contributions from major leaders in the field of plant gene editing |
| crispr guide rna design: Plant Genome Editing with CRISPR Systems Yiping Qi, 2019-01-05 This volume provides readers with wide-ranging coverage of CRISPR systems and their applications in various plant species. The chapters in this book discuss topics such as plant DNA repair and genome editing; analysis of CRISPR-induced mutations; multiplexed CRISPR/Cas9 systems; CRISPR-Cas12a (Cpf1) editing systems; and non-agrobacterium based CRISPR delivery systems. 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. Comprehensive and thorough, Plant Genome Editing with CRISPR Systems: Methods and Protocols is a valuable resource for any researcher interested in learning about and using CRISPR systems in plants. |
| crispr guide rna design: DNA-Protein Interactions Andrew Arthur Travers, 1993-04-30 The binding of proteins to DNA and the manipulation of DNA by proteins are crucial aspects of the biological role of DNA in the living cell. This book provides a comprehensive and lucid discussion of the molecular interactions involved. |
| crispr guide rna design: CRISPR in Animals and Animal Models , 2017-11-10 CRISPR in Animals and Animal Models, Volume 152, the latest release in the Progress in Molecular Biology and Translational Science series, explores the genome editing CRISPR system in cells and animal models, its applications, the uses of the CRISPR system, and the past, present and future of CRISPR genome editing. Topics of interest in this updated volume include a section on CRISPR history, The genome editing revolution, Programming CRISPR and its applications, CRISPR Delivery methods, CRISPR libraries and screening, CRISPR investigation in haploid cells, CRISPR in the generation of transgenic animals, CRISPR therapeutics, and Promising strategies and present challenges. Accessible to students and researchers alike Written by leading authorities in the field |
| crispr guide rna design: Gene Drives on the Horizon National Academies of Sciences, Engineering, and Medicine, Division on Earth and Life Studies, Board on Life Sciences, Committee on Gene Drive Research in Non-Human Organisms: Recommendations for Responsible Conduct, 2016-08-28 Research on gene drive systems is rapidly advancing. Many proposed applications of gene drive research aim to solve environmental and public health challenges, including the reduction of poverty and the burden of vector-borne diseases, such as malaria and dengue, which disproportionately impact low and middle income countries. However, due to their intrinsic qualities of rapid spread and irreversibility, gene drive systems raise many questions with respect to their safety relative to public and environmental health. Because gene drive systems are designed to alter the environments we share in ways that will be hard to anticipate and impossible to completely roll back, questions about the ethics surrounding use of this research are complex and will require very careful exploration. Gene Drives on the Horizon outlines the state of knowledge relative to the science, ethics, public engagement, and risk assessment as they pertain to research directions of gene drive systems and governance of the research process. This report offers principles for responsible practices of gene drive research and related applications for use by investigators, their institutions, the research funders, and regulators. |
| crispr guide rna design: Ribozymes Robert J Scarborough, Anne Gatignol, 2021-08-09 This volume provides protocols designed to study the function and the structure of diverse ribozymes. Chapters guide readers through different techniques to identify and characterize new ribozymes and methods to use ribozymes to alter the function of CRISPR-based guide RNAs, AgoshRNAs and aptamers or to study RNA capping and long non-coding RNAs. 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, Ribozymes: Methods and Protocols aims to help in accelerating ribozyme research and inspiring others to develop new methods to study ribozyme structure and function. |
| crispr guide rna design: Modulating Gene Expression Aditi Singh, Mohammad W. Khan, 2019-05-29 RNA interference (RNAi) is a widely used technology for gene silencing and has become a key tool in a myriad of research and lead discoveries. In recent years, the mechanism of RNAi agents has been well investigated, and the technique has been optimized for better effectiveness and safety. On the other hand, the clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas9/gRNA system is a recent, novel, targeted genome-editing technique derived from the bacterial immune system. Recent advances in gene-editing research and technologies have enabled the CRISPR Cas9 system to become a popular tool for sequence-specific gene editing to correct and modify eukaryotic systems. In this book, we will focus on the mechanisms, applications, regulations (their pros and cons), and various ways in which RNAi-based methods and CRIPSR-Cas9 technology have stimulated the modulation of gene expression, thereby making them a promising therapeutic tool to treat and prevent complex diseases and disorders. |
