Chapter 1 Synthetic Biology: Implications and Uses
2 DNA Assembly and Modification
3 Modular Parts and Circuits
6 Societal Challenges Posed by Synthetic Biology
Chapter 2 The Emergence of the First Cells
2 Origin of Prebiotic Metabolism and Compartments
2.1 ComparativeGenomics as aWay to Propose a Scenario for the Origins
2.3 The Origin of Nucleotides and the RNA-Metabolism World
2.4 From Substrates to Templates: the RNA-Genome World
3.1 Origin of the Archaea
3.2 Origin of the Bacteria
3.3 From Protokarya to Eukarya
3.4 Between Domains: the Perpetuation of Horizontal Gene Transfer
Chapter 3 Regulation of Gene Expression
2 Regulation of Gene Expression in Prokaryotes
2.1 Induction and Repression
2.2.1 The Lactose Operon (lac Operon)
2.2.2 The Histidine Operon
2.2.3 The Tryptophan Operon
2.2.4 The Arabinose Operon (ara Operon)
2.3 Positive and Negative Control
2.4 Attenuation: The Leader Sequence
2.5 Catabolite Repression
2.6 Cyclic AMP Receptor Protein
2.7 Guanosine-5'-Diphosphate,3'-Diphosphate
3 Regulation of Gene Expression in Eukaryotes
3.1 Transcriptionally Active Chromatin
3.2 Regulation of Gene Expression at the Initiation of Transcription
3.3 Regulation of Gene Expression in Chloroplasts
3.4 Regulation of Gene Expression in Mitochondria
4.2.1 Spliceosomal Introns
4.2.2 Spliceosome Formation and Activity
4.3 cis- and trans-Splicing Reactions
5 Role of microRNAs (miRNAs) in the Regulation of Gene Expression
6 Chromatin Structure and the Control of Gene Expression
7 Epigenetic Control of Gene Expression
8 Gene Regulation by Hormonal Action
9 Post-Transcriptional Regulation of mRNA
10 Transport of Processed mRNA to the Cytoplasm
11 Regulation of Gene Expression at the Level of Translation
2 Experimental Techniques for Detecting Protein Interactions
3 Computational Prediction of Protein Interactions
3.1 Interaction Prediction from the Gene Patterns Across Genomes
3.1.3 Phylogenetic Profiling
3.2 Predicting Interaction from Sequence Coevolution
3.4 Coexpression Networks
4 Exploring the Topology of the Interactome
4.2 Network Centrality and Protein Essentiality
4.4 Network Motifs and Related Concepts
5 Comparing Protein-Protein Interaction Networks
6 Databases of Protein and Domain Interactions
7.1 Predicting Protein Function
7.2 Application to Human Diseases
8 Looking Ahead: Towards the Dynamic Interactome
2 History of Microbial Diversity Studies
3.3 Host-Associated Microbiomes
5 Sequence Technologies and Tools
5.1 454 (Roche) GS Sequencing Technology
5.1.1 Illumina/Solexa GA Sequencing Technology
5.1.2 ABI SOLiD Sequencing Technology
5.3.1 Fragment Recruitment
Chapter 6 Dynamics of Biomolecular Networks
2 Boolean Dynamics Models
2.2 Generic Properties of (Random) Boolean Networks and Cell Behaviors: Cell Differentiations and the Cell Cycle
2.3 Topological and Dynamical Properties: Homeostasis, Flexibility, and Evolvability
2.4 Biologically Relevant Boolean Rules
2.5 Dynamical Simulation: An Example
2.6 Boolean Networks Inference from Experimental Data: Probabilistic Boolean Networks
3 Continuous Dynamics Models
3.1 ODE Formalisms: From Biochemistry to Mathematics
3.1.1 Biochemical Background-Based Models
3.1.2 Empirically Based Approaches
3.2 Summing Nodes and Links: From Math to Systems Biology
3.2.1 Simple but Subtle Structures: SIMs and SOMs
3.2.2 Oscillators, Clocks, and Bistable Switches: FB Dynamics
3.2.3 FFLs: Noise Management and Pulse Generation
Chapter 7 E-Cell: Computer Simulation of the Cell
2 Biological Modeling and Simulation Tools
3.2 Architecture of E-Cell
3.2.1 Elements of the Control Panel
3.2.2 Elements of the E-Cell Model
3.3 Features of E-Cell 2.0
3.4 Features of E-Cell 3.0
3.5 Advantages of the E-Cell System
3.6 Limitations of the E-Cell System
