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This second edition provides new and updated techniques and applications associated with synthetic biology. Chapters guide readers through the creation and regulation of gene circuits, manipulation of biochemical pathways, genome editing and modification, creating genome language and computing, as well as molecular assembly.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 key tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Synthetic Biology: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.
List of contents
Plant engineering to enable platforms for sustainable bioproduction of terpenoids.- Compartmentalized Terpenoid Production in Plants Using Agrobacterium-mediated Transient Expression.- Design Principles for Biological Adaptation: A Systems and Control-Theoretic Treatment.- Construction of Xylose-Utilizing Cyanobacterial Chassis for Bioproduction Under Photomixotrophic Conditions.- Allosteric-Regulation-Based DNA Circuits In Saccharomyces Cerevisiae To Detect Organic Acids And Monitor Hydrocarbon Metabolism In Vitro.- dCas12a:Pre-crRNA: A New Tool To Induce mRNA Degradation In Saccharomyces Cerevisiae Synthetic Gene Circuits.- CRISPRi-Driven Genetic Screening for Designing Novel Microbial Phenotypes.- Enzymatic Preparation of DNA with an Expanded Genetic Alphabet Using Terminal Deoxynucleotidyl Transferase and Its Applications.- Single-Nucleotide Microbial Genome Editing Using CRISPR-Cas12a.- Multiplex Marker-less Genome Integration in Pichiapastoris using CRISPR/Cas9.- Genome Editing, Transcriptional Regulation and Forward Genetic Screening Using CRISPR-Cas12a Systems in Yarrowia lipolytica.- An Improved Method for Eliminating or Creating Intragenic Bacterial Promoters.- Genetic Code Expansion in Pseudomonas putida KT2440.- Genome-Wide Screen for Enhanced Noncanonical Amino Acid Incorporation in Yeast.- Positive Selection Screens for Programmable Endonuclease Activity using I-SceI.- CRISPR-Cas9-mediated Genome Editing in Paenibacillus polymyxa.- Programming Juxtacrine-Based Synthetic Signaling Networks in a Cellular Potts Framework.- Encoding Genetic Circuits with DNA Barcodes Paves the Way for High-throughput Profiling of Dose-response Curves of Metabolite Biosensors.- Machine Learning for Biological Design.- A machine learning approach for predicting essentiality of metabolic genes.- The Causes for Genomic Instability And How To Try And Reduce Them Through Rational Design Of Synthetic DNA.- Genetic Network Design Automation with LOICA.- Flapjack: Data Management and Analysis for Genetic Circuit Characterization.- In Vivo DNA Assembly Using the PEDA Method.- Cell-Free Synthesis and Quantitation of Bacteriophages.- Multimodal Control of Bacterial Gene Expression by Red and Blue Light.- In silico design, in vitro construction and in vivo application of synthetic small regulatory RNAs in bacteria.