| crispr guide rna design: CRISPR Magnus Lundgren, Emmanuelle Charpentier, Peter C. Fineran, 2015-05-20 This volume presents a list of cutting-edge protocols for the study of CRISPR-Cas defense systems and their applications at the genomic, genetic, biochemical and structural levels. CRISPR: Methods and Protocols guides readers through techniques that have been developed specifically for the analysis of CRISPR-Cas and techniques adapted from standard protocols of DNA, RNA and protein biology. 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, CRISPR: Methods and Protocols provides a broad list of tools and techniques to study the interdisciplinary aspects of the prokaryotic CRISPR-Cas defense systems. |
| crispr guide rna design: Reprogramming the Genome: Applications of CRISPR-Cas in non-mammalian systems part A , 2021-03-28 Reprogramming the Genome: Applications of CRISPR-Cas in Non-mammalian Systems, Part A presents a collation of chapters written by global, eminent scientists. CRISPR-Cas9 system is an RNA-mediated immune system of bacteria and archaea that protects from bacteriophage infections. It is one of the revolutionized technologies to uplift biology to the next stages. Chapters in this release include An Introduction and applications of CRISPR-Cas Systems, History, evolution and classification of CRISPR-Cas associated systems, CRISPR based bacterial genome editing and removal of pathogens, CRISPR based genome editing and removal of human viruses, CRISPR based development of RNA editing and diagnostic platform, and much more. Additional sections cover Genome engineering in insects for control of vector borne diseases, Development of insect cell line using CRISPR technology, CRISPRing protozoan parasites to better understand the biology of diseases, CRISPR based genome editing of Caenorhabditis elegans, and a variety of other important topics. - Offers a basic understanding and clear picture of genome editing CRISPR-Cas systems in different organisms - Explains how to create an animal model for disease diagnosis/research and reprogram CRISPR for removal of virus, bacteria, fungi, protozoan, and many more - Discusses the advances, patents, applications, challenges and opportunities in CRISPR-Cas9 systems in basic sciences, biomedicine, virology, bacteriology, molecular biology, and many more |
| crispr guide rna design: Bioinformatics in Agriculture Pradeep Sharma, Dinesh Yadav, R.K. Gaur, 2022-04-28 Bioinformatics in Agriculture: Next Generation Sequencing Era is a comprehensive volume presenting an integrated research and development approach to the practical application of genomics to improve agricultural crops. Exploring both the theoretical and applied aspects of computational biology, and focusing on the innovation processes, the book highlights the increased productivity of a translational approach. Presented in four sections and including insights from experts from around the world, the book includes: Section I: Bioinformatics and Next Generation Sequencing Technologies; Section II: Omics Application; Section III: Data mining and Markers Discovery; Section IV: Artificial Intelligence and Agribots. Bioinformatics in Agriculture: Next Generation Sequencing Era explores deep sequencing, NGS, genomic, transcriptome analysis and multiplexing, highlighting practices forreducing time, cost, and effort for the analysis of gene as they are pooled, and sequenced. Readers will gain real-world information on computational biology, genomics, applied data mining, machine learning, and artificial intelligence. This book serves as a complete package for advanced undergraduate students, researchers, and scientists with an interest in bioinformatics. - Discusses integral aspects of molecular biology and pivotal tool sfor molecular breeding - Enables breeders to design cost-effective and efficient breeding strategies - Provides examples ofinnovative genome-wide marker (SSR, SNP) discovery - Explores both the theoretical and practical aspects of computational biology with focus on innovation processes - Covers recent trends of bioinformatics and different tools and techniques |