3.7 E-Cell with 127 Genes
3.8 Applications of the E-Cell System
3.9 Simulation of Erythrocyte Enzyme Deficiencies
Chapter 8 SynBioSS Designer Modeling Suite
2 Modeling Synthetic Systems Made by BioBricks
2.2 Inserting and Modifying BioBricks
2.3 Protein Input and Specifics
2.4 Effector Input and Specifics
3 Modeling Synthetic SystemsMade by User-Defined Genetic Constructs
3.1 Modeling User-Defined Genetic Constructs
3.2 Inserting and Modifying User-Defined Parts
3.3 Protein Input, Specifics, and Generation of Output
4 Current Limitations of the Designer
Part III Modular Parts and Circuits
Chapter 9 Synthetic Gene Circuits
1 Introduction to Synthetic Gene Circuits
2 Building Blocks of Synthetic Gene Circuits
2.1 The Chassis: Choice of the Host Cell
2.2 Inputs and Outputs of Synthetic Circuits
2.3 Properties of Synthetic Building Blocks
2.4 Building Blocks of Synthetic Transcriptional Regulation
2.5 Post-Transcriptional Regulation: RNA-Based Circuit Engineering
2.7 Post-Translational Regulation and Protein-Based Circuits
5 Boolean Logic and Digital Circuits
7 Intercellular Communication and Synthetic Multicellular Devices
7.1 Intercellular Communication Mechanisms
7.2 Examples of Synthetic Multicellular Systems
8 Synthetic Circuit Construction: Challenges and Solutions
8.1 Circuit Design: Topology and Parameters
8.2 Circuit-Host and Circuit-Environment Interactions
9 Applications of Synthetic Circuits
9.2 Therapeutic Applications
9.3 Synthetic Biology in Manufacturing
Chapter 10 DNA Origami Nanorobots
1 Introduction to Robotics
1.1 A Brief History of Robotics
1.2 Robotic Control of Molecules
2.5 DNA Actuators and Motors
2.6 Miscellaneous Functions of Nucleic Acids
2.8 Computer-Aided Design (CAD) Tools for DNA Nanostructures
2.9 Designing Scaffolded Origami in caDNAno: A Guided Tour
3.1 Case Study: A DNA Nanorobot
3.2 Sensing the Environment
3.3 Information Processing and Logic Types
3.5 Synthetic Genetic Circuits and DNA Nanorobotics
4 Challenges of Applying DNA Nanorobots to Therapeutics
5 Summary and Conclusions
Chapter 11 RNAi Synthetic Logic Circuits for Sensing, Information Processing, and Actuation
2 Overview of RNA Interference
2.1 MicroRNA-Mediated Regulatory Motifs
2.3 Information Processing and Actuation for RNAi-Based Logic Circuits
3.2 Learning by Engineering
4 Conclusions and Perspectives
Chapter 12 Synthetic Hybrid Biosensors
3 Electrochemical Biosensors
3.1 Amperometric Biosensors
3.2 Potentiometric Biosensors
3.3 Conductometric Biosensors
4.1 Conjugated Polymer-Based Biosensors
4.2 Surface Plasmon Resonance-Based Biosensors
4.2.2 Surface Chemistry in SPR Technique
4.2.3 Surface Plasmon Fluorescence Technique
4.3 Surface-Enhanced Raman Spectroscopy-Based Biosensors
5 Piezoelectric Biosensors
5.1 Bulk Acoustic Wave (BAW) Sensors
5.2 Surface-Generated Acoustic Wave (SGAW) Sensors
Chapter 13 Synthetic Biology in Metabolic Engineering: From Complex Biochemical Pathways to Compartmentalized Metabolic Processes-a Vitamin Connection
1 Industrial Production of Vitamin B12
2 Modular Assembly of Cobalamin
2.1 Cellular Resource Procurement
2.2.1 Building Block 1: ALA
2.2.2 Building Block 2: SAM
2.3 Synthesis of the Tetrapyrrole Macrocycle, Uroporphyrinogen III (Uro'gen III)
2.4 Different Molecular Assemblies
2.4.1 Section 1: The Last Common Step; Uro'gen III to Precorrin-2
2.4.2 Section 2a: The Ancestral Pathway; Precorrin-2 to Cobyrinic Acid a,c-Diamide
2.4.3 Section 2b: The Modern Pathway; Precorrin-2 to Cobyrinic Acid a,c-Diamide
2.4.4 Section 3: Both Pathways, from Cobyrinic Acid a,c-Diamide to Adenosyl-Cobinamide
2.5 Biosynthesis of the Lower Axial Ligand, ***alpha***-Ribazole Phosphate
2.6 Biosynthesis of Aminopropanol-O-2-Phosphate (APP)
3 Nature Has Evolved Different Ways to Catalyze Ring Contraction
4 The Methylases in the Cobalamin Biosynthetic Pathway Are Largely Derived From One Common Ancestor
5 CobA: Enhancing Pathway Productivity through Protein Engineering
7 Biosynthesis of Mismethylated Analogs of Cobalamin
8 Substitution of the Metal Ion
9 Tailoring of the Nucleotide Loop
11 Physical Compartments for Pathway Sequestration
11.1 Bacterial Protein-Based Microcompartments and Their Functions
11.2 Architecture of Bacterial Microcompartments
11.3 Protein Sequestration into Microcompartments
11.4 Engineering Microcompartments
11.5 Designing and Customizing Microcompartments
Part IV Synthetic Genomes
Chapter 14 The Minimal Gene-Set Machinery
2 Top-Down Approaches to the Minimal Gene Set
2.1 Preserved Genes to Approach the Minimal Genetic Core: The Power and Pitfalls of Comparative Genomics
2.2 Experimental Genetics: Mutational Approaches to Detect Essential Genes
2.3 Comparative Proteomics: Preserved versus Active Genes
2.4 Minimal Cell Modeling
3 The Minimal Gene-Set Machinery
3.1 The First Pillar. Storage and Processing of Genetic Information: From Genes to Gene Products
3.1.3 Protein Processing, Folding, and Secretion
3.2 The Second Pillar. Energetic and Intermediary Metabolism
3.3 The Third Pillar. The Cell Envelope and Its Involvement in EssentialCellular Processes
Chapter 15 Production of Mitochondrial Genome and Chromosomal DNA Segments Highly Engineered for Use in Mouse Genetics by a Bacillus subtilis-Based BGM Vector System
2 Giant DNA Handled by the BGM System
2.1 Differential Principles of DNA Uptake between E. coli and B. subtilis
2.2 DNA Cloned in the Plasmid Form in B. subtilis
2.3 DNA Cloned in the B. subtilis Genome
2.4 Assembly of Contiguous DNAs in the B. subtilis Genome: the Domino Method
3 Production of a Full-Length Mouse Mitochondrial Genome by the BGM System
3.1 Cloning and Engineering of mtDNA in E. coli
3.2 Direct Cloning by Use of Purified mtDNA by BGM
3.3 Synthesis of mtDNA by the Domino Method
4 Production of Heavily Manipulated DNA for Mouse Genetics
4.1 BAC Plasmid Vectors for Large DNA Handling in E. coli
4.2 BAC Domino Transfer in BGM
4.2.1 Complex Engineering for BAC Inserts (Deletion, Inversion)
4.2.2 Connection of Two Adjacent BACs in BGM
4.2.3 Isolation and Purification of BAC in BGM
4.3 Applications for Heavily Engineered BACs Produced in Transgenic Mice
4.4 Comprehensive BAC/BGM Library Construction Proposals
4.5 Long-Term Storage of Valuable DNA Resources in the BGM System
5 Future Perspectives for the BGM System in Molecular Cloning and Genome Design
Chapter 16 Synthetic Genetic Polymers Functioning to Store and Propagate Information by Genetic Alphabet Expansion
2.1 Bidirectionally Complementary Base Pairs
2.1.3 5SICS-MMO2 and 5SICS-NaM Pairs
2.2 Unidirectionally Complementary Base Pairs
3.1 PCR Amplification and qPCR
Part V Diseases and Therapeutics
Chapter 17 Synthetic Biology Approaches for Regenerative Medicine
1 Introduction: Current Problems in Regenerative Medicine
2 Synthetic Biology as a Promising Source of Solutions
2.1 Production and Expansion of Stem Cells
2.2 Control of Differentiation/Potency
2.3 Addressing the Danger of Tumorigenicity
2.4 Targeting in the Host
2.5 Population Control in the Host
2.6 Reporting of Cell Fate
3 Ethical, Legal, and Social Implications
Chapter 18 The Synthetic Biology Approach to Stem Cells and Regenerative Medicine
2 Synthetic Gene Circuits for Directing Stem Cell Differentiation and Establishing Intercellular Communication Networks within 3D Tissue-Engineered Constructs
3 Precise Gene Targeting and Genome-Editing Technologies to Allay Safety Concerns of Synthetic Gene Circuits Encoded by Recombinant DNA
4 Non-integrating Vectors for the Expression of Transgenes: Episomal Plasmids and Sendai Virus