| crispr guide rna design: Genome Engineering for Crop Improvement Bidyut Kumar Sarmah, Basanta Kumar Borah, 2021-04-18 This book serves the teachers, researchers and the students as a handy and concise reference as well as guidebook while designing and planning for use of the advanced technologies for crop improvement. The content of the book is designed to cover the latest genome engineering techniques for crop improvement. The conventional breeding has got its limitations such as non-availability of desired genes within the genepool. In many cases, breeding has been highly used and it has nearly reached its highest limit so far as the productivity and production of crops are concerned. However, with increasing need of food and decreasing resources, including water, land, labour, etc., to feed the growing population, the alternative available ways of increasing crop productivity need to be explored and exploited. Genome engineering has a wide scope that includes technologies such as genetic engineering and transgenesis, RNA technologies, CRISPR, cisgenics and subgenics for better productivity and more efficient biotic and abiotic stress management. Therefore, the book is planned to enlighten the readers with the advanced technologies with examples and case studies, whenever possible. Efforts will be made to emphasize on general efforts on various major food crops; however, it would also be made clear that such efforts could be taken as proofs of concepts and that this could be extrapolated keeping the demand in mind. |
| crispr guide rna design: CRISPR Rodolphe Barrangou, Erik J. Sontheimer, Luciano A. Marraffini, 2022-09-14 “An excellent compendium of all things CRISPR from some of the leading minds in the field. With thorough coverage from every angle and beautifully detailed illustrations, this book is not to be missed!” Jennifer A. Doudna, Professor of Chemistry, Biochemistry & Molecular Biology, UC Berkeley; Founder, Innovative Genomics Institute; Nobel Laureate and coinventor of CRISPR technology “This journey through CRISPR biology and several of its breakthrough applications offers an exciting glimpse into one of the most beautiful and compelling fields in the life sciences.” David R. Liu, Director of the Merkin Institute at the Broad Institute of MIT and Harvard; Professor of Chemistry and Chemical Biology at Harvard University; coinventor of base editing and prime editing “A must read! The CRISPR topics, written by world-leading experts, span from the fascinating mechanistic underpinnings to the ingenious applications. One can read from start to finish or pick and choose themes. Either way, the book delivers utterly enjoyable learning!” Bonnie Bassler, Squibb Professor and Chair, Princeton University Department of Molecular Biology; Howard Hughes Medical Institute Investigator CRISPR-Cas systems have revolutionized the science of gene editing and their possible applications continue to expand, from basic research to potentially groundbreaking medical and commercial uses. Led by a distinguished team of editors, CRISPR: Biology and Applications explores the subject matter needed to delve into this fascinating area. Topics covered include: Classification and molecular mechanisms of CRISPR-Cas systems CRISPR-Cas evolution, regulation, expression, and function Uses for gene editing and modulation of gene expression CRISPR-based antimicrobials and phage resistance for medical and industrial purposes Written by internationally renowned authors, CRISPR: Biology and Applications serves as both an introductory guide for those new to the field and an authoritative reference for seasoned researchers whose work touches this evolving and headline- making science. |
| crispr guide rna design: The CRISPR/Cas System Muhammad Jamal, 2017 The use of CRISPR/Cas technology for genome editing suggests many potential applications, including the alteration of the germline of humans, animals and food crops. The speed and efficiency of the CRISPR/Cas system make it a potentially useful system for gene therapy. In this volume expert international authors provide a useful and timely review of the applications of the CRISPR/Cas system across diverse fields and explore further avenues and research directions of this novel and powerful editing technology. The technology and its application are reviewed with respect to reproduction and development, immunity and genetic diseases, system structure and system specificity. Some of the potential problems of the CRISPR/Cas system are also discussed, in particular the specificity of the system: this remains an important topic as improvement could lead to the more direct and efficient use of the CRISPR/Cas system in clinical settings. The authors also debate ethical concerns associated with this powerful new technology. This volume is a rigorous review of the applications and new opportunities for the CRISPR/Cas system and provides a stimulus for current and future research. An invaluable guide for all scientists working in the fields of genome editing and gene therapy the book is also recommended for all life sciences libraries. |