5 Modulating Gene Expression through Direct Delivery of Proteins and RNA into the Cell: A Safer Alternative for Stem Cell Differentiation and Reprogramming Compared with Recombinant DNA Transfection
6 Breakthrough: Chemical-Based Reprogramming to Pluripotent Stem Cells with Small Molecules Alone
7 Overcoming the Limited Plasticity and Proliferative Potential of Adult Stem Cells Using a Synthetic Biology Toolkit
8 Conclusions: Safety Issues and Future Outlook
Chapter 19 Synthetic Biology Approaches to Cell Therapy
2.1 Hematopoietic Stem Cell Transplantation
2.2 Engineered Immunotherapy
2.4 Enhancing the Microbiome
2.5 Liposomal Encapsulations
3.1 Engineering Synthetic Gene Circuits
3.2 Engineering Synthetic Protein Circuits
3.3 Deploying Circuits in Mammalian Cells
4 Cell Therapies Enabled by Synthetic Biology
4.1 Cell Therapy with Engineered Bacteria
4.2 Optimizing Immunotherapy with Synthetic Biology
4.3 Deploying Synthetic Circuits in Mammalian Cells to Treat Broad Diseases
4.4 Artificial Cell Nanofactories as Therapeutics
Chapter 20 Synthetic Biology Approaches for Vaccine Development
2 Synthetic Approaches to Vaccine Design
3 Attenuation by CPB Recoding
4 Mechanisms of Attenuation by Recoding
5 Eradication as the Goal of Vaccines
Part VI Chemicals Production
Chapter 21 Metabolic Engineering for the Production of Diols
2 1,2-Propanediol (1,2-PD)
2.1 Microbiological Synthesis of 1,2-PD
2.2 Factors Influencing 1,2-PD Formation by Microorganisms
2.2.1 Medium Composition and Environmental Conditions
2.3 Genetic Engineering in 1,2-PD Production
3.1 Microbial Production of 1,3-PD
3.2 Glycerol Metabolism in Microorganisms Producing 1,3-PD
3.3 Influence of Medium Composition on the Microbial Production of 1,3-PD from Glycerol
3.4 Influence of Process Parameters on the Microbial Production of 1,3-PD from Glycerol
3.5 Genetic Engineering of 1,3-PD
4.1 2,3-BD Metabolic Pathway
4.3 Fermentation Conditions
4.3.4 Medium Supplementation with Acetic Acid
4.4 Recovery of Biologically Produced 2,3-BD
4.5 Genetic Engineering of 2,3-BD
Chapter 22 Synthetic Biology in Biofuels Production
2 Synthetic Biology: The Tools and Applications
2.3 Metabolic Engineering
2.4 Predicting Fabricated Genes or Pathways Behavior in a Biological System
2.4.1 Metabolic Network Modeling
2.4.2 Analysis of the Model
3 Role of Synthetic Biology in Feedstock Improvement
3.1 Feedstock Engineering for Efficient Hydrolysis
3.1.1 Feedstock Engineering for Low Lignin Content
3.1.2 Change in Lignin Structure
3.2 Feedstock Engineering for Increased Biomass
3.2.1 Delay in Reproductive Phase
3.2.2 Genetic Manipulation of Plant Growth Regulators
3.2.3 Modulation of Nutrient Metabolism
3.2.4 Facilitation of Phosphorus Utilization
3.3 Feedstock Engineering for Heterologous Expression of Hydrolyzing Enzyme
4 Enzyme Engineering for Hydrolysis of Biomass
4.1 Enzymes with Higher Catalytic or Specific Activity
4.2 Enzymes with Improved Thermostability and pH Optima
4.3 Enzymes with Bifunctional or Multifunctional Activities
5 Microbial Engineering to Expand the Substrate Range
6 Microbial Engineering to Produce Various Biofuel Molecules
6.1 Lignocellulosic Ethanol
6.2 Butanol and Higher-Chain Alcohols
6.3 Fatty Acid-Based Biofuels
6.4 Isoprenoid-Based Biofuels
7 Role of Synthetic Biology in Algal Fuels
Chapter 23 Synthetic Biology of Antibiotic Production
2 The Need for Chemical Diversity
3 Classical Approaches to Antibiotic Biosynthesis
4 Synthetic Biology Methods for Genome Prospecting of New Bioactive Molecules
5 Synthetic Biology Approaches for the Rapid Generation of Chemical Diversity
6 Engineering of Versatile Chassis for the Synthetic Biology of Antibiotics
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