| crispr guide rna design: Synthetic Genomics Miguel Fernández-Niño, Luis H. Reyes, 2022-02-02 The current advances in sequencing, data mining, DNA synthesis, cloning, in silico modeling, and genome editing have opened a new field of research known as Synthetic Genomics. The main goal of this emerging area is to engineer entire synthetic genomes from scratch using pre-designed building blocks obtained by chemical synthesis and rational design. This has opened the possibility to further improve our understanding of genome fundamentals by considering the effect of the whole biological system on biological function. Moreover, the construction of non-natural biological systems has allowed us to explore novel biological functions so far not discovered in nature. This book summarizes the current state of Synthetic Genomics, providing relevant examples in this emerging field. |
| crispr guide rna design: 10th International Conference on Theory and Application of Soft Computing, Computing with Words and Perceptions - ICSCCW-2019 Rafik A. Aliev, Janusz Kacprzyk, Witold Pedrycz, Mo Jamshidi, Mustafa B. Babanli, Fahreddin M. Sadikoglu, 2019-11-19 This book presents the proceedings of the 10th Conference on Theory and Applications of Soft Computing, Computing with Words and Perceptions, ICSCCW 2019, held in Prague, Czech Republic, on August 27–28, 2019. It includes contributions from diverse areas of soft computing and computing with words, such as uncertain computation, decision-making under imperfect information, neuro-fuzzy approaches, deep learning, natural language processing, and others. The topics of the papers include theory and applications of soft computing, information granulation, computing with words, computing with perceptions, image processing with soft computing, probabilistic reasoning, intelligent control, machine learning, fuzzy logic in data analytics and data mining, evolutionary computing, chaotic systems, soft computing in business, economics and finance, fuzzy logic and soft computing in earth sciences, fuzzy logic and soft computing in engineering, fuzzy logic and soft computing in material sciences, soft computing in medicine, biomedical engineering, and pharmaceutical sciences. Showcasing new ideas in the field of theories of soft computing and computing with words and their applications in economics, business, industry, education, medicine, earth sciences, and other fields, it promotes the development and implementation of these paradigms in various real-world contexts. This book is a useful guide for academics, practitioners and graduates. |
| crispr guide rna design: Rice Functional Genomics Narayana M. Upadhyaya, 2010-10-29 Rice has been chosen as a model cereal for functional genomics because of its well understood genetics. In addition, there is great similarities among all the cereals and grasses: any understanding of rice genes is directly applicable to the genes of other cereals. This book details rice functional genomics. It takes a multi-pronged genome-wide approach using structural similarities, expression profiles, and mutant phenotypes. Coverage includes the current status of genome sequencing and annotation, various tools, and resources being developed worldwide. |
| crispr guide rna design: Mammalian Cell Engineering Ryosuke Kojima, 2022-07-21 This volume explores the latest engineering methods of mammalian cells that are useful for controlling the performance of engineered mammalian cells for future cell-based therapeutics and for better understanding of complex biological systems. The chapters in this book are organized into five parts. Part One described methods to engineer mammalian cells to sense biologically relevant inputs, such as cell contacts and soluble proteins. Part Two looks at techniques to engineer mammalian cells to sense artificial inputs, such as light and ultrasound. Part Three provides cutting-edge CRISPR-Cas-based methods to carry out highly multiplexed genome editing and spatiotemporally controlled genome editing. Part Four discusses ways to control and engineer biological events in mammalian cells in combination with chemical compounds and systems. Part Five explores techniques to engineer specific mammalian cells in targeted manners. 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. Comprehensive and authoritative, Mammalian Cell Engineering: Methods and Protocols is a valuable resource that allows scientists to successfully carry out their research, thus ultimately contributing to the future advancement of this field. |
| crispr guide rna design: A Crack in Creation Jennifer Doudna, Samuel Sternberg, 2018-06-14 A handful of discoveries have changed the course of human history. This book is about the most recent and potentially the most powerful and dangerous of them all. It is an invention that allows us to rewrite the genetic code that shapes and controls all living beings with astonishing accuracy and ease. Thanks to it, the dreams of genetic manipulation have become a stark reality: the power to cure disease and alleviate suffering, to create new sources of food and energy, as well as to re-design any species, including humans, for our own ends. Jennifer Doudna is the co-inventor of this technology - known as CRISPR - and a scientist of worldwide renown. Writing with fellow researcher Samuel Sternberg, here she provides the definitive account of her discovery, explaining how this wondrous invention works and what it is capable of. She also asks us to consider what our new-found power means: how do we enjoy its unprecedented benefits while avoiding its equally unprecedented dangers? The future of humankind - and of all life on Earth - is at stake. This book is an essential guide to the path that now lies ahead. |
| crispr guide rna design: Modern Prometheus Jim Kozubek, 2016-10-18 This book tells the dramatic story of Crispr and the potential impact of this gene-editing technology. |
| crispr guide rna design: CRISPR Genome Surgery in Stem Cells and Disease Tissues Stephen H. Tsang, 2021-10-20 CRISPR Genome Surgery in Stem Cells and Disease Tissues focuses uniquely on the clinical applications of CRISPR/Cas9 based technology. Topics include the latest advances in gene editing and its translational applications to various diseases, including retinal degenerative disease, recessively inherited diseases, and dominantly inherited diseases, to name a few. The book's target audience includes researchers, students, clinicians and the general public. This space that is not currently served by any existing resource, so this publication fills a gap in current literature. - Provides a thorough review of CRISPR-Cas9, from discovery to therapy - Covers the latest advances in gene editing and its translational applications to various diseases - Written by global leaders in the fields of gene editing and stem cell therapy |
| crispr guide rna design: Microinjection David J. Carroll, 2008-12-12 As the number of sequenced genomes continues to increase, understanding the functions of newly discovered molecules will require greater efficiency and further study within the context of live cells. In Microinjection: Methods and Applications, expert researchers contribute methods utilizing microinjection techniques ranging from expression of RNA to the integration of DNA into the genome with the ultimate goal of learning about gene expression, signal transduction, and protein function within these living cells. This versatile volume updates established techniques such as cRNA expression in Xenopus oocytes, and examines new, cutting-edge technologies, including antisense morpholino oligonucleotides, RNAi for knockdown experiments, and the use of integrase to produce transgenic animals, all through microinjection techniques that can be easily adopted by any lab. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include brief introductions to the topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and Notes sections, highlighting tips on troubleshooting and avoiding known pitfalls. Comprehensive and easily accessible, Microinjection: Methods and Applications is an ideal source for new ideas and techniques certain to aid in the advance of biological research. |
| crispr guide rna design: The Glycome Adeel Malik, Tanveer A. Dar, 2021-07-07 This volume provides a comprehensive understanding of the enigmatic identity of the glycome, a complex but important area of research that has been largely ignored due to its complexity. The authors thoroughly deal with almost all aspects of the glycome, i.e., elucidation of the glycan identity enigma and its role in regulation of the cellular process, and in disease etiology. The book bridges the knowledge gap in understanding the glycome, from being a cell signature to its applications in disease etiology. In addition, it details many of the major insights regarding the possible role of the glycome in various diseases as a therapeutic marker. The book systematically covers the major aspects of the glycome, including the significance of substituting the diverse monosaccharide units to glycoproteins, the role of glycans in disease pathologies, and the challenges and advances in glycobiology. The authors stress the significance and huge encoding power of carbohydrates as well as provide helpful insights in framing the bigger picture. The Glycome: Understanding the Diversity and Complexity of Glycobiology details state-of-the-art developments and emerging challenges of glycome biology, which are going to be key areas of future research, not only in the glycobiology field but also in pharmaceutics. |
| crispr guide rna design: Epigenetic Reprogramming During Mouse Embryogenesis Katia Ancelin, Maud Borensztein, 2020-10-20 This volume explores the latest techniques used to study and understand chromatin reprogramming in embryos and germ cells. Various culture systems are presented, which consist of invaluable tools to investigate many developmental processes. This book also looks at methods for direct examination of DNA, RNA, and proteins in embryos, along with low-input and single-cell assays for exploring these features at the genome-wide scale. 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, Epigenetics Reprogramming During Mouse Embryogenesis: Methods and Protocols is a valuable resource for any scientist and researcher looking to make new discoveries in this fascinating field of chromatin reprogramming. |
| crispr guide rna design: RNA Design Alexander Churkin, |
| crispr guide rna design: CRISPR Handbook Zhi-Yan Du, 2024-11-26 CRISPR Handbook: Applications, Tools and Resources presents a detailed introduction to the CRISPR technology. This handbook summarizes the current CRISPR applications in diverse organisms, shares useful tools for starting a CRISPR experiment, and provides information on software and services for CRISPR technology.Written by an expert in the field of biotechnology and molecular biology of diverse experiment models, including plants, microalgae, and fungi. This handbook will serve as a guide for those who are interested in learning about CRISPR technologies and their applications in research and industry. - Introduces CRISPR technology, which includes the history and molecular basics of the approach - Covers applications and available methods and tools for starting a CRISPR experiment or project - Includes case studies of the model species of different kingdoms |
Designing of guide RNA constructs for CRISPR/Cas9 …
An A-T rich leader sequence is present upstream of the CRISPR array and it has conserved genes coding for the Cas proteins at the end of the loci [10]. It also includes a single guide …
Data Visualization of CRISPR-Cas9 Guide RNA Design Tools
Y. Jain et al. / Data Visualization of CRISPR-Cas9 Guide RNA Design Tools 771. 3. Results CHOPCHOP (Figure 1), CRISPOR (Figure 2), GT-SCAN (Figure 4), and CCTOP (Figure 6) …
Designing Guide Rna For Crispr Copy - cie-advances.asme.org
Designing Guide Rna For Crispr: CRISPR Guide RNA Design Tudor A. Fulga,David J. H. F. Knapp,Quentin R. V. Ferry,2020-11-19 This detailed volume focuses on the CRISPR …
CRISPR-GPT: An LLM Agent for Automated Design of Gene …
works by interacting with the RNA of a short "guide" sequence (guide RNA) that binds to a specific target sequence in a cell's DNA, much like the RNA segments bacteria produce from the …
Deep learning enhancing guide RNA design for …
SMART GUIDE RNA DESIGN FOR CRISPR/CAS12A DIAGNOSTICS | 3of15. FIGURE 1 Preparation and evaluation of the Cas12a‐based crRNA data set for deep learning models …
Research Paper crispRdesignR: A Versatile Guide RNA …
crispRdesignR: A Versatile Guide RNA Design Package in R for CRISPR/Cas9 Applications Dylan Beeber and Frédéric JJ Chain Department of Biological Sciences, University of …
Quick reference guide - Thermo Fisher Scientific
Quick reference guide Our Invitrogen ™ GeneArt CRISPR Search and Design Tool allows you to search our database of >600,000 predesigned CRISPR guide RNA (gRNA) sequences or …
REVIEW ARTICLE CRISPR guide RNA design for research …
CRISPR guide RNA design for research applications Stephanie E. Mohr1,2, Yanhui Hu1,2, Benjamin Ewen-Campen2, Benjamin E. Housden2, Raghuvir Viswanatha2 and Norbert …
Guide RNA structure design enables combinatorial CRISPRa …
Guide RNA structure design enables combinatorial CRISPRa programs for biosynthetic profiling Jason Fontana 1,2,3,8, ... CRISPR-Cas transcriptional control systems are emerging as
0000-0002-3005-526X) Accepted Article - ResearchGate
CRISPR-Cereal: A Guide RNA Design Tool Integrating Regulome and Genomic Variation for Wheat, Maize and Rice Chao He1,5, Hao Liu2,5, Dijun Chen3, Wen-Zhao Xie2, Mengxin …
CRISPR–Cas9-mediated genome editing and guide RNA …
the basic mechanism of CRISPR–Cas9 derived from Streptococcus pyogenes was elucidated (Deltcheva et al. 2011; Jinek et al. 2012). CRISPR–Cas9 is an RNA-guided DNA …
With the Alt-R CRISPR-Cas system
PROTOCOL GUIDE Select a Cas enzyme The CRISPR-Cas system has 2 components: 1. Cas enzyme—an RNA-guided endonuclease (e.g., Cas9 or Cas12a) 2. Guide RNA Cas enzymes …
GeneFix-AI: AI-Powered CRISPR-Cas9 System for Real …
May 4, 2025 · the CRISPR-Cas9 system, streamlining the mutation prediction, guide RNA design, and real-time monitoring of gene-editing outcomes Choi et al., 2020. The system’s core func …
iMeta | 之江实验室/农科院基因组所联合开发CRISPR/Cas12a …
基于crispr的检测被誉为下一代核酸检测平台，为临场精准分子诊断提供了新技术支持。 设计筛选获得高检测活性的crRNA仍具挑战性且耗时较长。 深度学习为高效设计筛选crRNA提供了可能 …
CRISPR Design tool FAQ - Horizon Discovery
CRISPR Design tool FAQ . Or, if you closed the pop-up window, you can click the “Change nuclease for more results” button towards the bottom of the screen: ... What is a PAM, and is it …
GuideScan software for improved single and paired CRISPR …
single and paired crisPr guide rna design. Alexendar R Perez. 1– 4, Yuri Pritykin ,, Joana A Vidigal. 2, Sagar Chhangawala. 1,3, Lee Zamparo. 1, Christina S Leslie & Andrea Ventura. 2. …
CRISPR guide RNA design for research applications
RNAs (gRNAs). Here, we review the state of the art in CRISPR gRNA design for research applications of the CRISPR-Cas9 system, including knockout, activation, and inhibition. …
Guide-it™ CRISPR/Cas9 Systems User Manual - Takara Bio
The Guide-it CRISPR/Cas9 Systems are complete kits for the cloning and expression of a target single guide RNA \(sgRNA\) for mammalian gene modification studies using CRISPR/Cas9 …
Single Guide RNA Library Design and Construction - Broad …
Single Guide RNA Library Design and Construction Tim Wang,1,2,3,4,5 Eric S. Lander,1,3,6,7,8 and David M. Sabatini1,2,3,4,5,7,8 1Department of Biology, Massachusetts Institute of …
IDT_Alt-R HDR Design Tool & Templates (CRS-10176-FL …
The Alt-R HDR Design Tool enables greatly increased HDR rates by providing optimized donor template design and Cas9 guide RNA selection. The higher HDR rates result from clear …
CRISPR-Cas technology in corn: a new key to unlock genetic …
where CRISPR-Cas will act, the intended DNA sequence change or regulatory modification. Guide design is the work to produce the guide RNAs that program CRISPR-Cas reagents to …
Edit-R CRISPR Design Tool - horizondiscovery.com
The Edit-R™ CRISPR Design Tool allows you to quickly and easily generate guide RNA sequences for ordering either synthetic and lentiviral guides. There are several options for …
EuPaGDT: a web tool tailored to design CRISPR guide …
Current guide RNA (gRNA) design tools for the CRISPR-Cas9 system have limitations when applied to gRNA design for eukaryotic pathogens. For example, the genomes of most …
Crackling Cloud: an event-driven, cloud-based CRISPR …
Dec 4, 2024 · CRISPR-Cas9, guide design, cloud computing, event-driven architectures, serverless Correspondence: jake.bradford@qut.edu.au; dimitri.perrin@qut.edu.au Introduction …
Edit-R CRISPR Design Tool - horizondiscovery.com
The Edit-R™ CRISPR Design Tool allows you to quickly and easily generate guide RNA sequences for ordering either synthetic and lentiviral guides. There are several options for …
Faster and better CRISPR guide RNA design with the …
Feb 14, 2020 · Faster and better CRISPR guide RNA design with the Crackling method Jacob Bradford1, Timothy Chappell1 and Dimitri Perrin1 1School of Computer Science, Queensland …
Data Visualization of CRISPR-Cas9 Guide RNA Design …
visualizations used in guide RNA design tools, their advantages, their shortcomings, and the minimum set of visualization components needed to deliver results effectively. 2.
CRISPR-GRIT: Guide-RNAs with Integrated Repair …
Nov 27, 2023 · CRISPR-Cas 56 systems utilize a guide RNA (gRNA) and a Cas endonuclease to target and cleave a gene of 57 interest. The induction of DNA double-strand breaks (DSBs) at …
CRISPR-Cas9 protein for genome editing - Thermo Fisher …
CRISPR-Cas9 protein GeneArt Platinum Cas9 Nuclease CRISPR design tool GeneArt CRISPR Search and Design Tool CRISPR-Cas9 delivery Lipofectamine CRISPRMAX Cas9 …
1. Identify target and find genomic sequence - Promega …
PROTOCOL: Adding HiBiT Tag to an Endogenous Gene Using CRISPR 2. Design crRNA and order guide RNA (crRNA + tracrRNA) Select a region to search for guide RNA. Start with 40 …
LentiCRISPRv2 and lentiGuide-Puro: lentiviral CRISPR/Cas9 …
Page 1 of 2 rev20140722 LentiCRISPRv2 and lentiGuide-Puro: lentiviral CRISPR/Cas9 and single guide RNA CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a …
CRISPR guide RNA design for research applications
RNAs (gRNAs). Here, we review the state of the art in CRISPR gRNA design for research applications of the CRISPR-Cas9 system, including knockout, activation, and inhibition. …
DeepCRISPR: optimized CRISPR guide RNA design by …
METHOD Open Access DeepCRISPR: optimized CRISPR guide RNA design by deep learning Guohui Chuai1,2†, Hanhui Ma5†, Jifang Yan1,2, Ming Chen4, Nanfang Hong1,2, Dongyu …
Alt-R CRISPR-Cas9 System
(Recommended for option 1, 2-part guide RNA) Alt-R CRISPR-Cas9 Control Kit IDT (cat # 1072554 [human], 1072555 [mouse], ... For other species, use our proprietary algorithms to …
CRISPR Reagent Description - Addgene
the guide RNA. Two forms of guide RNAs can be used to facilitate Cas9-mediated genome cleavage, using a CRISPR RNA array and tracrRNA or a synthetic guide RNA fusing the …
sgRNA Brochure 07082021 - GenScript
CRISPR gRNA/Cas9 Plasmids Synthetic gRNAs & Cas9 Nucleases Single-Stranded DNA Synthesis Customized CRISPR Libraries Mammalian Cell Line Services ... Guide RNA design …
Design and cloning gRNA oligo’s into Cas9 vectors from F
2) Design sgRNA oligos (fwd and rev) and order along with U6 fwd primer (standard desalted value oligos at 50N scale of synthesis work fine). 3) Once arrived, dilute oligos to 100 μM in …
LentiCRISPRv2 and lentiGuide-Puro: lentiviral CRISPR/Cas9 …
LentiCRISPRv2 and lentiGuide-Puro: lentiviral CRISPR/Cas9 and single guide RNA CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a microbial nuclease system …
DeepCRISPR: optimized CRISPR guide RNA design by …
A major challenge for effective application of CRISPR systems is to accurately predict the single guide RNA (sgRNA) on-target knockout efficacy and off-target profile, which would facilitate the ...
Model-directed generation of artificial CRISPR–Cas13a guide …
CRISPR–Cas13a guide RNA sequences improves nucleic acid detection ... Cas13a-based detection assays; specifically, we design artificial 28 nt CRISPR guide RNA spacer …
CRISPR-P 2.0: an improved CRISPR-Cas9 tool for genome …
21 Running title: An improved tool for CRISPR guide RNA design in plants 22 . T D ... It supports to design guide sequences for various CRISPR-Cas systems 58 including Cpf1 (Zetsche et al., …
Development of the CasCADE CRISPR Detection guide …
specific guide RNA (gRNA) sequences must be developed per genomic target which can be a ... The Cas-CRISPR Automated Design and Evaluation (CasCADE) bioinformatics pipeline is a …
WheatCRISPR: a web-based guide RNA design tool for …
endonuclease and a single guide RNA (sgRNA) formed by fusing two small RNA molecules, namely CRISPR RNA (crRNA) and an auxiliary trans-activating crRNA (tracrRNA) that …
Tudor A. Fulga David J. H. F. Knapp Quentin R. V. Ferry …
guide RNA. In this volume, we focus on the CRISPR-associated guide RNA and how it can be designed, modified, and validated for a broad repertoire of purposes. The chapters fall into …
Rational design of minimum CRISPR guide RNA by site
Rational design of minimum CRISPR guide RNA by site-specific Cas9–RNA conjugation† Xinyu Ling,‡ Xiaoqin Gao,‡ Liying Chang, Heqi Chen, Xiaomeng Shi and Tao Liu *
T CI - Lubio
Forming of RNP (step 1) can occur either inside of cells or on the bench. First, CRISPR RNA (crRNA) and transactivating CRISPR RNA (tracrRNA) anneal together, forming a complete …
Agilent Integrated Solutions for Design, Synthesis, and …
(CRISPR) and CRISPR-associated (Cas) protein system, is gaining interest due to the ease and versatility in editing the genome. The system consists of an RNA-guided nuclease (Cas9), and …
CRISPR/Cas9 Genome Editing Application Guide - OriGene
protein and a guide RNA for effective double-stranded breakage at a desired site. OriGene has developed many CRISPR vectors, including All-in-one vectors which contain both guide RNA …
LentiCRISPRv2 and lentiGuide-Puro: lentiviral CRISPR/Cas9 …
Page 1 of 2 rev20140722 LentiCRISPRv2 and lentiGuide-Puro: lentiviral CRISPR/Cas9 and single guide RNA CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a …
CRISPR-Cereal: a guide RNA design tool integrating …
Brief Communication CRISPR-Cereal: a guide RNA design tool integrating regulome and genomic variation for wheat, maize and rice Chao He1,†, Hao Liu2,†, Dijun Chen3, Wen-Zhao Xie2, …
